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DEVELOPl\1ENT AND EVALUATION OF A
NASBA SYSTEM FOR THE DIAGNOSIS OF CHOLERA
USING ELISA AND BIOSENSOR METHODS
by
LEESUYIN
Thesis submitted in fulfillment of the
requirements for the degree of
Doctor of Philosophy
April2008
ACKNOWLEDGEMENTS
I would like to express my deepest gratitude to my supervisor, Dr P. Lalitha, who
has been helpful and supportive throughout this study. Her critical comments and valuable
insights have guided me in the preparation of this thesis. I am grateful to my co-supervisor,.
Prof. Zainul F. Zainuddin and Assoc. Prof. M. Ravichandran for their guidance and advice
that have motivated me to become a better student and researcher.
To my dear friends and comrades, Melissa Chan, Yean Yean and Kurunathan, I
express my heartfelt appreciation for their encouragements and support that have helped me
through numerous failed experiments and mental roadblocks. My appreciation also goes out
to my labmates and friends who have helped me in one way or another during the course of
this study: Elina, Balqis, Donn, Chua, Siew Keah, Nik, Nurul, Kak Shikin, Nas, Nisha,
Chandrika, Syazwan, Kun Lee, Narjit and Kavitha. In addition, I am grateful to the lecturers,
administrative staff and lab technologists from the Department of Medical Microbiology and
Parasitology, and Institute for Research in Molecular Medicine, Universiti Sains Malaysia
for their help and the use of their excellent facilities.
I would like to thank Prof. Mitsuaki Nishibuchi from the Center for Southeast Asia
Studies, Kyoto University, Japan; Communicable Disease Hospital, Thandiarpettai, Chennai,
India; National Public Health Laboratory, Ministry of Health, Malaysia; Institute for Medical
Research (IMR), Malaysia and Kak Liza from the Medical Microbiology and Parasitology
laboratory, Universiti Sains Malaysia for providing the various bacterial strains used in this
study. I am also grateful to the Ministry of Science, Technology and Innovations (MOSTI)
for the IRPA and NBD grants that have funded part of this study.
On a more personal note, my family has been my strongest motivation and
inspirati6n. No words could ever express my gratitude to them. As a sign of appreciation, I
dedicate this thesis to them and hope that I have made them proud.
11
TABLE OF CONTENTS
Acknowledgement. ................................................................................................................... ii
Table of Contents .................................................................................................................... .iii
List ofTables ........................................................................................................................... .ix
List of Figures .......................................................................................................................... x
List of Symbols, Abbreviations and Acronyms ..................................................................... xiii
Abstrak ................................................................................................................................. xvii
Abstract. ................................................................................................................................. xix
CHAPTER 1 - INTRODUCTION
1.1 History of cholera ......................................................................................................... 1
1.2 Prevalence of cholera ................................................................................................... 1
1.3 Characteristics of V. cholerae ...................................................................................... 2
1.4 Ecology of V. cholerae ... .............................................................................................. 5
1.5 Viable but non-culturable (VBNC) state ...................................................................... 5
1.6 Epidemiology of cholera .............................................................................................. 6
1. 7 Pathophysiology of cholera .......................................................................................... 6
1.8 Clinical manifestations of cholera ................................................................................ 7
1.9 Treatment of cholera .................................................................................................... 8
1.10 Prevention of cholera ................................................................................................... 8
1.11 Diagnosis of cholera ..................................................................................................... 9
1.11.1 Conventional laboratory methods ................................................................... 9
1.11.2 Alternative methods of cholera diagnosis ..................................................... 11
1.11.2.1 Immunological-based tests for cholera .............................................. 11
1.11.2.2 Molecular-based tests for cholera ...................................................... 12
1.11.2.2.1 Characteristics and advantages of molecular-based tests
over conventional methods ........................................................ 13
1.11.2.3 Nucleic acid sequence-based amplification (NASBA) ....................... 14
1.12 Rationale of the study ................................................................................................. 17
1.13 Objectives of the study ............................................................................................... 18 I
1.14 Overview of the study ................................................................................................ 19
lll
CHAPTER 2- MATERIALS AND METHODS
2.1 Materials ..................................................................................................................... 20
2.1.1 Bacterial strains ............................................................................................. 20
2.1.1.1
2.1.1.2
2.1.1.3
2.1.2
2.1.3
2.1.3.1
2.1.3.2
2.1.4
2.1.5
2.1.6
2.1.6.1
2.1.6.2
Reference strains .................................................................................. 20
Clinical isolates .................................................................................... 20
Growth and maintenance of bacterial strains ........................................ 21
Culture Media ................................................................................................ 21
Primers and probes ........................................................................................ 25
Preparation of primer stock solutions ................................................... 25
Preparation of primer working solutions .............................................. 25
Deoxyribonucleotide triphosphates (dNTP, 20 !J.M) ..................................... 25
Ribonucleotides (NTP, 20 1-!M) ..................................................................... 26
Buffers and chemical stock solutions ............................................................ 26
Diethylpyrocarbonate (DE PC) treatment of water and solutions ......... 27
Diethylpyrocarbonate (DEPC) treatment of glasswares and
plasticwares .......................................................................................... 27
2.2 Methods ...................................................................................................................... 27
2.2.1 RNA Isolation ............................................................................................... 27
2.2.2 Quantitation of RNA ..................................................................................... 28
2.2.3 Plasmid Isolation ........................................................................................... 29
2.2.4 Genomic DNA Isolation ............................................................................... 29
2.2.5 Quantitation of DNA ..................................................................................... 30
2.2.6 Polymerase Chain Reaction (PCR) assay ................. , .................................... 31
2.2.7 Purification ofPCR product .......................................................................... 31
2.2.8 Agarose gel electrophoresis .......................................................................... 32
2.3 Experimental overview of Phase 1 study: Development and optimization of a
cholera NASBA assay ................................................................................................ 35
2.3.1 Designing primers and probes for cholera NASBA assay ........................... 36
2.3.2
2.3.2.1
2.3.2.2
2.3.2.3 i
2.3.2.4
2.3.2.5
2.3.2.6
2.3.2.7
Construction of in vitro RNA transcripts ...................................................... 38
Cloning of V. cholerae lo!B gene ......................................................... 38
PCR ofthe lolB gene ............................................................................ 38
Ligation ofPCR product into pTZS7R vector. ..................................... 38
Preparation of competent E. coli Top 10 cells ....................................... 40
Transforn1ation ..................................................................................... 40
PCR screening of transformed colonies ............................................... 41
DNA sequencing .................................................................................. 43
IV
2.3.2.8
2.3.2.9
2.3.2.10
Plasmid linearization by restriction endonuclease digestion ................ 43
In vitro transcription ............................................................................. 43
Purification of RNA using phenol-chloroform and ethanol
precipitation .......................................................................................... 44
2.3.3 Cholera NASBA assay ................................................................................. 46
2.3.3.1
2.3.3.2
Preparation of cholera NASBA reaction mix and enzyme mix ............ 46
Detection ofNASBA amplicons by agarose gel electrophoresis ......... 49
2.3 .3 .3 Optimization of cholera NASBA reaction conditions .......................... 49
2.3.3.4 Analytical specificity of the cholera NASBA assay ............................. 51
2.3.3.5 Analytical sensitivity of the cholera NASBA assay ............................. 51
2.3.3.5.1 Analytical sensitivity at the gene level ........................................ 51
2.3.3.5.2
2.3.3.6
Analytical sensitivity at the bacterial cell level ........................... 52
Reproducibility and efficiency of the RNA isolation technique .......... 53
2.3.4
2.3.4.1
Analysis of the NASBA reaction and its amplicons ..................................... 54
Northern Blotting .................................................................................. 54
2.3.4.2 Dot-blotting .......................................................................................... 55
2.3.4.2.1 Hybridization with biotinylated DNA probe ................................ 55
2.3.4.2.2 Hybridization with Streptavidin-HRP ........................................... 56
2.3.4.2.3 Colorimetric detection ofblots ..................................................... 56
2.3.4.3 RNase and DNase digestion ofNASBA amplicons ............................. 57
2.3.4.4 Amplification of DNA by NASBA ...................................................... 59
2.3.4.5 Viability assay ...................................................................................... 59
2.4 Experimental overview of Phase 2 study : Development and optimization of
ELISA for detection ofNASBA amplicons (NASBA-ELISA) ................................. 61
2.4.1 Cholera NASBA-ELISA assay ..................................................................... 62
2.4.1.1 Preparation of 3 '-end biotin-tailed capture probe
2.4.1.2
2.4.1.3
2.4.1.4
2.4.1.5
2.4.1.6
2.4.1.7
(VHA-S4-Biotin3 ') ............................................................................... 64
Optimization and comparison of the hybridization efficiency of
3 '-end biotin-tailed capture probe (VHA-S4-Biotin3 ')and
5' -end biotin- labelled capture probe (VHA-S4-5'Biotin) ................... 64
Optimization ofVN2F-Flu concentration as detection probe for
unlabelled NASBA amplicons .............................................................. 65
Optimization of fluorescein-12-UTP concentration for internal
labeling ofNASBA amp1icons ............................................................. 65
Detection ofNASBA amplicons by ELISA ......................................... 65
Analytical specificity of the cholera NASBA-ELISA assays ............... 67
Analytical sensitivity of the cholera NASBA-ELISA assays ............... 67
v
2.4.2
2.4.2.1
2.4.2.2
Clinical evaluation of cholera NASBA-ELISA using spiked stool
samples ......................................................................................................... 68
Preparation of spiked stool samples ..................................................... 68
Limit of detection (LoD) of cholera NASBA-ELISA at the
bacterial cell level using spiked stool samples ..................................... 69
2.4.2.3 Statistical analysis ................................................................................ 69
2.4.2.3.1 Calculation of sample size for spiked stool sample evaluation .... 69
2.4.3.3.2 Calculation of diagnostic performance for spiked stool
sample evaluation ......................................................................... 70
2.5 Experimental overview of Phase 3 study: Development of electrochemical
biosensor detection for cholera NASBA-ELISA ....................................................... 71
2.5.1 Biosensor detection for cholera NASBA-ELISA .......................................... 72
2.5.1.1 Biosensor and electrode design ............................................................ 72
2.5.1.2 Optimization of biosensor detection of cholera NASBA-ELISA
signal .................................................................................................... 72
2.5.1.3 Analytical specificity of the cholera NASBA-ELISA with biosensor
detection ............................................................................................... 73
2.5.1.4 Analytical sensitivity of the cholera NASBA-ELISA with biosensor
detection ................................................................................................ 73
2.6 Experimental overview of Phase 4 study: Optimization of a thermostabilized
cholera NASBA mix .................................................................................................. 75
2.6.1 Thermostabilization of cholera NASBA mix (reaction mix and
enzyme mix) .................................................................................................. 76
2.6.1.1 Preparation offreeze-dried reaction mix .............................................. 76
2.6.1.2 Preparation of freeze-dried enzyme mix .............................................. 77
2.6.1.2.1 Optimization of enzymes and enzyme stabilizer concentrations ... 77
2.6.1.3 Freeze-drying ofNASBA reaction and enzyme mixes ........................ 77
2.6.1.4 Reconstitution ofthe freeze-dried NASBA mix.. ................................. 78
2.6.1.5 Analytical sensitivity of the freeze-dried cholera NASBA mix at
the bacterial cell level.. ......................................................................... 78
2.6.1.6 Determination of periodic stability of the freeze-dried cholera
NASBA mix at different temperatures ................................................. 79
vi
CHAPTER 3- RESULTS AND DISCUSSION ·
3.1 Designing primers and probes for cholera NASBA assay ......................................... 80
3.2 Construction of RNA transcript ................................................................................. 84
3.2.1 Cloning of lolB gene into pTZ57R vector .................................................... 84
3.2.2 Confirmation of clones by PCR screening and DNA sequencing ................. 86
3.2.3 In vitro transcription of the linearized pTZ-lolB plasmid ............................. 89
3.3 Cholera NASBA assay ............................................................................................... 91
3.3.1 Optimization of cholera NASBA reaction conditions ................................... 91
3.3.1.1 MgCh concentration ............................................................................. 91
3.3.1.2 KCl concentration ................................................................................. 91
3.3.1.3
3.3.1.4
3.3.1.5
3.3.2
3.3.3
3.3.4
3.3.5
Primers concentration ........................................................................... 93
DMSO concentration ............................................................................ 93
Enzymes concentration ......................................................................... 95
Detection ofNASBA amplicons by agarose gel electrophoresis .................. 98
Analytical specificity of the cholera NASBA assay ..................................... 98
Analytical sensitivity ofthe cholera NASBA assay .................................... 100
Reproducibility and efficiency of the RNA isolation technique ................. 103
3.3.6 Analysis of the NASBA reaction and its amplicons ................................... 105
3.3.6.1 Probe-based hybridization ofNASBA amplicons .............................. 105
3.3.6.1.1 Northern Blotting ........................................................................ 105
3.3.6.1.2
3.3.6.2
3.3.6.3
Dot-blotting ................................................................................. 105
RNase and DNase digestion ofNASBA amplicons ........................... 107
Amplification of DNA by NASBA .................................................... 109
3.3.6.4 Viability assay .................................................................................... 111
3.4 Cholera NASBA-ELISA .......................................................................................... 113
3.4.1 Optimization and comparison of 3 '-end biotin-tailed capture probe
(VHA -S4-Biotin3 ') and 5 '-end biotin-labelled capture probes
(VHA-S4-'Biotin) ....................................................................................... 113
3.4.2 Optimization ofVN2F-Flu concentration as detection probe for
unlabelled NASBA amplicons .................................................................... 115
3.4.3 Optimization of fluorescein-12-UTP concentration for internal labeling
ofNASBA amplicons ................................................................................. 117
3.4.5 Analytical specificity of the two NABSA-ELISA formats ......................... 119
3.4.6 Analytical sensitivity of the two NASBA-ELISA formats at the gene
and bacterial cell level.. ............................................................................... 122
3.4.7 Comparison of performance ofthe two NASBA-ELISA formats .............. 126
Vll
3.4.8
3.4.8.1
3.4.8.2
Evaluation of cholera NASBA-ELISA using spiked stool samples ............ 128
Diagnostic performance of the cholera NASBA-ELISA assay .......... 131
Limit of detection (LoD) of cholera NASBA-ELISA at the
bacterial cell level using spiked stool samples ................................... 131
3.5 Electrochemical biosensor detection of cholera NASBA-ELISA ........................... 134
3.5.1 Analytical specificity ofthe cholera NASBA-ELISA assay with
biosensor detection ...................................................................................... 134
3.5.2 Analytical sensitivity of the cholera NASBA-ELISA assay with
biosensor detection ...................................................................................... 137
3.5.3 Comparison and correlation between biosensor- and spectrophotometric-
based ELISA results .................................................................................... 139
3.6 Thermostabilization of cholera NASBA mix .......................................................... 141
3.6.1 Optimization of enzymes and enzyme stabilizer concentrations ................ 141
3.6.2 Analytical sensitivity of the freeze-dried NASBA mix at the bacterial
cell and gene level ....................................................................................... 144
3.6.3 Periodic stability of the freeze-dried NASBA mix ..................................... 146
3.7 Discussion ................................................................................................................ 148
CHAPTER 4- SUMMARY AND CONCLUSION ......................................................... 167
REFERENCES ..................................................................................................................... 170
APPENDICES
Appendix A- Preparation of Culture Media, Buffers and Chemical Stock
Solutions .......................................................................................................................... A 1
Appendix B- Alignment result of V cholerae lo!B gene (AF227752) with the
lo!B or hemM gene of other enteric bacteria .................................................................. All
Appendix C -lo!B (hemM) sequence (Genbank accession no: AF227752) and
NASBA primers and probes binding sites ...................................................................... Al6
Appendix D- Partial sequence of pTZ-lolB plasmid (position 551 - 1350)
showing the binding sites of primers used for PCR screening of clones and restriction
enzymes sites .................................................................................................................. A 17 I
Appendix E- Alignment of pTZ-lolB sequencing result with the /alB gene
sequence (AF227752) ..................................................................................................... Al8
LIST OF PUBLICATIONS
Vlll
LIST OF TABLES
Table 1.1: Tests for differentiation of Classical and El Tor biotypes of V. cholerae
serogroup 0 1 .......................................................................................................... 4
Table 1.2: V. cholerae serogroups and their antigenic determinants ...................................... .4
Table 2.1: Details of the reference strains used in this study ................................................ 22
Table 2.2: Details of the clinical isolates used in this study ................. .-................................ 23
Table 2.3: Composition of a standard PCR mix .................................................................... 34
Table 2.4: Standard thermal cycling programme .................................................................. 34
Table 2.6: Details of the cholera NASBA primers and probes used in this study ................ 37
Table 2.5: Details ofPCR primers, annealing temperatures and expected product sizes
used in the PCR screening of transformed colonies ............................................. 42
Table 2. 7: Composition of the cholera NASBA mix before optimization ............................ 48
Table 2.8: Optimization of cholera NASBA reaction components ....................................... 50
Table 3.1: Result of PCR screening for two positive pTZ-lolB clones to confirm the
gene insert size and orientation ............................................................................ 88
Table 3.2: Composition of the optimized cholera NASBA mix ........................................... 97
Table 3.3: Reproducibility of the RNA isolation technique. RNA isolation was
performed on a culture of V. cholerae 01 El Tor in six replicates ..................... 104
Table 3.4: Efficiency of the RNA isolation technique. RNA isolation was performed
on four replicate samples spiked with 10 Jlg of RNA from V. cholerae
01 El Tor ............................................................................................................ 104
Table 3.5: Reproducibility ofNASBA-ELISA using unlabelled and labelled NASBA
amplicons based on the analytical sensitivity assays .......................................... 127
Table 3.6: Summary of cholera NASBA-ELISA evaluation with spiked stool samples .... 130
Table 3.7: Statistical analysis ofthe diagnostic performance of the cholera
NASBA-ELISA ................................................................................................. 132
ix
LIST OF FIGURES
Figure 2.1: Procedures involved in the cloning of lolB gene of V. cholerae ........................ 39
Figure 2.2: Plasmid map ofpTZ-lolB showing the exact position of the cloning site,
genetic elements, restriction sites and T7 promoter site ..................................... 39
Figure 2.3: In vitro transcription of the Sad linearized pTZ-lolB plasmid to produce
RNA transcripts ................................................................................................... 45
Figure 2.4: Procedures involved in NASBA and detection of its amplicons by agarose
gel electrophoresis ............................................................................................... 4 7
Figure 2.5: Procedures involved in the viability assay to determine whether the lolB
mRNA can be used as an indicator of cell viability ............................................ 60
Figure 2.6: Diagrammatic representation of the two ELISA formats evaluated in this
study using unlabelled NASBA amplicons (A) or fluorescein-labelled
NASBA amplicons (B) ........................................................................................ 63
Figure 2.7: Experimental overview ofthe cholera NASBA-ELISA assay with biosensor
detection ............................................................................................................. 74
Figure 3.1: Mfold result showing a possible structure for the 784 nucleotide region of
the lolB mRNA molecule and the NASBA primers binding sites ....................... 82
Figure 3.2: Mfold result showing a possible structure of the 203 nucleotide NASBA
amplicon and probes binding sites ...................................................................... 83
Figure 3.3: Agarose gel electrophoresis result of the lolB gene PCR product for cloning
into pTZS7R vector ............................................................................................. 85
Figure 3.4: PCR screening of two positive clones for the correct lolB gene insert size
and orientation ..................................................................................................... 87
Figure 3.5: Linearization ofpTZ-lolB plasmid with Sad enzyme ........................................ 90
Figure 3.6: In vitro transcription oflinearized pTZ-lolB plasmid ......................................... 90
Figure 3. 7: Optimization ofMgCh concentration ................................................................. 92
Figure 3.8: Optimization ofKCl concentration ..................................................................... 92
Figure 3.9: Optimization of primers concentration ............................................................... 94
Figure 3.10: Optimization ofDMSO concentration .............................................................. 94
Figure 3.11: Optimization ofT7 RNA polymerase (A) and AMV-RT (B) enzymes
concentration ..................................................................................................... 96
Figure 3.12: Analytical specificity evaluation of the cholera NASBA assay with
agarose gel electrophoresis detection ................................................................ 99
Figure 3.13: Analytical sensitivity of the cholera NASBA assay at the gene level using
agarose gel electrophoresis detection .............................................................. 101
X
Figure 3.14: Analytical sensitivity ofthe cholera NASBA assay at the bacterial cell
level using agarose gel electrophoresis detection ............................................ 102
Figure 3.15: Northern blotting ofNASBA amp1icons from agarose gel (A) onto a
positively-charged nylon membrane (B) ......................................................... I 06
Figure 3.16: Dot-blotting ofNASBA amplicons onto a positively-charged nylon
membrane ........................................................................................................ 106
Figure 3.17: Analysis ofNASBA amplicons by RNase A and DNase I digestion ............. 108
Figure 3.18: Analysis ofRNase A and DNase I digested NASBA amplicons by
RT-PCR (A) and PCR (B) ............................................................................... 108
Figure 3.I9: Amplification of DNA by NASBA ................................................................. II 0
Figure 3.20: Evaluation of the stability of the /olB mRNA after lethal treatments and
incubation at different times and temperatures .............................................. 112
Figure 3.21: Comparison ofELISA signal using 3'-end (VHA-S4-Biotin3') and 5'-end
(VHA-S4-5'Biotin) biotin-labelled capture probes ......................................... 114
Figure 3.22: Optimization ofVN2F-Flu detection probe concentration using unlabelled
NASBA ampiicons from positive control. ...................................................... 116
Figure 3.23: Optimization offluorescein-12-UTP concentration using /olB RNA transcripts
with amplicon detection by agarose gel electrophoresis(A) and ELISA(B) .... Il8
Figure 3.24: Analytical specificity of ELISA detection using unlabelled NASBA amplicons
evaluated using a panel of 41 reference bacterial strains ............................... 120
Figure 3.25: Analytical specificity of ELISA detection using fluorescein-labelled NASBA
amplicons evaluated using a panel of 41 reference bacterial strains ............ 121
Figure 3.26: Analytical sensitivity ofNASBA-ELISA at the (A) gene and (B) bacterial cell
level using unlabelled and fluorescein-labelled NASBA amplicons ......... 123
Figure 3.27: Analytical sensitivity at the gene level using unlabelled (A) and fluorescein-
labelled (B) NASBA amplicons by agarose gel electrophoresis ..................... 124
Figure 3.28: Analytical sensitivity at the bacterial cell level using unlabelled (A) and
fluorescein-labelled (B) NASBA amplicons by agarose gel electrophoresis .. .l25
Figure 3.29: Clinical evaluation of cholera NASBA-ELISA using spiked stool samples .. 129
Figure 3.30: Limit of detection (LoD) of cholera NASBA-ELISA at the bacterial cell
level with spiked stool samples ....................................................................... 133
Figure 3.31: Analytical specificity of cholera NASBA-ELISA with signal measurement by 1 spectrophotometry (microplate reader) and biosensor. ................................... 136
Figure 3.32: Analytical sensitivity ofNASBA-ELISA at the gene (A) and bacterial
cell (B) level with signal measurement by spectrophotometry (microplate
reader) and biosensor ....................................................................................... 138
XI
Figure 3.33: Correlation analysis of biosensor and spectrophotometry results ................... 140
Figure 3.34: First round optimization of enzymes and enzyme stabilizer concentrations
for thermostabilization of enzyme mix ............................................................ 142
Figure 3.35: Second round optimization of enzymes and enzyme stabilizer concentrations
for thermostabilization of enzyme mix ............................................................ 142
Figure 3.36: Optimization using higher concentrations of enzyme stabilizer for
thermostabilization of enzyme mix ................................................................. 143
Figure 3.37: Analytical sensitivity of the freeze-dried NASBA mix at the bacterial
cell level (A) and gene level (8) ...................................................................... 145
Figure 3.38: Periodic evaluation of the stability of freeze-dried NASBA mix .................... 147
xii
LIST OF SYMBOLS, ABBREVIATIONS AND ACRONYMS
nil eDNA complimentary deoxyribonucleic acid
% percent CPU colony forming unit
approximately cr chlorine ion
+ positive em centimeter
negative/ minus CT cholera toxin
< less than CTP cytidine 5 '-triphosphate
> more than cv coefficient of variation
± plus I minus dATP deoxyadenosine triphosphate
~ to dCTP deoxycytidine triphosphate
oc degree Celsius ddt dideoxythymidine
A adenine I adenosine; DEPC diethylpyrocarbonate absorbance
A26o absorbance at 260 nm dG Gibbs free energy
A2so absorbance at 280 nm dGTP deoxyguanosine triphosphate
A4so absorbance at 450 nm dH20 distilled water
ADP adenosine diphosphate DMSO dimethyl sulfoxide
Ag/AgCl silver/silver chloride DNA deoxyribonucleic acid
AMV-RT avian myeloblastosis virus- DNase deoxyribonuclease reverse transcriptase
APW alkaline peptone water dNTP deoxynucleoside triphosphate
ATP adenosine 5 '-triphosphate DTT dithiothreitol
BLAST Basic Local Alignment dTTP deoxythymidine triphosphate Search Tool
bp basepair ECL electrochemiluminescence
BSA bovine serum albumin EDTA ethylenediaminetetraacetic acid
c cytosine; current ELGA enzyme-linked gel assay
cAMP adenosine 3 ',5 '-cyclic ELISA enzyme-linked monophosphate immunosorbent assay
xiii
eta/. et alii I and other IU infectious unit; international unit
FAM carboxyfluorescein J Joule
FDA Food and Drug k kappa value Administration
Flu fluorescein K+ potassium ion
G guanine I guanosine kcallmol kilocalories per mol
g gram KCl potassium chloride
GHKB General Hospital Kota Bharu kDa kilodalton
GITC guanidine thiocyanate KIA Kligler iron agar
GM1 monosialotetrahexosylganglio L/hour liter per hour side
GMO genetically modified LB Luria Bertani organism
GTP guanosine 5 '-triphosphate LCD liquid crystal display
H2 hydrogen LCR ligase chain reaction
H20 water LoD limit of detection
H202 hydrogen peroxidase M molar I molarity
H2S hydrogen sulphate mbar millibar
HCl hydrogen chloride MCS multiple cloning site
HC03- hydrogen carbonate ion mg milligram
HIV-1 human immunodeficiency MgCh magnesium chloride virus 1
HPLC high performance liquid mm minute chromatography
hr hour MKAK National Public Health Laboratory
HRP horseradish peroxidase ml milliliter
HUSM Hospital Universiti Sains mm millimeter Malaysia
I.e. id est I that is mM millimolar
IFU 1 inclusion-forming unit M-MLV Moloney murine leukemia RT virus reverse transcriptase
IMR Institute for Medical MOPS 3-(N-Research morpholino )propanesulfonic
IPA intermittent pulse mRNA messenger ribonucleic acid amperomehy
XIV
N normal psi pounds per square inch
n sample size Psn specificity
N/A not available I not applicable Psp sensitivity
Na+ sodium ion R correlation coefficient
NAO nicotinamide red reduced I reduction
NaOH sodium hydroxide RNA ribonucleic acid
NASBA nucleic acid sequence-based RNase ribonuclease amplification
NCBI National Center for RNase H Ribonuclease H Biotechnology Information
nm nanometer RNasin RNasin Ribonuclease Inhibitor
nmol nanomol rpm revolutions per minute
NPV negative predictive value rRNA ribosomal ribonucleic acid
nt nucleotide RSO relative standard deviation
NTP nucleoside triphosphate RT room temperature
Oz oxygen RT-PCR reverse transcription-polymerase chain reaction
00 optical density s Svedberg unit
00450 optical density at 450 nm SAM salf-assembled monolayer
00600 optical density at 600 nm SO standard deviation
OH hydroxyl group SOA strand displacement amplification
ORS oral rehydration solution SOS sodium dodecyl sulphate
ox oxidized I oxidation s second
PBS phosphate buffered saline SPCE screen-printed carbon electrode
PBST phosphate buffered saline- SPE screen-printed electrode Tween 20
PCR polymerase chain reaction spp. species
PFU PCR-forming unit SPR surface plasmon resonance
pmol picomole sse sodium chloride/sodium citrate
PPV positive predictive value SSCT sodium chloride/sodium citrate/Tween 20
XV
T thymine I thymidine UTP uri dine 5 '-triphosphate
Ta annealing temperature uv ultraviolet
TAE Tris-acetate-EDT A v volts
TBE Tris-borate-EDTA v/v volume/volume
TCBS thiosulphate citrate bilesalt VBNC viable but non-culturable sucrose
tcp toxin coregulated pili vs versus
TdT terminal deoxynucleotidyl w/v weight/volume transferase
TE Tris-EDTA www World Wide Web
Tm melting temperature X precision
TMA transcription-mediated xg relative centrifugal force amplification
TMB 3,3',5,5'- JlA microamperes tetramethylbenzidine
Tris tris(hydroxymethyl)aminomet jlg microgram hane
tRNA transfer ribonucleic acid jll microliter
TSI triple sugar indole jlm micrometer
u units J.!M micromolar
xvi
PEMBANGUNAN DAN PENILAIAN SISTEM NASBA UNTUK DIAGNOSIS
PENYAKIT TAUN MENGGUNAKAN KAEDAH ELISA DAN BIOSENSOR
ABSTRAK
Taun (kolera) ialah penyakit ciri-birit yang disebabkan Vibrio cholerae. Taun boleh
membawa maut jika tidak dikesan dengan serta-merta. Justeru, pengesanan awal adalah
penting untuk rawatan pesakit dan kawalan wabak taun. Ujian kultur dan biokimia
konvensional adalah rumit, lambat dan kurang sensitif. Walaupun ujian berasaskan teknik
molekul adalah lebih pantas, sensitif dan spesifik, kaedah ini memerlukan peralatan mahal
dan penyimpanan sejuk bahan-bahan reagen. Ujian DNA seperti PCR tidak dapat
membezakan sel hidup dengan sel mati. Kaedah amplifikasi berasaskan asid nukleik
(NASBA) yang menggandakan RNA secara isoterma dapat mengesan sel hidup sahaja.
Maka, objektif kajian ini adalah untuk membangunkan dan menilai suatu ujian NASBA
ELISA yang stabil haba dengan biosensor untuk mengesan V. cholerae berasaskan gen lolB.
Pada peringkat permulaan, transkrip RNA sebagai kawalan positif dikonstruk dan primer
serta prob khusus direka. Pengoptimuman ujian NASBA dan ELISA dilakukan dan
spesifisiti analitikal diuji dengan 41 bakteria rujukan yang terdiri daripada V. cholerae,
Vibrio spesis dan patogen enterik. Sensitiviti analitikal diuji dengan cairan bersiri transkrip
RNA dan sel-sel V. cholerae. Penilaian klinikal dijalankan dengan menggunakan najis yang
ditokok sampel (n=200). Seterusnya, kaedah biosensor dioptimurnkan dan keputusannya
dibandingkan dengan kaedah spektrofotometri. Campuran NASBA dijadikan stabil haba
melalui pengeringbekuan dan kestabilannya dinilai pada suhu berlainan untuk jangkamasa
tertentu. Selain itu, kesesuaian lolB mRNA sebagai penunjuk kebolehhidupan diselidiki
dengan rhembunuh sel-sel V. cholerae melalui pelbagai kaedah dan mengesan isyarat
NASBA daripadanya. Ujian kolera NASBA-ELISA yang telah dioptimurnkan berdasarkan
pengesanan produk amplifikasi melalui prob berlabel fluorescein dan isyarat TMB/HRP.
· Spesifisiti analitikal ujian adalah l 00% manakala sensitiviti analitikal ujian adalah 102
xvn
molekul/J..Ll transkrip RNA dan 10 CFU/ml sel. Penilaian klinikal memberikan keputusan
100% sensitif, 84.52% spesifik, 89.92% nilai ramalan positif dan 100% nilai ramalan negatif.
Kaedah biosensor didapati setanding kaedah spektrofotometri dengan mencatatkan kepekaan
analitikal yang sama, korelasi yang rapat (R2<0.964) dan persetujuan kappa yang hampir
sempuma (95.1%, k = 0.828). Penstabilan campuran NASBA mampu mengekalkan
kestabilannya pada 8°C dan -20°C selama dua bulan. Dalam ujian kebolehhidupan sel, gen
lolB masih dapat dikesan daripada kultur sel V. cholerae yang telah dibunuh selepas 48 jam,
justeru gen ini tidak sesuai dijadikan penunjuk sel bemyawa. Kesimpulannya, buat pertama
kalinya, kami telah membangunkan suatu ujian kolera-NASBA-ELISA dengan pengesanan
biosensor yang sensitif dan dapat dilakukan dengan peralatan mudah dalam empat jam.
Campuran NASBA kering mengurangkan langkah-langkah mempipet serta memudahkan
penghantaran dan penyimpanan ujian. Ujian ini sesuai sebagai ujian diagnostik pantas dan
ujian saringan di lapangan.
xviii
DEVELOPMENT AND EVALUATION OF A NASBA SYSTEM FOR THE
DIAGNOSIS OF CHOLERA USING ELISA AND BIOSENSOR METHODS
ABSTRACT
Cholera is a diarrheal disease caused by Vibrio cholerae. Cholera is potentially
lethal if not diagnosed on time. Hence, early detection is crucial for patient treatment and
containment of outbreak. Conventional culture and biochemical tests are laborious, time
consuming and less sensitive. Although molecular-based methods are rapid, more
sensitive and specific; they require expensive equipments and cold storage of reagents.
Furthermore, DNA-based tests such as PCR, do not distinguish between viable and non
viable cells. Nucleic acid sequence-based amplification (NASBA) is an isothermal RNA
amplification technique that specifically detects viable cells. Hence, the objective of this
study was to develop and evaluate a thermostabilized cholera-NASBA-ELISA assay with
biosensor detection for V. cholerae based on the lo/B gene. RNA transcripts as positive
control were first constructed and specific primers and probes were designed. NASBA and
ELISA conditions were optimized and the analytical specificity was tested with 41
reference strains comprising of V. cholerae, Vibrio species and enteric pathogens. The
analytical sensitivity was tested with serial dilutions of RNA transcripts and V. cholerae
cells. Clinical evaluation of the assay was performed using spiked stool samples (n=200).
Subsequently, biosensor detection for the NASBA-ELISA assay was optimized and the
results compared to spectrophotometry. The NASBA mix was thermostabilized by freeze
drying and its stability at different temperatures was determined periodically. In addition,
suitability of lo/B mRNA as a viability indicator was investigated by subjecting cultures to
lethal tl1eatments and detecting the NASBA signal. The optimized cholera-NASBA
ELISA assay detected amplicons using fluorescein-labeled probes and TMB/HRP signal.
The analytical specificity of the assay was 100%, while the analytical sensitivity was 102
molecules/Ill RNA transcripts and 10 CFU/ml cells. Clinical evaluation gave 100%
XIX
sensitivity, 84.52% specificity, 89.92% PPV and 100% NPV. Biosensor detection was
comparable to spectrophotometry, yielding similar analytical sensitivity level, excellent
correlation (R2 <0.964) and near perfect kappa agreement (95.1 %, k= 0.828).
Thermostabilization of the NASBA mix was able to preserve its stability at 8°C and -20°C
for two months. In the viability assay, lolB mRNA was detected even after 48 hours post
treatment, therefore precluding its use as a viability indicator. In conclusion, we have for
the first time, developed a sensitive cholera-NASBA-ELISA assay with biosensor
detection that can be performed using simple equipments within four hours. The dry
NASBA mix reduces multiple pipetting steps and facilitates transportation and storage.
The test is suitable for use as a rapid diagnostic test or screening test in the field.
XX
1.1 History of cholera
CHAPTER 1
INTRODUCTION
Cholera is a potentially life-threatening secretory diarrheal disease caused by the
bacteria Vibrio cholerae. Cholera is thought to originate from the Ganges Delta of the Indian
subcontinent. In the nineteenth century, seven distinct pandemic waves of cholera spread
from Asia to many parts of the world. Six pandemics arose from the Indian subcontinent,
while the seventh pandemic originated from the island of Sulawesi, Indonesia in 1961 (Parsi,
2001). In the late 1992, a possible eighth pandemic was reported when a large epidemic
cholera spread throughout Bangladesh, India, Pakistan, Nepal, China, Thailand and Malaysia
(Blake, 1994).
There are more than 150 serogroups of V. cholerae, however only the serogroups 01
and 0139 cause epidemic and pandemic diseases (Sack et al., 2004). The Classical biotype
of V. cholerae serogroup 01 was responsible for the fifth and sixth pandemics and is
believed to have been associated with the earlier pandemics as well. The seventh cholera
pandemic is caused by the El Tor biotype of V. cholerae serogroup 01 and this biotype has
completely displaced the Classical biotype worldwide, except in Bangladesh where it
appeared in epidemic proportions in 1982 and now seems to have become extinct again
(WHO, 2002). The newly emerged serogroup 0139 or 'Bengal' in the late 1992 has been
attributed to the eighth cholera pandemic and this serogroup is closely related to the Asian
V. cholerae 01 El Tor strains associated with the seventh pandemic (Blake, 1994).
1.2 Prevalence of cholera
Cholera is one of the oldest and best-known diseases in the world, yet it continues to
cause considerable suffering and needless deaths. In 2006 alone 131,943 cases of cholera
were reported worldwide with 2272 fatalities (WHO, 2007). However, this number is just the
tip of the iceberg because poor surveillance and fear of travel and economic sanctions lead to
under-reporting of actual cholera cases in certain countries (WHO, 2007). It is estimated that
in reality, the number of deaths from cholera is probably 100 times more than was officially
reported (WHO, 2007). In Malaysia, the Ministry of Health reported the incidence rate of
cholera in 2005 (per 100,000 population) was 1.48 with a 0.01 mortality rate (Ministry of
Health Malaysia, July 2007).
1.3 Characteristics of V. cholerae
Vibrio cholerae is a member of the family Vibrionaceae. It is a facultative anaerobe,
short, curved rod about 1.4 - 2.6 f.!m, capable of fermentative and respiratory metabolism. It
is a non-halophilic vibrio, oxidase-positive, reduces nitrate and is highly motile by means of
a single sheathed polar flagellum. Even though growth of V. cholerae is stimulated by
addition of 1% sodium chloride, it can grow in nutrient broth without added sodium chloride,
which is an important distinction from other Vibrio spp. (Kay et al., 1994). It can grow at 16
- 40°C, with an optimum temperature of37°C and at pH 7.4-9.6 (WHO, 2002).
The species V. cholerae is divided into more than 150 serogroups based on the
differences in their somatic (0) antigens. These variations are secondary to differences in the
oligosaccharide side chains in parts of the cell wall (Parsi, 2001). The serogroup 01 is
divided into two biotypes, Classical and El Tor, which can be differentiated by tests such as
hemolysis, hemagglutination, phage typing, polymyxin B sensitivity and Voges-Proskauer
reaction (table 1.1). Each of the 01 biotype can be further subdivided into two major
serotypes, Ogawa and Inaba, based on variations in the polysaccharide component of the 0
antigen. Ogawa strains possesses only the A and B antigens while lnaba strains possesses
only the A and C antigens. A third and rare serotype, Hikojima possesses all three A, Band
C antigens (Kay et al., 1994).
2
The new serogroup 0139 Bengal was thought to have evolved as a result of
horizontal gene transfer between 01 and non-01 strains. The 0139 strain does not produce
01 lipopolysaccharide and lacks some of the genetic material necessary for production of the
01 antigen. It has potential for capsule expression and an increased capacity for spread and
proliferation within the environment (Morris and Cholera Laboratory Task Force, 1994).
Strains of V. cholerae identified by biochemical tests but do not agglutinate with 01
and 0139 antisera are referred to as non-01, non-0139 V. cholerae. The non-01, non-0139
strains can produce enterotoxins that are similar to cholera toxin (Morris, 1994). Although
this strain is not involved in cholera epidemics, it can be pathogenic and is frequently
associated with small sporadic outbreaks of diarrheal disease caused by the consumption of
contaminated shellfish and from a variety of extraintestinal infections (Morris, 1994).
Besides the somatic (0) antigen, all V. cholerae possess common heat-labile flagella
(H) antigen, and this property may be used to distinguish V. cholerae from all other vibrios
(Kay et al., 1994). Table 1.2 summarizes the different V. cholerae serogroups and their
antigenic determinants.
3
Table 1.1: Tests for differentiation of Classical and El Tor biotypes of V. cholerae serogroup 01
Hemolysis of sheep erythrocytes
Hemagglutination with fowl erythrocytes
Susceptibility to bacteriophage: i) classical phage (group IV) ii) El Tor phage (group V)
Sensitivity to Polymyxin B (50 U)
Produces acetoin in Voges Proskauer test (modified with 1% NaCl)
+
+
+ +
+
+
Table 1.2: V. cholerae serogroups and their antigenic determinants
Serogroup
Biotypes
Serotypes
01 Antigens
Toxin production
Polysaccharide capsul~
01
Classical El Tor
Ogawa Inaba
Hikojima
Ogawa- A and B Inaba- A and C
Hikojima- A, B and C
Produces cholera toxin
None
0139
None
None
Does not have 01 somatic
antigen
Produces cholera toxin
Yes
Non-01
None
Does not have 01 somatic
antigen
Usually does not produce cholera toxin, sometimes
produce other toxins
None
Adapted from Kay, B., Bopp, C. & Wells, J. (1994) In Vibrio cholerae and Cholera: Molecular to global perspectives (Eds, Wachsmuth, I., Blake, P. and Olsvik, 0.) American Society for Microbiology, Washington DC (table 1, pp. 4)
4
1.4 Ecology of V. cholerae
Until the late 1970s and early 1980s, it was believed that V. cholerae was highly
host-dependant and incapable of surviving longer than a few hours or days outside the
human intestine. However, studies have shown that V. cholerae is a normal inhabitant of
brackish water and estuarine systems (Colwell and Huq, 1994a). V. cholerae non-01, non-
0139 strains are frequently isolated from aquatic ecosystems while 01 and 0139 strains are
less frequently isolated. Outside of the host and in the aquatic environment, V. cholerae can
be found as free swimming cells, attached to aquatic plants, filamentous green algae,
copepods, crustaceans, insects and egg masses of chronomids. Environmental persistence of
V. cholerae within natural aquatic habitats during periods between epidemics is facilitated by
biofilm formation and entry into a viable but non-culturable (VBNC) state (Colwell and
Huq, 1994b ).
1.5 Viable but non-culturable (VBNC) state
V. cholerae 01 and non-01, non-0139 strains can enter into a VBNC state in
response to nutrient deprivation, elevated salinity and reduced temperatures. In this dormant
state, the V. cholerae cells are reduced in size, become ovoid and do not grow at all on
standard laboratory media used to isolate V. cholerae. However, Colwell eta/. (1994b) found
that when the VBNC cells of V. cholerae were inoculated into rabbit ileal loops or ingested
by human volunteers, it caused large accumulation of fluid in the rabbit ileal loops or
diarrhea in the human volunteers. This may explain the reason attempts to culture and isolate
V. cholerae from water sources between epidemics often fail. Since V. cholerae in the
VBNC state in environmental samples may not grow on conventional bacteriologic media, it
may go undetected unless other detection methods such as immunologic, molecular or direct I
microscopy are employed. Huq et al. (1990) showed that V. cholerae 01 could be detected
by direct immunofluorescence microscopy throughout the year in their water reservoirs even
when culturing could not isolate the organism itself. Rapid detection kits for V. cholerae that
do not require culture called CholeraScreen (a coagglutination test), Cholera DFA (direct
5
fluorescent monoclonal antibody staining kit) and Cholera SMART (a colorimetric
immunoassay) have been developed and these were also able to detect VBNC cells of
V. cholerae (Colwell and Huq, i994b).
1.6 Epidemiology of cholera
Cholera is the classic water-borne disease and an epidemiological study by John
Snow in 1849 showed the association of the disease with contaminated drinking water (Parsi,
200 I). Poor sewerage and sanitation practices that resulted in contamination of water
supplies used for drinking and food preparation are often the causes of cholera epidemics
(Mintz eta/., 1994). This mode of transmission is more common in less developed countries
under conditions of famine, war and natural disaster. Cholera transmission has also been
linked to drinking water from shallow wells, rivers, bottled water and ice (Parsi, 2001 ).
Food is another vehicle for transmission. Seafood, particularly raw or undercooked
shellfish harvested from sewage-contaminated seabeds, meat, cooked grains, fruit and
vegetables irrigated with raw sewerage have been implicated in cholera outbreaks (Parsi,
2001, Mintz eta/., 1994).
1. 7 Pathophysiology of cholera
Upon ingestion, V. cholerae cells colonize the small intestines, particularly the
duodenum and jejunum because the alkaline pH, nutrients and bile salts provide a suitable
environment. They adhere to the microvilli with the help of a long filamentous fimbriae
called toxin-coregulated pili (Tcp pili), hemagglutinins, mucinase and neuraminidase. Their
motility also enables them to penetrate the mucus layer. They penetrate the host cells by
elaborating a potent enterotoxin, called cholera toxin (CT), a 84 kDa protein consisting of 2
regions, )Nhich are the A region and B region (Sack eta/., 2004).
6
The B region (56 kDa) binds the glycolipid, GMl ganglioside on the host intestinal
epithelial cell membrane, enabling the A region (28 kDa) to penetrate the cell. The A region
will enzymatically transfer ADP-ribose from NAD to a GTP-binding regulatory protein
associated with membrane-bound adenylate cyclase enzyme. The ADP-ribosylation reaction
activates adenylate cyclase, which leads to an increase of intracellular cAMP levels. This is
followed by the secretion of H20, Na+, K+. cr and HC03- into the lumen (Kaper et al., 1994).
The patient may lose several litres of protein-free fluid and associated electrolytes,
bicarbonates and ions within hours. The watery diarrhea (rice-water stool) is speckled with
flakes of mucus, epithelial cells and contains large number of vibrios. Excessive loss of fluid
may lead to dehydration, uremia, metabolic acidosis, hypovolemic shock and subsequently,
death in untreated cases (Sack et al., 2004, Parsi, 2001). The severity of a cholera infection
depends on many factors, and it is increased with the absence of a local intestinal immunity,
a high infectious dose (> l 08 bacteria), low gastric acid production and possession of blood
group 0 (Sack et al., 2004, Parsi, 2001 ).
1.8 Clinical manifestations of cholera
Most individuals infected with V. cholerae have no symptoms or only mild diarrhea,
indistinguishable from other mild diarrheal diseases. Only a minority will develop cholera, a
disease characterized by the sudden onset of vomiting and profuse watery diarrhea,
following an incubation period of 6 to 48 hours. The most distinctive feature of cholera is the
painless purging of voluminous stools resembling rice-water and having a fishy odour. In
adults with severe cholera, the volume of watery stool may exceed 1 Llhour, leading to
severe dehydration, hypovolemic shock, metabolic acidosis and renal failure. This condition
may lead to death within a few hours of onset if rapid treatment is not given (Bennish, 1994,
Parsi, 2001 ).
7
1.9 Treatment of cholera
Without proper treatment the case-fatality for severe cholera is about 50% (Sack et
a!., 2004). Treatment is very simple and effective based on fluid replacement. Oral
rehydration solution (ORS) should be given for mild cases of diarrhea, while intravenous
fluid replacement using lactated Ringer's solution should be given for more severe cases
(Parsi, 2001 ). The use of antibiotics shortens the duration and severity of the illness. In most
cases, tetracycline and doxycycline is the antibiotic of choice. In cases of tetracycline
resistance, erythromycin, cotrimoxazole, ciprofloxacine, azithromycin and trimethoprim
sulfamethoxazole may be used (Parsi, 2001 ).
1.10 Prevention of cholera
Transmission of V. cholerae through contaminated food and water can be prevented
by minimizing contamination and reducing survival and growth of the organism (Sack et a!.,
2004). The level of contamination can be minimized by practicing personal and domestic
hygiene such as hand washing with soap before food handling and safe sewage disposal.
Survival of the organism may be diminished by boiling or disinfecting drinking water and
proper cooking and refrigeration of food. Prophylactic prevention of cholera can be achieved
through the use of vaccines. Three oral vaccines (two inactivated and one live attenuated) are
currently available (Sack eta!., 2004). These vaccines have been licensed in some countries
and are mainly used by travellers. However, these vaccines are for V. cholerae serogroup 01
and do not give cross-protection against other serogroups such as 0139 or non-01, non-
0139. Although a number of vaccine candidates for V. cholerae serogroup 0139 are under
development (Ravichandran eta!., 2006), they are not commercially available. Prevention of
cholera using vaccines may be beneficial as a public health intervention if they are cost
effective,' give long lasting protection and easy to administer.
8
1.11 Diagnosis of cholera
1.11.1 Conventional laboratory methods
Due to the clinical and epidemiological severity of cholera, rapid diagnosis of V.
cholerae in clinical samples, water and food is very critical so that appropriate monitoring
and effective preventive measures can be undertaken to prevent a cholera outbreak. The
conventional laboratory methods employed are culturing, microscopy and biochemical
testing.
Faecal specimens should be collected as early as possible in the illness, as the
number of V. cholerae begins to decline soon after onset of symptoms, and before initiation
of antibiotic therapy (Kay et al., 1994). Faecal specimens or rectal swabs should be collected
from patients into a sterile bottle containing transport medium such as alkaline peptone water
(APW). APW is also the standard medium for enrichment of V. cholerae as its high pH
condition preferentially supports the growth of vibrios while inhibiting other organisms and
it can be used to recover low levels ofvibrios in faecal specimens (Kay et al., 1994).
If specimen is collected on the first day of illness, the vibrios are likely to be present
in large numbers (107-109 CFU/ml), hence it is possible to make a provisional diagnosis by
direct microscopy examination of a film of faeces using dark-field or phase-contrast
microscopy (Kay et al., 1994). Vibrios are highly motile and can be seen darting about
rapidly. When specific antiserum is added to the film, the vibrios are immobilized.
For culture, fresh faecal specimens or APW-enriched specimens are plated onto
thiosulfate-citrate-bile salts-sucrose (TCBS) agar, a highly differential and selective medium
for V. cholerae. Its selective ingredients suppress the growth of most of the interfering
organisms such as coliforms, psedomonads, aeromonads and other Gram-positive bacteria
(WHO, 2002). The sucrose-fermenting V. cholerae grow on TCBS as large, slightly
flattened,1yellow, smooth colonies with a diameter of 2-4 mm.
9
Identification of 01 or 0139 serogroups is perfonned using slide agglutination test
with antiserum raised against V. cholerae 01 or 0139. Agglutination in polyvalent 01
antiserum provides presumptive identification of serogroup 01, which must then be
confirmed by agglutination with monovalent Ogawa and Inaba antisera. Identification of
serogroup 0139 should be perfonned with specific 0139 antiserum (Kay et al., 1994).
A series of biochemical tests may be used for further identification in addition to
serological identification. A crucial biochemical test for distinguishing V. cholerae from
other members of Enterobacteriaceae is the oxidase test. V. cholerae is oxidase-positive
while all Enterobacteriaceae are oxidase-negative. Other important traits that may be used to
distinguish V. cholerae include fermentation of glucose with acid production (without gas),
maltose, mannitol, sucrose and trehalose. In a string test, a loopful of V. cholerae suspended
in a drop of 0.5% aqueous deoxycholate gives a mucoid "string" when drawn. Inoculation of
V. cholerae into Kligler iron agar (KIA) or triple sugar iron agar (TSI) produces an alkaline
slant (K) over acid (A) butt, with no gas or H2S (Kay et al., 1994).
Conventional culture methods are time-consuming and labour-intensive. It takes at
least 2 days to obtain results and may lack sensitivity, especially for poorly handled samples
or clinical samples of patients previously treated with antibiotics as the number of viable and
culturable organisms may be diminished. Detection may also be difficult if the number of
viable organism is low, as in some environmental samples where V. cholerae can exist in a
metabolic state that is non-culturable, but still remain viable and capable of causing disease
(Colwell and Huq, 1994b).
10
1.11.2 Alternative methods of cholera diagnosis
1.11.2.1 Immunological-based tests for cholera
As an alternative to conventional culture methods, several rapid immunological
based tests have been developed. The earlier studies employed antibodies against V cholerae
01 antigen in enzyme-linked immunosorbent assay (ELISA) format (Martinez-Govea et al.,
2001, Osek eta/., 1992, Bhadra eta/., 1991, Gustafsson, 1984, Cooper eta/., 1983), bead
ELISA format (Ramamurthy eta/., 1996, Ramamurthy eta/., 1992, Uesaka et al., 1992,
Cooper et a/., 1983), immunofluorescence microscopy (Goel et a/., 2005, Hasan et a/.,
1994a, Huq eta/., 1990), coagglutination test (Goel et al., 2005, Hasan eta/., 1995, Colwell
eta/., 1992, Rahman eta/., 1989, Rahman eta/., 1987) and colloidal gold-based colorimetric
immunoassay (Hasan et a/., 1994b). Immunoassays for V cholerae 0139 have also been
developed using coagglutination test (Qadri et al., 1994), immunofluorescence microscopy
(Hasan et al., 1995), colloidal gold-based colorimetric test (Qadri eta/., 1995) and dot-blot
ELISA (Chaicumpa eta/., 1998).
More recently, antibody-based biosensors, called immunosensors, have been
described. Jyoung et a/. (2006) immobilized monoclonal antibodies against V cholerae 01
on a self-assembled monolayer (SAM), whereby binding of 01 antigen to the antibody can
be detected using surface plasmon resonance (SPR) spectroscopy. Rao eta/. (2006) utilized
an indirect ELISA method in developing an amperometric immunosensor for detection of V
cholerae 01 on disposable screen-printed electrodes.
Most of the immunological assays offer the advantages of speed, simpler reagents
and equipments, better sensitivity and specificity over culture methods. Several tests such as
CholeraScreen, Cholera DF A and Cholera SMART have been reported to be able to detect
VBNC cells from faecal specimens (Colwell and Huq, 1994b). However, only a few tests are
commerdally available, namely SMART™ and Medicos™ Cholera Dipstick to detect the
01 serogroup but these tests are quite expensive and well beyond the reach of medical
providers in areas at risk of cholera (Kalluri et al., 2006).
11
1.11.2.2 Molecular-based tests for cholera
Recently, there has been a move to adopt molecular-based methods as a gold
standard to replace the traditional culture methods. The use of molecular techniques that rely
on nucleic acid amplification, such as polymerase chain reaction (PCR), ligase chain reaction
(LCR), transcription-mediated amplification (TMA), strand displacement amplification
(SDA) and nucleic acid sequence-based amplification (NASBA) have greatly improved the
speed, sensitivity and specificity of diagnostic tests. This, in turn, would facilitate early and
informed decision-making related to patient management, infection control, treatment and
prevention.
PCR assays have been developed to detect the cholera enterotoxin operon, since
most of the cholera pandemic and epidemics were associated with enterotoxin producing
V. cholerae (Koch et al., 1993, Fields et al., 1992, Shirai et a/., 1991). Subsequently, a
multiplex PCR assay was developed to detect toxigenic strains of V. cholerae based on the
cholera toxin gene and to identify its biotype based on the hyl gene (Shangkuan et al., 1995).
As the new cholera pandemic involving the serogroup 0139 began to emerge,
various PCR tests were developed to detect this new serogroup 0139 alone (Albert et a/.,
1997), or both the serogroups 0139 and 01 (Gubala, 2006, Lipp et al., 2003, Lyon, 2001,
Singh et al., 2001, Albert et al., 1997, Rivera eta!., 1995). Besides detecting the serogroups
01 and 0139, Nandi eta!. (2000) and DiPinto eta!. (2005) have developed PCR assays
based on non-virulence genes such as the ompW and collagenase gene, respectively, which
were able to detect certain non-toxigenic V. cholerae strains of the serogroups non-0 1, non-
0139. This serogroup is often found in environmental samples and causes sporadic and
localized diarrheal outbreaks (Vital-Brazil eta!., 2002, Kaper eta!., 1994).
12
11.2.2.1 Characteristics and advantages of molecular-based tests over conventional
methods
The advantage of PCR over conventional culturing in detecting viable but non-
ulturable (VBNC) cells of V. cholerae was proven in a study by Chaiyanan et al. (200 l ).
~onservation of cholera toxin-associated genes like ctxA, tepA, toxR and zot in chromosomal
)NA of VBNC cells was demonstrated using PCR. It was shown that VBNC cells retained
heir viability, along with their genes and chromosomal integrity up to one year.
PCR assays are rapid, highly sensitive, specific and can detect more than one gene at
the same time. Although the advantages ofPCR-based test over conventional culture method
are numerous, there are certain limitations to the test. PCR requires the use of a thermal
cycler and even with recent advances in this field, the cost and size of a thermal cycler limit
its use in laboratories with limited resources (Lai et a!., 2006). In addition, PCR reagents
must be transported and stored at -20°C and maintaining a constant cold chain may not be
possible when transporting to far or remote places.
These are important considerations in developing a diagnostic test for cholera, as
cholera is a disease that affects most of the poor under-developed countries, or countries
ravaged by war or natural disasters. Hence, there are not many PCR-based tests for cholera
in the market, while those that are available commercially are immunochromatographic-
based assays, which can be quite expensive and still require refrigeration for long term
storage (Kalluri et al., 2006).
PCR can amplify DNA from both live (viable) and dead (non-viable) cells, since
DNA can remain intact and undegraded long after cell death. Thus, PCR-based tests cannot
differentiate viable from non-viable cells. Since cholera is transmitted mainly by
contaminated food and water, detection of viable cells from these samples is desirable during I
an epidemic to identify the source of infection and implement control measures. It is
important that positive test results are associated with live cells and not the remains of dead
cell. Identification of live cells would also help clinicians in monitoring the effectiveness of
l3
antimicrobial treatments in patients (Bej et al., 1996). Detection of viable microorganisms
after sterilization procedures is also important in the medical and food industry to ensure
effectiveness of the process.
RNA has been suggested as a suitable indicator of cell viability as it rapidly degrades
after cell death (Sheridan et al., 1999, Sheridan et al., 1998). Detection of RNA is possible
through reverse-transcription PCR (RT-PCR), a modification of the PCR process, which first
converts the RNA to eDNA, and subsequently the eDNA is amplified by PCR. RT-PCR is a
multiple step process and even small amounts of DNA in the RNA sample might get
amplified, thus giving a false-positive result. Therefore, all RNA samples need to be treated
with DNase enzyme prior to RT-PCR.
1.11.2.3 Nucleic acid sequence-based amplification (NASBA)
Besides RT-PCR, another RNA-based amplification technique is nucleic acid
sequence-based amplification (NASBA). NASBA is an isothermal amplification assay that
specifically amplifies RNA. The reaction occurs at a relatively low temperature of 41 oc that
does not promote the denaturation of double-stranded DNA, hence DNA is not amplified
(Deiman et al., 2002). Furthermore, it can be performed using a simple water bath or heating
block. NASBA produces more amplicons in a shorter time than PCR, requiring only 60- 90
minutes of assay time, compared to 2- 3 hours for RT-PCR. Amplification of approximately
106 to 109-fold is obtained within 90 minutes (Compton, 1991).
The single-stranded RNA amplicons can be detected using various methods, such as
agarose gel electrophoresis (Jean et al., 2004, Jean et al., 2002b), molecular beacon-based
real-time amplification technique (Loens et al., 2008, Churruca et al., 2007, Deiman et al.,
2007, Fykse et al., 2007, Nadal et al., 2007) and probe hybridisation techniques, such as
Northern blotting (Jean et al., 2004, Jean et al., 2002b), ELISA (Lau et al., 2008, Jean et al.,
2002a, Jean et al., 2002b), electrochemiluminescence (ECL) (Lau et al., 2008, Collins et al.,
2003, Hibbitts et al., 2003), enzyme-linked gel assay (ELGA) (Lau et al., 2008, Hibbitts et
14
al., 2003) and biosensors (Baeumner et al., 2004a, Baeumner et al., 2004b, Zaytseva et al.,
2004). These features make NASBA a suitable molecular-based test for cholera. Figure 1.1
shows an overview of the NASBA reaction.
NASBA was first reviewed in 1991 by Compton (1991), who described the salient
features of the technology and its applications. Kievits et al. (1991) was among the earliest to
describe the use ofNASBA for the diagnosis ofHIV-1 infection. Since NASBA is an RNA
amplification technology, it is suitable for detection of RNA viruses, such as norovirus (Kou
et al., 2006, Patterson et al., 2006, Rutjes et al., 2006), enterovirus (Casper et al., 2005,
Landry et al., 2005), hepatitis A virus (Abd el-Galil et al., 2005) and cytomegalovirus
(Bergallo et al., 2006, Revello et al., 2003).
NASBA provided researchers with a way of detecting viable microorganisms in
clinical samples, food and environmental samples, as presence of intact RNA is a valuable
indicator of viability. Detection of viable microorganisms is important for screening of
contaminated food (Cook, 2003, Gore et al., 2003) and environmental samples (Fykse et al.,
2007, Rutjes et al., 2006, Baeumner et al., 2003); monitoring the clinical course of a disease
(Yoo et al., 2005); and assessing the efficacy of antimicrobials and other treatments (de
Vries et al., 2006).
A real-time NASBA assay for V. cholerae was developed by Fykse et a!. (2007)
targeting genes encoding cholera (etxA), toxin-corregulated pilus (tepA), ctxA toxin regulator
(toxR), hemolysin (hlyA) and the 60 kDa chaperonin product (groEL). The assay was able to
detect V. eholerae from various environmental water samples and has a strong potential for
detecting toxigenic strains using the tepA and etxA markers.
Besides detection of medically important microorganisms, other clinical applications
of NASBA include detection of biomarkers and important human genes. NASBA has also
been used to detect disease-causing microorganisms in the marine, agriculture and livestock
industries (Lau et al., 2008, Lau et al., 2006, Olmos et al., 2007, Teng et al., 2006).
15
RNA(+)
T7 primer '-
1
NON-CYCLIC PHASE
t Reverse transcriptase
TIRNA polymerase
------...
'-
1 Reverse T transcriptase
~ RnaseH
eDNA
1 Reverse • tra.nscriptase
I TIRNA T polymerase
....................... ············-········ ••••w•••••••••••••••• .....•............... .....................
RNA(-)
CYCLIC PHASE
Figure 1.1: Overview of the NASBA reaction
16
1 Reverse + transcriptase
1.12 Rationale of the study
Most of the molecular-based diagnostic tests that have been developed for
V. cholerae are either PCR or real-time based PCR assays. These assays require constant
cold chain for transport and storage of the PCR reagents, skilled laboratory technicians and
sophisticated equipments to perform the tests. Moreover PCR assays detect DNA, which
may still be present in dead cells; therefore it cannot be used to differentiate between viable
and non-viable cells. Identification of viable V. cholerae is important especially during a
cholera epidemic, where detection of viable cells from food and water samples is desirable to
identify the source of infection and implement control measures. It is also useful for testing
environmental samples for reservoirs of viable V. cholerae.
We have identified a non-virulence gene called lolB (hemM), which codes for an
outer membrane protein in V. cholerae. The lolB gene sequence has been submitted to the
Genbank under the accession number AF227752. The lolB gene sequence was found to be
highly conserved among the different serogroups of V. cholerae. A PCR assay was
developed that was able to detect 01, 0139 and non-01, non-0139 serogroups of
V. cholerae from clinical and environmental samples with 98.5% sensitivity and 100%
specificity (Lalitha et al., 2008).
The present study used the lolB gene as a candidate in the development of a cholera
NASBA-ELISA assay for detection of V. cholerae. The cholera NASBA-ELISA assay with
biosensor detection would be a suitable detection method for viable V. cholerae as it does
not require expensive and specialized equipments. The present study also aims to make
NASBA easy to perform and to eliminate the need for cold storage of NASBA reagents
through the use of our patent-pending thermostabilization technology (Ravichandran et al.,
2005), which has been successfully applied in thermostabilization PCR assays for typhoid
and cholera (Aziah et al., 2007, Ravichandran et al., 2003). To the best of our knowledge,
this is the first time a them1ostabilized cholera NASBA-ELISA assay featuring the use of a
portable biosensor is described.
17
1.13 Objectives ofthe study
Phase 1: Development and optimization of a cholera NASBA assay
1. To design specific primers and probes for cholera NASBA assay
2. To construct in vitro RNA transcripts as positive control
3. To develop and optimize a cholera NASBA assay targeting the lolB gene of V. cholerae
4. To analyze the NASBA reaction and its amplicons
5. To test the suitability of lolB mRNA as an indicator of cell viability
Phase 2: Development and optimization of ELISA for detection of cholera NASBA
amplicons (cholera NASBA-ELISA)
6. To develop and to optimize an ELISA test for detection of NASBA amplicons by
comparison of two ELISA formats
7. To evaluate the cholera NASBA-ELISA assay with spiked stool samples
8. To calculate the diagnostic sensitivity, specificity, positive predictive value (PPV) and
negative predictive value (NPV) of the clinical evaluation
Phase 3: Development of an electrochemical biosensor detection for cholera NASBA
ELISA assay
9. To optimize detection of the NASBA-ELISA signal with an electrochemical biosensor
10. To compare the biosensor results with spectrophotometric measurements
Phase 4: Optimization of a thermostabilized NASBA mix
10. To optimize the enzymes and enzyme stabilizer concentrations for thermostabilization of
the NA5BA mix
11. To detennine the stability of the thermostabilized NASBA m1x stored at different
temperatures over a certain period of time
18
1.14 Overview of the study
Development and optimization of a NASBA assay targeting the
lo!B gene of Vibrio cholerae
• Detection ofNASBA amplicons by
agarose gel electrophoresis
• Determination of
analytical specificity
• •
Determination of analytical sensitivity
Analysis ofNASBA reaction and amplicons
••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••
Development and optimization of ELISA for detection ofNASBA amplicons (NASBA-ELISA)
• Determination of analytical specificity and sensitivity
• Evaluation ofNASBA-ELISA with spiked stool samples
• Determination of diagnostic sensitivity, specificity,
PPV, NPV and limit of detection (LOD)
••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••
Optimization of an electrochemical biosensor method for detection of ELISA reaction
• Comparison of biosensor and
spectrophotometry results
• Determination of analytical sensitivity and specificity
••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••
Optimization of a thermostabilized formulation for lyophilization of the NASBA mix
• Periodic stability evaluation of the
lyophilized NASBA mix
19
• Determination of
analytical sensitivity
2.1 Materials
2.1.1 Bacterial strains
2.1.1.1 Reference strains
CHAPTER2
MATERIALS AND METHODS
Six V. cholerae strains comprising of 01, 0139 and non-01, non-0139 serogroups
were used as reference strains for optimization and evaluation of the sensitivity of the
NASBA assay. Six other Vibrio species strains and 29 enteric pathogen strains were used as
reference strains for evaluating the specificity of the NASBA assay. The V. cholerae, Vibrio
spp. and 10 enteric pathogen strains were obtained from Prof. Mitsuaki Nishibuchi, Centre
for Southeast Asia Studies, Kyoto University, Japan as a gift. The remaining 19 enteric
pathogen strains were obtained from the culture collection of the Department of
Microbiology and Parasitology, Universiti Sains Malaysia, Malaysia. Details of the reference
strains used in this study are given in table 2.1.
2.1.1.2 Clinical isolates
For evaluation of the NASBA assay using spiked stool samples, 110 well
characterized strains of V. cholerae isolated from clinical samples were obtained from Centre
for Southeast Asia Studies, Kyoto University, Japan; Communicable Diseases Hospital,
Thandiarpettai, Chennai, India; Hospital Universiti Sains Malaysia (HUSM) and General
Hospital Kota Bharu (GHKB), Kota Bharu, Kelantan; National Public Health Laboratory
(MKAK), Ministry of Health, Sungai Buloh; and Institute for Medical Research (IMR),
Selangor, Malaysia.
In addition, 45 well-characterized strains of other Vibrio species and various enteric
pathogens isolated from clinical samples were also obtained from Centre for Southeast Asia
20
Studies, Kyoto University, Japan; Hospital Universiti Sains Malaysia (HUSM), Kota Bharu,
Kelantan and Institute of Medical Research (IMR), Selangor, Malaysia.
All 41 reference strains were also included in the evaluation of the NASBA assay
using spiked stool samples as these were originally isolated from clinical samples. Details of
the clinical isolates used in the study are given in table 2.2.
2.1.1.3 Growth and maintenance of bacterial strains
All bacterial strains were preserved and maintained as glycerol stock in LB broth
with 15% glycerol and kept at -70°C. For experimental purposes, the bacterial strains were
revived from glycerol stocks by inoculating a loopful of culture into LB broth and incubated
overnight at 37°C. For V. cholerae strains, the overnight cultures were then subcultured onto
TCBS agar while for other enteric bacteria, the overnight cultures were subcultured onto LB
agar and incubated overnight at 37°C. V. cholerae appeared as yellow, convexed and mucoid
colonies on TCBS agar. A single colony was picked with a sterile wire loop, streaked onto
LB agar and incubated overnight at 3 7°C again. These cultures were used to perform the
NASBA assay.
2.1.2 Culture Media
Culture media were prepared using molecular biology or biotechnology grade
chemicals. Distilled water was used for preparing media solutions. The appropriate media
were autoclaved at 121 °C, 15 psi for 15 minutes. Sterility check was performed by
incubating the media at 37°C overnight. Sterile agar media were stored at 4°C while broth
and other liquid media were stored at room temperature. The list of culture media used in
this study is given in appendix A.
21
Table 2.1: Details of the reference strains used in this study
Vibrio Centre for V. cholerae, 01 Classical 2 cholerae Southeast Asia V. cholerae, 01 El Tor 2 (n =6) Studies, Kyoto V. cholerae, 0139 Bengal 1
University, Japan V. cholerae, non-01, non-0139 1
Other Centre for V. cincinnatiensis 1 Vibrio spp. Southeast Asia V. fluvial is 1 (n= 6) Studies, Kyoto V. furnissii 1
University, Japan V. mimicus 1 V. parahaemolyticus 1 V. vulnificus 1
Enteric Centre for Aeromonas hydrophila 1 pathogens Southeast Asia Escherichia coli 2 (n = 29) Studies, Kyoto Pleisiomonas shigelloides 1
University, Japan Salmonella enteritidis 1 Salmonella typhi 1 Shigella boydii 1 Shigella dysenteriae 1 Shigella jlexneri 1 Shigella sonnei 1
Department of Acinetobacter spp. 1 Microbiology Acinetobacter baumanii 1 and Parasitology, Bacillus cereus 1 Universiti Sains Bacillus subtilis 1 Malaysia Burkholderia pseudo mallei 1
Citrobacter freundii 1 Enterobacter cloacae 1 Klebsiella spp. 1 Klebsiella pneumoniae 1 Morganella morganii 1 Proteus mirabilis 1 Proteus vulgaris 1 Providencia stuartii 1 Pseudomonas aeruginosa 1 Salmonella spp. 1 Salmonella para typhi A 1 Salmonella para typhi B 1 Serratia marsescens 1 Yersinia enterocolitica 1
22
Table 2.2: Details of the clinical isolates used in this study
Vibrio Hospital Universiti Sains V cholerae, 01 8 cholerae Malaysia (HUSM), (n = 116) Kelantan, Malaysia
General Hospital, Kota V cholerae, 01 17 Bharu (GHKB), Kelantan, Malaysia
National Public Health V. cholerae, 01 6 Laboratory, Ministry of Health, Sungai Buloh, Selangor, Malaysia
Institute for Medical V cholerae, 01 55 Research (IMR), V cholerae, 0139 Bengal 1 Selangor, Malaysia V cholerae, non-01, non-0139 3
Communicable Diseases V cholerae, 0139 Bengal 9 Hospital, Thandiarpettai, Chennai, India
Centre for Southeast V cholerae, 01 14 Asia Studies, Kyoto V cholerae, 0139 Bengal 2 University, Japan V. cholerae, non-01, non-0139 1
Other Centre for Southeast V. cincinnatiensis 1 Vibrio Asia Studies, Kyoto V. jluvialis 3 spp. University, Japan V. furnissii 2 (n =12) V. mimicus 2
V parahaemolyticus 1 V. vulnificus 2
Institute for Medical V vulnificus Research (IMR), Selangor, Malaysia
Enteric Centre for Southeast Aeromonas hydrophila 1 pathogens Asia Studies, Kyoto Escherichia coli 4 (n = 68) University, Japan Pleisiomonas shigelloides 1
Salmonella enteritidis 1 Salmonella typhi 1 Shigella boydii 1 Shigella dysenteriae 1 Shigella jlexneri 1 Shigella sonnei 1
23
Table 2.2 (continued)
Enteric Department of Acinetobacter spp. 1 pathogens Microbiology and Acinetobacter baumannii 1 (n = 68) Parasitology, Universiti Bacillus cereus 1
Sains Malaysia Bacillus subtilis 1 Burkholderia pseudomallei 1 Citrobacter freundii 2 Enterobacter cloacae 1 Escherichia coli 1 Klebsiella spp. 1 Klebsiella pneumoniae 1 Morganella morganii 1 Proteus vulgaris 1 Pseudomonas aeruginosa 2 Salmonella enteritidis 1 Salmonella typhi 1 Serratia marsescens 1 Shigella boydii 1 Staphylococcus aureus 1 Streptococcus group G 1
Institute for Medical Aeromonas hydrophila 1 Research (IMR), Acenitobacter baumanii 1 Selangor, Malaysia Bacillus cereus 1
Burkholderia pseudomallei 1 Enterococus faecalis 1 Klebsiella spp. 1 Klebsiella pneumoniae 1 Proteus mirabilis 1 Providencia stuartii 1 Salmonella spp. 4 Salmonella enteritidis 1 Salmonella para typhi A 5 Salmonella para typhi B 3 Salmonella typhi 4 Shigella boydii 2 Shigella dysenteriae 2 Shigella jlexneri 1 Shigella sonnei 2 Staphylococcus aureus 1 Yersinia enterocolitica 1
24