10/24/2018 objectives - scacm

10/24/2018

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Clinical and Public Health Microbiology of Carbapenem Resistant Enterobacteriaceae

WI SCACM October 30, 2018

Allen Bateman, PhD, MPH, D(ABMM) Assistant Director, Communicable Diseases

Wisconsin State Laboratory of Hygiene

WISCONSIN STATE LABORATORY OF HYGIENE - UNIVERSITY OF WISCONSIN

Objectives

At the conclusion of the presentation, participants will be able to:

1. Define the difference between CRE and CP-CRE, and explain why

it matters to differentiate the two.

2. Describe the ARLN and clinical laboratories' role in surveillance.

3. Describe the overall epidemiology of CP-CRE in Wisconsin.

4. Appreciate the complexity of carbapenemases and

susceptibility profiles.


Acknowledgement: Ann Valley, ARLN coordinator at WSLH

Antimicrobial Resistance- U.S.

WISCONSIN STATE LABORATORY OF HYGIENE - UNIVERSITY OF WISCONSIN 3

National Action Plan

Wisconsin State Laboratory of Hygiene- University of Wisconsin 4

Carbapenem-Resistant Enterobacteriaceae (CRE)

Wisconsin State Laboratory of Hygiene- University of Wisconsin 33

• Any Enterobacteriaceae that is resistant to a carbapenem • Resistance an be due to many mechanisms

Carbapenemase-producing CRE (CP-CRE)

Carbapenemases cleave carbapenems

Render carbapenems inactive

Main classes

Class A (Serine in active site): KPC

Class B (Zinc in active site): NDM, VIM, IMP

Metallo beta-lactamases

Class D (Serine in active site; Oxacillinases): OXA


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Carbapenemase-producing CRE (CP-CRE)

Carbapenemases typically plasmid-borne

Can transmit from one bacteria to another

Higher transmission potential than chromosomally-encoded enzymes

Plasmids often carry other resistance genes


WISCONSIN STATE LABORATORY OF HYGIENE - UNIVERSITY OF WISCONSIN Acknowledgement: Nick Florek, ARLN fellow at WSLH

KPC-CRE in the US


Other ‘common’ carbapenemases


ARLN- Regional Approach

Wisconsin State Laboratory of Hygiene- University of Wisconsin 5 Wisconsin State Laboratory of Hygiene- University of Wisconsin

• Select isolates and specimens sent from clinical/reference labs to state labs

• All state labs perform Core Testing

• Regional labs perform Additional Testing

ARLN Structure

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ARLN

Wisconsin State Laboratory of Hygiene- University of Wisconsin

Testing at WSLH


CRE/CRPA Isolate Characterization

• Species confirmation

• Susceptibility testing

• Phenotypic screening (mCIM)

• PCR (KPC, NDM-1, OXA-48, IMP, VIM, mcr-1&2)

Outbreak Response CRE Colonization

Screening

Confirmed CRE Case

Engage HAI Program

Identify Patient Contacts

Coordinate Swab Collection

CRE Colonization Screening from Rectal

Swabs

Results to Facility, Epidemiologist, and

Lab in 2 Days

WS L H

ARLN Organisms


Carbapenem-resistant Enterobacteriaceae (CRE) All E. coli, Klebsiella oxytoca, Klebsiella pneumoniae, and

Enterobacter spp. resistant to any carbapenem Any Enterobacteriaceae species non-susceptible to any

carbapenem

Carbapenem-resistant Pseudomonas aeruginosa (CRPA)

P. aeruginosa isolates resistant to any carbapenem

Candida C. auris identification using MALDI-TOF C. auris colonization screening Antifungal susceptibility for resistant Candida such as C. auris,

C. haemulonii, and C. glabrata


mCIM – Phenotypic Testing


• Screening for carbapenemases

• Grow organism in presence of meropenem disc

• After 4 hr incubation, place disc on bacterial lawn

• If no carbapenemase, meropenem disc kills lawn

• If organism had carbapenemase, lawn grows up to disc

Note: does not work well with Acinetobacter

Colonization Testing

If patient has confirmed carbapenemase producing (CP) infection, IP and HAI coordinator may consider screening for transmission within facility

Patient contacts vary from setting to setting

May include roommates of the index patient

Longer stays may require broader testing

Point prevalence study(s) on the unit or ward

If transmission documented, may conduct follow-up surveys to document halted transmission


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Rectal Swabs


Must be tested within 5 days of collection

Cepheid GeneXpert System

• Tests for 5 PCR targets straight from swabs

• KPC, NDM, OXA, VIM, IMP

• Capacity: at WSLH up to 16 at once


Regional Laboratory Role

Provide facility with Cepheid dual swab collection kit for use with GeneXpert Carba-R assay

Provide requisitions

Will be moving to electronic test ordering and reporting (ETOR)

Provide collection and transport instructions

Test rectal swabs using Xpert Carba-R molecular assay


Regional Laboratory Role

Report results

1-2 Day TAT

Sent by secure communications (FAX) or through the APHL web portal

Sent to submitting healthcare facility, HAI coordinator, and the jurisdictional public health laboratory

Monthly summary of testing activities to CDC


CRE Surveillance- WI

WISCONSIN STATE LABORATORY OF HYGIENE - UNIVERSITY OF WISCONSIN 11

4 8 24 31

46 74 83

9 39

90 121

150

384

715

0

100

200

300

400

500

600

700

800

2010 2011 2012 2013 2014 2015 2016

Nu

mb

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Te

ste

d a

nd

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Year

Number Tested and Positive for KPC and NDM-1 PCR

KPC gene detected. NDM-1 gene detected. Total Isolates Received

First 10 months of ARLN


Acknowledgement: Megan Lasure, ARLN epidemiologist

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2017 Wisconsin ARLN Testing


All tests 1971

Wisconsin CRE 746

Non-Wisconsin CRE 89

CR-PA 407

Colonization swabs 729

2017 Carbapenemases in WI


Isolate Submission WI January-July 2018


• Total isolates submitted: 428 • Total CRE: 213 • Total CP-CRE: 56

CP-CRE in WI (January-July 2018)


KPC 42

OXA 5

IMP 5

NDM 4

VIM 0

CP-CRE Rates per 100,000


Northern

Western

Northeastern

Southern

Southeastern

0.0

0.26

0.57

0.71 1.84

Response

Patient in a LTCF has a urine isolate that tests positive for KPC at WSLH.

• WDPH/LHD is notified and calls IP

• Dates of admission/discharge

• Healthcare exposures in past 12 months

• Any history of travel (and if so, hospitalization abroad)

• Is colonization screening appropriate?

• Was patient on contact precautions the entire stay?

• Did patient have any roommates?

• Any other patients overlap for ≥ 3 days?

• Are there multiple positive specimens from a facility within a short time range?


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CRE Colonization Testing January-July 2018

n=1521


CP Mechanisms by State for colonization testing


KPC

NDM

OXA

VIM

Detect Respond Contain

WISCONSIN STATE LABORATORY OF HYGIENE - UNIVERSITY OF WISCONSINn

How you can help

Send in isolates CRE

CR-PA (but only some)

Candida

We’ll be calling for all CP+ patients and asking for: Dates of admission/discharge

Healthcare exposures in past 12 months

Any history of travel (and if so, hospitalization abroad)

Determine whether colonization screenings would be appropriate:

Was patient on contact precautions the entire stay?

Did patient have any roommates?

Any other patients overlap for ≥ 3 days?

Slide courtesy of Chicago Department of Public Health. Slide courtesy of Chicago Department of Public Health.

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Slide courtesy of Chicago Department of Public Health.

Interpretive reading of AST profiles

Interpreting AST profiles to identify carbapenemases: can it be done?

Beta-lactams 101 • Penicillins

• Penicillin, ampicillin, amoxicillin

• Penicillin + beta-lactamase inhibitor • Piperacillin-tazobactam (pip-tazo) • Ticarcillin-clavulanate (tic-clav)

• Cephalosporins

• 1st-generation: cefazolin • 2nd-generation: cefoxitin • 3rd-generation: ceftazidime, ceftriaxone, cefotaxime • 4th-generation: cefepime

• Carbapenems

• Ertapenem, meropenem, imipenem, doripenem

Typical ESBL vs AmpC profiles

Drug ESBL AmpC

1st-gen ceph R R

2nd-gen ceph S R

3rd-gen ceph R R

4th-gen ceph R S

Pip-tazo S R

carbapenems S Erta R, others S

Highly expressed AmpC enzymes cause CRE, but not CP-CRE

Klebsiella pneumoniae by MALDI-TOF

KPC-positive by PCR

Susceptibility profile:

Aztreonam (R)

Ampicillin/sulbactam (R)

Piperacillin/tazobactam (R)

Cefazolin (R)

Ceftazidime (R)

Ceftriaxone (R)

Cefepime (R)

Ertapenem (R)

Meropenem (R)

Imipenem (R)

Doripenem (R)

Isolate 1: KPC

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Isolate 2

• Enterobacter asburiae isolate from tracheal aspirate

• AST profile: • R to first-third generation cephalosporins • R to carbapenems

• Ertapenem, imipenem, meropenem

• S to cefepime

• mCIM result:

Case courtesy of Stephanie Mitchell, PhD D(ABMM)

Isolate 2, mCIM result

• Per CLSI, a positive mCIM: • 6-15mm zone • Presence of colonies within a 16-18mm zone

Negative control This isolate Thoughts on what this could be?

Isolate 2, ARLN results

• KPC positive • KPC that spares cefepime?

Isolate 3 (NDM are nasty)

• E. coli urine isolate • Beta-lactam susceptibilities:

• aztreonam (R) • cefepime (R) • ceftazidime (R) • doripenem (R) • ertapenem (R) • imipenem (R) • meropenem (R) • piperacillin/tazobactam (R)

Kim Y, et al. Structure of Apo- and Monometalated Forms of NDM-1—A Highly

Potent Carbapenem-Hydrolyzing Metallo-β-Lactamase. PLOS ONE 2011.

Isolate 4 Klebsiella pneumoniae from CRE colonization

Isolate 4

• mCIM positive (6mm)

• At WSLH: blaKPC and blaNDM • At CDC: blaKPC and blaNDM

• WSLH routinely culturing for non-KPC

carbapenemases identified by Carba-R

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Cases 5 and 6 A tale of two isolates

1. 37 y.o. F, rectal swab isolate • Enterobacter cloacae • mCIM, 6mm

2. 83 y.o. F, urine isolate • Enterobacter cloacae • mCIM, 6mm

#1 #2

Cases 5 and 6 A tale of two isolates

1. Negative for all 5 PCRs • WT colistin

2.Negative for all 5 PCRs

• NWT colistin • Negative mcr-1/2

Thoughts on what this could be?

Cases 5 and 6

• blaIMI/blaNMC

• CDC results: “A Research Use Only (RUO) conventional PCR was positive for blaIMI/blaNMC genes. This RUO conventional PCR can't differentiate blaIMI from blaNMC genes; targeted sequencing or whole genome sequencing is required to differentiate these two very similar genes (95% similarity).”

WGS results

#1. NMC-A

Coverage Identity ResFinder, IMI-2 100% 99.09% CARD, IMI-2 100% 99.09% NCBI, IMI-9 100% 100%

Coverage Identity ResFinder 100% 100% CARD 100% 100% NCBI 100% 100%

#2. IMI

Isolates 7-10 OXA-48: The Phantom Menace

OXA-48-like enzymes weakly hydrolyze carbapenems and broad spectrum cephalosporins

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Isolates 7-10: 4 OXA positive isolates (2 WI, 1 KY, 1 IN)

Drug #1 #2 #3 #4

Cefepime S R R R

Ceftazidime S R S S

Doripenem R S S S

Ertapenem R I I R

Imipenem R I S R

Meropenem R I S S

IMPs

• 8 in Wisconsin since 2017 • Non-big 3 feature prominently • Variable resistance, even with imipenem

Isolate ID Species Dori Erta Imi Mero

1 Enterobacter cloacae S S S S

2 Providencia rettgeri R R I R

3 Enterobacter cloacae R R R R

4 Providencia rettgeri S R S S

5 Providencia rettgeri R R I I

6 Providencia rettgeri R R S S

7 (same

patient as #2) Providencia rettgeri pending

8 Proteus mirabilis pending

VIM

• “VIM belt” • 41 VIM-CRE reported to CDC to date • Indiana and neighboring states account for 29 (71%)

VIM-CRE organisms (MMWR paper)

• Klebsiella pneumoniae (n=3) • Klebsiella oxytoca • Enterobacter cloacae complex (n=2) • Proteus mirabilis • Providencia rettgeri • Citrobacter freundii complex

VIM-CRE beta-lactam profiles (Thanks to Indiana!)

Enterobacter cloacae complex outside lab: cefazolin (R), ceftazidime (R), ceftriaxone (R), meropenem (R) ISDH: pan-R E. coli, outside lab: cefazolin (R), ceftriaxone (R), cefepime (R), ertapenem (R), imipenem (R) E. coli, outside lab: ampicillin (R), piperacillin/tazobactam (R), cefazolin (R), ceftazidime (R), ceftriaxone (R), cefepime (R), meropenem (R) K. pneumoniae, outside lab: cefazolin (R), cefepime (R), ceftazidime (R), ceftriaxone (R), meropenem (R), piperacillin/tazobactam (R)

Main points

• If it’s uniformly R to beta-lactams, likely a KPC or NDM • But no guarantee; VIM also quite R

• If the profile like below, think IMI/NMC

• R to ‘weak’ beta-lactams (like ampicillin) • S to 3rd- and 4th-gen cephs, pip-tazo • R to all carbapenems tested

• For IMP and OXA, beware odd patterns and not super R

• IMP and VIM commonly seen in non-big-3 Enterobacteriaceae

• Interpreting AST profiles to identify carbapenemases: can it be done?

• Not really • It’s a good thing we have PCR!

10/24/2018 objectives - scacm

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