the role of plasmid-located mucab genes in emergence of...

The role of plasmid-located mucAB genes in emergence

Of quinolone resistant Escherichia coli (Mutators)

Master thesis in Biotechnology (30 ECTS)

Signe Tanja Andersen

September 2009

Supervisors

Henrik Hasman

The National Food Institute Department of Microbiology and Risk Assessment

Technical University of Denmark, DTU

Lasse Engbo Christiansen

Department of Informatics and Mathematical Modelling

Technical University of Denmark, DTU

http://www.dtu.dk/?lang=en

Signe Tanja Andersen, The National Food Institute DTU, Copenhagen, 2009

The role of plasmid-located mucAB genes in emergence of quinolone resistant Escherichia coli

2

Preface

This report is the written outcome of the experimental work performed at the National Food

Institute Copenhagen, The Technical University of Denmark (DTU) in the period from March 2009

to July 2009. The aim was to examine the role of plasmid-located mucAB genes in emergency of

quinolone resistant Escherichia coli.

I would like to thank my internal supervisor Henrik Hasman, The national Food Institute (DTU), for

his guidance in the theoretical as well as the experimental work and his ideas to the project. Further

I would like to thank my external supervisor Lasse Engbo Christiansen, Department of Informatics

and Mathematical Modelling (DTU), for his participation in the design of the mutation frequency

determination and the statistical analysis following.

For providing bacterial strains I would like to thank Mona-Lise Binderup from the National Food

Institute, Department in Mørkhøj, who provided two of Ames Salmonella strains; TA100 and 1535.

Anne Mette Seyfarth and Gitte Sørensen, Department of Zoonosis, who provided the Salmonella

strains used for mucAB screening. Per Klemm, Department of Systems Biology, who provided

E.coli MG1655.

I would like to thank Lisbeth Andersen as well as all the other technicians, students and staff at the

resistance department for helping me with the theoretical and practical things and for making my

stay at the department pleasant and rewarding every day.

Finally I would like to thank my family and friends for supporting me whenever it was needed.

_______________________________

September 2009, Signe Tanja Andersen



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Abstract

Antibiotic resistance has in the recent years received an increasing attention, due to the decrease in

effectiveness caused by development of bacterial resistance mechanisms. In the latest report from

the Danish Integrated Antimicrobial Resistance Monitoring and Research Programme (DANMAP)

in 2007, a strong correlation between the quantity of the antibiotics and the development of

resistance has been found. The transfer of resistance genes have been found to be caused by mobile

genetic elements such as plasmids, transposons and integrons.

Escherichia coli are one common cause of infections in human and animals. In human diagnostic E.

coli, which are resistant to beta-lactam antibiotics due to production of Extended-spectrum Beta-

Lactamases (ESBL), has become more and more prominent. Fluoroquinolone is one alternative

antibiotic used to treat infections caused by ESBL producers. But in the year 2000 until today the

resistance towards fluoroquinolones has increased in correlation with the increased consumption.

The main focus of this study was to investigate the role of plasmid-located mucAB genes in

emergence of quinolone resistant E. coli. This was done by determining the distribution of the

plasmidic mucAB genes in animal reservoirs and by analyzing in what degree mucAB is activated

when fluoroquinolones are used.

Isolates collected from pigs and cattle in Denmark were selected and screened for the presence of

mucAB genes, which are carried on resistance plasmids. Isolates included 81 indicator and 58

diagnostic E. coli O149 isolated from pigs in 2008, 81 indicator and 45 diagnostic E. coli K99

isolated from cattle in 2008, 12 diagnostic E. coli ESBL producers from humans in Spain obtained

in the period 2000-2003. Additionally, 33 diagnostic S. typhimurium isolated from pigs and 36

diagnostic S. ssp. isolated from cattle in 2008, were examined. It was found that approximately 26

% of the diagnostic E. coli from pigs and 8 % of the diagnostic Salmonella from cattle contained

mucAB. None of the indicator strains contained mucAB, along with the diagnostic E. coli from cattle

and human.

When examining the impact of mucAB on resistance development, transformants of E. coli with a

plasmid carrying mucAB, were constructed. Additionally two Salmonella strains from Ames test,

TA1535 and TA100 were used. A fluctuation assay was constructed and the mutation frequency

measured in the presence or absence of mucAB. The mutation frequency was expected to increase

when ciprofloxacin was used as inducer by activation of the SOS response and thereby mucAB. The



4

result did not show any significant increase of the mutation frequency in induced cells containing

mucAB compared to the negative control strain. Neither was a significant increase in the mutation

frequency found in cells induced by 4-nitroquinoline-N-oxide, a compound known to activate

mucAB.

The target modifications in gyrA and parC were found by PCR and sequencing. This was done to

investigate if mucAB induce certain basepair substitution events. All the quinolone resistant strains

had a mutation in gyrA, while none of them had a mutation in parC. None of them was

fluoroquinolone resistant.

Transversion events accounted for 50 % of the basepair substitutions where the bases adenine,

guanine and thymine were substituted equally. Thymine was the most prevalent base inserted,

accounting for 47 % of the inserted bases. In GyrA, Asp87 to Tyr87 and Gly87 as well as Ser83 to

Leu83, were the most frequent amino acids substitutions found.

The minimum inhibitory concentration (MIC) was examined to find out if the target specificity

mediated by ciprofloxacin mediated strains with higher MIC values than strains produced when 4-

nitroquinoline-N-oxide was used. No difference was found between the two compounds, both

produced quinolone resistant strains with most predominant MIC values in the range of 0,125 to 0,5

µg/ml ciprofloxacin.

Based on the data in this study the conclusions were that mucAB are distributed in animal reservoirs

in Denmark, primarily in diagnostic E. coli from pigs. In the study mucAB were not activated by

ciprofloxacin and 4-nitroquinoline-N-oxide and therefore a correlation between an increased

mutation frequency and resistance development mediated by mucAB was not established. The target

modifications could therefore not be correlated with the effects of mucAB, but was rather the result

of spontaneous mutations. The MIC values in the quinolone resistant strains correlated with

previous findings.



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Resumé

I de seneste år har antibiotika resistens fået stigende opmærksomhed, grundet den nedsatte

effektivitet forårsaget af udviklingen af bakterielle resistens mekanismer. I den seneste rapport fra

the Danske Integrerede Antimikrobielle Resistens Overvågning og Forskningsprogram (DANMAP)

fra 2007, blev en signifikant sammenhæng fundet mellem mængden af antibiotika of udviklingen af

resistens. Overførslen af resistens gener skyldes tilstedeværelsen af mobile genetiske elementer som

plasmider, transposoner og integrons.

Escherichia coli forårsager ofte infektioner i mennesker og dyr. I mennesker er

sygdomsfremkaldende E. coli resistente overfor beta-latam antibiotika, grundet produktionen af

”Extended-spectrum Beta-Lactamase” (ESBL), blevet mere og mere udbredt. Fluorokinoloner kan

bruges til at behandle infektioner forårsaget af ESBL producerende E. coli. Men i perioden 2000 til

i dag er resistensen overfor fluorokinoloner øget i sammenhæng med det stigende forbrug.

Hovedformålet med dette studie var at undersøge rollen for plasmid lokaliserede mucAB gener in

udviklingen af kinolone resistente E. coli. Målet var at finde ud af hvor udbredt de plasmide mucAB

gener var i dyre reservoirs og at analysere i hvilken grad mucAB er aktiveret når fluorokinoloner

anvendes.

Isolater indsamlet fra grise og kvæg fra Danmark, blev udvalgt og screenet for tilstedeværelsen af

mucAB gener som bæres på resistens plasmider. Isolaterne bestod af 81 indikator og 58 diagnostiske

E. coli O149 isoleret fra grise i 2008, 81 indikator og 45 diagnostiske E. coli K99 fra kvæg i 2008,

12 diagnostiske ESBL producerende E. coli fra mennesker fra Spanien isoleret i perioden 2000-

2003. Derudover blev 33 diagnostiske S. typhimurium isoleret fra grise og 36 diagnostiske S. ssp.

isoleret fra kvæg i 2008, undersøgt. Det blev fundet at cirka 26 % af de diagnostiske E. coli fra grise

og 8 % af de diagnostiske Salmonella spp. fra kvæg havde mucAB. Ingen af indikator isolaterne

indeholdt mucAB og heller ingen af de diagnostiske E. coli fra kvæg og mennesker.

Da mucAB’s effekt på resistens udvikling blev undersøgt, blev transformanter konstrueret bestående

af E. coli med et plasmid bærende på mucAB. Derudover blev to Salmonella stammer fra Ames test,

TA1535 og TA100 brugt. Et fluktuations assay blev konstrueret og mutations frekvensen målt ved

mucAB’s tilstedeværelse eller fravær. Mutationsfrekvensen var forventet at stige når ciprofloxacin

var tilføjet som inducerende stof fordi det aktiverer SOS responset i E. coli og dermed mucAB.

Forsøget viste ikke nogen signifikant øgning af mutationsfrekvensen i mucAB inducerede celler. Ej



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heller var en signifikant stigning i mutationsfrekvensen fundet i celler induceret af 4-nitroquinoline-

N-oxide, et stof der vides at aktivere mucAB.

Target modifikationer i gyrA og parC blev fundet ved PCR og sekventering. Dette blev udført for at

undersøge om mucAB inducerer specifikke basepar ændringer. Det blev fundet at alle kinolone

resistente stammer havde en mutation i gyrA, hvorimod ingen af dem havde en mutation i parC.

Ingen af dem var dog fluorokinolone resistente.

Transversioner udgjorde 50 % af alle basepar substitutionerne og baserne adenin, guanin og thymin

var substitueret ligeligt. Thymin var den base der var hyppigst indsat, dermed udgørende 47 % af

alle indsatte baser. I GyrA var de mest almindelige aminosyrer substitutioner Asp87 til Tyr87 eller

Gly87, såvel som Ser83 to Leu83.

Den mindste inhiberende koncentration (MIC) blev undersøgt, for at se om den target specificitet

som ciprofloxacin har, medierede stammer med en højere MIC, end de stammer der var produceret

når 4-nitroquinoline-N-oxide var inducer. Der blev dog ikke fundet nogen forskel, begge

producerede kinolone resistente stammer med MIC værdier mest hyppigt beliggende i området

0,125 to 0,5 µg/ml ciprofloxacin.

Ud fra de data der blev indsamlet i dette studie, blev det konkluderet at mucAB er udbredt i

produktions dyr i Danmark, primært i diagnostiske E. coli fra grise. I studiet var mucAB ikke

aktiveret af hverken ciprofloxacin eller 4-nitroquinoline-N-oxide og en sammenhæng mellem en

øget mutationsfrekvens og resistens udvikling medieret af mucAB blev ikke fundet. Target

modifikationerne kunne derfor ikke blive relateret til effekterne af mucAB, men var nærmere et

resultat af spontane mutationer. MIC værdierne i de kinolone resistente stammer passede med hvad

der har været påvist i andre studier.



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Table of contents

1 INTRODUCTION ......................................................................................................................... 11

2 AIM OF THE PROJECT ............................................................................................................. 13

LIST OF ABBREVIATIONS ......................................................................................................... 14

3 ESCHERICHIA COLI................................................................................................................... 16

3.1 CHARACTERISATION OF ESCHERICHIA COLI .............................................................................. 16

3.2 RESISTANCE PLASMIDS .............................................................................................................. 16

3.3 TRANSMISSION AND DISEASES CAUSED BY E. COLI .................................................................... 17

3.3.1 Transmission and diseases in humans .............................................................................. 17

3.3.2 Transmission and diseases in animals .............................................................................. 18

4 QUINOLONES AND FLUOROQUINOLONES ....................................................................... 19

4.1 ANTIBIOTICS IN GENERAL .......................................................................................................... 19

4.2 THE FIRST QUINOLONE NALIDIXIC ACID: DEVELOPMENT AND USE ............................................. 19

4.3 FLUOROQUINOLONE DEVELOPMENT AND ANTIBACTERIAL ACTIVITY ........................................ 19

4.4 DNA GYRASE AND TOPOISOMERASE IV; THE TARGETS OF QUINOLONES ................................... 20

4.5 MUTATIONS IN GYRA AND PARC ............................................................................................... 22

4.6 MUTATIONAL HOTSPOTS IN GYRA AND PARC ........................................................................... 23

5 FLUOROQUINOLONE RESISTANCE IN E. COLI ............................................................... 24

5.1 THE RISE OF FLUOROQUINOLONE RESISTANT BACTERIA ............................................................ 24

5.2 ANTIMICROBIAL CONSUMPTION AND RESISTANCE IN HUMANS .................................................. 25

5.3 ANTIMICROBIAL CONSUMPTION AND RESISTANCE IN ANIMALS ................................................. 26

6 THE MUC OPERON AND ITS ROLE IN AMES TEST AND THE SOS RESPONSE ....... 27

6.1 AMES BACTERIAL REVERSION TEST ........................................................................................... 27

6.2 AMES TESTER STRAINS AND PLASMID PKM101 ......................................................................... 28

6.3 IDENTIFICATION OF THE MUC OPERON ....................................................................................... 29

6.4 PROOFREADING STRATEGIES ..................................................................................................... 29

6.5 THE SOS REPAIR SYSTEM .......................................................................................................... 30

6.6 THE GENE PRODUCTS OF MUCAB .............................................................................................. 30

6.7 DNA POLYMERASES INVOLVED IN SOS REPAIR ........................................................................ 32



8

7. DNA DAMAGING AGENTS ..................................................................................................... 35

7.1 THE MUTAGENIC POTENTIAL OF MUCAB ................................................................................... 35

7.2 MUTAGENIC COMPOUNDS ACTIVATING MUCAB ........................................................................ 35

7.3 BASE PAIR SUBSTITUTIONS INDUCED BY MUCAB ...................................................................... 36

7.4 QUINOLONES AS MUTAGENIC COMPOUNDS................................................................................ 37

8 INTRODUCTION TO THE METHODS USED ....................................................................... 39

8.1 SELECTION OF INDICATOR AND DIAGNOSTIC STRAINS ............................................................... 39

8.2 TRANSFORMATION .................................................................................................................... 39

8.3 POLYMERASE CHAIN REACTION ................................................................................................. 40

8.4 MUTATIONS RATE DETERMINATION BY FLUCTUATION TESTS .................................................... 40

8.4.1 Luria-Delbrück experiments ............................................................................................. 40

8.4.2 The Poisson distribution ................................................................................................... 41

8.5 HANDLING MUTAGENIC COMPOUNDS- 4NQO ........................................................................... 42

8.6 GROWTH DETERMINATION BY BIOSCREEN C ............................................................................. 43

8.7 RESISTANCE DETERMINATION ................................................................................................... 43

8.7.1 Minimum inhibitory concentration ................................................................................... 43

8.7.2 Resistance breakpoints ...................................................................................................... 43

8.7.3 MIC by Broth dilution testing, the Sensititre method........................................................ 44

8.7.4 Disk diffusion antibiotic sensitivity testing ....................................................................... 44

9. MATERIALS AND METHODS ............................................................................................... 45

9.1 BACTERIAL STRAINS.................................................................................................................. 45

9.2 CONSTRUCTION OF TRANSFORMANTS ........................................................................................ 45

9.2.1 Preparation of electro competent cells ............................................................................. 45

9.2.2 Transformation.................................................................................................................. 46

9.3 POLYMERASE CHAIN REACTION (PCR) ...................................................................................... 47

9.3.1 Boiling lysates as PCR templates...................................................................................... 47

9.3.2 Amplification of mucAB genes .......................................................................................... 47

9.3.3 Amplification and sequencing of QRDRs of DNA gyrase and topoisomerase IV genes ... 47

9.3.4 Agarose gel electrophoresis .............................................................................................. 48

9.3.5 Sequencing of QRDRs of DNA gyrase and topoisomerase IV genes ................................ 48

9.4 MUTATION FREQUENCY DETERMINATION ................................................................................. 49



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9.4.1 Initiating the assay ............................................................................................................ 49

9.4.2 Procedure 1- the microtiter plate procedure .................................................................... 50

9.4.3 Procedure 2- the 24 well plate procedure ........................................................................ 50

9.4.4 Statistical analysis............................................................................................................. 51

9.4.5 Growth determination ....................................................................................................... 52

9.5 RESISTANCE DETERMINATION ................................................................................................... 52

9.5.1 Disk diffusion antibiotic sensitivity testing ....................................................................... 52

9.5.2 MIC by Broth dilution testing, the Sensititre method........................................................ 52

9.5.3 MIC by broth microtiter bouillon dilution testing ............................................................ 53

10 RESULTS .................................................................................................................................... 54

10.1 THE DISTRIBUTION OF THE PLASMIDIC MUCAB GENES ............................................................ 54

10.1.1 Distribution of mucAB in E. coli and Salmonella spp. from indicator and diagnostic

pigs and cattle ............................................................................................................................ 54

10.1.2 Presence of mucAB among ESBL producing E. coli from humans ................................ 55

10.2 MUTATION FREQUENCY DETERMINATION ............................................................................... 57

10.2.1 Procedure 1- Mutations induced by 4NQO .................................................................... 57

10.2.2 Procedure 2- Mutations induced by 4NQO .................................................................... 59

10.2.3 Procedure 2- Mutations induced by Ciprofloxacin......................................................... 60

10.2.4 Statistical analysis of the results ..................................................................................... 61

10.2.5 Mutation frequency in Ames tester strains S. typhimurium TA1535 and TA100 ............ 61

10.4 TARGET MODIFICATION THROUGH MUTATIONS IN QRDR ....................................................... 66

10.5 RESISTANCE AND SENSITIVITY TOWARDS CIP IN THE NAL RESISTANT STRAINS ..................... 69

10.5.1 Ciprofloxacin resistant strains ........................................................................................ 69

10.5.2 Ciprofloxacin sensitivity in NALR strains ....................................................................... 69

11. DISCUSSION ............................................................................................................................ 71

11.1 THE DISTRIBUTION OF THE PLASMIDIC MUCAB GENES ............................................................ 71

11.1.1 Distribution of mucAB among E. coli from pigs and cattle ............................................ 71

11.1.2 Distribution of mucAB among Salmonella spp. from pigs and cattle ............................. 72

11.1.3 Distribution of mucAB among 12 E. coli from humans harbouring ESBL ..................... 72

11.2 MUTATION FREQUENCY DETERMINATION ............................................................................... 73

11.2.1 MucAB mediated mutation frequencies .......................................................................... 73



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11.2.3 Experimental setup- problems faced ............................................................................... 74

11.2.3 Strain specificity .............................................................................................................. 75

11.2.4 Target specificity of 4NQO and CIP ............................................................................... 76

11.2.5 MIC of ciprofloxacin and the correlation with 4NQO or CIP induction........................ 78

11.2.6 Gene expression analysis ................................................................................................ 79

11.3 TARGET MODIFICATION THROUGH MUTATIONS IN QRDR-PART I ........................................... 79

11.3.1 Target modifications through QRDR mediated by mucAB ............................................. 79

11.3 TARGET MODIFICATION THROUGH MUTATIONS IN QRDR- PART II ......................................... 80

11.3.2 Mutations in gyrA............................................................................................................ 81

11.3.3 Mutations in parC ........................................................................................................... 82

12 CONCLUSION............................................................................................................................ 84

13 PERSPECTIVES ........................................................................................................................ 85

14 REFERENCES ............................................................................................................................ 86

15 APPENDIX .................................................................................................................................. 92

R-CODES ......................................................................................................................................... 92



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1 Introduction

E. coli is mainly harmless when present as commensal flora, but do also appear pathogenic,

causing gastrointestinal infections as well as being the main cause of urinary tract infections (36).

Diseases caused by E. coli can be treated with fluoroquinolones, which are broad-spectrum

antimicrobials, routinely used in humans. Before the early 1990s fluoroquinolone resistance was

rarely found in E. coli isolated from humans as well as animal. But since then, the frequency of

resistance has significantly increased worldwide (41).

Resistance towards fluoroquinolones is rare, since at least two base pair substitutions in the

quinolone resistance determining regions (QRDR) of the targets; DNA gyrase and topoisomerase

IV, are required (58,67). Consequently a low resistance level was expected when

fluoroquinolones was introduced in the 1980´s. In 1997 no fluoroquinolone resistance was

observed in humans in Denmark. But in the period 1997 to 2007 fluoroquinolone resistance

increased significantly both in Denmark and other countries and in 2007 resistant E. coli strains

was found in 8% of urine isolates from hospitals and 6% in the primary health care, with a

significantly increase in the period from 2006 to 2007 (36). This was consistent with a parallel

increase in consumption of fluoroquinolones both in the primary health care and hospitals (18,20).

The increasing resistance is a problem since the consequence could be untreatable infections

given that fluoroquinolones often is the only alternative to broad-spectrum penicillins and

cephalosporin’s in infections caused by bacteria producing extended spectrum β-lactamases

(ESBL) (80).

When acting on bacteria, fluoroquinolones initiate a number of cellular events, of which

mutations may be mediated. These events are closely associated with events increasing resistance

to killing by chemicals and radiation and this is why these compounds activate the SOS repair

system (85). The SOS system is the last system of repair when the others repair systems have

failed. Different polymerases are activated of which the last one is the dormant polymerase V

encoded by the chromosomal umuDC or the homolog polymerase RI encoded by the plasmidic

mucAB genes. E. coli with R-plasmids carrying mucAB could pose a threat to the society due to

the increased mutagenic potential, which may favour the emergence of antibiotic resistance.

However mucAB are only activated by mutagenic compounds and respond in different ways to

each mutagen (59). Fluoroquinolones in the environment may therefore induce an increased

mutation frequency by activating the SOS system and mucAB, mediating error-prone repair and

due to translesion DNA synthesis.



12

The effects mediated by mucAB should be of concern when thinking of emergence of resistant

strains. An increase in ESBL producing E. coli has been observed in the recent years, being nearly

always highly resistant to penicillins and many cephalosporins’ (32). If one such strain posses an

R-plasmid with mucAB an increased chance of gaining fluoroquinolone resistance occurs due to

the increased mutation frequency. If the strain already has a mutation mediating quinolone

resistance, the chances of gaining fluoroquinolone resistance are significantly increased. This

could be extremely dangerous to the patients, since now they cannot be treated with

fluoroquinolones, which was the only alternative to penicillins (32,80). The same aspect could

happen in the veterinary industry in the future, since as described an increase in ESBL producers

have been found. Even so fluoroquinolones are not used in animals in Denmark, resistance

towards other antimicrobials, could occur by the same mechanism.



13

2 Aim of the project

Given the knowledge described in the introduction, the aim of this project was to examine the role

of the plasmid located mucAB genes in emergence of quinolone resistant E. coli. This was done by

the following:

A screening of the distribution of mucAB in indicator and diagnostic strains of E. coli,

isolated from the intestines or faeces from pigs and cattle, to find the extent of the

distribution. The selection was based on randomly selected E. coli samples, a new farm

and a new pig or cattle each time. Thereby, the occurrence of repetitions of the same clone

should be minimized. The strains chosen where E. coli O140 from pig’s and E. coli K99

from cattle’s, since those subtypes are well characterized and known to be disease causing.

Strains of S. typhimurium and S. spp. were examined.

Secondly the mutation frequency was examined to find out the level of mutations per cell

division, when mucAB was activated as well to examine the mutagenic potential of

ciprofloxacin on mucAB activation. This was examined by constructing E. coli strains,

with or without the plasmid pHHA45, which encoded mucAB. The strains were grown in

the absence or presence of the mutagenic compounds 4NQO (positive control) and

ciprofloxacin, to induce transcription of mucAB. The selection for mutants was based on

nalidixic acid resistance.

Mutagenic compounds have an effect on the types of mutations that occur. Further 4NQO

and ciprofloxacin does not share target specificity. Therefore the nalidixic acid resistant

strains that emerged in the mutation frequency determination were sequenced for

mutations in sites of gyrA and parC of QRDR, to study the types of basepair substitutions

that were produced and what amino acids that were changed. This was done to see if

mucAB induced certain basepair substitutions as well as transition and transversion events.

Mutations in parC were only expected if the nalidixic acid resistant strains were

ciprofloxacin resistant. The sequencing results were compared with the MIC values of

ciprofloxacin to study the effect of certain amino acid changes on low-level

fluoroquinolone resistance.



14

List of abbreviations

A Adenine

BA Blood Agar

bp basepair

C Cytosine

cd cell division

CI Confidence interval

CIP Ciprofloxacin

CLSI Clinical Standard Laboratory Institute

CTX Cefotaxime

DANMAP Danish Integrated Antimicrobial Resistance Monitoring and Research Programme

DNA Deoxyribonucleic acid

DsDNA Double-stranded DNA

ESBL Extended-spectrum Beta-Lactamase

FQ Fluoroquinolone

G Guanine

Inc Incompatibility

kb kilo base

kD kilo Dalton

MH Müeller Hinton

MIC Minimum Inhibitory Concentration

Muc Mutagenesis UV-like chemicals

NAL Nalidixic Acid

NALR

Nalidixic acid resistant

NER Nucleotide excision repair

4NQO 4-nitroquinolone-N-oxide

OD Optical Density

OECD Organisation for economic co-operation and development

OriC Origin of replication

PCR Polymerase Chain Reaction

Pol Polymerase

QRDR Quinolone Resistance Determining Region



15

RNA Ribonucleic acid

rpm rounds per minute

R-plasmid Resistance plasmid

SSB Single strand-binding protein

SsDNA Single stranded DNA

TLS Translesion synthesis

T Thymine

UTI Urinary tract infection



16

3 Escherichia coli

3.1 Characterisation of Escherichia coli

Escherichia coli is a gram negative, rod shaped, non-sporulating, facultative anaerobic bacterium

belonging to the group of Enterobacteriaceae. It is one of the most well characterized bacterial

specie. Strains of E. coli are usually motile, fimbriate and grow in the temperature interval 15-45°C,

with optimal growth at 37°C, driven by aerobic or anaerobic respiration. E. coli grow well on non-

selective media and can be differentiated from other enteric gram-negative bacteria by the ability to

utilize certain sugars, such as lactose, producing large red colonies on MacConkey agar (32,89).

The E. coli specie may appear purely as a commensal, pathogenic or opportunistic pathogenic

bacterium in both human and animals. Strains of non-pathogenic E. coli predominates the aerobic

intestinal flora in the gut of humans and animals from the day of birth, acting as mutualistic

symbionts, by producing vitamin K2 and preventing the establishment of pathogenic bacteria within

the intestine, thereby being a benefit to the host (66,89).

E. coli is used as a prokaryotic model organism in many fields of microbial investigation of which

being used as indicator bacteria for antibiotic resistance in animals and humans is one (20).

3.2 Resistance plasmids

E. coli posses the ability to transfer DNA via bacterial conjugation, transduction or transformation.

This allows genetic material, such as plasmids, to spread horizontally through an existing

population. Thus E. coli and the other Enterobacteriaceae are important reservoirs of transferable

antibiotic resistance.

Plasmids are usually rather short, circular, dsDNA molecules, which occur extra chromosomally

and therefore replicates independently as stable components of the cells genome (61,71). Naturally

plasmids vary in size from one to several hundred kilo bases (kb) and have a copy number between

one to several hundred per cell (7,61). Many Resistance plasmids (R-plasmids) are self-

transmissible, due to transfer genes (tra). The transfer often occurs by conjugation, which is the

transfer of one copy of a plasmid from one bacterial cell to another. Conjugation is considered the

primary route for distribution of antibiotic resistance in clinical bacteria such as E. coli and

Salmonella, which have used this strategy of transfer for a long time (6,7,72).

R-plasmids carry genes for resistance towards elements otherwise stress-full for the host. For this

reason R-plasmids are considered the major cause of clinical drug resistant bacteria since its

abilities may be essential for host survival in certain environments, such as hospitals (7). For

http://en.wikipedia.org/wiki/Enterobacteria



17

instance some R-plasmids consequently carry in linkage one or more specific antibiotic resistance

determinants, such as Extended spectrum beta-lactamases (ESBL) genes, whose products provide

resistance towards antibiotics such penicillins and cephalosporin’s (6).

Plasmids borne resistance may pose a fitness cost to the host, due to the expense of metabolic

energy. But after a period of co-evolution some compensation mutations can arise, which makes the

plasmid carrying strain more fit than its plasmid free derivative (26,73).

Besides plasmids, other transposable elements can be acquired through horizontal gene transfer,

such as bacteriophages and transposons, both of which are mobile, generally dsDNA molecules,

always found within another DNA molecule (49, 61).

3.3 Transmission and diseases caused by E. coli

3.3.1 Transmission and diseases in humans

The main routes of transmission to humans are by the oral and aseptic routes, therefore urinary tract

infections (UTI) and gastrointestinal infections are the most common diseases in humans caused by

pathogenic E. coli today (Figure 1). Strains that cause UTI often originate from the gut of a patient,

with infection occurring in an ascending manner. Uropathogenic E. coli (UPEC) is responsible for

approximately 90 % of the cases of uncomplicated UTI’s at hospitals as well as causing hospital

associated urinary tract sepsis (84). Enteropathogenic E. coli cause gastrointestinal disease, ranging

from mild, self-limiting diarrhoea, to haemorrhagic colitis (66,89). Although virulent strains

typically cause no more than diarrhoea in healthy adult humans, they can cause serious illness or

death in elderly, very young or immune-compromised humans. Other common E. coli infections are

neonatal meningitis, sepsis in operation wounds and abscesses (32,66,89).

Faecal-oral contamination of water sources and food is another common way of transmission to

humans as well as animals (Figure 1), (9,32). Contaminated food can be the source of food

poisoning, which is acute illness due to the ingestion of food, which can lead to infectious

diarrhoea. In humans, common food products associated with food poisoning caused by E. coli

include unwashed vegetables and meat contaminated post-slaughter. Other pathways of

transmission are shown in Figure 1.

Depending on the type of infection, treatment of E. coli usually involves administration of co-

trimoxazole, nitrofurantoin or a fluoroquinolone in humans (37,66).



18

3.3.2 Transmission and diseases in animals

In the veterinary industry the dairy and beef animals, pigs, swine and broilers, may carry pathogenic

E. coli asymptomatically and shed the bacteria in their faeces (32). By this, transmission of

pathogenic E. coli from one animal to another is easily achieved through the oral-faecal route or by

directly contact and may spread throughout the farm, causing sporadic outbreaks of serious illness

or diarrhoea (9). Other routes of transmissions is through the drinking water or by contact with

companion animals (Figure 1).

Figure 1. The pathways of resistance transmission. This diagram has been used in various incarnations to

depict the epidemiology of antimicrobial resistance and plausible pathways of spread between various

environments. The version is from Boerlin and Reid-Smith (2008), which adapted the version from Presctott

(2000). The circles represent potential anthropogenic antimicrobial selection pressure. Some pathways are

well described, while others are plausible but lacks substantive evidence. Not all plausible pathways are

depicted (9).



19

4 Quinolones and fluoroquinolones

4.1 Antibiotics in general

Antimicrobial agents are defined as natural, synthetic or semi-synthetic chemicals that kill or inhibit

growth of microorganisms. Antibiotics are produced as natural metabolites by microorganisms to

kill or inhibit other microorganisms, whereas semi-synthetic antibiotics are produced by

pharmaceutical companies to enhance the mechanism of action of a given antibiotic. Antimicrobial

agents are divided into eleven major groups based on the structure and are classified as broad or

narrow spectrum antibiotic, depending on the range of action of the compound. Today most

antibiotics used in treatment of infections are synthetic or semi synthetic (49).

4.2 The first quinolone nalidixic acid: development and use

Quinolones are synthetic antibacterial compounds used to treat infections in humans and in

veterinary use. The introduction of quinolones goes back to 1962, in the form of nalidixic acid,

which was approved for clinical use in 1965. The spectrum was limited to Enterobacteriaceae

mainly causing UTI. Over time and in association with clinical needs, quinolones became adapted

to become broad spectrum agents (2,4). More active derivatives of nalidixic acid were evolved

from two parallel pathways: The naphthyridones, with the original naphthyridine core of nalidixic

acid, and the fluoroquinolones (FQ), which are modified nalidixic acid compounds with a

piperazine substitution at the 7-position and a fluorine substitution at the 6-position of the

naphthyridine nucleus, illustrated in Table 1 (4,74).

4.3 Fluoroquinolone development and antibacterial activity

FQ’s became clinically available in the 1980´s (74). They are fully synthetic antibiotics and to a

large extent more potent against Enterobacteriaceae than nalidixic acid, due to superior

antibacterial and pharmacokinetic features (24,65).

A second generation of FQ’s were developed, shortly after the first one, epitomized by

ciprofloxacin (Table 1 ), (4). Ciprofloxacin has a wide spectrum of in vitro antibacterial activity,

particular against gram negative bacteria and is effective in treatment of many types of infections.

Today ciprofloxacin has become the most widely described FQ in the world, typically used in the

treatment of UTI’s in humans, caused by E. coli (74).

Other FQ’s have been developed of which some are listed in Table 1. The mutual factor is the

increased antimicrobial activity per generation (16,24), however due to different side effects, the



20

most potent FQ’s used in human medicine today are ciprofloxacin, moxifloxacin and gatifloxacin

(4).

Table 1. Fluoroquinolones used as antibacterial agents. Along with the development the

fluoroquinolone compounds became divided into defined generations, each with a increased antimicrobial

activity. The quinolone pharmacore and ciprofloxacin structure are illustrated (4,74,81).

Generation Fluoroquinolone Structure

I Nalidixic acid

The quinolone pharmacore (81)

IIa Ciprofloxacin,

Ofloxacin

IIb Grepafloxacin,

Sparfloxacin

IIIa Moxifloxacin,

Gatifloxacin, Sitafloxacin,

Clinafloxacin

Ciprofloxacin (74)

IIIb In development

4.4 DNA gyrase and topoisomerase IV; the targets of quinolones

To understand how resistance towards quinolones and FQ’s occur it is necessary to know the

functions of the topoisomerase enzymes DNA gyrase and topoisomerase IV, which quinolones

and FQ’s target. Common for topoisomerases is the production of breaks and rejoinings of the

DNA to relieve stress in the helical molecule during replication. They also have an important role

in DNA packaging, a feature that makes bacteria able to contain their entire DNA (49). For

example, E. coli has a chromosomal size of about 4.64 Mb, which is around 1000 times

compacted to occupy 15 % of the cell volume. Hence DNA packaging is essential for existence

and survival (23,71).



21

DNA packaging is carried out by two complementary processes; supercoiling and relaxation

(Figure 2). Supercoiling is the twisting of dsDNA and occurs uniquely in a negative direction in

bacteria. Supercoiling is mediated by DNA gyrases belonging to the highly conserved

topoisomerase type II enzymes (25, 36, 74). DNA gyrase act in an ATP-dependant process by

breaking one of the duplex DNA strands, which facilitates the movement of replication- and

transcription complexes along the strands, passing the DNA strand through the break and

resealing the initial broken strand (24,35,74).

DNA gyrase can also remove positive supercoils to avoid stalling of replication forks, an event

also catalyzed by topoisomerase IV. Furthermore, topoisomerase IV is the principal enzyme that

removes the interlinking of daughter chromosomes at the completion of a round of DNA

replication, thereby allowing for their segregation into daughter cells (35, 36). The mechanisms

and structure of the two enzymes are illustrated in Figure 2.

DNA gyrase and topoisomerase IV both have a hetero-tetramer. DNA gyrase is composed of two

GyrA (97 kDa) and two GyrB (90 kDa) subunits, encoded by the gyrA and gyrB genes

respectively. The GyrA subunits form the catalytic core of the enzyme and ensure DNA breaking

and rejoining, while the GyrB subunits are responsible for ATP binding and hydrolysis (16).

Topoisomerase IV is composed of the two ParC and ParE subunits, which is homologous to the

subunits of DNA gyrase. ParC and parE is encoded by the parC and parE genes respectively

(35,36,58).

Fluoroquinolones act by binding and stabilizing the breaking-rejoining intermediates, made by the

type II topoisomerases. Thereby, the passage of RNA and DNA polymerases, are prevented. The

effects are stalled DNA replication and accumulation of lethal double stranded DNA breaks, which

eventually leads to cell death (Figure 2), (16, 74). The huge advantage of FQ’s lies in their target,

since DNA gyrase is found in all bacteria, both gram negatives and gram positives. For this reason

FQ’s can be used in broad spectrum treatment of bacterial infections. In gram negative bacteria

DNA gyrase is the primary target for FQ’s, whereas in gram positive bacteria topoisomerase IV is

the primary target. (36).



22

Figure 2. Structure and mechanisms of DNA gyrase and topoisomerase IV. Quinolones block these

activities by stabilizing an enzyme-DNA complex, which also functions as a barrier to the movement of

other proteins such as RNA and DNA polymerase along the DNA (35).

4.5 Mutations in gyrA and parC

To become FQ resistant at least one mutation in gyrA and parC in the quinolone resistance

determining regions (QRDR) in E. coli is required, whereas nalidixic acid resistance only requires

one mutation in gyrA (74). The mutations occur in a stepwise manner, where the first mutation

occurs in gyrA, causing resistance towards the first generation of quinolones, i.e. nalidixic acid,

and low-level resistance to FQ’s. The gyrA mutation is usually followed by a mutation in parC,

resulting in high-level fluoroquinolone resistance (10,58,75). ParC mutations are found only in

combination with gyrA mutations (10,58,75).

The step-wise resistance pattern was recently proved by Morgan-Linnell et al. (2009), who found

that all of the tested FQ resistant isolates had gyrA mutations and that 85 % of these had mutations

in parC. Furthermore, all the gyrA and parC mutations observed in the study, had been

documented previously for clinical isolates (58).



23

Mutations of the gyrB and parE genes in QRDR may also contribute to resistance although they

are secondary and less frequent and will not be discussed further (27, 36, 58).

4.6 Mutational hotspots in gyrA and parC

Many Enterobacteriaceae have similarities in the QRDR of any of the four topoisomerase genes;

gyrA, gyrB, parC and parE (87). Consequently, quinolone resistance is mainly due to target

modification by mutations occurring in the QRDRs of DNA gyrase and topoisomerase IV. Such

mutations induce changes in the active sites of the enzymes, preventing or reducing quinolone

activity (10,36). In E. coli the mutations in gyrA are localized at the 5′ end (N-terminus) at

nucleotide 199 to 318. The majority of the mutations have been found within the defined QRDR,

encoding the amino acids Ala67 to Glu106, in the GyrA protein and in the homolog areas in ParC

(35,87,90). Diminished quinolone binding may occur when a single amino acid is changed in

gyrA, leading to a changed protein structure (36,48,74).

The most frequent amino acid substitutions observed in gyrA and parC of E. coli and its nearly

associated family member Salmonella spp. are shown in Table 2. The results have been found in

several studies (10,36,58). In GyrA Ser83 is the most common changed amino acid, generally to

Leu83. Also Asp87 are frequently mutated to construct Asn87 or Tyr87 respectively (27, 87).

Ser83 and Asp87 changes are the most common amino acid changed in GyrA in quinolone

resistant isolates in clinical, veterinary and laboratory strains of E. coli. Further, the changes have

been associated with high level quinolone resistance and low-level fluoroquinolone resistance

(10,11,36,78). Lastly they have been found to be the prevalent type of mutations involved in high-

level ciprofloxacin resistance (11).

Crystal structure of GyrA have shown that the Ser83 and Asp87 typically are located to a

positively charged surface near the active site of DNA gyrase, near Tyr122 which possible

interacts with the cleaved DNA, which DNA is thought to bind. Additionally, it has been found

that when polar amino acids are mutated to less polar amino acids the affinity for quinolone

binding is reduced (35).

The most frequent amino acid substituted in parC is Ser80, corresponding to Ser83 in gyrA.

Minor frequent is the substitution of Glu84, corresponding to Asp87 in gyrA (Table 2), (27,58). It

seems that mutations of topoisomerase IV emerge, when DNA gyrase has mutated, thereby being

resistant or at least less sensitive than topoisomerase IV. Therefore is topoisomerase IV

considered a secondary target to quinolones (24).



24

Table 2. Section of the most common mutations detected in the DNA gyrase and topoisomerase IV

genes of E. coli and Salmonella spp. mediating quinolone resistance. Mutations in parC are usually

associated with gyrA mutations and often mediates fluoroquinolone resistance (35, 36, 58).

Specie GyrA ParC

Amino

acid

position

Wild type

amino acid

Mutant amino acid Amino

acid

position

Wild type

amino acid

Mutant

amino

acid

E. coli 67 Ala Ser*

81 Gly Cys*, Asp* 78 Gly Asp*

82 Asp Gly

83 Ser Leu*, Trp*, Ala*,

Val

80 Ser Leu*, Ile.

Arg

84 Ala Pro*, Val

87 Asp Asn*, Val*, Gly,

Tyr, His

84 Glu Lys*,

Gly, Val

106 Gln His*, Arg*

Salmonella

spp.

67 Ala Pro

72 Asp Gly

73 Val Ile

81 Gly Cys, Ser, His, Asp 78 Gly Asp

82 Asp Gly, Asn

83 Ser Phe*, Tyr*, Ala 80 Ser Arg, Ile

87 Asp Asn*, Tyr*, Gly,

Lys

84 Glu Lys, Gly

98 Leu Val

Do to the homology between the subunits of DNA gyrase and topoisomerase IV, codons 81, 83 and 87 in the QRDR

of gyrA correspond to codons 78, 80 and 84 in parC.

*Amino acids for which genetic data support a role for the mutation in causing resistance. The other mutant amino

acids have been associated with resistance in clinical isolates.

5 Fluoroquinolone resistance in E. coli

5.1 The rise of fluoroquinolone resistant bacteria

The target specificity of FQ’s may pose a problem, regardless of whether they are used in clinical

or veterinary medicine, since resistance towards one fluoroquinolone probably will confer

resistance towards all FQ’s (36).

In the past 25 years that have elapsed since the introduction of fluoroquinolones, resistance by

Enterobacteriaceae have been found worldwide (25,74). It is unlikely that selective pressure have

mediated resistance towards FQ’s in such a short time by random, independent mutational events,

since FQ’s are fully synthetic antibiotics and most bacteria have a low spontaneous mutation rate,



25

general once per 107

to 1011

cell division due to errors in DNA replication and DNA repair events

(5,16,49,64). In addition multiple mutations in the DNA gyrase and topoisomerase IV would be

needed and since the frequency of FQ mutations would be <10-7

mutations per cell division,

therefore in theory a bacterial population of >1014

cells would be needed for two concurrent

resistance mutations to arise. In clinical infections such large bacterial population sized are

considered unlikely (5,62). Instead intermediate strains, with a mutation frequency between 10-7

to 10-9

, are typically selected in heterogeneous or rapidly changing environments, which have

been shown in clinical isolated antibiotic-resistant gram-negative pathogens (5,25,49).

The stress and DNA alterations provided by the antimicrobials may induce error prone repair

mechanisms (SOS) which results in a transient mutator state. Thus exposure to FQ’s would then

increase the mutation frequency to this class of antimicrobials in an exposed bacterial population

(9). Some disadvantages follows with an increased mutation rate due to the huge amount of non-

beneficial mutations or harmful mutations (5,6). Only 1 out of 150 newly arising mutations in

Enterobacteriaceae are beneficial about 10 % of these increases the fitness of the individual

carrying it (64). Instead another explanation of the FQ resistance could be the use of nalidixic acid

as treatment of choice, before development of FQ’s. Therefore a selection of quinolone resistant

strains has occurred and only one additional mutation in the quinolone resistance determination

regions (QRDR) is needed to become fluoroquinolone resistant. This increases the possibility of

development of FQ resistance significantly (62).

Besides target modification other mechanisms can be acquired by mutations to gain FQ

resistance, such as changes of permeability, development of efflux pumps and target protection

(e.g. qnr), (10,74,78). Thereby may high level resistance towards FQ’s be the result of the

selection of nalidixic acid resistant strains in combination with resistance mechanisms in the same

strain (6,25,74).

5.2 Antimicrobial consumption and resistance in humans

Among diagnostic E. coli (connected with disease) a higher frequency of resistance is often

observed than among those from healthy humans and animals (indicator). This can be explained by

several factors, such as the acquirement of resistance genes located on plasmids, or that the bacteria

originate from environments where antibiotics have been used in consequence of disease problems

(18).

Antibacterial consumption in Denmark, both in the community and in hospitals, has been

considered one of the lowest compared to other European countries and one of the most narrow-



26

spectrum. Although 90 % of antibacterial agents are consumed in primary healthcare, there is

evidence to suggest that antibacterial selection pressure is much higher in hospitals. The use of

broad spectrum and new antibiotics has increased at Danish hospitals, from 19 % in 2001 to 34 % in

2007 (20).

In general, E. coli infections are treated with antibiotics such as amoxicillin as well as other semi-

synthetic penicillins, ciprofloxacins, cephalosporins and aminoglycocides etc. In the 1990’s

resistance towards FQ were rare in clinical isolates of E. coli (18,36). But since year 2000, an

extensive increase in the consumption of FQ’s have been found (Figure 3, shows from 2003), (20).

The consequences are evident, since the resistance towards FQ’s in E. coli isolates from blood

infections have increased intensively from 4 % in 2003 to 13 % in 2007, to a level almost the same

as the amount of nalidixic acid resistance. The increase in FQ resistance occurs in correlation with

an increased use of FQ’s, especially ciprofloxacin, through the last years, both in the primary sector

and at hospitals (20).

One explanation to the increase in FQ resistance is the high correlation between the increased use of

cephalosporin’s and FQ’s and selection of ESBL producing Enterobacteriaceae, since ESBL genes

are located on plasmids, which often carry genes that cause resistance to amino glycosides and

fluoroquinolones (20,32,63). The ESBL production makes these strains nearly always highly

resistant to penicillins and many cephalosporins’ (32). Therefore treatment options are limited and

FQ’s tend to be used as treatment instead.

5.3 Antimicrobial consumption and resistance in animals

In animal production the total consumption of antimicrobials has increased gradually since 1996, as

described in the latest DANMAP report from 2007 (20). The antibiotic use increased 6,3 % from

2006 to 2007 in the production of pigs, corresponding to an increase of 3,9 % per kg meat

produced. However from 2006 to 2007 the increase in resistance was 5,2 % showing the correlation

between antimicrobial consumption and resistance development. Pigs comprised 80 % of the total

veterinary consumption while cattle comprised 12%.

The most commonly used antimicrobials in pigs are tetracyclines, macrolides and pleuromutilitins.

In cattle beta-lactamase sensitive penicillins are the most common ones used, followed by

tetracyclines. In pigs and cattle FQ’s are normally not applied to treat for microbial diseases (20).

In 2005 the first two ESBL producing E. coli from domestic bred pigs and cattle were reported and

in the following year, the first ESBL producing Salmonella was detected in a Danish pig herd. In

2007, 23 ESBL producers were found out of 1.175 examined isolates, corresponding to a 77 %



27

increase from 2006 to 2007 (20). If the number of ESBL producers increase in animals, then other

antimicrobials such as FQ’s probably will be needed if the infections should be overcome, being the

same problem that were see in humans.

Figure 3. Trends in the use of fluoroquinolones and occurrence of fluoroquinolone resistance among E.

coli from blood infections at Danish hospitals in the period of 2003 to 2007 (20). a) Estimated number of

occupied bed days.

6 The muc operon and its role in Ames test and the SOS response

6.1 Ames bacterial reversion test

Ames test was developed in the early 1970s by a group at the University of California in Berkeley

under the direction of Bruce Ames, who laid name to the test (28). The revised and now standard

method is described in a paper written by Maron and Ames (1983), (52).

Ames test is one of the most useful screens for determining the potential toxicity and

carcinogenicity of many compounds (28,34). The Organisation for economic co-operation and

development (OECD) has made some guidelines for the performance of Ames test and the use of

specially constructed mutants of E. coli and S. typhimurium (29,92).

The Standard Ames test was designed for detection of potential mutagenic compounds, through

the induction of reverse mutations in the gene encoding synthesis of the amino acid histidine, of

modified S. typhimurium strains (28). The mutagenesis was tested by looking for an increased



28

reversion rate in auxotrophic strains of S. typhimurium in the presence of the suspected mutagen

(49).

The mutagenic activity of the test compound is evaluated through calculations of the ratio

between the number of revertant colonies scored at a test concentration and the number revertant

colonies scored in the solvent controls (28). Besides using bacteria as sensitive indicators of DNA

damage, mammalian liver extracts (S9-mix) may be used for metabolic conversion of carcinogens

to their active mutagenic form, since many mutagenic compounds inactive in their native form

(55).

Ames tester strains does almost exclusively use error-prone repair pathways, whereas normal

repair mechanisms are thus thwarted (1). So far have histidine auxotrophs of S. enterica and S.

typhimurium and tryptophan auxotrophs of E. coli been the major tools of Ames test (28,49,68).

In the standard Ames test OECD recommend six different Salmonella strains; TA98, TA100,

TA1535, TA1537, TA102 and TA1538 as well as E. coli WP2uvrA/pKM101, which is excision

repair deficient and have an A:T substitution at trpE56 (28, 34).

For a more detailed description of Ames test and the recommendation of performance see Maron

and Ames (1983) and Gatehouse et al. (1994), (29,52).

6.2 Ames tester strains and plasmid pKM101

Besides carrying genes promoting resistance, some R-plasmids carry additional genes that

promote increased resistance and survival by interactions with DNA repair and replication

mechanisms of the host. This event can be ascribed to plasmids from over 10 different

incompatibility (Inc) groups (44). One of the best studied of these plasmids is the 34.5 kb

resistance plasmid pKM101 belonging to the IncN group. PKM101 increase the mutagenic

potential of bacteria, by increase of the rate of mutations, an effect termed the “mutator effect”

(56,59). Further, it has retained the ability to enhance UV-survival and spontaneous UV-induced

mutagenesis (59). It was utilized by McCann et al. 33 years ago (55). The abilities of pKM101

made it optimal for testing mutagenic compounds in Ames bacterial reversion test (56,59,85).

Thus when plasmid pKM101 was introduced into S. typhimurium TA1535, the resulting strain

TA100 became the most sensitive of all the S. typhimurium tester strains, being highly suitable for

detection of mutagens causing frameshift and base-pair substitutions (54,56,68).



29

6.3 Identification of the muc operon

In the work with pKM101, Perry and Walker (1982) constructed some Tn5 insertion mutants of

pKM101, which led to the complete loss of the ability to influence mutagenesis and repair.

Mapping of these insertions led to the identification of the approximately 1.6 kb long muc region,

which was necessary for the mutator effects of pKM101. The muc region got its name do to the

fact that mutagenesis occurs when the host harbouring the plasmid is exposed to UV or chemicals

(59,65). It encodes the two genes mucA and mucB. PKM101 is the best studied R-plasmid, which

posses the ability to increase the survival and mutation rate of their UV-irradiated bacterial host,

due to the carriage of the muc operon (30,44). The presence of the muc operon has been ascribed

to plasmids from over 10 different Inc groups (44).

The muc locus consists of the two genes mucA and mucB, organized in an operon with the mucA

gene located upstream the mucB gene. Sequencing studies have revealed that the reading frames

of the two genes overlap by 10 base pairs. The muc genes lies within a region between 1.9 kb to

2.4 kb of the pKM101 genome and is surrounded by inverted repeats, suggesting that it might be,

or might once have been a part of a transposable element (44,45,59,85).

The muc region has been shown to increase the susceptibility of cells to mutagenesis and their

resistance to killing by UV to a greater extent than the chromosomal umu region in E. coli, which

is involved in DNA repair and mutagenesis as well (46,59). When pKM101 was introduced into

umuC deficient mutants, mucB suppressed the deficiencies in mutagenesis and repair, and actually

increased the repair and mutagenesis above the level observed in the regular umuC strain.

Moreover it was found that mucAB suppress the umuDC phenotype. The simplest interpretation of

the results was, that mucAB codes for functions analogous to those of the umuCD genes, but in a

faster and more effective way (13,77).

6.4 Proofreading strategies

During prokaryotic DNA replication different proofreading strategies lowers the mutation rate

mostly due to the large amount of special cell enzymes and processes, which serves as

checkpoints during replication (49). Some of the almost error-free repair processes are DNA

proofreading, nucleotide excision repair (NER), mismatch repair and homologous recombination

(42,49). Many of these repair systems are activated fulltime and require template instruction,

thereby leading to an almost error-free DNA replication. However these systems are often not

sufficient to repair the large scale damage done by some DNA damaging agents (77). Fortunately

other networks of genes have induced expression in response to DNA damaging agents. One such



30

network is the error-prone SOS system found among others in E. coli and Salmonella, which

activates umuDC and mucAB (38,54).

6.5 The SOS repair system

In E. coli, the expression of approximately 40 unlinked SOS genes is induced in response to

exposure of DNA damaging agents. Most of the genes encode proteins engaged in protection,

repair, replication and mutagenesis of DNA (38,77).

The SOS repair is a post replication system, consisting of a series of complex cellular mechanisms

mainly regulated by the two key genes lexA and recA (Figure 4), (49,85). The LexA repressor acts

by binding to operator sequences, referred to as “SOS boxes”, with a high degree of sequence

conservation, near promoters of each gene. This binding interferes with the binding of RNA

polymerase and thereby represses the SOS system (79,85).

When chromosomal DNA in a cell is damaged, regions of single stranded DNA (ssDNA)

accumulates, which is the internal indicator of damaged DNA (85,86). The few free RecA

molecules that are present, are polymerized on the ssDNA molecules in an ATP hydrolysis driven

reaction, to form a helical, nucleoprotein filament; RecA-ssDNA (77,79). RecA-ssDNA is often

referred to as RecA′ or RecA*, which describes the activated form of RecA. RecA′ functions as a

co-protease that facilitates LexA cleavage by stimulating the latent ability of LexA to autodigest.

The decrease in the LexA repressor pool induces the transcription of various SOS genes,

including recA, umuDC or mucAB (54,79,86). As the cell begins to recover the amount of ssDNA

is decreased, the RecA molecules return to their proteolytically inactive state and LexA repress

the SOS system once again (85).

The plasmidic mucA′B system is believed to be a functional homolog to the chromosomal

umuD′C system when referring to SOS regulation, as both operons contain the highly conserved

SOS-boxes for LexA, showing that mucAB probably are repressed by LexA and partly because

the protective effects of mucAB are not expressed in recA deficient strains (30, 86).

6.6 The gene products of mucAB

The gene products of mucA and mucB are the two proteins MucA and MucB. They have a

molecular weight of approximately 16 kD and 45 kD, similar to the size of the chromosomal

umuC and umuD gene products: UmuD and UmuC (59, 65). In Figure 4 the genes products of

umuDC and their effects is illustrated, this correspond to the effects of the mucAB products.

MucA has a higher affinity for RecA than UmuD, and consequently a faster processing of MucA



31

to MucA′ (13, 30). MucA is cleaved in a posttranscriptional process, to generate the active form

MucA′. MucA′ forms a homodimer Muc(A′)2, which forms a complex with MucB and this

Muc(A′)2B protein complex switches DNA repair from homologous recombination to SOS

mutagenesis (Figure 4), (13,33,77).

Figure 4. Regulation of the umuDC operon by RecA and LexA. DNA damage generates a signal that

converts RecA to the activated form RecA* that mediates the cleavage of the LexA repressor. This results

in the induction of the umuDC operon and the other SOS response genes. RecA* can also mediate the

processing of UmuD to the shortened UmuD’ molecule. UmuD and UmuD’ can interact with UmuC in a

variety of combinations. The Umu(D)2C complex seems to be involved in regulating the E. coli cell cycle

after DNA damage. The UmuD(D’)2C complex is active in SOS mutagenesis (translesion synthesis). The

third complex UmuDD’C does not appear to have an activity, but it may play a role in shutting off SOS

mutagenesis by sequestering UmuD’ (77).



32

6.7 DNA polymerases involved in SOS repair

Three potential mutagenic DNA polymerases (Pol) are activated in the SOS response; Pol II, Pol

IV and Pol V. These polymerases compete hierarchically; Pol II > Pol IV > Pol V (Fejl!

Henvisningskilde ikke fundet.). Pol II (polB) and pol IV (dinB) appear in the early stages of SOS

induction whereas pol V (umuC) is a dormant polymerase only synthesized in SOS induced cells

(17,30,38). Pol IV and pol V belongs to the Y family of polymerases, who possess the ability to

replicate through damaged DNA to fill in the gaps, a process called translesion synthesis (TLS).

This is an error-prone repair process due to the lack of template instructions (54). Further, both

polymerases have the ability to catalyze the shifting of a functional group from one position to

another within the same molecule (54,79).

Genotoxic compounds, such as ciprofloxacin, may cause stalled replication forks and gaps in the

daughter strands. Normally, RecA recognize and fill these gaps by using a homologous DNA

sequence from the replicated sister chromatid, by recombination (54). If this isn’t possible the

SOS regulated polymerases mediate TLS as shown in Figure 5.

Pol V is the most error-prone TLS polymerase and plays an important role in mutagenesis

induced by UV light and a variety of genotoxic compounds. It is the last polymerase activated,

acting as a last response for survival (38,54). Pol V, encoded by umuC, are homologous to the

polymerase RI, encoded by mucB (17,30).

The mechanism of activation of pol RI is as follows; when LexA is cleaved free RecA molecules

are produced. These are stimulated by single strand-binding proteins (SSB) to form RecA-ssDNA.

Pol RI probably binds SSB to target RecA-coated ssDNA. The binding of pol RI to the RecA-

ssDNA complex is mediated by MucA. This alters the conformation of pol RI, without including

dissociation of SSB from DNA (30).

An increased bypass effect for pol RI compared to pol V have been found, probably due to a

different dependency of UmuDC and MucAB on interactions with the RecA protein (Figure 7).

Goldsmith et al. (2000) have proven that mucB encodes the polymerase RI, since it is highly

activated by MucA′, RecA and SSB and have no or little polymerase activity on its own, as shown

in Figure 6. Furthermore, they showed that all the mentioned components are essential for DNA

bypass, since no TLS occurred when each of the four elements was left out (30).

So far, pKM101 encoding mucAB has played a major role in the success of the SOS system, when

testing for mutagenesis. However umuDC deficient strains should still be used, since some



33

chemicals produce direct mispairing lesions, which do not require SOS processing to cause a

mutation (59, 85).

Figure 5 The model of SOS mutagenesis via translesion synthesis. (A) The DNA polymerase is replicating a

DNA template normally (active replication is indicated by: →). (B) The polymerase encounters a damaged

nucleotide (X). (C) The polymerase incorporates a nucleotide opposite the lesion but cannot replicate

through the lesion. (D) RecA*, UmuD’ and UmuC are required for the polymerase to replicate through the

lesion (TLS). If the nucleotide incorporated opposite the lesion was incorrect (C), TLS will fix the mutation

in the organism’s genome (D) (77).



34

Figure 6. DNA polymerase activity of MucB.

Gap-filling bypass replication was performed with

MucB alone or in the presence of MucA’, RecA

and SSB using the gap-lesion plasmid GP21 as a

substrate. Reaction products were restricted,

fractionated by urea-PAGE, and visualized by

phosphoimaging. The DNA bands of 19, 29 and

47 nucleotides long represent the unextended

primer, the replication products blocked at the

abasic site, and the bypass product, respectively.

M, size marker for the 47-mer bypass product

(30).

Figure 7. Kinetics of translesion replication by

MucB in the presence of MucA’, RecA and

SSB. The quantification is showing the percent of

lesion bypass, calculated as the total amount of

DNA extended beyond the abasic site, divided by

the total amount of extended primers (30).



35

7. DNA damaging agents

7.1 The mutagenic potential of mucAB

Activation of mucAB is induced by mutagenic compounds, which are chemicals or physical

agents that generate changes in the genetic material, usually DNA, of an organism and increase

the frequency of mutations above the natural background level. Hence mutagen means “origin of

change” in Latin, since the DNA or replication is mostly affected and the frequency of mutations

is increased (55). Some of the mutations may be lethal. However, E. coli possessing mucAB may

have a better chance to adapt to and survive these mutations, since the repair mechanisms can be

switched to SOS repair and survival, due to TLS mediated by pol RI (30,54).

One type of DNA lesions commonly produced by a variety of mutagens is abasic sites, which

strongly block DNA replication by inhibition of elongation. The muc operon was tested for

mutagenic properties to promote replication past this site. The result was that mucAB strongly

promotes replication past each abasic site (46). This feature may be the explanation to why some

R-plasmids carry mucAB.

The mutagenic compounds listed in Table 3 are known to activate mucAB. Examples of the results

found in Ames test with S. typhimurium strains and some of the mutagens are shown as well. S.

typhimurium TA1535 and TA1538, both lacking pKM101, were found to be poorly activated by

the mutagens, shown by the amount of induced revertants per plate. But when pKM101 was

present, in the isogenic S. typhimurium strains TA100 and TA98, the amount of induced

revertants per plate increased significantly (59). From the data presented in Table 3, along with

the previous findings mentioned, the mucAB genes were found to possess a strong mutagenic

potential (33,46).

7.2 Mutagenic compounds activating mucAB

In general, most mutagens are carcinogenic, such as 4-nitroquinolone oxide (4NQO), methyl

methanesulfonate (MMS) and Furylfuramide (AF-2), since the many mutations they provoke,

promotes cancer (Table 3). The degree of activation of the SOS response depends of the

mutagenic compound, indicated by the amount of induced revertant per plate (59,85). In addition

to the chemicals listed, UV light and ionizing radiation are two well known mutagenic agents.

Mutagens induce either transition or transversion events. Transition is the substitution of a purine

for another purine, A→G or G→A, or a pyrimidine for another pyrimidine, C→T or T→C.



36

Transversion is the substitution of a purine for a pyrimidines, or reverse, e.g. A→ T, C→ G (49).

Transversions can be caused by ionizing radiation and alkylating agents (22). Alkylating agents

are typically clinically used for treatment of a variety of cancers. The other compounds in Table 3

are typically used for research purposes.

EMS produces random mutations by nucleotide substitutions, specifically guanine alkylation. The

product is typically point mutations. It is most likely that pol RI bypass ethyl, but not methyl

adducts in DNA since it has been found that ENNG but not MNNG induce mutagenesis in the

presence of pKM101 (54).

The nitro-compound 4NQO is a quinoline derivative and a tumorigenic compound used in the

assessment of the efficacy of drugs and procedure in the prevention and treatment of cancer in

animal models. It induces DNA lesions and is used as positive control compound in Ames test as

well as in other mutagenicity assays (52,54). 4NQO has been shown to produce transversion and

transition events, predominately G→A and C→T transitions, accounting for approximately 90 %

of the total events. A tenfold lower prevalence for G→T and C→A transversions has been found,

however this may vary depending on the target site (15).

The consequences of transversion events are more severe than transition events, since this type of

mutation changes the chemical structure dramatically. For this reason although there is twice as

many possible transversion events, transitions appear more often in genome, possibly due to the

molecular mechanisms that generate them (49).

7.3 Base pair substitutions induced by mucAB

When DNA is damaged and Pol RI fills in the gaps, it tends to produce base pair substitutions or

-1frameshift mutations, depending on the type of mutagenic compound. Recently Curtis et al.

(2009) have found that transversions accounts for 51 % of the total number of basepair substitutions

mediated by pol RI (17). Since transversion mediates more drastically changes, this could be the

result of the Pol RI mediated repair.

Generally Pol RI tends to enhance mutations at AT base pairs and especially transversions of

AT→CG (59). Lawrence et al. (1996) described the insertion of bases at abasic sites by mucAB

encoded TLS, with or without induction by UV irradiation. The most prevalent base substitution

mediated by mucAB was adenine, with a total account of 75% and 78 % of the basepair

substitutions in two independent abasic sites. The base substitutions with guanine and thymine was

more seldom and none substitutions with cytosine was found at all (46).



37

7.4 Quinolones as mutagenic compounds

It has been speculated whether quinolones act as mutagenic compounds. Firstly, it was concluded

that they did not act in this manner, since only negative results were observed in in vivo

eukaryotic assays (80). But later on the results were referred to the experimental setups, since the

activity of quinolones towards prokaryotic and eukaryotic topoisomerases type II is different (80).

Now in vitro tests have shown that quinolones do act in a mutagenic manner, yielding

mutagenesis at levels more than 2-fold lower the bactericidal effects (34,67). Today the mutagenic

effects have been shown in both E. coli WP2uvrA/pKM101 and different strains of Ames S.

typhimurium containing pKM101 (12,34,91). This indicates that error-prone repair pathways can

participate in mutagenesis induced by quinolones. As it have been discussed whether this feature

should be related to the induction of the SOS-response due to the effects quinolones have on DNA

gyrase. Thereby they potentiate mutations towards themselves, by causing mutations in the genes

coding for their target enzyme (9,67). Additional mutagens usually target DNA itself. Therefore,

FQ and other quinolone agent’s are not direct-acting mutagens (67). This further supports that the

detection of quinolones mutagenic effects could be influenced by the location of the bacterial

target studied and that quinolones instead should be classified as genotoxic compounds

(12,13,16). In general fluorinated compounds have shown to be better inducers than the non-

fluorinated precursor nalidixic acid (67).



38

Table 3. Mutagens and their carcinogenicity and mutagenic effects observed in Salmonella

typhimurium strain TA1535 and TA1538 with and without pKM101. Modified version from Mortelmans,

K. 2006 (59).

Mutagen Abbreviations Carcinogenic TA1535 TA100 TA1538 TA98

Alkylating agents

Induced revertants per plate

N-Methyl-N’-nitro-N-

nitrosoguanidine

MNNG + 1511 18701 0 22

Methyl methanesulfonate

MMS + 5 3244 0 5

Ethyl methanesulfonate EMS (+) 220 406 2 13

Nitro compounds

2-Nitrosofluorene 2-NFI + 0 462 3936 3841

4-Nitroquinoline- N-oxide

4NQO + 118 7640 339 641

Other compounds

Furylfuramide

+ 0 1674 0 169

Aflatoxin B1*

AF-2 + 0 2260 80 1940

Benzopyrene* + 7 2398 196 685

* Activated by Araclor-induced rat liver S-9.



39

8 Introduction to the methods used

8.1 Selection of indicator and diagnostic strains

When searching for specific characteristics, randomly collected bacteria are usually chosen, of

which two types of strains are examined, namely the indicator strains and the diagnostic strains.

The indicator strains are isolated from animals or humans, without being involved in causing

disease, whereas the diagnostic strains are isolated from diseased animals or humans. The

information about the indicator strains can be used to estimate the frequency of each type of

resistance in the whole population. This can be compared the level found in the diagnostic strains to

estimate the occurrence of each type of resistance in the population of diagnostic strains (18).

Specific subtypes can be chosen, such as E. coli O149, which is well characterized and known to be

disease causing. Thereby, the study of diagnostic strains is limited to one subtype with clonality, but

yet heterogeneity, to ideally represent the whole population of E. coli.

8.2 Transformation

Transformation is a way that bacteria acquire foreign DNA, such as plasmids, by uptake through the

cell wall. Transformation can be performed in the laboratory. Firstly, competent cells are produced.

These cells are able to take up exogenous DNA from the environment due to the laboratory

induction where the cells are made passively permeable to DNA uptake. The competent cells can be

electroporated, where the cell membranes are made permeable for smaller DNA fragments, due to

the short lasting electric shock. Additionally could a Lysogeny Broth medium (LB-medium) be

added, which results in higher transformation efficiencies of plasmids due to the multiplication of

the cells, and to secure the expression of the resistance genes (88).

Another transformation method is transformation by chilling cells in the presence of high

concentrations of divalent Ca-ions (in CaCl2) at 0°C, whereby the cell membrane becomes

permeable, following by incubated on ice with the DNA and lastly a brief heat shock (30-120 sec)

at 42°C, which causes the DNA to enter the cell (49).

Since transformation usually produces a mixture of few transformed cells and numerous non-

transformed cells, a selection for transformants can be carried out on selective agar plates, since the

vector usually contain a gene conferring resistance to an antibiotic that the recipient strain is

sensitive to. Therefore, the cells that grow on selective plates are the ones that have been

transformed by the vector, since the cells lacking the plasmid are unable to grow. For instance if the



40

vector carries the cefotaxime (CTX) resistance marker, the selection is carried out on agar plates

containing CTX. Thereby only the transformed cells will grow. Another marker, typically used for

identifying E. coli cells that have acquired recombinant plasmids, is the lacZ gene, which codes for

β-galactosidase. The cells that are able to metabolize galactose sugar (X-gal) have been transformed

and blue colonies will appear. Hence the selection is based on whether or not blue colonies appear

(43).

8.3 Polymerase chain reaction

The polymerase chain reaction (PCR) is a molecular method used to amplify and identify specific

DNA fragments. The knowledge of some DNA sequences must be known, which flank the

fragment of DNA to be amplified, to chemically synthesize two oligonuclotide primers, each being

complementary for each stretch of DNA to the 3’ side of the target DNA. One forward and reverse

primer for each strand of DNA is produced.

The PCR consist of three major steps: Denaturation of the DNA by heating the reaction to above

90°C; Annealing where the two oligonucleotide primers hybridize to their complementary sites that

flank the target DNA. The annealing temperature depends on the GC content and the length of the

fragment that should be amplified; Extension of the annealed oligonucleotides by binding of the

DNA polymerase to the free 3’-hydroxyl groups. The extension step is carried out by a thermo

stable DNA polymerase, usually Taq polymerase. Each step is usually repeated between 30 and 40

times, termed cycles. In each cycle the DNA amount is doubled (exponential amplification) and

new complementary DNA strands generated based upon the existing ones (88).

To analyze the PCR product 1,5 % agarose electrophoresis gels are usually used and the sizes of the

amplified bands are compared to the size of a molecular weight standard (typically 100 bp lambda).

8.4 Mutations rate determination by fluctuation tests

8.4.1 Luria-Delbrück experiments

The Luria-Delbrück experiment (1943) is a test used to demonstrate that mutations arise in the

absence of selection in bacteria, rather than being a response to selection. It therefore apply

Darwin’s theory of natural selection acting on random mutations to bacteria (40,69). Fluctuations

test can be performed in many versions. One type is Ames test which was described previously.



41

Some fluctuation tests measure the amount of induced mutants. The mutation frequency is

determined by comparison to the control plates. This method takes into account if two or more

types of resistant strains occur. Other takes advantage of a positive outcome, thereby is the amount

of mutants unimportant, but rather the presence or absence of mutants. The mutation frequency is

instead estimated based on the CFU counts of control wells.

8.4.2 The Poisson distribution

The Luria-Delbrück test still serves as the basis for estimating microbial mutation rates today,

although later developments have resulted in much improved methods (40,69). In fluctuation

experiment each of n (number of replicates) parallel cultures is seeded a time zero with N0

nonmutant cells for incubation. At a later time T, each culture has NT nonmutant cells. The content

of each culture are plated to facilitate counting of mutants existing at time T in n cultures. This

process results in experimental data in the fromX1, X2,…. Xn. The numbers of mutants existing in

the n cultures still remain devoid of mutant cells at time T. The original Lurie-Delbrück (1943) P0

method estimates the mutation rate by :

𝜇0 = 𝑙𝑜𝑔2−log (𝑃 𝑕𝑎𝑡 0)

𝑁𝑇−𝑁0 ,with P(hat)0 = z/n

They used mutations per bacterium per division cycle. This is the mutation rate, which is the

probability that a cell undergoes a mutation during the cells life cycle (Article 69 cited in specific

words). As shown the mutation rate is Poisson distributed.

The Poisson distribution is a discrete probability distribution without an upper limit, corresponding

to a counting in a series of experiments. It was discovered by Siméon-Denis Poisson (1781-1840)

who derived the distribution in 1837. The Poisson distribution is applied to systems with

spontaneous events within a defined area. The sample space is therefore the unlimited set N0

={0,1,2,...n}. The Poisson distribution is an approximation of the Binomial distribution, where n is

high and p (possibility) is small (76). In Figure 8 the distribution is shown, when 1000 estimated

mutations rates are obtained, by simulating fluctuation experiments.



42

Figure 8. Distribution of 1000 estimated mutation rates obtained by simulating fluctuation

experiments. Each simulated experiment consists of 30 cultures and the probability of mutation per cell

division is x10-8

(69).

8.5 Handling mutagenic compounds- 4NQO

4-nitroquinoline-N-oxide (4NQO) is a well known mutagenic compound used in Ames test as a

positive control compound (Table 3), (52). Many mutagenic compounds needs the presence of

mammalian liver extract (S9-mix), to generate a metabolic conversion of carcinogens to their active

mutagenic from, since many of the mutagenic compounds are not active in their native form (55).

However 4NQO does not need the presence of S-9 mix, since the compound is already in its active

form, which makes it easier to work with in other studies. It is however recommended to use S-9

mix anyway since this has been shown to increase the effects of 4NQO (52).

The use of 4NQO is limited to research studies due to the toxicity and carcinogenic effects. For this

reason 4NQO should always be handed in the fume hood. Compared to other mutagens 4NQO is

easy to handle in the laboratory, since it can be dissolved in acetone. Other mutagens, such as

MMS, should typically be dissolved in organic compounds such as dimethylformamide (DMF)

which are somewhat hazardous, since exothermic decompositions have been reported at

temperatures as low as 26 °C. DMF has also been linked to cancer in humans and cause birth

defects.



43

8.6 Growth determination by Bioscreen C

Bioscreen C is an incubator/reader/shaker and a culture growth monitoring device (OD reader),

used to monitor kinetically growth of 200 microbial samples at a time. The system generates

automatically growth curves, one for each well, and perform microbiological calculations

automatically by the use of the Research express® software, by measurements of changes in OD

versus time. Bioscreen C measures the sample turbidity, produced by multiplication in broth,

kinetically and displays the turbidity versus time graph (growth curves) on the screen. Growth data

is recorded kinetically to a computer hard disk.

Bioscreen C is an open system thereby the user can decide which microorganisms, broths or

chemicals to use. Therefore broth cultures of bacteria, yeast, fungi or cells can be used in the

system. It is a useful tool to measure the effect of an environmental parameter by miniaturized

bioassay measurement of effects such as chemicals, pH, temperature, antibiotic susceptibility test

and others. Additionally Bioscreen C can be used for both aerobic and anaerobic bacterial strains.

The advantages of Bioscreen C lies in the possibilities of changing programme parameters,

therefore it is possible to cover a wide range of research application in a routine work. Seven

wavelengths can be chosen; 405, 420, 450, 492, 540, 580 and 600 nm plus wide-band for turbidity

measurements (unaffected by change in colour in wells), Bioscreen is more sensitive than a

spectrophotometer. There is no evaporation of the sample, since the cover on is kept on and the

temperature can range from 1 to 60 °C (+/- 0.1 °C), (93).

8.7 Resistance determination

8.7.1 Minimum inhibitory concentration

The minimum inhibitory concentration (MIC) is the lowest concentration of an antibiotic in a given

culture medium, e.g. broth or agar that inhibits the visible growth of a bacterium after overnight

incubation. MIC is a diagnostic method to confirm or reject the resistance of bacteria to

antimicrobial agents as well as a method to measure the activity of antimicrobial agents. Therefore

MIC is regarded one of the most basic measurements of the activity of antimicrobial agents towards

bacteria (20).

8.7.2 Resistance breakpoints

MIC interpretations can be made by following the guidelines of a committee such as BSAC (British

Society for Antimicrobial Chemotherapy), EUCAST (The European Committee on Antimicrobial



44

Susceptibility Testing) and CLSI (The Clinical Standard Laboratory Institute), of which the CLSI

guidelines is followed in this study. CLSI defines clinical (pharmacological) breakpoints, thereby it

is defined whether at clinical bacterial isolate is sensitive, intermediate or resistant towards a

specific antibiotic. This measurement is used to define the treatment directions of the patient (14).

Epidemiological breakpoints state the upper MIC level for the normal wild type population.

Thereby are the bacteria either wild type or not. Epidemiological cut-off values are mostly used for

monitoring antimicrobial resistance. The same epidemiological breakpoint can be used for

monitoring resistance in bacteria obtained from animals, foods and humans as done in the

DANMAP 2007 report (14,20).

8.7.3 MIC by Broth dilution testing, the Sensititre method

Generally, broth dilution testing is a way to measure the MIC values of a bacterium to several

different antibiotics. Each well contains a dehydrated antibiotic and this is made in a series of

dilutions. The wells are incubated with specific inoculums of bacteria in a bouillon.

The Sensititre method is a commercial variant of the broth dilution test, where about 18 different

dehydrated antibiotics are tested. Typically two positive growth controls are made, where no

antibiotics are present. To make sure that the test is performed correctly a negative control can be

applied, by the use of a strain known to be sensitive to the antibiotics of interest. When working

with E. coli one such standard strain could be E. coli ATCC® 25922.

Another test that can be used to measure the MIC of an antibiotic is Etest®, which is a plastic strip

containing a concentration gradient of antibiotic. The strip is placed on an inoculated agar plate and

the antibiotic diffuse in to the media. The MIC value can be read directly at the inhibition line.

8.7.4 Disk diffusion antibiotic sensitivity testing

Disk diffusion antibiotic testing is a method, which uses antibiotic impregnated wafers, to test

whether a particular bacterium are susceptible to specific antibiotics. A known amount of bacteria is

inoculated on agar plates in the presence of thin wafers containing relevant antibiotics. After

incubation, the susceptibility of the bacteria to the antibiotic is measured, since an area of clearing

surrounds the wafer where bacteria are not able of growing, this is the zone of inhibition The size

(mm) of the inhibition zone and the rate of antibiotic diffusion are used to estimate the sensitivity of

the bacteria to the particular antibiotic give by CLSI guidelines (14). In general larger zones

correlate with smaller MIC values of antibiotics.



45

9. Materials and methods

9.1 Bacterial strains

When studying the distribution of mucAB genes, E. coli O149 from pigs and E. coli K99 from cattle

were chosen, since those subtypes are well characterized and known to be disease causing. The

isolates were obtained from the continuous surveillance program for antimicrobial resistance in

Denmark (DANMAP) during the year 2008. The selected strains ideally represent the total

population of E. coli in pigs and cattle. In summary, 81 indicators and 58 diagnostic E. coli O149

from the faeces or intestines from pigs were examined. Further, 81 indicators and 45 diagnostic E.

coli K99 isolated from the faeces or intestines from cattle were examined. Additionally, 33

diagnostic S. typhimurium isolated from pigs and 36 diagnostic S. ssp. isolated from cattle, isolated

from the faeces or intestines were examined. No specific subtype of Salmonella was chosen.

Twelve E. coli strains isolated from healthy humans were also examined. for the presence of

mucAB, since they contained R-plasmids conferring ESBL production (CTX-M-1) and besides were

classified as being weak mutators with a mutation frequency between 4x10-8

and 4x10-7

(5).

When studying the impact of mucAB on the mutation frequency, E. coli MT102 and MG1655 were

recipient strains for the R-plasmid pHHA45, purified from the donor strain H10. H10 is an E. coli

isolated from a bacterial culture from a pig in 2006. The recipient strains were chosen, to work with

isogenic strains have been fully sequenced. The R-plasmid pHHA45 encode the mucAB genes as

well as the CTX-M-1 gene. The two routinely used strains in Ames test, S. typhimurium TA1535

and TA100 were used to study the mutation frequency, since they were known to be activated by

4NQO and are routinely used to test potential mutagenic compounds (52). Further the sensitivity

between E. coli and Salmonella are equivalent (29). Both Salmonella strains have deleting

mutations in hisG46, rfa and chl-uvrB-bioΔ. TA100 additionally carry pKM101, encoding the

mucAB genes and ampicillin resistance.

All bacterial strains were stored at -80°C in LB-medium, 15% glycerol (SSI Diagnostica).

9.2 Construction of transformants

9.2.1 Preparation of electro competent cells

E. coli MT102 and MG1655 were made competent. The procedure was as follows. The strain of

choice was inoculated in 10 ml of selective media and incubated at 37°C, at 125 rpm overnight.

2x500 ml selective media was prepared in two 1000 ml ehrlenmeyer bottles and stored at 37°C over

night. At the day of preparation 2500 µl of the overnight culture was inoculated into the two



46

prepared ehrlenmeyer bottles, to reach an OD ~0.02. The bottles were incubated at 37°C, 125 rpm

until an OD600nm=0.8-1.0 or at least 5 generations (4-5 hours) was reached. As soon as the right cell

density was reached, the bottles were placed in an ice bath and shaken a couple of minutes until the

cells were cold. The cells were harvested in six 50 ml tubes and centrifuged at 5000 rpm, 6 min

(Eppendorf centrifuge 5810R), 5°C, until all the 2x500 ml was used. Decantations were performed

quickly. The pellets were resuspended in 5-10 ml glycerol afterwards the tubes were filled with

glycerol to the 50 ml mark and centrifuged at 5000 rpm 6 min, 5°C. The step was repeated 3 times.

The pellet was resuspended in 5-10 ml glycerol and the six tubes were reduced to three. Again the

tubes were filled with glycerol to the 50 ml mark and centrifuged at 5000 rpm, 6 min, 5°C. The step

was repeated 2 times. The pellet was then resuspended and the three tubes were reduced to two,

centrifuged at 5000 rpm, 6 min, 5°C. Lastly the pellet was resuspended and the two tubes were

reduced to one, centrifuged at 5000 rpm, 6 min, 5°C. The supernatant was poured and the pellet was

resuspended in 1 ml ice cold 10 % glycerol to a final volume of 2-3 ml. The competent cells were

distributed to 40 µl in ice cold 0.5 ml eppendorph tubes and were stored at -80°C.

9.2.2 Transformation

Competent cells, cuvettes and plasmids were placed on ice. 1 µl of plasmid and 20 µl of cells were

transferred to a new eppendorph tube and mixed. Afterwards, the mixture was transferred to a

cooled cuvette. Electroporation was performed (BIO-RAD Micropulser) at a pulse time around 5ms

and an electric field of 1.8 kV to generate holes in the bacterial cells. 600 µl BHI broth was added

to the cuvette, mixed and transferred to an eppendorph tube. The step was repeated. The cells were

incubated for 1-2 hours at 37°C to allow for recovery, since natural membrane repair mechanisms

close the holes in the cell membrane after the electric shock and antibiotic resistance is expressed.

Afterwards the tubes with the cells were centrifuged at 13.000 rpm, 5 min (Eppendorf Minispin).

The supernatants were poured and the pellet was mixed with the remaining supernatant. Half of it

was transferred to a selective BHI plate (CTX) and the other half no a non-selective BHI plate, as

positive control. Competent cells were streaked on both types of BHI plates as control. The plates

were incubated at 37°C over night. If the transformation was successful, colonies become visible at

the selective BHI plate after 24 h at 37°C. Several colonies were re-streaked to another selective

BHI plate and incubated at 37°C overnight. Subsequently the cells were ready for use.



47

9.3 Polymerase chain reaction (PCR)

All primers (Ordered at TAG Copenhagen A/S, Copenhagen, Denmark) are listed in Table 4. The

PCR reactions were performed using a 3T Thermocycler (Biometra, Göttingen, Germany). PCR

Buffer (10x Extra Buffer) and Taq polymerase were supplied by VWR (10.000 units), (WVR

Belgium).

9.3.1 Boiling lysates as PCR templates

Template DNA for all PCR reactions were made as boiling lysates from bacteria streaked on C-calf

5% blood agar (BA) plates (SSI Diagnostica, Denmark) and grown at 37°C overnight. An amount

corresponding to a minor inoculation loop was suspended in 1 ml PBS and centrifuged 5 min. at

20.000xg, the supernatant was discarded. The pellet was resuspended in 100 µl TE (10:1) and boiled

for 10 min. followed by centrifugation in 5 min. at 20.000xg. The boiled lysates were diluted 1:10

in TE (10:1) and stored at 20°C. DNA preparations were stored at -20ºC until use in PCR assays.

9.3.2 Amplification of mucAB genes

DNA was extracted by the boiling method described in the previous section. When screening for

mucAB, five isolates were pooled in a single tube and PCR was run. If a pool was found to be

positive for mucAB, single DNA extracts were made and PCR was run once again. When PCR was

used for verification of the presence of mucAB, single DNA extracts were used. The mucAB genes

were amplified by PCR using the mucAB primers (Table 4). PCR was performed in a 50 µl PCR

mixture, including 5 µl 10x Extra Buffer, 0,5 µl forward and reverse primer, 0,5 µl dNTPs, 0,1 µl

polymerase and 5 µl DNA template. PCR was run with the programme 94°C, 5 min+(94°C, 30 sec

+ 56°C, 30 sec + 72°C, 1 min)x30 cycles + 72°C, 10 min.

9.3.3 Amplification and sequencing of QRDRs of DNA gyrase and topoisomerase IV genes

DNA was extracted by the boiling method. The QRDRs of DNA gyrase and topoisomerase IV

genes, gyrA and parC, were amplified by PCR using the primers listed in Table 4. PCR was

performed in a 50 µl PCR mixture, including 5 µl 10x Extra Buffer, 0,5 µl forward and reverse

primer, 0,5 µl dNTPs, 0,1 µl polymerase and 5 µl DNA template. PCR was run with the same

programme 94°C, 5 min+(94°C, 1 min + 55°C, 1 min + 72°C, 1 min)x30 cycles + 72°C, 10 min,

except for parC where the annealing temperature was 57°C.



48

9.3.4 Agarose gel electrophoresis

The PCR products were visualized by gel electrophoresis on a 1.5% (w/v) agarose gel (SeaKem®

LE Agarose, Lonza). The gel was submerged with 1xTBE in the gel electrophoresis tank (Agagel

Mini Biometra). A 100 bp ladder was the weight marker (New England Biolabs). 2 µl of Loading

Dye Blue (6x) was mixed with 8 µl PCR product and loaded. The electrophoresis was run for 0.25 h

at 130 V, 430mA (Consort 300V-500mA E835) in1xTBE buffer. The gel was stained in 10 µl/ml

ethidium in bromide (BIO-RAD) in 15 min and destained in distilled water for 10-15 min.

Visualization of DNA-bands was done by UV-light. A picture of the gel was taken by the use of

Gel Doc 2000 equipment; this was processed by Quantity One ® software (Both BIO-RAD).

9.3.5 Sequencing of QRDRs of DNA gyrase and topoisomerase IV genes

PCR products were purified for sequencing using GFX purification kit (GFXTM

, GE Healtcare).

DNA purification was performed according to the user manual. Briefly, a GFX- column was placed

in the collection tube, 500 µl Capture Buffer was applied to each column as well as the PCR

product. Centrifugation was performed in a microcentrifuge (VWR Bie & Berntsen 5418), at 13.000

rpm in 30 sec. The liquid in the collection tube was discarded and 500 µl Wash Buffer was added to

each column. Centrifugation was performed again at 13.000 rpm in 30 sec. Afterwards the column

was moved to a new eppendorph tube and 50 µl MilliQ water was added. Incubation was performed

at room temperature in 1 min, followed by 1 min of centrifugation at 13.000 rpm to recover the

purified DNA. The purified DNA product was checked on a 1.5% agarose gel, the amount of loaded

DNA was 5 µl. All sequencing work was performed by Macrogen Laboratories (Seoul, South

Korea), with the same primers as used in the PCR (both forward and reverse (Table 4).

Sequence analysis was performed using the Vector NTI Software (Informax Vector NTI, version

10) where sequences were assembled, aligned and compared for detection of mutations involved in

quinolone resistance. The analyses were performed through alignment of corresponding protein

sequences for detection of amino acid changes (Vector NTI-AlignX). Reference strains were found

in Genebank (http://www.ncbi.nlm.nih.gov) and were as follows: gyrA: AF038431 (Fuchs &

Heisig, 1997) and X06373 (Swanberg & Wang, 1897), parC: AY065817 (Gómez et al. 2004) and

DQ447146 (Petersen et al. 2006).

The sequencing of gyrA and parC was performed in E. coli nalidixic acid (NAL) strains, produced

in the mutation frequency determination study described next.

http://www.ncbi.nlm.nih.gov/



49

Table 4. Primers used in this study

Target gene Primer sequence (5’-3’) Annealing

temp. (°C)

Amplicon size

(bp)

Reference

gyrA

5'-ACGTACTAGGCAATGACTGG-3'

5'-TGTTCCATCAGCCCTTC-3'

55

475

Modified from

Everett et al.(27)

parC

5'-TGTATGCGATGTCTGAACTG-3'

5'-CTCAATAGCAGCTCGGAATA-3'

57 264 Cavaco et al.(10)

mucAB

5'-GTCACCCTTCAGCAACTTAC-3'

5'-CAGGATGCTCATTAATTTCTTCAG-3'

56 820 This study

9.4 Mutation frequency determination

To examine the effects of mucAB on the mutation frequency in E. coli a fluctuation test, was made.

The transcription of mucAB was induced by the mutagenic compounds 4-Nitroquinoline-N-oxide

(4NQO), (Sigma) and Ciprofloxacin (CIP), (Bayer). The concentrations of 4NQO were as follows;

0.3, 0.6, 1.3 µg/ml, previously used by others (8). As positive compound control 2.0 µg/ml 4NQO

was used, a level with bactericidal effect. The concentrations of CIP were; 0.0015, 0.0025, 0.005,

0.0075 and 0.01 µg/ml, previously used by others (12). As positive compound control 0.015 µg/ml

CIP was used, corresponding to the MIC level of the wild type. As positive growth control 4NQO

or CIP was absent.

9.4.1 Initiating the assay

For all dilutions 0.9 % NaCl was used, forward this will be mentioned as NaCl. Firstly, the test

strains were streaked out on 5% BA plates and incubated 37°C overnight, CTX disk were added if

the strains contained pHHA45, to ensure the presence of the plasmid. Afterwards a single colony

was picked and inoculated in 10 ml BHI broth and left for incubation at 37°C, 125 rpm, overnight. 1

ml of the overnight culture was spun down at 12.000 g, 5 min. The media was poured and the pellet

resuspended in 1.5 ml of NaCl. The density was measured by OD600nm reading on a

spectrophotometer (UV mini 1240, Shimadzu), the blind test being NaCl. Based on the measured

OD600nm, a sample with 106 cells/ml was made, corresponding to an OD600nm=0.05, diluted 100

times. Serial 10-fold dilutions in Eppendorph tubes were made to be sure that the amount of cells

were correct. As a negative control 100 µl of the sample was spread on a 64 µg/ml NAL- BHI agar

plate, to make sure that none NAL resistant cells were present at this point. The equivalent

resistance breakpoint is ≥ 32 µg/ml NAL according to CLSI standards (14).



50

Two independently procedures were afterwards performed, described separately in the following

two sections.

9.4.2 Procedure 1- the microtiter plate procedure

To ensure that mutants were absent a low amount of cells, 104 cells/ml, was transferred to each well

of the 96 well microtiter plate (Nunc). This corresponds to 10 µl of the OD600=0.05 suspension and

100 µl BHI broth. The suspension was mixed. As blank sample the BHI broth was used. If a

mutagenic compound was used, this was mixed with BHI broth, before adding it to the wells. Two

samples were selected for cell count on BHI agar plates, to secure the amount of cells were correct.

The microtiter plates were left for incubation at 37°C until an OD570nm of either 0.05, 0.1 or 0.2 was

reached, measured on the ELISA reader (Opsys MR, Dynex Technologies) by the programme

Revelation Quicklink (Dynex Technologies). The ELISA reader measures the intensity of the

colour in each well by comparing the blank wells with the test wells thereby the cell density is

measured. When the correct OD570nm was reached the growth was stopped by adding 100 µl 64

µg/ml NAL-BHI broth, leading to a final concentration of 32 µg/ml NAL in each well, the

equivalent MIC breakpoint defined by CLSI (14). One plate was made for each concentration of the

mutagenic compound as well as for the negative control (no mutagen). The plates were incubated at

37°C in 48 hours and then read in the ELISA reader to know the initial OD570nm, which is a

measurement of the presence of mutants, since growth was either observed or not. From the positive

wells, containing mutants, an inoculation loop was dipped and the cells were streaked on a 64 µg/ml

NAL-BHI agar plate, to ensure that the cells were NAL resistant.

9.4.3 Procedure 2- the 24 well plate procedure

To ensure that no mutants were present a low amount of cells, 104 cells/ml, was transferred to each

well of a 96 well microtiter pate (Nunc). This corresponds to 25 µl of the OD600=0.05 suspension

and 250 µl BHI broth. The suspension was mixed. As blank sample the BHI broth was used. If a

mutagenic compound was used, this was mixed with BHI broth, before adding it to the wells.

Two samples were selected for cell count on BHI agar plates to secure the amount of cells was

correct. The microtiter plates were left for incubation at 37°C until an OD570nm of ~0.3 was reached,

measured on the ELISA reader. This OD value was chosen, to secure that exponential growth was

occurring. When OD570nm was equivalent with 0.3, growth was stopped by transferring 250 µl of

each sample to a new microtiter plate containing 24 wells. 2 ml of 36 µg/ml NAL-BHI broth was

added, leading to a final concentration of 32µg/ml NAL in each well, the equivalent MIC



51

breakpoint defined by CLSI. One plate was made for each concentration of the mutagenic

compound as well as for the negative control (no mutagen). The plates were incubated at 37°C in 48

hours. Since the plates were too large to be read in the ELISA reader, mutants were measured by the

visible eye, since wells with no mutants were blank compared to the ones containing mutants. From

the positive wells, containing mutants, an inoculation loop was dipped and the cells were streaked

on a 64 µg/ml NAL-BHI agar plate, to ensure that the cells were NAL resistant.

9.4.4 Statistical analysis

The mutation rate was calculated by the use of the Poisson distribution. The CFU per well was used

to calculate the mutation frequency by analysis of the number of positive wells (X) out of 23 or 92

possible, depending of the procedure of choice. The statistic programme R (R Foundations) was

used (R-codes are shown in the Appendix).

Firstly the amount of cells from different counts in different dilutions could be calculated (CFU) by

the use of a logarithm:

𝑦 = 𝑐 × 𝑓

log 𝑦 = log 𝑐 × 𝑓 = log 𝑐 + log(𝑓)

𝑦′ = log 𝑦 − log 𝑓 = log 𝑐 = 𝑐′

1

n= log(yi − log(fi)) = log(c′)

𝑛

𝑖=1

,with y = CFU, f = dilution, c = concentration

Secondly the mutation rate could be calculated by the use of the P0 method and given that the setup

was Poisson distributed:

𝑃0 = exp(−𝑚)

𝑚 = −ln(𝑝0)

𝑚𝑢𝑡𝑎𝑡𝑖𝑜𝑛 𝑟𝑎𝑡𝑒 = 𝑚 𝑐′

,with P0 = amount without mutations, m = expected number of mutations



52

9.4.5 Growth determination

The Bioscreen C incubator (Thermo Labsystems) was used for measurements of the growth of S.

typhimurium 1535 and TA100. This was done, since the two strains did not grow in the mutation

fluctuation assays. Graphs corresponding to the OD600m value were made. 20 µg/ml histidine was

added in to the BHI media due to the hisG45 deletions that prevent the production of this essential

amino acid. The concentrations of 4NQO were; 0.01, 0.025, 0.05, 0.075, 0.1, 0.15, 0.2 and 0.3

µg/ml. Double determinations were made for each concentration. As positive growth control wells

were 4NQO were absent, was done.

The cells were prepared in the same way as described in section 9.4.1, by the use of procedure 1,

however 20 µl cells was mixed with 200 µl BHI broth (104 cell/ml) in each well and incubated at

37ºC, 125 rpm for 48 hours in the Bioscreen C incubator. The growth curves were automatically

produced on the computer by the programme Research Express version 1.0.

9.5 Resistance determination

Resistance determination was performed according to the CLSI instructions.

Four strains; E. coli MT102, E. coli MT102 (NALR, CIP

R), E. coli MT102 (NAL

R) and E. coli

ATCC® 25922 were controls. Ciprofloxacin resistance was examined in all strains by the disc

diffusion method. The MIC of ciprofloxacin was examined by the Sensititre® plate method for the

control strains, but the E. coli (NALR) produced in the fluctuations assays, were examined by the

broth microtiter bouillon dilution testing, due to the prize of a MIC panel.

9.5.1 Disk diffusion antibiotic sensitivity testing

Ciprofloxacin susceptibility was done by disk diffusion antibiotic sensitivity testing of E. coli

NALR strains, produced in the fluctuation assay. Briefly, an inoculation loop of bacteria grown

37°C overnight on 5 % BA plates were suspended in sterile 0.9 % NaCl and the density was

measured on a McFarland Nephelometer (Sensititre) towards 0.5, corresponding to 108 cells/ml.

With a cotton bud, the cells were streaked on a MH-agar plate, followed by the addition of a 5

µg/ml CIP disk. The plates were incubated at 37°C for 20 hours. The disk results interpreted were

according to the CLSI breakpoints.

9.5.2 MIC by Broth dilution testing, the Sensititre method

The minimum inhibitory concentration (MIC) was found by microtiterbroth dilutions by the use of

Sensititre® plates (DKMVN4). An inoculation loop of bacteria grown 37°C overnight on 5 % BA

plates, was suspended in sterile 0,9 % NaCl and the density measured on a McFarland



53

Nephelometer (Sensititre) towards 0.5, corresponding to 108 cells/ml. Afterwards, 50 µl of the

suspension was transferred to MüellerHinton (MH) broth to reach a concentration of 106 cells/ml.

The bacteria were spread to the Sensititre® plates by the use of an Autoinoculator, followed by an

incubation period of 18-20 hours at 37°C. The purity of the diluted bacteria was controlled by

plating each bacterial suspension on a 5% BA plate, which was incubated together with the

inoculated Sensititre® plate. The Sensititre® plates were read by the use of an inverted mirror.

MIC was defined as the first visible minimum inhibitory concentration of growth compared to the

control wells without antibiotic. MIC results were interpreted according to the breakpoints

described by CLSI.

The antibiotics tested were: 4-64 µg/ml NAL (Nalidixic acid), 0.015-4 µg/ml CIP (Ciprofloxacin),

1-32 µg/ml AMP (Ampicillin), 2/1-32/16 µg/ml AUG2 (Amoxicillin+Clavulanic acid (2:1)), 4-32

µg/ml APR (Apramycin), 0.125-4 µg/ml FOT (Cefotaxime), 0.5-8 µg/ml XNL (Ceftiofur), 2-64

µg/ml CHL (Chloramphenicol), 1-16 µg/ml COL (Colistin), 2-64 µg/ml FFN (Florfenicol), 0.5-16

µg/ml GEN (Gentamicin), 2-32 µg/ml NEO (Neomycin), 16-256 µg/ml SPE (Spectinomycin), 8-

128 µg/ml STR (Streptomycin), 64-1024 µg/ml SMX (Sulphamethoxazole), 2-32 µg/ml TET

(Tetracycline), 1-32 µg/ml TMP (Trimethoprim).

9.5.3 MIC by broth microtiter bouillon dilution testing

The MIC of CIP was examined by performing microtiterbroth dilutions in microtiter plates (Nunc).

Briefly an inoculation loop of bacteria grown 37°C overnight on 5 % BA plates was suspended in

sterile 0.9 % NaCl and the density measured on a McFarland Nephelometer (Sensititre) towards 0.5,

corresponding to 108 cells/ml. Afterwards, 50 µl of the suspension was transferred to MH broth to

reach a concentration of 106 cells/ml. The cells were distributed in the microtiter plate with dilutions

of CIP being: 0.015, 0.03, 0.06, 0.125, 0.25, 0.5, 1, 2 and 4 µg/ml respectively. For each isolate one

well was used as positive control of growth without CIP. The microtiter plates were incubated 18-

20 hours at 37°C, followed by reading of the results by the use of an inverted mirror.



54

10 Results

10.1 The distribution of the plasmidic mucAB genes

10.1.1 Distribution of mucAB in E. coli and Salmonella spp. from indicator and diagnostic pigs

and cattle

To the knowledge of this report, the distribution of mucAB in animals in Denmark has not

previously been examined. By PCR examination the distribution of the plasmidic genes mucAB

were examined among E. coli (O149) and Salmonella spp. (K99) isolated from pigs or cattle,

belonging to the DANMAP 2008 collection. The results are shown in Table 5.

When examining E. coli from pigs, none of the 81 indicator strains contained mucAB. However in

the diagnostic strains 15 out of 58 had the genes, corresponding to 25,86 % of the total diagnostic

population from pigs (Table 5). When examining E. coli from cattle none of the 81 indicator strains

or the 45 diagnostic strains contained mucAB.

In addition to E. coli, the distribution of mucAB was examined in the family member Salmonella,

which belongs to the family of Enterobacteriaceae. Samples from 33 diagnostic S. typhimurium

strains from pigs and 36 diagnostic S. ssp. from cattle were examined. None of the 33 strains from

pigs contained mucAB. But in cattle, 3 out of the 36 examined strains did contain mucAB,

corresponding to a total of 8,33 % of the diagnostic population. Due to the sample limitation the 95

% confidence interval (CI) was wide and more samples would be needed to find a more precise

estimate of the mucAB distribution (Table 5). None indicator strains of Salmonella spp. or S.

typhimurium were examined and for this reason, the results could not be compared with the

distribution in the total population.

In addition the resistance patterns of the pig isolates were examined. MIC by Sensititre had been

performed in the DANMAP surveillance programme (2008, data not yet published) and the data is

shown in Figure 9. The data showed that resistance towards all the examined antibiotics were

significantly higher in the diagnostic strains (n=58), with a distribution of antibiotic resistance being

at least twice the level observed in the indicator strains (n=43), (Figure 9). It should be emphasised

that these results are not due to the presence of mucAB, but rather an indication of the presence of

R-plasmids and other resistance determining factors. No correlation between the presence of mucAB

and resistance towards nalidixic acid and ciprofloxacin, as well as to any of the other antibiotics

were found (not shown).



55

10.1.2 Presence of mucAB among ESBL producing E. coli from humans

This examination was done to examine the twelve diagnostic E. coli from humans (provided by

Baquero et al. 2004, Spain) (5), which were known to contain R-plasmids conferring ESBL

production (CTX-M-1). Therefore is does not show the total distribution of mucAB in the human

population. All the strains were weak mutators (4x10-8

to 4x10-7

), thereby having a mutation

frequency above the normomutable level (8x10-9

to 4x10-8

), (5). Therefore the presence of mucAB

was examined in these twelve isolates. The result was that none of the 12 strains contained plasmids

encoding mucAB.

Table 5. Distribution of mucAB genes among E. coli and Salmonella spp. from healthy and diagnostic

pigs, cattle and human isolates.

Straina Samples

(n)

Distribution

of mucAB

Distribution % [95 % CI]

E. coli

Indicator pigs 81 0 0 [0-4,45]

Diagnostic pigs 58 15 26,86 [15,26-39,04]

Indicator cattle 81 0 0 [0-4,45]

Diagnostic cattle 45 0 0 [0-7,87]

Indicator Humanb 12 0 0 [0-26,46]

Salmonella

Diagnostic pigs 33 0 0 [0-10,57]

Diagnostic cattle 36 3 8,33 [1,75-22,47]

a All isolates was from pigs and cattle from the DANMAP 2008 collection.

bThe human isolates were provided by Baquero et al. 2004 (5).



56

Figure 9. The distribution (%) of antibiotic resistance among E. coli isolates from pigs towards 14

different antibiotics. Distribution (%) of antibiotic resistance (vertical line) towards the antibiotics

Apramycin, Ceftiofur, Chloramphenicol, Ciprofloxacin, Florfenicol, Gentamicin, Nalidixic acid, Neomycin,

Spectinomycin, Streptomycin, Sulphonamide, Tetracycline and Trimethoprim (horizontal line) in indicator

(blue) and diagnostic (red) strains of E. coli from pigs from the DANMAP 2008 collection. Error rates (5 %)

are indicated in each column.

0,0010,0020,0030,0040,0050,0060,0070,0080,0090,00

100,00

Dis

trib

uti

on

(%

) o

f re

sist

an

ce

Distribution (%) of antibiotic resistance among E. coli isolates

Indicator 2008 (n=43) Diagnostic 2008 (n=58)



57


The mutagenesis mediated by mucAB was examined, to find out how beneficial the genes were in

resistance development. The amount of induced mutations was found by selection for NAL resistant

strains (NALR) and CFU counts. The effects were examined in strains of E. coli; MT102,

MT102/pHHA45, MG1655, MG1655/pHHA45 and the wild type strain H10/pHHA45, of which

the strains with pHHA45 contain mucAB.

The results are divided into three sections. The first section covers the results of procedure 1 were

4NQO was used as mutagen. The second section covers the results of procedure 2 were 4NQO was

used as mutagen. The third section covers the results of procedure 2 were CIP was used as mutagen.

For all the results the mutation frequency corresponds to the number of mutations mediating NAL

resistance per cell division, from now on abbreviated NALR/cd.

4NQO was selected as a control compound to test that the assay worked and that mucAB was

activated, since the SOS response and mucAB is known to be induced by this compound, whereas

CIP was used to examine the mutagenic effect of CIP on bacteria containing mucAB, to see if

resistance towards ciprofloxacin would occur more frequently.

10.2.1 Procedure 1- Mutations induced by 4NQO

Before examining the effects of 4NQO and CIP on the mutation frequency, the mutation frequency

of E. coli MT102 and MT102/pHHA45 in the absence of 4NQO were determined. This was done to

know the initial level and to verify that the mutation level was the same in the two isogenic strains,

since mucAB should not be activated in the absence of an inducer. H10 was also examined.

When E. coli MT102 was used, between zero to three positive wells out of 92 possible was found,

corresponding to a maximal mutation frequency of 2x10-10

NALR/cd. This value corresponds with

the spontaneous mutation rate normally found. Estimates were calculated as described in the

method section, based on the CFU count and amount of positive wells. The same background level

was observed in E. coli MT102/pHHA45 and H10. The 95 % CI showed that it was possible to find

between 0 to 5 positive wells simply due to spontaneous mutations.

Firstly the initial OD level was examined, since the cells should be in exponential growth before

adding NAL. The cells were grown to a OD570nm of 0,05 or 0,1 or 0,2 respectively. The mutation

frequency do not change due to the different OD values since the calculations takes the CFU per

well into account. It was expected that the cells grown to OD570nm=0,2 was nearer the exponential



58

phase rather than the ones grown to OD570nm=0,05. The result was that no difference in the success

rate was observed, irrespectively of the OD value used when adding 4NQO. The determination was

carried out twice (data not shown). For this reason OD570nm of 0,1 were chosen as being the

preferred value in the next trials.

New determinations were made with five concentrations of 4NQO; 0, 0.3, 0.6, 1.3 and 2.0. µg/ml.

The results are shown in Figure 10. The mutation frequency in MT102 was 6x10-10

NALR/cd when

4NQO was absent, which was a level equally to the spontaneous level found. When 0.3 µg/ml

4NQO was added, the mutation rate decreased to 3x10-11

NALR/cd. When 0.6 µg/ml 4NQO was

used it was again in the spontaneous range, being 3x10-10

NALR/cd. The mutation frequency found

in MT102/pHHA45 was lower than the one MT102, being in the range of 1x10-10

and 2x10-10

NALR/cd. No positive wells were observed in the plates without 4NQO. H10 were not tested.

Due to the results MG1655 and MG1655/pHHA45 was tested instead, to see if mucAB were

activated in this strain. The results were the same as for MT102 and MT102/pHHA45 (data not

shown).

Since no difference between the mutation frequency in MT102 and MT102/pHHA45 was observed,

the setup of the assay was either not good enough or there was actually not a difference between the

mutation frequency in MT102 and MT102/pHHA45 when 4NQO was used as inducer. Since the

theory was that mucAB should mediate error-prone repair when induced by 4NQO the procedure

was modified. The results for the new procedure, procedure 2, are shown in the next sections.

Besides procedure 2 another method, described by Mandsberg et al. 2009 (51), was applied. But

since the outcome was a mutation rate far below the one detected in procedure 1 (results not

shown), this method was not used further.



59

Figure 10. Mutation frequencies in cells induced by 4-nitroquinoline-N-oxide in procedure 1. The 5

different concentrations of 4NQO are shown in the vertical line being: 0, 0.3, 0.6, 1.3 and 2.0 µg/ml. The

mutation frequency (NALR/cd) is shown in the horizontal line. The two E. coli strains examined were

MT102; dark grey, MT102/pHHA45; light grey.

10.2.2 Procedure 2- Mutations induced by 4NQO

In procedure 2, 24 large wells were used of which one was used as positive test. The amount of cell

material was the same, but the volume was increased 250 µl. Double determinations were made, by

making two independent trials.

The results when 4NQO was inducer is shown in Table 6 and illustrated in Figure 11. In MT102 the

number of positive wells for each plate was between zeros to five positive wells out of 23 possible.

Once in each determination a well with zero positives were found but at different concentrations of

4NQO. In both trials the mutation frequency reached a level between 2x10-11

to 9x10-11

NALR/cd,

no matter the 4NQO concentration. The lowest mutation frequency was observed when 4NQO were

absent. The highest mutation frequency in both trials was found when 0,6 µg/ml 4NQO was added,

to reach a level of 1.5x10-10

NALR/cd. The mutation frequency was the same no matter the 4NQO

concentration.

0 1E-10 2E-10 3E-10 4E-10 5E-10 6E-10 7E-10

0

0.3

0.6

1.3

2.0

NALR/cd)

4N

QO

ug/

ml

Mutation frequency in E. coli induced by 4-nitroquinoline-N-oxide

MT102

MT102/pHHA45



60

For MT102/pHHA45 the number of positive wells for each plate was between zeros to nine out of

23 possible wells. In both trials the mutation frequency reached a level between 4.7x10-11

to 1x10-10

NALR/cd. The highest and the lowest mutation frequency were observed when 0,9 µg/ml 4NQO

was used, being 2x10-10

and 8.5x10-12

NALR/cd.

Lastly, the mutation frequency of H10 was examined. The mutation frequencies observed

corresponded to the ones found in MT102 and MT102/pHHA45, being in the range of 10-11

NALR/cd. When 4NQO was absent, zero positive wells were observed. H10 mutated in trial one

when 1,3 µg/ml 4NQO was used, while none of the other two strains did. However they did mutate

in the second trial. An isogenic strain of H10 without pHHA45 was not available.

In summary the results found for MT102 and MT102/pHHA45 in the presence of 4-NQO were that

both had a mutation frequency similar the spontaneous mutation level and no difference between

the two strains was found.

10.2.3 Procedure 2- Mutations induced by Ciprofloxacin

The results of the double determinations of CIP are shown in Table 6 and illustrated Figure 12. For

MT102 the number of positive wells for each plate was between zeros to four positive out of 23

possible wells. In both trials the mutation frequency reached a level between 3x10-11

to 4x10-11

NALR/cd, no matter the CIP concentration. In trial two frequency dropped once at 0,0075 µg/ml

CIP, to 9x10-12

NALR/cd.

For MT102/pHHA45 the number of positive wells for each plate was between zeros to five wells.

The mutation frequency was 1.9x10-11

to 9.9x10-11

NALR/cd. The mutation frequency was the same

no matter the CIP concentration.

Common for both trials was that, both with MT102 and MT102/pHHA45, a whole tray with zero

positives were found at different CIP concentrations.

Lastly, the mutation frequency of H10 was examined. The level was once again similar to the level

observed in the two other strains.

In summary, none of the three strains showed an increased mutation frequency, when any of the 6

CIP concentrations was used. The mutation frequency in all the strains was between 10-11

to 10-12

NALR/cd, no matter the CIP concentration. The result was identical to the result found with 4NQO.



61

10.2.4 Statistical analysis of the results

To find out whether the counts in the two trials were significant, statistical analysis using the

statistical programme R (codes are shown in Appendix) was done. The Poisson distribution was

used. The objective was to determine the uncertainty of the amount of mutants for each well, given

that growth was observed in X out of 23 possible wells. Examples of the results are shown in Figure

13, where the cumulative distribution function of 2 or 10 positive wells out of 23 are shown. The 95

% CI found by this analysis is shown in Table 6.

The conclusion of the statistical analysis was, that there have to be a large degree of difference in

the amount of positive wells in the experiments with MT102 compared to the same experiment

performed with MT102/pHHA45 to reach a significant degree of difference between the two

strains. Therefore the few differences observed between the strains were not significant.

10.2.5 Mutation frequency in Ames tester strains S. typhimurium TA1535 and TA100

The mutation frequency in the two routinely used Ames tester strains S. typhimurium TA1535 and

TA100, was also examined. The two strains were known to be activated by 4NQO. However none

of the strains survived when 4NQO was added, not even when the lowest concentration 0,3 µg/ml

4NQO, was used (data not shown). Therefore growth determination was performed in the

Bioscreen, with and without 4NQO, being in even lower concentrations in the range of 0.01 to 0,3

µg/ml. The result was the same namely that the strains did not survive the treatment (data not

shown). Therefore further work with these strains was not performed.



62

Table 6. The mutation frequency in E. coli induced by 4-nitroquinoline or ciprofloxacin.

MT102 MT102 (pHHA45) 2006-40-1139

4NQO

(µg/ml)

Counts per plate

NAL

R/cd

Counts per

plate

NAL

R/cd

Counts per

plate

NAL

R/cd

0 1 2.00E-11 5 1.00E-10 0 0 0 0 5 4.73E-11

0.3 2 4.29E-11 8 1.83E-10 16 3.48E-11 3 9.00E-11 5 4.73E-11

0.6 3 6.58E-11 6 1,29E-10 21 7.14E-11 5 1.58E-10 8 8.25E-11

0.9 2 4.29E-11 9 2.12E-10 22 9.17E-11 2 5.86E-11 1 8.58E-12

1.3 0 0 0 0 17 3.93E-11 1 2.86E-11 5 4.73E-11

MT102 MT102 (pHHA45) 2006-40-1139

CIP (µg/ml)

Counts per plate

NAL

R/cd

Counts per

plate

NAL

R/cd

Counts per

plate

NAL

R/cd

0 3 4.68E-11 4 1.36E-10 2 3.19E-11 0 0 1 9.41E-12

0.0015 2 3.05E-11 3 9.93E-11 2 3.19E-11 3 2.96E-11 0 0

0.0025 2 3.05E-11 2 6.46E-11 5 8.60E-11 3 2.96E-11 2 1.93E-11

0.005 2 3.05E-11 1 3.16E-11 1 1,56E-11 4 4.04E-11 5 5.19E-11

0.0075 2 3.05E-11 1 3.16E-11 1 1,56E-11 1 9.41E-12 3 2.96E-11

0.01 0 0 0 0 0 0 3 2.96E-11 2 1.93E-11

Counts per plate is the number of well were growth were observed, out of 23 possible wells.

Confidence intervals (95 %) of the counts per plate:0 [0-0], 1 [0-3], 2 [0-5], 3 [0-6], 4 [1-8], 5 [1-9], 6 [2-10], 8 [4-13],

9 [5-14], 16 [12-20], 17 [13-21], 21 [18-23], 22 [20-23].



63

Figure 11. Mutation frequencies in 4-nitroquinoline-N-oxide induced cells by procedure 2. The 5

different concentrations of 4NQO are shown in the vertical line being: 0, 0.3, 0.6, 1.3 and 2.0 µg/ml. The

mutation frequency (NALR/cd) is shown in the horizontal line. The two E. coli strains examined are MT102;

dark green trial 1, light green trial 2, MT102/pHHA45; dark blue trial 1, light blue trial 2.

0 5E-11 1E-10 1,5E-10 2E-10 2,5E-10

0

0.3

0.6

0.9

1.3

NALR/cd

4N

QO

(u

g/m

l)

Mutation frequency in E. coli induced by 4-nitroquinoline-N-oxide

MT102-1

MT102-2

MT102 (pHHA45)-1

MT102 (pHHA45)-2



64

Figure 12. Mutation frequencies in ciprofloxacin induced cells by procedure 2. The 6 different

concentrations of CIP are shown in the vertical line being: 0, 0.0015, 0.0025, 0.005, 0.0075 and 0.01 µg/ml.

The mutation frequency (NALR/cd) is shown in the horizontal line. The two E. coli strains examined are

MT102; dark purple trial 1, light purple trial 2, MT102/pHHA45; dark orange trial 1, light orange trial 2.

0 2E-11 4E-11 6E-11 8E-11 1E-10 1,2E-10 1,4E-10 1,6E-10

0

0.0015

0.0025

0.005

0.0075

0.01

NALR/cd

CIP

(u

g/m

l)

Mutation frequency in E. coli induced by ciprofloxacin

MT102-1

MT102-2

MT102 (pHHA45)-1

MT102 (pHHA45)-2



65

Figure 13. The cumulative distribution function. The parameter x represents number of wells. Fn(x) are

the cumulative distribution function showing how the amount of positive well could be distributed when x

equals 2 or 10. The Empirical distribution is discrete, no matter if the sample space for the single event is

discrete or continual, thereby ascribing the same emphasize (1/n) to all the observations. When the amount of

events is high enough the Empirical distribution is close to the theoretical distribution (76).



66

10.4 Target modification through mutations in QRDR

The originally idea was, that the mutants should be sequenced following the mutation assays, to

find out if mucAB induce certain basepair substitutions and to what degree the MIC’s towards

ciprofloxacin were changed when CIP was used as mutagen. But due to the many problems with the

mutation frequency assays, these final tests were carried out last. Therefore, the NALR strains that

had emerged in procedure 1 were the only ones being sequenced.

All the PCR amplifications of the QRDR regions of gyrA and parC, gave fragments of the band size

475 bp and 264 bp, as expected (Table 4). DNA purification by GXF columns was performed and

sufficient amounts of DNA were sent to sequencing. Alignments of the sequences were done with

MT102, H10 and the reference strains found in Genbank. The analysis was based on basepair

mutations of which all mutations (including silent mutations) were considered.

The sequencing results for the 37 mutants are shown in Table 7. However 3 samples of gyrA and 2

samples of parC did not succeed in being sequenced.

All of the 34 successfully sequenced isolates had one mutation in gyrA. No silent mutations were

found in any of these.

The most prevalent base inserted was thymine in both MT102 and MT102/pHHA45, accounting for

53 % of all the insertions. Following was guanine insertions accounting for 26 % of all insertions.

The most frequent mutation site was Asp87, which was changed in 17 isolates, corresponding to

50,0 % of the total amount of isolates. Asp87 was most frequently changed to Tyr87 or Gly87. The

Asp87 mutations increased the MIC of CIP from <0,03 µg/ml in MT102 or MT102/pHHA45 to

either 0,06 or 0,125 µg/ml CIP (Figure 14).

The second most frequently mutations site was Ser83. Seven isolates were mutated to Leu83,

corresponding to 20 % of the total amount of isolates. Of these strains all seven had a MIC of 0,25

µg/ml CIP, being the highest value found in the NALR strains, only found when Ser83 was changed

to Leu83.

Gly81 to Cys81 were found within 5 isolates, corresponding to 15 %. The strains had a MIC of

0,125 µg/ml CIP. Other less frequently mutation sites were Asp82 and Ala119 (Table 7) with a

MIC of either 0,06 or 0,125 µg/ml CIP. None of the NALR mutants had a MIC below 0,06 µg/ml

CIP.

When testing for mutations in parC, 35 isolates were successfully sequenced. None of them had

mutations in the parC region of QRDR (result not shown).



67

Table 7. Distribution of point mutations in the Quinolone resistance-determining region (QRDR) of

GyrA among E. coli.

GyrA

a

Amino

acid

positio

n

Amino

acid

WT

Amino

acid

NALR

Basepa

ir

changeb

Freque

ncy

Distributio

n (%)

MT

102

MT102

(pHHA

45)

2006-

40-

1139

81

Gly

Cys81

G→T

5

14,71

3

2

82

Asp

Asn82

Gly82

Ala82

G→A

A→G

A→C

1

1

1

2,94

2,94

2,94

1

1

1

83 Ser Leu83 C→T 7 20,59 3 3 1

87

Asp

Tyr87

His87

Asn87

Gly87

G→T

G→C

G→A

A→G

6

2

1

8

17,65

5,88

2,94

23,53

1

1

3

3

1

1

5

2

119

Ala

Glu119

C→A

2

5,88

1

1

Total 34 100 %

a Single mutation events in gyrA.

b G, Guanine; C, Cytosine, A, Adenine, T, Thymine.

Gly, Glycine; Asp, Aspartic acid; Ser, Serine; Ala, Alanine; Cys, Cysteine; Asn, Asparagine; Leu, Leucine; Tyr,

Tyrosine; His, Histidine, Glu, Glutamic acid.



68

Figure 14. MIC of ciprofloxacin in nalidixic acid resistant isolates and their corresponding mutations

sites in gyrA. All the mutations sites were within the defined Quinolone resistance determining region

(QRDR), except for the mutation site Alanine119. Only one mutation was found in gyrA of each isolate

(n=34). The amino acid changes occurred at the mutation sites; Alanine119 (yellow), Aspartic acid82

(green), Aspartic acid87 (orange), Glycine81 (purple) and Serine 83 (blue). No silent mutations were found.

0

1

2

3

4

5

6

7

8

9

10

<0,03 0,06 0,125 0,25

Hyp

pig

he

d (

n=3

4)

MIC ciprofloxacin ug/ml

MIC of ciprofloxacin in nalidixic acid resistant isolates

Ala119

Asp82

Gly81

Asp87

Ser83



69

10.5 Resistance and sensitivity towards CIP in the NAL resistant strains

10.5.1 Ciprofloxacin resistant strains

The number of NALR strains that emerged in the mutation assay in procedure 2, are listed in Table

6. All the NALR isolates had a MIC >64 µg/ml NAL as found in the mutation frequency

determination. The NALR strains were also tested for ciprofloxacin resistance by disk diffusion

antibiotic sensitivity testing. In summary, none of the NALR strains of either MT102 or

MT102/pHHA45 were ciprofloxacin resistant, with a zone of inhibition below 21 mm (CLSI

guidelines),(14). The NALR strains of H10 were not examined.

10.5.2 Ciprofloxacin sensitivity in NALR strains

The ciprofloxacin sensitivity was expected to be decreased in the NALR strains due to the gyrA

mutations. Therefore the MIC of CIP was examined. The recommended clinical breakpoint of

resistance is > 0.06 µg/ml CIP (19). MIC was found to be <0,015 µg/ml CIP for MT102 (NALS,

CIPR) and ATCC® 25922. MIC was >4 µg/ml CIP for MT102 (NAL

R, CIP

R).

The results for 4NQO and CIP induced mutations are shown independently, given their different

target specificity (Figure 15, Figure 16).

When 4-NQO was added, 19 MT102 (NALR) and 52 MT102/pHHA45 (NAL

R) were found). Of

these approximately 3 % of MT102 and MT102/pHHA45 were CIP sensitive with a MIC < 0,06

µg/ml CIP (Figure 15). In MT102 6 % were characterized as intermediate sensitive (MIC=0,06

µg/ml CIP) whereas none of MT102/pHHA45 was within this category. The rest of the NALR

strains were low-level CIP resistant with a MIC > 0,06 and with a maximum MIC of 1 µg/ml CIP (a

single isolate). Most strains had a MIC of 0,25 µg/ml CIP, corresponding to 54 % of MT102 and 71

% of MT102/pHHA45.

When CIP was added as inducer, 25 MT102 (NALR) and 22 MT102/pHHA45 (NAL

R) were found

(Table 6). Of these none of MT102 and 4 % of MT102/pHHA45 were CIP sensitive with a MIC <

0,06 µg/ml CIP. None strains of either MT102 or MT102/pHHA45 was intermediate sensitive. Of

MT102 13 % had an MIC of 0,125 µg/ml CIP, thereby being low-resistant and the same was found

in 4 % of MT102/pHHA45. In general most of the strains had an MIC of 0,25 µg/ml CIP,

corresponding to 32 % of MT102 and 68 % of MT102/pHHA45. But many did also have a MIC of

0,5 µg/ml CIP, being 41 % of MT102 and 20 % of MT102/pHHA45. Few isolates had a MIC > 0,5

µg/ml CIP.

In general no difference in the MIC was found between CIP and 4NQO induced cells.



70

Figure 15. MIC for ciprofloxacin in NAL resistant strains produced by 4-nitroquinoline-N-oxide

induction. The MIC for ciprofloxacin (CIP) is shown in the vertical line, the percentages of the total strains

are shown in the horizontal line for MT102 (n=19) and MT102/pHHA45 (n=54) respectively. Each clinical

breakpoint definition is marked by a colour, purple (sensitive), red (intermediate) and blue (low-level

resistant).

Figure 16. MIC for ciprofloxacin NAL resistant strains produced by ciprofloxacin induction. The MIC

for ciprofloxacin (CIP) is shown in the vertical line, the percentages of the total strains are shown in the

horizontal line for MT102 (n=25) and MT102/pHHA45 (n=22) respectively. Each clinical breakpoint

definition is marked by a colour, orange (sensitive), green (low-level resistant).

0

10

20

30

40

50

60

70

80

<0,015 0,03 0,06 0,125 0,25 0,5 1

% o

f N

AL

resi

sta

nt

stra

ins

MIC of ciprofloxacin ug/ml

MIC among 4-nitroquinoline-N-oxide induced NAL resistant strains

MT102

MT102

MT102

MT102 (pHHA45)

MT102 (pHHA45)

0

10

20

30

40

50

60

70

80

<0,015 0,03 0,06 0,125 0,25 0,5 1 2

% o

f N

AL

resi

sta

nt

stra

ins

MIC of ciprofloxacin ug/ml

MIC among ciprofloxacine induced NAL resistant strains

MT102

MT102 (pHHA45)

MT102 (pHHA45)



71

11. Discussion

11.1 The distribution of the plasmidic mucAB genes

11.1.1 Distribution of mucAB among E. coli from pigs and cattle

The increased mutation frequency mediated by mucAB when bacteria is stressed, becomes useful

when the environment changes, for instance when new antibiotics are used. Therefore, mucAB

could be widely distributed among E. coli from animal reservoirs.

To the knowledge of this report, the distribution of mucAB from animals in Denmark has previously

not been examined. However back in 2006 the E. coli strain H10 was isolated from a bacterial

culture from a pig in Denmark. H10 contained mucAB on the IncN plasmid pHHA45.

Given that the muc operon has been found on plasmids from over 10 different Inc groups (44), the

muc region is not restricted to R-plasmids of certain Inc groups, which potentiate the spread and

presence of the genes. Further a putative insertion element that is characteristic of a transposable

genetic element has been identified immediately downstream of the muc operon and the muc operon

is surrounded by inverted repeats. Therefore it has been suggested that the mucAB genes could be

closely associated with mobile genetic elements and this association might enable the muc genes to

move between plasmids and to perhaps to chromosomal locations (44,45,59).

For this reasons it was examined if the muc operon was distributed among E. coli isolated from pigs

as well as cattle. The result was positive as shown in Table 5, were the distribution among diagnostic

E. coli isolated from pigs were ~ 26 %. In the diagnostic cattle and the indicator strains mucAB were

not found. The results were not surprisingly, since the indicator strains probably not have been

exposed to the same selective pressure as the diagnostic strains and therefore do not carry R-

plasmids to the same extent. In addition plasmids tend to be lost when the features of the plasmids

are not required (49). Further due to the use of different antibiotics, variants with an increased

mutation frequency will tend to be selected, since they have an increased probability of forming

beneficial mutations mediating survival (5). This explains why diagnostic strains contain mucAB,

since these have been selected due to the R-plasmid mediated antibiotic resistance they confer. It

also explains why the diagnostic strains from pigs had significantly more resistance than the

indicator strains (Figure 9).

All together the ability of mucAB to increase the mutation frequency by the error-prone repair

mechanism is an ability that contributes to the vast potential for adaption and may partly explain

how antibiotic resistance and virulence evolve so quickly. Other resistance mediating factors could

be development of efflux pumps, enzyme production and target protection (qnr) etc. (10,74,78).



72

11.1.2 Distribution of mucAB among Salmonella spp. from pigs and cattle

Since E. coli belongs to the family of Enterobacteriaceae, the distribution of mucAB in the familiar

pathogenic strain Salmonella was examined as well (54). Among these family members genetic

material can be shared by transfer of genetic elements, and therefore were Salmonella spp.

examined. Further mucAB have been shown to be activated in Ames Salmonella strains by SOS

repair, being the key element for the mutagenesis mediating effects in plasmid pKM101 (46,59).

It was found that 8 % of the diagnostic isolates from cattle contained mucAB. None of the

diagnostic Salmonella from pigs contained mucAB. The result shows that environmental Salmonella

probably also use mucAB in the SOS response. Further, since mucAB have been found in both

Salmonella spp. and E. coli, a vast potential for the sharing and spread of the genes are present.

11.1.3 Distribution of mucAB among 12 E. coli from humans harbouring ESBL

When focusing on antibiotic resistance, the spread of the muc operon is a reason to be concerned,

since mucAB typically are located on R-plasmids already encoding resistance towards at least one

type of antibiotic (7,30). Thus, when mucAB are activated, the chance of mutations mediating

resistance towards other types of antibiotics is increased. Further, most R-plasmids contain tra

genes, making them able to be transferred to other hosts by conjugation (7).

Fortunately, mucAB were not found in any of the 12 examined E. coli isolates from humans. It was

expected that the R-plasmids might had carried mucAB, since they had the CTX-M-1 gene which

was also found on the plasmid pHHA45 from H10. Further they had a mutation frequency above

the normomutable level (5). This was interesting, since among E. coli UTI isolates, a mutator

phenotype is strongly associated with fluoroquinolone resistance. Besides the mutator phenotype

was most frequently the intermediate strength (48,82). This correlates with a modest increase in the

mutation rate, which additionally has been shown to be advantageous during adaptive evolution of

bacteria (53). Additionally, it has been found that a specific base change in the LexA box of mucAB

mediates independency of LexA and thereby an increased mucAB synthesis, resulting in a weak

mutator strain (57). It has been found by other that the frequency of mutations increase, when

bacteria repeatedly are exposed to antibiotics. The result is selection of bacteria that have a much

higher mutation rate than the original population (9,48). In E. coli cultures, mutators have been

found to accumulate once per < 10-5

genome replication (23).



73

It have been found that mucAB only have a modest influence on the spontaneous mutation rate

(31,85). This correlates with the fact that the mucAB genes are SOS regulated. Therefore an

increased mutation frequency could not be directed to the presence of mucAB, since the 12 strains

were grown without any selection or stress (5). This correlated with the result found here, were

none of the twelve isolates carried mucAB (Figure 9).

The isolates were interesting due to their ESBL production, since strains with antibiotic resistance

and mucAB have an increased possibility of becoming multi-resistant, compared to the strains

without thee abilities. If the ESBL producers already were quinolone resistant, then only one

additional mutation would be required to become fluoroquinolone resistant.

It would be interesting to make a collection of bacterial isolates from humans, which are ESBL

producers and then examine the distribution of the mucAB genes. This could give an indication of

how widespread this type of bacterial strain is and explain one mechanism that contribute to the

evolvement of resistant strains.


11.2.1 MucAB mediated mutation frequencies

In this study the occurrence of resistance towards NAL was examined, when cells were grown in

the presence of a mutagenic compound, either 4NQO or CIP. Both are mutagenic compounds

known to induce the SOS response. The level of mutations in induced E. coli was found (Table 6,

Figure 11, Figure 12). Generally the level of spontaneous mutations is in the range of 10-7

to 10-11

errors per base pair due to a single round of replication (6,23,49). This correlated with the observed

mutation frequency in this study in either 4NQO or CIP induced cells, which was 10-10

to 10-12

NALR/cd. The mutation frequency found was in the lowest level of the spontaneous mutation range.

Based on the finding that MT102 and MT102/pHHA45 had the same mutation frequency in the

presence of the positive test compound 4NQO as well as the test compound CIP, it was concluded

that mucAB probably were not activated. Besides, the statistical analysis showed that no significant

difference among MT102 and MT102/pHHA45 was present.

In this study no data of the frequency of mutations mediated by mucAB was found. For this reason it

was difficult to define whether mucAB were activated or not. However, it is known that cells

induced by mutagens or other stressful factors change the repair process to SOS response and

thereby activate TLS polymerases which mediates error-prone repair (38,54).



74

11.2.3 Experimental setup- problems faced

Ideally Ames test could have been used, since this test is used to test for the potential of mutagenic

compounds and at the same time, shows the mutation frequency. Thereby, the test could have been

used as a measurement of whether the mutation frequency was increased in the strains or not.

However Ames test requires specially constructed strains, due to the selection process, which is

based on histidine depletion in the media. Therefore histidine deficient strains are used of which

only the cells that revert the deletion in the his gene survives.

In this study, strains without target modifications were used and therefore another type of mutation

assay was applied, which ideally should give the same result as Ames test. However the procedure

did face some essential problems.

Firstly the cells were grown in 96 microtiter trays (both in procedure 1 and 2). It was observed that

growth was not equally distributed in the wells. In some wells the desired cell density was reached

faster than in others. Given the many samples, this was difficult to handle, since taking the

microtiter trays in and out of the incubator many times to measure the OD affects the growth, which

tended to stop. Therefore the CFU counts were based on selection of representative wells and

double counts were performed, thereby representing the average cell value in each well. However

even so different cell densities occurred, the CFU stayed within the same 10-fold limit (e.g. 1x108

to 8x108 cells/ml), tested by CFU of different OD values (0.3, 0.35 and 0.4). However, the

differences in the cell density should be kept in mark.

Regarding the use of H10, this was rather difficult, since this strain grew much faster than MT102.

For this reason the cell density reached the climax many hours before MT102. When H10 was

induced by 4NQO, 76 NALR strains emerged. This probably was due to the cells grew very fast and

therefore the amount of cells was 10-fold higher than the intended level. This was not a problem

when calculating the mutation frequency, since the CFU counts were taken into account. However,

the following NAL selection seemed be non-sufficient, given the many positive wells, which was

not found in previous experiments with H10 and 4NQO (data was not shown). But following, the

NALR strains were tested on 64 µg/ml NAL plates and were found to be resistant. Two things could

explain this. Either the NALR mutants emerged when the cells were incubated in 32 µg/ml NAL-

BHI broth, due to sub-lethal NAL concentrations mediated by the high cell number and this induced

QRDR mutations. Or the H10 strain was in fact induced by 4NQO, thereby activating the SOS

response and the mucAB transcription. These findings could not be compared with the ones found



75

with CIP, since here the cells were stopped at the correct OD value. Therefore, H10 should have

been examined again, induced by 4NQO, to examine if the assay worked and activated mucAB.

It was desirable that large populations of bacteria were available, since mutational events are rare.

Therefore, it was desired to have a high cell number. In the revised method protocol, which is still

used when performing Ames test, it is given that maximum sensitivity is achieved by plating 2x108

cells, since fewer cells would give an normal amount of spontaneous revertants (52). Fortunately a

cell density of 108 to 10

9 cells/ml was used in this study. In addition the cells in this study were in

exponential growth. It has been found that stationary phase bacteria give a weak mutagenic

response when exposed to 4NQO, whereas bacteria from exponentially growing cultures result in a

strong dose-related response (70). Therefore the cells prepared were expected to be as inducible as

possible given the circumstances.

Another issue was the selection. Since the focus was on quinolone resistance the selection was

based upon the emergency of NAL resistant strains. NAL resistance was easy to examine, since the

mutations occur in the QRDR of gyrA gene. This offered the advantage that a single pairs of

oligonucleotide primers could be used for PCR amplification and DNA sequencing. Therefore NAL

was regarded a good indicator of the general frequency of mutations in the cell. The same could

have been found if rifampicin was chosen to be the antibiotic for selection, since 88 % of all rpoB

mutations are localized in the central 202 bp region of the gene (39,48).

Regarding the statistical analysis, the Poisson distribution was used. Given that the amount of

replicates were set high (n.rep=1000) the significance of the estimated distribution was high.

Different statistical approaches could have been chosen, but given that the Poisson distribution is a

discrete distribution and it covers the number of events in a fixed interval it was chosen. It is also

usually used in fluctuation tests and others have used for calculating the mutation frequency in

Ames test (40,52,69,70,76). The Poisson distribution is a double sided test. The single sidet

binomial distribution could also have been used. It was examined (data not shown, R-codes in

Appendix) and found to give almost the same result as for the Poisson distribution, due to the high

number of replicates. This was not surprisingly since the Poisson distribution is an approximation of

the binomial distribution, just with a large n (n→∞).

11.2.3 Strain specificity

The original setting of this study was to examine a system as “natural” as possible, thereby without

deleting any genes affecting the mutation frequency. Of course mutator clones do exist, mostly



76

under intermediate rates of environmental changes (82). However the theory was, that most

environmental E. coli due not posses such extreme changes as knock out of NER, since a deleted

repair free system would cause an increase in error-prone repair pathways of which most of the

mutations would be non-beneficial or even harmful to the host (64). Instead bacteria that carry

genes that are induced, when NER are not sufficient, would have a better chance of survival than

the ones with deletions of important proofreading mechanisms.

The laboratory strain MT102 was used in this study. One might expect this strain had a tendency to

mutate faster, however this was not the case, when comparing the results found with

MT102/pHHA45 and H10 (Figure 11, Figure 12). Actually the strains were less fragrant compared

with the two Salmonella strains TA1535 and TA100, which did not grow in the presence of 4NQO.

If a laboratory strains was unwanted and a wild type strains should have been used instead, perhaps

the standard susceptible E. coli isolate Nu14, isolated from a patient with UTI, could have been

used as recipient of the plasmid. NU14 have been found previously to have a mutation frequency of

5x10-9

per cell generation (48). The strain H10 could also have been modified by constructing

knock out mutants of the muc genes. Thereby, it would be possible to examine to what degree

mucAB were expressed when the cells were stressed, compared to the KO strain. However, H10 is

not a well characterised strain as the laboratory strain MT102.

When examining what others have done in the work with mucAB and mutagenesis, strains with

deleting mutations in the uvr genes encoding the UvrABC endonuclease have been constructed.

Thereby is the NER system knocked out (60). The NER system acts before TLS, since this repair

pathway exceeds proofreading mechanisms. When NER is knocked out an increased sensitivity in

detecting many mutagens occurs, since now the NER system do not interfere with the TLS

mediated by pol RI (42,60). This gives reason to speculate whether NER activity was the reason to

the lack of mucAB activity in this study. Other deletions that could have been used was deleting the

rfa genes, causing partial loss of the lipopolysaccharide barrier that coats the surface of the bacteria

and increase the permeability of large molecules (52). However, the construction of such strains

depends on what to examine, for instance Ames Salmonella tester strain TA102 does not contain the

deletion of uvr since it is used for detecting mutagens that require an intact excision repair system

(52).

11.2.4 Target specificity of 4NQO and CIP

Regarding the target specificity, 4NQO is a quinoline derivative, not to be mistaken for being a

quinolone. 4NQO is known to induce DNA lesions and thereby target genetic material of the



77

bacteria and every function of the cell. 4NQO is also known to induce mucAB due to its DNA

damaging effects (Table 3), (52,54). CIP is known to target DNA replication due to its specific

binding and inhibition of DNA gyrase (36,54). Therefore, differences in the mutation frequency

could be observed when 4NQO and CIP were used as inducers, since the selection was based on

NAL resistance. Both compounds were used in bacteriostatic concentrations, to interfere with the

DNA replication, without killing the bacteria.

The common factor for CIP and 4NQO is the activation of the SOS response, however whether CIP

is a mutagenic compound have been discussed. It is known that genotoxic compounds are

potentially mutagenic. Genotoxic effects of CIP have been found, due to its action were it

specifically binds the DNA gyrase complex, leading to genetic instability i.e. point and frame-shift

mutations, deletions and generally inhibition of DNA synthesis (13,16,50). But whether CIP is a

mutagen or not have not yet been defined precisely. However it is known that CIP induce the SOS

repair system and specifically the mucAB genes, since mutagenesis of fluorinated compounds have

been found to be affected by the absence of plasmid pKM101 (13,34,67).

Clerch et al. (1996) made a study were they expected an increased mutagenic response in CIP

induced strains carrying mucAB and that this would correlate with an increase in bacterial resistance

to killing by this compound. However the results were, that the strain with a hisG420 mutation had

similar levels of survival after quinolone treatment, regardless of the presence of pKM101. Further

investigations showed that the mutagenic repair of quinolone damage by MucAB is not a very

efficient process and that the level of expression of the mucAB operon might be critical for SOS

mutagenesis (13). These findings might explain why some studies have failed to show the

mutagenic effect of ciprofloxacine, since a higher copy number of mucAB plasmids would be

needed.

In the mutation assay neither 4NQO nor CIP succeed in inducing the SOS regulated mucAB genes.

Both compounds are known to be mutagenic or at least genotoxic and this was confirmed by the use

of a maximum level of each compound (2,0 µg/ml 4NQO and 0,15 µg/ml CIP) which was

bactericidal levels. However, at lower concentrations they were not found to have an significant

effect on the mucAB transcription, even so the mutagenic effect should have been detectable in a

dose-response linear manner. Actually a maximal induction have been found at the MIC=0,015

µg/ml for CIP. However in this study this level fully killed the cells and therefore it was not

possible to observe anything at this concentration. However the cells were able to grow in 0,1 µg/ml

CIP, which could be a good concentration for induction of mucAB, due to the dose and response



78

association of CIP and that CIP have been found to induce mucAB at sub-inhibitory concentrations

(67). However, this was not found in this study.

No difference in the mutation frequency was found when comparing 4NQO and CIP induced

mutagenesis (Table 6). This can be explained by the mechanisms of the SOS response. The first

SOS repair mechanism to be induced is nucleotide excision repair (NER), which repair DNA in an

error-free manner by removal of a short ssDNA segment that includes the lesion, creating a single

strand gap in the DNA, which is filled in by a DNA polymerase that use the undamaged strand as

templates. If NER does not sufficient repair the damage, the LexA concentration is further reduced,

and the expression of genes with stronger LexA boxes such as dinB and mucAB, are induced (85).

Therefore Pol RI is the last polymerase of the three SOS polymerases mentioned, to be activated

(17,30,38). Therefore the transcription of mucAB is the last activated response of the SOS response.

Therefore if CIP induced mutations can be repaired by NER, mucAB are not activated and perhaps

this was what happened in this study.

In combination all these factors explain why an increased mutation rate in MT102/pHHA45 was not

found and that no difference was observed between the two inducers 4NQO and CIP.

11.2.5 MIC of ciprofloxacin and the correlation with 4NQO or CIP induction

The data from 4NQO and CIP was illustrated separately due to their different target specificity

(Figure 15, Figure 16). However the findings was the same, namely that most isolates had an

MIC=0,25 µg/ml and most mutants were in the range of 0,06 µg/ml ≤ MIC ≤1µg/ml CIP no matter

the mutagenic compound used. The data corresponded with previous findings, namely that

resistance to quinolones cause low-level FQ resistance (10,58,75). Further, the MIC of NALR

strains have been showed to be ≥0,06 CIP, which was equal to what was found here (3,75,90).

It was rather interesting to find that a few NALR mutants had MIC >0.015 µg/ml CIP a level equal

to the wild type level. Saenz et al. (2003) have found, the NALS strains (MIC ≤ 1-16 µg/ml) with an

maximally MIC =0.007 to 0,06 µg/ml CIP, whereas the NALR strains (MIC =32 µg/ml to MIC>256

µg/ml) had an MIC ≥ 0,06 µg/ml CIP (75). Since the MIC=0,06 µg/ml CIP was the lowest found in

the NALR strains by Saenz et al (2003), the mutants with an MIC >0.015 µg/ml CIP found in this

study were probably not NALR. It could have been examined by QRDR sequencing and of course

resistance check on the 64 µg/ml NAL plates once again. It is also possible, but less likely, that the

resistance was caused by other mechanisms, such as changed membrane permeability or changed

antibiotic efflux (25).



79

None of the mutants had an MIC of CIP above the MIC level previously found for isolates with one

mutation in gyrA (3,90). Unfortunately a correlation between target modifications in QRDR and

MIC of CIP could not be examined, due to the lack of sequencing of the mutants from procedure 2.

However, this was examined in the NALR mutants from procedure 1, discussed in section 11.3.

11.2.6 Gene expression analysis

To examine whether mucAB were expressed and the MucA and MucB proteins were produced,

gene expression analysis could have been performed.

To find out if the proteins were produced, western blotting could have been used, to detect the

presence of MucA and MucB by antibody binding of the Muc proteins. However the procedure

does not measure the quantity of the proteins. Therefore quantitative PCR (qPCR) could have been

applied as well. The key feature of qPCR is that the amplified DNA is quantified as it accumulates

in the reaction in real time after each amplification cycle. The quantification are based on

fluorescent dyes that intercalate with double stranded DNA or modified oligonucleotide probes that

fluoresce when hybridized with a complementary DNA (88).

The regulation of the genes could also have been examined by reverse transcriptase PCR (RT-

PCR), which is a highly sensitive technique. It determines the abundance of even low copy numbers

of specific RNA molecules within a cell, which is a measurement of gene expression. In RT-PCR,

cDNA are produced from RNA, denaturated and extended. The products are visualized by agarose

gel electrophoresis. A housekeeping gene can be used as reference to the expression level.

Microarray analysis could also have been applied, since then the expression of many genes could be

examined at once, hence the genes involved in SOS repair, such as uvr, dinB, mucAB, lexA and recA

e.g., could have been examined (47,54). However this technique is rather expensive.

11.3 Target modification through mutations in QRDR-Part I

11.3.1 Target modifications through QRDR mediated by mucAB

The original plan of this project was to find out whether mucAB induce certain basepair

substitutions. This was done by studying mutations in QRDR. However it requires that the mutagen

damages the DNA encoding DNA gyrase, since mucAB do not damage the DNA but rather is an

error-prone DNA repair mechanism due to the TLS polymerase activity.



80

As summarised by Mortelmans et al. (2006), the most prevalent findings in the work with pKM101,

was that mucAB enhance mutations at AT basepairs and especially transversions of AT→CG and

that transversions accounts for 51 % of the total number of basepair substitutions mediated by pol

RI (17,59). Given that transversions changes the chemical structure drastically compared to

transitions, these findings is rather interesting. On the other hand, mucAB have been found to

specifically induce GC→TA transversions followed by GC→AT transitions (60). Lastly mucAB

have also been found not to induce certain basepair changes compared to the wild type (31).

In this study the bases A, G and C were substituted equally. The transversion events accounted for

50 % of the basepair substitutions, which correspond to the level found by Curtis et al (2009), (17).

Nevertheless these results cannot be related to the TLS mediated by mucAB, since the genes

probably were not activated, as concluded from the results of the mutation frequency and since the

same types of basepair substitutions were found in MT102 without mucAB. The findings therefore

were accounted to be the result of spontaneous mutations rather than to the effect of mucAB.

In this study thymine (T) was found to be the most prevalent base inserted accounting for 47 % of

the total inserted bases in MT102/pHHA45. The same was found in MT102. This was differently

than what was found by Lawrence et al. (1996), who found that adenine was the predominant base

inserted found in 75% and 78 % of the basepair substitutions in two independent abasic sites (46).

This is rather interesting, since Ser83 is one of the prevalent amino acids that are changed in GyrA.

If adenine were inserted instead of thymine in Ser83 in gyrA, a stop codon would be created. Sine

Ser83 is located near the active site in DNA gyrase a stop codon would either decrease the

enzymatic activity of DNA gyrase or produce a fully inactivated protein (36). Thereby would the

strain not survive due to the lack of DNA gyrase essential for DNA supercoiling and twisting.

11.3 Target modification through mutations in QRDR- Part II

The next section do not focus on the mucAB mediated basepair substitutions, since the genes were

probably not activated, but rather focus on what types of amino acid substitutions that have been

found in QRDR of gyrA and parC and the correlation with the MIC for ciprofloxacin.

The findings of the laboratory work were that all of the sequenced NALR strains had one mutation

in gyrA, distributed on 10 mutation sites (Table 7). This was expected since a single mutation in

gyrA of E. coli is sufficient to become high-level resistant to NAL (36,48,74). As at least one

mutation in gyrA and one in parC of QRDR, is required for E. coli to become fluoroquinolone

resistant (10,58,75), it was not surprisingly that none of the 37 NALR isolates had mutations in

parC, since none of the isolates were CIP resistant. Further, none silent mutations, (no amino acid



81

change) in gyrA or parC were observed. This correlated with, that silent mutations generally make

the same amino acid and for this reason, the binding of quinolones and fluoroquinolones is not

changed and the strains do not survive NAL selection (49).

11.3.2 Mutations in gyrA

All the mutations in gyrA were missense mutations mediating diminish of quinolone binding. The

mutation sites Asp87 and Ser83 were the most frequent mutation sites observed, corresponding to

50 % and 20 % of the total amount of mutations, respectively. This was not surprisingly since as

described in the theory section, Ser83 and Asp87 are the most common mutated amino acids

substituted when quinolone resistance is mediated, found in both clinical, veterinary and laboratory

strains of E. coli (11,36,41). Further, both sites are associated with high level quinolone resistance

(NAL) and low-level fluoroquinolone resistance (10,36,87). Additionally they are also found to be

the prevalent type of mutations involved in high-level ciprofloxacin resistance (11). Perhaps the

high prevalence of mutations in these sites is due the fact that they are located near the active sites

of DNA gyrase. Mutations in the active site may alter the quinolone binding leading to resistance to

quinolones and low-level resistance to fluoroquinolones (36).

The resistance contribution of the Ser83 to Leu83 amino acid change has in other in vitro studies

been found to affect the MIC from being MIC=0,01 µg/ml in the wild type to 0,1 µg/ml in the

mutant (90) and in another study from being MIC=0,015 µg/ml in the wild type to 0,4 µg/ml in the

mutant (3). This correlates with what was found in this study, with a MIC=0,25 µg/ml for all the

Ser83 to Leu83 mutants, whereas the wild type MIC=0,015 µg/ml.

The resistance contribution of the Asp87 was MIC=0.06 µg/ml or 0.125 µg/ml CIP. This mutation

does also only contribute to low ciprofloxacin resistance when occurring alone. The most prevalent

substitutions observed were Asp87 to Tyr87 and Gly87. In vitro studies has shown that changes of

Asp87 to Tyr87 and Gly87 single mutations were associated MIC=0.06 µg/ml CIP (75). This

correlates with what was found here.

One interesting found was that 5 strains had a mutation, changing Gly81 to Cys81. The construction

of cysteine usually are not preferred due to its thiol side chain (-SH), which can participate in the

formation of S-S bonds. But perhaps the hydrophobic and polar features favours cysteine as being a

building stone of GyrA in change of the non-hydrophobic and non-polar amino acid glycine. This

corresponds with what was found with Gly84 in topoisomerase IV, which is negatively charged at

pH=7 and typically changed to a positively charged amino acid (83). In this study the resistance



82

contribution of Gly81 to Cys81 changed the MIC=0,015 µg/ml CIP in the wild type to MIC=0.06

µg/ml or 0.125 µg/ml CIP. This was reasonable compared to an in vitro study, which has shown a

resistance change from MIC=0,01 µg/ml in the wild type to MIC=0,1 µg/ml CIP in the mutant (90).

In summary 10 different mutations were found, as shown in Table 7. All of them have been

described previously. The 9 sites were within the originally defined QRDR (Ala67 to Glu106),

(35,36,90). But the tenth mutation site, Ala119, was outside this region. It was changed to Glu119 a

mutation that to the knowledge of this report, has not have been described previously in E. coli. But

for the family member, Salmonella, mutations in Ala119 to Ser119, Glu119 or Val119 have

previously been described. For this reason the mutations observed in Ala119 were not surprisingly

since many Enterobacteriaceae have similarities in the QRDR of any of the four topoisomerase

genes gyrA, gyrB, parC and parE (87). Mutations of gyrA in Ala119 in Salmonella and in Ala196

in E. coli, have also been associated with fluoroquinolone resistance (36). The Ala119 to Glu119

did give NAL resistance as well as low-level fluoroquinolone resistance, with MIC=0.06 to 0.125

µg/ml CIP, corresponding to the level mediated by the other amino acid changes found in this

study.

11.3.3 Mutations in parC

All the 34 isolates sequenced, were ciprofloxacin sensitive, examined by disk test. Given that

mutations mediating fluoroquinolone resistance occurs in a stepwise manner, where parC

mutations are found only in combination with gyrA mutations, the finding that none of the strains

had mutations in parC was not surprisingly (10,58,78). This shows once again that DNA gyrase is

the primary target of fluoroquinolones in E. coli and that topoisomerase IV is the secondary

target. Thereby seems the mutations of topoisomerase IV to emerge, when the gyrA has mutated

and DNA gyrase thereby have become resistant or at least less sensitive than topoisomerase IV

(24).

Had the strains in this study been CIP resistant, 85 % of them were expected to have a mutation in

gyrA in combination with a mutation in parC (58,75). Further the most frequent mutations sites of

parC are Ser80 and Gly84 as found by others (36,75). This is probably due to the structural

similarity of the gyrA and parC products, since Ser80 and Glu84 in parC corresponds to Ser83 and

Asp87 in gyrA and thereby are the changes in the protein structure of DNA gyrase and

topoisomerase IV similar (27,58).

None of the NALR isolates were sequenced for changes in gyrB and parE since mutations were not

found in parC and the order of the occurrence of the QRDR mutations are being;



83

gyrA→parC→(gyrA),parE→gyrB (27,36). Thus mutations in parE and gyrB were not expected. In

addition it has been found that mutations in gyrB and parE are secondary and less frequent

(27,36,58).



84

12 Conclusion

In this study, the potential of mucAB in mediating quinolone and fluoroquinolone resistance was

examined, mainly in E. coli and to a less extent in Salmonella.

One major finding was, that mucAB seems to be widespread in both E. coli and Salmonella, given

that the genes were found in both species. MucAB were especially predominant in pigs, being

present in 26 % of the diagnostic isolates. It would be interesting to examine if the distribution of

mucAB were just as extensive in humans, due to the common oral-faecal transmission routes that

animals and humans share described previously. This knowledge would be useful if we wanted to

identify strains that potentially carry the highest risk of becoming fluoroquinolone resistant, due to

the mutator effects mediated by mucAB (48).

The mutator effects of mucAB were not detected in this study, neither when CIP or 4NQO was used

as inducers and even not in the wild type strain H10, of which the plasmid pHHA45 was purified.

MT102 without any modifications other than the plasmid pHHA45 was used to examine the effects

of ciprofloxacin and to keep the system as “natural” as possible. However an increased mutation

frequency was not observed. This was probably since the NER system repaired the mutations

mediated by the mutagenic compounds in an error free way. The conclusion was that some other

repair mechanisms probably prevented the activation of mucAB, since perhaps the NER was

sufficient enough to repair the damage done by ciprofloxacin.

It could not be proven that mucAB had an effect on the type of basepair substitutions produced in

the gyrA region of QRDR, since mucAB probably were not activated. For this reason this is still an

area to examine. However from the data observed and the theoretically knowledge found, it was

concluded that quinolone resistance occur when mutations in gyrA of QRDR occur, mediating

changes of DNA gyrase. Serine83 and Asp87 substitutions were the most prevalent events,

accounting together for 70 % of all the amino acid changes found in the NALR mutants,

corresponding to what others have found. Further, Ser83 to Leu83 was the amino acid change that

mediated the highest MIC of ciprofloxacin.

In summary this study has given an insight in the abilities of mucAB and shown the vast potential of

these genes for adaption in bacteria. It can be concluded that the presence of mutator genes, such as

mucAB, to some extent are involved in mutations mediating resistance towards antibiotics and

thereby contribute to the rapid evolvement of antibiotic resistance and virulence, however it could

not be proven by the experimental setups in this study.



85

13 Perspectives

Since the muc operon has been found in plasmids from over 10 different Inc groups, it would be

interesting to examine what Inc groups the 15 mucAB carrying plasmids from pigs belonged to,

since the isolates were from different animals and farms and therefore a correlation of the Inc

groups could give an indication on what types of plasmids mucAB would be found on. Replicon

typing could be used with multiplex PCR followed by gel electrophoresis and visualisation.

Thereby, patterns of bands are found, which can be related to the Inc type.

In connection with the fluoroquinolone resistance it would be interesting to find out how many of

the 15 mucAB plasmids that encoded other resistance determining factors such as the resistance

gene aac(6’)Ib-cr, which mediates enzymatic modifications or the qnr genes mediating target

protection (10) as well as how many that carried the CTX-M-1 gene encoding ESBL production.

It would also be interesting to examine the distribution of mucAB in E. coli from humans, to clarify

how widespread mucAB are, perhaps along with ESBL production. This would give an idea of the

spread and their impact on resistance development in humans. This could be done by PCR and gel

electrophoresis.

As discussed the copy number of the mucAB genes may be essential for their effects. It would

therefore be interesting to examine this feature in the 15 mucAB strains. This could be done by

southern blotting, in which restriction enzyme digested genomic DNA is hybridized to a probe. The

DNA that was uncut by the restriction enzyme produce a single band, whereas multiple bands are

likely observed when the probe hybridizes to several highly similar sequences, e.g. those that may

are the result of the sequence duplication (88). This would give an indication of the copy number.

Since no effects of mucAB were observed in this study, further work is needed to be done to find out

to what extent these genes contribute to resistance development. As discussed expression analysis

could be performed, perhaps along with specially constructed strains. Also the assay need to be

optimized, by an increase in the sample amount, to get a significant result.

Further, if the mucAB genes were activated in a fluctuation assay, it would be relevant to examine

what types of base pair events they induce when ciprofloxacin is used as mutagenic compound, due

to the importance of what types of amino acids that are changed in QRDR of DNA gyrase and

topoisomerase IV. This would only require PCR and sequencing.



86

14 References

1. Ames, B. N., Lee, F. D. and Durston, W. E. (1973) An improved bacterial test system for the detection and

classification of mutagens and carcinogens. Proc. Nat. Acad. Sci., Vol. 70 (3), p. 782-786.

2. Andersson, M. I and MacGowan, A. P. (2003) Development of the quinolones. Journal of antimicrobial

chemotherapy, Vol. 51, p. 1-11.

3. Bagel, S., Hüllen, V., Wiedemann, B. and Heisig, P. (1999) Impact of gyrA and parC Mutations on Quinolone

Resistance, Doubling Time and Supercoiling Degree of Escherichia coli. Antimicrobial Agents and chemotherapy, Vol.

43 (4), p. 868-875.

4. Ball, P. (2000) Quinolone generations: natural history or natural selection? Journal of Antimicrobial

Chemotherapy, Vol. 46, p. 17-24.

5. Baquero M-R., Nilsson, A. I., Turrientes, M. del C., Sandvang, D., Galán, J. C., Martínez, J. L., Frimodt-

Møller, N., Baquero, F. and Andersson, D. I. (2004) Polymorphic mutation frequencies in Escherichia coli:

Emergency of weak mutators in clinical isolates. Journal of Bacteriology, Vol. 186 (16), p. 5538-5542.

6. Bastarrachea, F. (1998) On the origin of Plasmid-borne, Extended-spectrum, Antibiotic Resistance Mutations in

Bacteria. Journal of theoretical biology, Vol. 190, p. 379-387.

7. Bennet, PM. (2008) Plasmid encoded antibiotic resistance: acquisition and transfer of antibiotic resistance genes in

bacteria. British Journal of Pharmacology, Vol. 153, p. 347-357.

8. Birosová, L., Mikulasová, M. and Chroma, M. (2005) The effect of phenolic and polyphenolic compounds on the

development of drug resistance. Biomedical Papers (Olamouc), Vol. 149 (2), p. 405-407.

9. Boerlin, P. and Red-Smith, R. J. (2008) Antimicrobial resistance: its emergence and transmission. Animal Health

Research Reviews, Vol 9, p. 115-126.

10. Cavaco, L. M., Frimodt-Møller, N., Hasman, H., Guardabassi, L., Nielsen, L. and Aarestrup, F. M. (2008)

Prevalence of quinolone resistance mechanisms and associations to minimum inhibitory concentrations in quinolone-

resistant Escherichia coli isolated from humans and swine in Denmark. Microbial drug resistance, Vol. 14 (2), p.

163-169.

11. Chen, J. Y, Siu, L. K, Chen, Y-H., Lu, P-L., Ho, M. and Peng, C-F. (2001) Molecular Epidemiology and

Mutations at gyrA and parC Genes of Ciprofloxacin-Resistant Escherichia coli Isolates from a Taiwan Medical Centre.

Microbial drug resistance, Vol. 7 (1), p. 47-53.

12. Clerch, B., Bravo, J. M. and Llagostera, M. (1996) Analysis of the Ciprofloxacin-Induced Mutations in

Salmonella typhimurium. Environmental and Molecular Mutagenesis, Vol. 27, p. 110-115.

13. Clerch, B., Bravo, J. M. and Llagostera, M. (1996) Efficiency of MucAB and Escherichia coli UmuDC

proteins in quinolone and UV mutagenesis in Salmonella typhimurium: effect of MucA and UmuD processing.

Mutation Reseacrh, Vol. 349, p. 201-208.

14. Clinical and Laboratory standards Institute (2008) Performance Standards for Antimicrobial Susceptibility

Testing; Eighteenth Informational Supplement. M100-S18, Vol. 28, No. 1. ISBN: 1-56238-653-0.

15. Coulondre, C and Miller, J. H. (1977) Genetic Studies of the lac Repressor, IV mutagenic specificity in the lacI

Gene of Escherichia coli. Journal of Molecular Biology, Vol. 117 (3), p. 577-606.

16. Couturier, M., Bahassi, E. M. and Meldern, L. V. (1998) Bacterial death by DNA gyrase poisoning. Trends in

Microbiology, Vol. 6 (7), p. 269-275.



87

17. Curtis, E., McDonald, J. P., Mead, S. and Woodgate, R. (2009) DNA polymerase switching: effects on

spontaneous mutagenesis in Escherichia coli. Molecular Microbiology, Vol. 71 (2), p. 315-331.

18. DANMAP 1997. Consumption of antimicrobial agents and occurrence of antimicrobial resistance in bacteria from

food animals, food and humans in Denmark. ISSN 1397-1409.

19. DANMAP 2006. Use of antimicrobial agents and occurrence of antimicrobial resistance in bacteria from food

animals, foods and humans in Denmark. ISSN 1600-2032.

20. DANMAP 2007. Use of antimicrobial agents and occurrence of antimicrobial resistance in bacteria from food

animals, foods and humans in Denmark. ISSN 1600-2032.

21. Dowden, S. B. and Strikes P. (1982) R46-Derived Recombinant Plasmids Affecting DNA Repair and Mutation in

E. coli. Molecular and General Genetics, Vol. 186, p. 140-144.

22. Doyle, N. and Strike, P. (1995) The spectra of base substitutions induced by the impCAB, mucAB and umuDC

error-prone DNA repair operons differ following exposure to methyl methansesulfonate. Mol. Gen. Genet., Vol. 247,

p. 735-741.

23. Drake, J. W., Charlesworth, B., Charlesworth, D. and Crow, J. F. (1998) Rates of spontaneous mutation.

Genetics Society of America, Vol. 148, p. 1667-1686.

24. Drlica, K. and Zhao, X. (1997) DNA gyrase, Topoisomerase IV, and the 4-Quinolones. Microbiology and

Molecular Biology Reviews, Vol. 61 (3), p. 377-392.

25. Ellington, M. J. & Woodford, N. (2006) Fluoroquinolone resistance and plasmid addiction systems: self-

imposed selection pressure. Journal of Antimicrobial Chemotherapy, Vol. 57, p. 1026-1029.

26. Enne, V. I., Delsol, A. A., Davis, G. R., Hayward, S. L., Roe, J. M. and Bennet, P. M. (2005) Assessment of

the fitness impacts on Escherichia coli of acquisition of antibiotic resistance genes encoded by different types of

genetic element. Journal of Antimicrobial Chemotherapy, Vol. 56, p. 544-551.

27. Everett, M. J., Jin, Y. F., Ricci, V. and Piddock, L. J. V. (1996) Contributions of Individual Mechanisms to

Fluoroquinolone Resistance in 36 Escherichia coli Strains Isolated from Humans and Animals. Antimicrobial Agents

and chemotherapy, Vol. 40 (10), p. 2380-2386.

28. Flamand, N., Meunier, J.-R., Meunier, P.-A. and Agapaksis-Caussé. (2001) Mini mutagenicity test: a

miniaturized version of the Ames test used in a prescreening assay for point mutagenesis assessment. Toxicology in

Vitro, Vol. 15, p. 105-114.

29. Gatehouse D., Haworth, S., Cebula, T., Gocke, E., Kier, L., Matsushima, T., Melcion, C., Nohmi, T., Ohta,

T., Venitt, S. and Zeiger, E. (1994) Recommendations for the performance of bacterial mutation assays. Mutation

Research, Vol. 312, pp. 217-233.

30. Goldsmtih, M., Sarov-Blat, L. and Livneh, Z. (2000) Plasmid-encoded MucB protein is a DNA polymerase

(pol RI) specialized for lesion bypass in the presence of MucA’, RecA, and SSB. PNAS, Vol. 10 (21), p.11227-11231.

31. Gordon, A. J. E., Bernelot-Moens, C. and Glickman, B. W. (1993) Spontaneous mutagenesis in Escherichia

coli harbouring plasmid pKM101: DNA sequence analysis of forward lacI- mutations. Mutagenesis, Vol. 8 (2), p.

133-139.

32. Greenwood, D., Slack, R., Peutherer, J. and Barer, M. (2007) Medical Microbiology, a guide to microbial

infections: Pathogenesis, immunity, laboratory diagnosis and control. Churchill Livingstone, Elsevier, 17 th edition.

ISBN: 978-0-443-10209-7.

33. Gruz, P., Matsui, K., Sofuni, T. and Nohmi, T. (1998) Roles of the mutagenesis proteins SamA′B and MucA′B

in chemically induced frameshift mutagenesis in Salmonella typhimurium hisD3052. Mutation Research, Vol. 398, p.

33-42.



88

34. Hayasaki, Y., Itoh, S., Kato, M. and Furuhama, K. (2006) Mutagenesis induced by 12 quinolone antibacterial

agents in Escherichia coli WP2uvrA/pKM101. Toxicology in Vitro, Vol. 20, p. 343-346.

35. Hooper, D. C (1999) Mechanisms of fluoroquinolone resistance. Drug resistance updates, Vol. 2, p. 38-55.

36. Hopkins, K. L., Davies, R. H. and Threlfall, E. J. (2005) Mechanisms of quinolone resistance in Escherichia coli

and Salmonella: Recent developments. International Journal of Antimicrobial Agents, Vol. 25, p. 358-373.

37. Højby, N. and Tvede, M. (1999) Økologiske of farmakodynamiske principper for antibiotikabehandling i almen

praksis. LEO Temabog, Leo Pharma.

38. Janion, C. (2008) Inducible SOS response System of DNA repair and Mutagenesis in Escherichia coli.

International Journal of Biological Sciences, Vol. 4 (6), p. 338-344.

39. Jin, D. J. and Gross, C. A (1988) Mapping and Sequencing of Mutations in the Escherichia coli rpoB Gene that

Lead to Rifampicin Resistance. Journal of Molecular Biology, Vol. 202, p. 45-58.

40. Jones, M. E., Thomas, S. M. and Rogers, A. (1994) Luria-Delbrück Fluctuations Experiments: Design and

Analysis. Genetics Society of America, Vol. 136, p. 1209-1216.

41. Jurado, S., Orden, J. A., Horcajo, P., Fuente, R. D. L., Ruiz-Sanat-Quiteria, J. A., Martínez-Pulgarin, S. and

Domínguez-Bernal, G. (2008) Characterization of fluoroquinolone resistance in Escherichia coli strains from

ruminants. Journal of Veterinary and Diagnostically Investigations, Vol. 20, p. 342-345.

42. Khare, V. and Eckert, K. A. (2002) The proofreading 3´→5´ exonuclease activity of DNA polymerases: a

kinetic barrier to translesion DNA synthesis. Mutation Research, Vol. 510, p. 45-54.

43. Kossoy, E., Lavid, N., Soreni-Harari, M., Shoham, Y. and Keinan, E. (2007) A programmable Biomolecular

Computing Machie with Bacterial Phenotype Output. Chemistry Biochemistry, Vol. 8 (11), p. 1255-1260.

44. Kulaeva, O. l., Koonin, E. V., Wootton, J. C., Levine, A. S. and Woodgate, R. (1998) Unusual insertion element

polymorphisms in the promoter and terminator regions of the mucAB-like genes of R471a and R446b. Mutation

Research, Vol. 397, p. 274-262.

45. Langer, P. J., Shanabruch, W. G. and Waker, G. C. (1981) Functional Organization of Plasmid pKM101.

Journal of bacteriology, Vol. 145 (3), p. 1310-1316.

46. Lawrence, C. W., Borden, A. and Woodgate, R. (1996) Analysis of the mutagenic properties of the UmuDC,

MucAB and RumAB proteins, using a site-specific abasic lesion. Mol. Gen. Genet., Vol. 251, p. 493-498.

47. LeClerc, J. E., Li, B., Payne, W. L. and Cebula, T. A. (1996) High Mutation Frequencies Among Escherichia

coli and Salmonella Pathogens. Science, New Series, Vol. 274 (5290), p. 1208-1211.

48. Lindgren, P. K., Karlsson, Å. and Hughes, D. (2003) Mutation Rate and Evolution of Fluoroquinolone Resistance

in Escherichia coli Isolates from Patients with Urinary Tract Infections. Antimicrobial Agents and Chemotherapy, Vol.

47 (10), p. 3222–3232.

49. Madigan, M. T. and Martinko, J. M. (2006) Brock, Biology of Microorganisms. Pearson Prentice Hall, Eleventh

Edition, p. 169-181.

50. Mamber, S. W., Kolek, B., Brookshire, K. W., Bonner, D. P. and Fung-Tomc, J. (1993) Activity of

Quinolones in the Ames Salmonella TA102 Mutagenicity Test and Other Bacterial Genotoxicity Assays.

Antimicrobial Agents and Chemotherapy, Vol. 37 (2), p. 213-217.

51. Mandsberg, L. F., Ciofu, O., Kirkby, N., Christiansen, L. E., Poulsen, H. E. and Høiby, N. (2009) Antibiotic

Resistance in Pseudomonas aeruginosa Strains with Increased Mutation Frequency Due to Inactivation of the DNA

Oxidative Repair System. Antimicrobial agents and chemotheraphy, Vol. 53 (6), p.2483-2491.



89

52. Maron, D. M and Ames, B. N. (1983) Revised methods for the Salmonella mutagenicity test. Mutation

Research, Vol. 113, pp.173-215.

53. Matic, I., Radman, M., Tadden, F., Picard, B., Doit, C., Bingen, E., Denamur, E. and Elion, J. (1997). Highly

Variable Mutation Rates in Commensal and Pathogenic Escherichia coli. Science, Vol. 277 (5333), p. 1833-1834.

54. Matsui, K., Yamada, M., Imai, M., Yamamoto, K. and Nohmi, T. (2006) Specificity of replicative and SOS-

inducible DNA polymerases in frameshift mutagenesis: Mutability of Salmonella typhimurium strains overexpressing

SOS-inducible DNA polymerases to 30 chemical mutagens. DNA repair, Vol. 5, p. 465-478.

55. McCann, J. and Ames, B. N. (1976) Detection of carcinogens as mutagens in the Salmonella/microsome test:

Assay of 300 chemicals: Discussion. Proc. Nat. Acad. Sct., Vol. 73 (3), p. 959-954.

56. McCann, J., Spingarn, N. E., Kobori, J. and Ames B. N. (1975) Detection of Carcinogens as Mutagens:

Bacterial Tester Strains with R Factor Plasmids. Proc. Nat. Acad. Sci. USA, Vol. 72 (3), p. 979-983.

57. McNally, K. P., Freitag, N. E. and Walker G. C. (1990) LexA- Independent Expression of a Mutant mucAB

Operon. Journal of Bacteriology, Vol. 172 (11), p. 6223-6231.

58. Morgan-Linnell, S. K., Boyd, L. B., Steffen, D. and Zechiedrich, L. (2009) Mechanisms accounting for

Fluoroquinolone Resistance in Escherichia coli Clinical Isolates. Antimicrobial Agents and Chemotherapy, Vol. 53 (1),

p. 235-242.

59. Mortelmans, K. (2006) Isolation of plasmid pKM101 in the Stocker laboratory. Mutation research, Vol. 612, p.

151-164.

60. Murata-Kamiya, N. Kaji, H. and Kasai, H. (1999) Deficient nucleotide excision repair increase base-pair

substitutions but decreases TGGC frameshifts induced by methylglyoxal in Escherichia coli. Mutation Research, Vol.

442, p. 19-28.

61. Novick, R. P (1987) Plasmid incompatibility. Microbial reviews, Vol. 51 (4), p. 381-395.

62. Olofsson, S. K., Marcusson, L. L., Lindgren, P. K., Hughes, D. ad Cars, O. (2006) Selection of ciprofloxacin

resistance in Escherichia coli in an in vitro kinetic model: relation between drug exposure and mutant prevention

concentration. Journal of Antimicrobial Chemotherapy, Vol. 57, p. 116-1121.

63. Paterson, D. L and Bonomo, R. A. (2005) Extended-Spectrum β-Lactamases: a Clinical Update. Clinical

Microbiology Reviews, Vol. 18 (4), p. 657-686.

64. Perfeito, L., Fernandes, L., Mota, C. and Gordo, I. (2007) Adaptive Mutations in Bacteria: High Rate and Small

Effects. Science, Vol. 317, p. 813-815.

65. Perry, K. L. and Walker, G. C. (1982) Identification of plasmid (pKM101)-coded proteins involved in

mutagenesis and UV resistance. Nature, Vol. 300 (5889), p. 278-281.

66. Piddock, L. J. V. (2006) Multidrug-resistance efflux pumps- not just for resistance. Nature reviews, Microbiology,

Vol. 4, 629-635.

67. Power, E. G. M. and Phillips, I. (1993) Correlation between umuC induction and Salmonella mutagenicity assay

for quinolone antimicrobial agents. FEMS Microbial Letters, Vol. 112, p. 251-254.

68. Prival, M. J. and Zeiger, E. (1998) Chemicals mutagenic in Salmonella typhimurium strain TA1535 but not in

TA100. Mutation Research, Vol. 412, p. 251-260.

69. Qi, Z. (2005) Update on estimation of mutation rates using data from fluctuation experiments. Genetics, Vol. 171

(2), p. 861-864.



90

70. Reiffercheid, G., Arndt, C. and Schmid, C. (2005) Further Development of the β-lactamase MutaGen Assay and

Evaluation by Comparison with Ames Fluctuation Tests and the umu Test. Environmental and Molecular Mutagenesis,

Vol. 46, p. 126-139.

71. Reyes-Lamothe, R., Wang, X. and Sherratt, D. (2008) Escherichia coli and its chromosome. Trends in

Microbiology, Vol. 16 (5), p. 238-244.

72. Richmond, M. H., Bennet, P. M., Choi, C.-L., Brown, N., Brunton, J., Grinsted, J. and Wallace, L. (1980)

The genetic basis of the spread of β-lactamase synthesis among plasmid-carrying bacteria. Philosophical

Transactions of the Royal Society of London, Vol. 289 (1036), p. 183-193.

73. Ricci, J.C. D. and Hernández, M. E. (2000) Plasmid effects on Escherichia coli metabolism. Critical Reviews

Biotechnology, Vol. 20 (2), p. 79-108.

74. Robicsek, A., Jacoby, G. A. and Hooper, D. C. (2006) The worldwide emergence of plasmid-mediated quinolone

resistance. Lancet infectional diseases, Vol. 6, p. 629-640.

75. Sáenz, Y., Zarazaga, M., Briñas, L., Ruiz-Larrea, F. and Torres, C. (2003) Mutations in gyrA and parC genes in

nalidixic acid-resistant Escherichia coli strains from food products, humans and animals. Journal of Antimicrobial

Chemotherapy, Vol. 51, p. 1001–1005.

76. Skovgaard, I., Stryhn, H. and Rudemo, M. (1999) Basal Biostatistik- Del 1. DSR Grafik, First Edition. ISBN:

87-7432-517-5.

77. Smith, B. T. and Walker, G. C. (1998) Mutagenesis and More: umuDC and the Escherichia coli SOS Response.

Genetics Society of America, Vol. 148, p. 1599-1610.

78. Sorlozano, A., Gutierrez, J., Jimenez, A., de Dios Luna, J. and Martínez, J. (2007) Contribution of a New

Mutation in parE to Quinolone Resistance in Extended-Spectrum-Lactamase-Producing Escherichia coli Isolates.

Journal of Clinical Microbiology, Vol. 45 (8), p. 2740–2742.

79. Sutton, M. D., Smith, B. T., Godoy, V. G. and Walker, G. C. (2000) The SOS response: Recent Insights into

umuDC-Dependent Mutagenesis and DNA Damage Tolerance. Annu. Rev. Genet., Vol. 34, p. 479-497.

80. Stahlmann, R. (1990) Safety profile of the quinolones. Journal of Antimicrobial Chemotherapy, Vol. 26, p. 31-44.

81. Tillotson, G. S. (1996) Quinolones: structure-activity relationship and future perspectives. Journal of medical

microbiology, Vol. 44, p. 320-324.

82. Travis, J. M. J. and Travis E. R. (2002) Mutator dynamics in fluctuating environments. Proceedings: Biological

Sciences, Vol. 269 (1491), p. 591-597.

83. Vila, J., Ruiz, J., Go´ni, P. and Jimenez de Anta, M. T. (1996) Detection of mutations in parC in Quinolone-

Resistant Clinical Isolates of Escherichia coli. Antimicrobial Agents and Chemotherapy, Vol. 40 (2), p. 491-493.

84. Wagenlehner, F. M. and Naber, K. G. (2006) Treatment of bacterial urinary tract infections: presence and future.

Uropean Urology, Vol. 49, p. 235-244.

85. Walker, G. C. (1984) Mutagenesis and Inducible Responses to Deoxyribonucleic Acid Damage in Escherichia

coli. Microbiological Reviews, Vol. 48 (1), p. 60-93.

86. Walker, G. C. (1995) SOS-regulated proteins in translesion DNA synthesis and mutagenesis. Trends Biochem

Sci., Vol. 20 (10), p. 416-420.

87. Weigel, L. M., Steward, C. D. and Tenover, F. C. (1998) gyrA Mutations Associated with Fluoroquinolone

Resistance in Eight Species of Enterobacteriaceae. Antimicrobial agents and chemotherapy, Vol. 42 (10), p. 2661-

2667.



91

88. Wilson K. & J. Walker. Principles and Techniques of Biochemistry and Molecular Biology (2005). Cambridge

University Press, USA, 6th

edition, p. 208-210. ISBN-12 978-0-521-82889-5.

89. Wilson M. (2005) Microbial Inhabitants of humans- Their Ecology and Role in Health and Disease. Cambridge

University press, UK. ISBN: 0521841585.

90. Yoshida, H., Bogaki, M., Nakamura, M. and Nakamura, S. (1990) Quinolone resistance-determining region in

the DNA Gyrase gyrA Gene of Escherichia coli. Antimicrobial Agents and Chemotherapy, Vol. 51 (6), p. 1271-1272.

91. Ysern, P. Chlerch, B., Castano, M., Gibert, I., Barbe, J. and Llagostera, M. (1990) Induction of SOS genes in

Escherichia-coli and mutagenesis in Salmonella-typhimurium by fluoroquinolones. Mutagenesis, Vol. 5 (1), p. 63-66.

92. Internet source: Introduction to the OECD Guidelines on genetic toxicology testing and guidance on the

selection and application of assays (August 2007). Organisation for economic co-operation and development;

http://www.oecd.org/dataoecd/9/11/33663321.pdf

93. Internet source: Microbiology Reader Bioscreen C and a softwase Research Express (2005). Transgalactic Ltd

(manufacturer of Biosreen C software), Finland; http://www.bionewsonline.com/index.html

http://www.oecd.org/dataoecd/9/11/33663321.pdf

http://www.bionewsonline.com/index.html



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15 Appendix

R-codes

Examination of the uncertainty of the amount of mutations for each well, given that growth

was observed in X out of 23 possible wells

Example: 2 positive wells

> ## Simulation:

> obs.pos <- 2 #amount of wells observed to be positive

> n.rep <- 10000 # Amount of replicates

> m.p0 <- -log((23-obs.pos)/23) #expected number of mutations for each well(m)

>## Experiment:

> sum(rpois(23, m.p0)>0)

>## And then with a lot of samples:

> tmp <- matrix(rpois(n.rep*23,m.p0)>0,nrow=23)

#tmp is a matrice with 23 rows and n.rep columns and represent n.rep experiments

> pos.sim <- colSums(tmp)

> summary(pos.sim)

>## Making a table, the first columns are the amount of positive well, the other column are the

amount of simulations, with this result:

##> cbind(0:max(pos.sim),tabulate(pos.sim+1))

>## Plotter den empiriske kumulerede fordeling:

>plot.ecdf(pos.sim,add=TRUE)

>## Adding a gren line with the theoretical distribution:

qp <- qbinom((1:999)/1000, 23, 2/23)

lines(qp, (1:999)/1000, col=3)

>## 95% confidence interval:

> m.95 <- qbinom(c(0.025,0.975), 23, 2/23)

> m.95

## If 2 positive wells were observed at start and these are thought of as the true value, then in 95 %

of the repeated experiment the results are between 0 and 5 positive wells out of 23.

##If a single side test was chosen-Binomial distribution:

>qbinom(0.95, 23, 2/23)

the role of plasmid-located mucab genes in emergence of...

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