CRO and CPE: Epidemiology and diagnostic tests · Overall European situation regarding occurrence...
Transcript of CRO and CPE: Epidemiology and diagnostic tests · Overall European situation regarding occurrence...
CRO and CPE: Epidemiology and
diagnostic tests
Scottish Microbiology and Virology Network Scientific Meeting
22nd April 2016
Katie Hopkins PhD Clinical Scientist, Antimicrobial Resistance and Healthcare Associated Infections
(AMRHAI) Reference Unit
Public Health England © Crown copyright
Walking through a minefield of acronyms
Acronym Better to spell it out ! ‘Translation’ Defined by
CRE Carbapenem-resistant
Enterobacteriaceae
Must be Enterobacteriaceae and resistant to
carbapenems. May or may not produce a
carbapenemase
AST
CRO Carbapenem-resistant
organisms
Any carbapenem-resistant species (strictly, also
those with intrinsic resistance). May or may not
produce a carbapenemase.
AST
CPE Carbapenemase-producing
Enterobacteriaceae
Must be Enterobacteriaceae and produce a
carbapenemase. May or may not be resistant to
carbapenems.
Mechanism
detection
CPO Carbapenemase-producing
organisms
Any carbapenemase-producing species (strictly,
also those with intrinsic carbapenemases). May
or may not be resistant to carbapenems.
Mechanism
detection
2 CRO and CPE: Epidemiology and diagnostic tests SMVN Meeting 2016 © Crown copyright
• So, “CPEs are always CPOs and may also be CREs or CROs (unless they have
low MICs); every CRE is a CRO, but not every CRE or CRO is a CPE or a CPO”
Gram-negative resistance ad infinitum
• 5 of 7 ‘ESKAPEEs’ are Gram-negative
•Increasing reliance on carbapenems
• detection of carbapenemases required for IPC and public health
Pathogen Established problems Emerging threats
E. faecium VRE, HLGR, Amp-R Lin-R, Dap-R, Tig-R
S. aureus MRSA (ha/ca) Van-R, Lin-R, Dap-R
Klebsiella ESBLs Carbapenemases, Col-R
Acinetobacter MDR, Carbapenemases Tig-R, Col-R
Pseudomonas MDR, except Col Carbapenemases, Col-R
Enterobacter AmpC, ESBLs Carba-R, Carbapenemases
E. coli Cip-R, ESBLs Carbapenemases
2 CRO and CPE: Epidemiology and diagnostic tests SMVN Meeting 2016 © Crown copyright
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Health Protection Report Vol 9 No. 2
– 16 January 2015
The ‘nightmare’ bacteria
CRO and CPE: Epidemiology and diagnostic tests SMVN Meeting 2016 © Crown copyright
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The “big 5” carbapenemases
KPC
OXA-48-like
NDM
VIM
IMP
(22 variants)
(>10 variants)
(14 variants)
(43 variants)
(48 variants)
CRO and CPE: Epidemiology and diagnostic tests SMVN Meeting 2016 © Crown copyright
Global perspective: KPC-producers
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Nordmann & Poirel, 2014
KPC: international strain epidemic of KPC +ve
K. pneumoniae
ST258
ST258
ST258
Nordmann et al. TLID 2009; 9: 228–36
NW England KPC outbreak:
K. pneumoniae STs 11, 25,
27, 248, (258 - Col-R), 321,
468, 490 and 491
plus Enterobacter, E. coli +
others
Global perspective: OXA-48-producers
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Nordmann & Poirel, 2014
OXA-48: international plasmid ‘epidemic’
OXA-48 (c. 62 kb) OXA-48
OXA-181 (c. 7kb)
Dimou et al. JAC 2012 ; Poirel et al. AAC 2012
• OXA-48 found on related plasmids in clonally diverse isolates of E. coli, K.
pneumoniae and E. cloacae.
Global perspective: NDM-producers
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Nordmann & Poirel, 2014
• Multiple plasmid backbones in
multiple clones of different
genera
NDM epidemiology is diverse
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Kumarasamy et al., 2010
Kumarasamy et al., 2010
Nordmann et al., 2011
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Global perspective: VIM- and IMP-producers
Nordmann et al., 2011
EARS-Net data: Proportion of carbapenem
resistant (R+I) invasive E. coli and K. pneumoniae,
2014
• Most countries <1% non-susceptibility in E.coli
• 6 countries reported >5% non-susceptibility in K. pneumoniae as judged by surveys
• Bacteraemia isolates account for <10% carbapenemase producers in UK
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E. coli K. pneumoniae
Overall European situation regarding occurrence of CPE
using an epidemiological scale of nationwide expansion
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N.B. epidemiological stage might
not represent the true extent of the
spread of CPE as it is a subjective
judgment by national experts
Albiger et al. submitted
Limiting the impact of carbapenemases
• Prompt detection essential for
identifying infected/colonized
patients: 1.appropriate patient management
2.rapid implementation of infection
control procedures
3.Prevent onwards transmission
• But how?
15 Bioconnections Masterclass 14th April 2015 © Crown copyright 15 CRO and CPE: Epidemiology and diagnostic tests SMVN Meeting 2016 © Crown copyright
The problem with spotting carbapenemase
producers
Carbapenem MIC
N
0.5 16
Wild-type Carbapenemase
ESBL / AmpC + porin loss
or true carbapenemase ?
•Not all carbapenemase producers are resistant to the carbapenems
•ESBL/AmpC + porin loss = not transferable, may have fitness cost rarely cause outbreaks
Phenotypic detection of ESBLs and carbapenemases - BSAC workshop 2015 © Crown copyright 16 CRO and CPE: Epidemiology and diagnostic tests SMVN Meeting 2016 © Crown copyright
Chromogenic screening media
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• Brilliance CRE, CHROMagar KPC, chromID CARBA,
chromID OXA-48, COLOREX KPC, chromID CARBA
SMART, COLOREX mSuperCARBA…
• stool/rectal swabs
• Not all detect the “big 5” carbapenemases
• Odd strains that ‘don’t play by the rules’
• Organisms resistant to carbapenems due to other
mechanisms may grow
• Non-fermenters appear as colourless colonies
• Be cautious in interpretation of study data!
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How can we identify a
carbapenemase-producing organism?
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Clinical specimen Bacterial isolate
-lactamase inhibitor tests
Detect carbapenem
hydrolysis
some assays
Detect carbapenemase
antigens
some of the “big 5” some of the “big 5”
Detect carbapenemase
genes
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EUCAST guidance for resistance
mechanism detection
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http://www.eucast.org/resistance_mechanisms/
How can we identify a
carbapenemase-producing organism?
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Clinical specimen Bacterial isolate
-lactamase inhibitor tests
Detect carbapenem
hydrolysis
some assays
Detect carbapenemase
antigens
some of the “big 5” some of the “big 5”
Detect carbapenemase
genes
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Cleavage of -lactam ring by carbapenemases
+18 Da - 44 Da
red
yellow
hydrolysis decarboxylation
pH change
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Detecting hydrolysis: CarbaNP test
• CarbaNP: yes/no answer:
– ‘in-house’ (Nordmann et al. [2012], Dortet et al. [2012])
– Rosco Diagnostica Rapid CARB Screen kit
– Biomerièux Rapid-Ec CarbaNP
• CarbaNP-II: determination of carbapenemase type (Dortet et al. [2012])
• Results ≤2 hrs with good sensitivity and specificity
• False-negatives with mucoid strains, some OXA-48
producers and other carbapenemases.
CPE screening – where are we now? IBMS Congress 2015 © Crown copyright 22 CRO and CPE: Epidemiology and diagnostic tests SMVN Meeting 2016 © Crown copyright
CarbaNP for direct detection of carbapenemase producers
in blood cultures
Phenotypic detection of ESBLs and carbapenemases - BSAC workshop 2015 © Crown
copyright
• Identification of a carbapenemase producer reduced from 24-48 hrs to 3-5 hrs
Dortet et al. 2013
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Phenotypic detection of ESBLs and carbapenemases - BSAC workshop 2015 © Crown
copyright
Detecting hydrolysis: MALDI-ToF
Meropenem solution
Negative control
NDM-1 K. pneumoniae
NDM-1 A. baumannii
• Potential for detection of resistance to carbapenems but
currently no standardized protocol
• Bruker detection kit and software in the pipeline
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MALDI-ToF for direct detection of
carbapenemase producers in blood cultures
Carvalhaes et al. 2014
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Detecting carbapenemase antigens:
immunochromatographic tests
• Coris RESIST K-SeT sets
– Currently only KPC and OXA-48
• 100% sensitivity/specificity from bacterial colonies (Meunier et al. in press)
and spiked blood cultures (Wareham et al. 2016)
CPE screening – where are we now? IBMS Congress 2015 © Crown copyright 26 CRO and CPE: Epidemiology and diagnostic tests SMVN Meeting 2016 © Crown copyright
Detection of carbapenemase genes
KPC OXA-48-like
NDM VIM
• RT-PCR validated vs. 450 isolates.
• Testing daily all ?CPE and ?MBL NFs positive results within 48 hours
• Aiming for deployment in regional PHE labs (and beyond…? Used at GRI)
• Already in use in Birmingham and Leeds PHE labs
• +es sent to AMRHAI for WGS (MICs, typing); -ves for further workup
+ internal
positive control
ACB ASM 2015 - Antimicrobial drug resistance: current challenges and future threats © Crown copyright 27 CRO and CPE: Epidemiology and diagnostic tests SMVN Meeting 2016 © Crown copyright
Detection of carbapenemase genes
Multiplex PCR assay for genes encoding acquired metallo-β-lactamases.
[Ellington et al. 2007]
Testing for other
carbapenemases still dictated by:
• information on
submission form
• MICs for rarer genes
ACB ASM 2015 - Antimicrobial drug resistance: current challenges and future threats © Crown copyright ACB ASM 2015 - Antimicrobial drug resistance: current challenges and future threats © Crown copyright 28 CRO and CPE: Epidemiology and diagnostic tests SMVN Meeting 2016 © Crown copyright
Commercial molecular assays
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Company Assay Basis Cultures Clinical
samples
Coverage* Platform Time
Amplex Eazyplex SuperBug
complete or
eazyplex SuperBug
CRE
(CE-marked)
LAMP yes “screening
swabs”
KPC, OXA-
48, VIM,
NDM
Proprietary 15 m
(isolates)
or 30 m
(swabs)
Cepheid GeneXpert Carba-R
(CE-marked)
RT-
PCR
yes Rectal swabs KPC, OXA-
48, NDM,
VIM, IMP-1
Proprietary 50 m
Check-
Points
Check-Direct CPE
(CE-marked)
RT-
PCR
Yes Rectal/perianal
swabs
KPC, OXA-
48, NDM,
VIM
Multiple RT-
PCR
machines
2 h
Nanosphere Verigene BC-GN PCR/
array
No(?) Blood cultures KPC, OXA-
48, NDM,
VIM, IMP
Proprietary <2 h
* Coverage within OXA-48, VIM and IMP families varies between kits
AMRHAI commercial kit evaluation [Findlay et al. 2015]
Amplex
Eazyplex SuperBug
Complete
Cepheid
GeneXpert Carba-R
Check-Points
Check-Direct CPE
on ABI 7500
Check-Points
Check-Direct CPE
on BD MAX™
Assay coverage
KPC, OXA-48*,
NDM, VIM
KPC, OXA-48*, NDM,
VIM, IMP-1
KPC, OXA-48-like,
NDM/VIM
KPC, OXA-48-like,
NDM, VIM
‘Big 5’
carbapenemases NOT
detected IMP family Some IMP variants IMP family IMP family
Hands on time per
sample <5 min <5 min <5 min <5 min
Assay runtime 20 min ~50 min ~1.75 hrs ~2.5 hrs
No of samples that can
be processed at once
1 or 2 independent
tests
Up to 80 independent
tests Up to 94 batched Up to 22 batched
• A commercial system may be an interim solution whilst PHE assay was
developed
• Tested against 450 pure bacterial cultures, mostly Enterobacteriaceae
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The Equipment
Cepheid GeneXpert Amplex Genie II
BD MAX (Check-Points)
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• 100% sensitivity for detecting KPC, NDM and VIM genes
• OXA-48-like: Amplex v.1 and Cepheid v.1 did not detect the OXA-181
variant • Both kits subsequently modified to detect this allele
• IMP: Cepheid detected IMP-1-like, but NOT other variants • more common in NFs
• AMRHAI starting to accept local lab results with these assays at face value
Assay Performance [Findlay et al. 2015]
Carbapenemases Detected
Isolates Tested Amplex v.1 Cepheid v.1 Check-Points ABI
7500
Check-Points BD
MAX™
KPC (n=100) 100% 100% 100% 100%
OXA-48-like (n=100) 83% 83% 100% 100%
NDM (n=100) 100% 100% 100% 100%
VIM (n=100) 100% 100% 100% 100%
IMP (n=24) n/a 71% (17/24) n/a n/a
NDM+OXA-48-like (n=2) 2x NDM; 1x OXA-
48-like
2x NDM; 1x OXA-
48-like
2x NDM; 2x OXA-
48-like
2x NDM; 2x OXA-
48-like
Non-carba (n=24) 0% 0% 0% 0%
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NICE medtech innovation briefing
• Based on AMRHAI evaluation and two others:
• Tenover et al (2013) – Xpert MDRO = earlier
version
• Anandan et al (2015) – no explanation of
discrepancies
• Provides objective information to aid local
decision making
• Is NOT NICE guidance or a recommendation
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https://www.nice.org.uk/advice/mib52
Molecular diagnostics to guide empiric
therapy
• Current molecular tests to detect/infer resistance mechanisms are
surrogates for rapid susceptibility testing
• Absence of a resistance mechanism doesn’t confirm susceptibility
• cannot indicate appropriate empiric therapy
• Presence of a resistance mechanism used to infer likely resistance
• false resistance (unexpressed/partial genes)
• Indicates potentially inappropriate empiric therapy
• carbapenemase detected: carbapenem NOT suitable as sole agent
• Still need to culture organism for :
– AST – still essential to confirm susceptibility for patient treatment
– Typing – needed to investigate transmission
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Allele diversity, assay coverage and
sensitivity
• For maximum sensitivity, molecular assays must include probes/primers to
detect all known gene variants
• >150 alleles in ‘big 5’ families (http://www.lahey.org/Studies/; 16th April ‘16)
• KPC: 24 variants
• NDM: 16 variants
• IMP: 53 variants
• VIM: 46 variants
• OXA-48-like: -48, -181, -232 (at least 10 variants)
• Family coverage ‘simple’ for KPC, NDM; harder for OXA-48-like; much
harder for IMP and VIM
• Solutions usually include compromises and won’t detect rarer or new
enzymes
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Carbapenemases come in many varieties
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Enzyme Type Classification by
Ambler Class
Activity Spectrum Organism(s)
KPC A All β-lactams Enterobacteriaceae,
P. aeruginosa,
A. baumannii
SME A Carbapenems and aztreonam,
but not 3rd/4th G
cephalosporins
S. marcescens
NMC–A
IMI
A Carbapenems and aztreonam,
but not 3rd/4th G
cephalosporins
Enterobacter species
GES A Imipenem and 3rd/4th
cephalosporins
P. aeruginosa and
Enterobacteriaceae
IMP
VIM
NDM
AIM, GIM, SIM, (not detected
in the UK yet)
DIM, SPM
B (metallo-β-lactamases) All β-lactams except
monobactams (aztreonam)
Pseudomonas species
Acinetobacter species
Enterobacteriaceae
OXA D Weakly active against
carbapenems
A. baumannii,
Enterobacteriaceae
and rarely P. aeruginosa
CRO and CPE: Epidemiology and diagnostic tests SMVN Meeting 2016 © Crown copyright
Other new carbapenemases
• FR1-1: class A carbapenemase [Dortet et al. 2015]
• Enterobacter cloacae
• Patient hospitalised in France; previous travel to Switzerland
• Plasmid-mediated
• BKC-1: class A carbapenemase [Nicoletti et al. 2015]
• Klebsiella pneumoniae
• Brazil
• Plasmid-mediated
• VCC-1: class A carbapenemase [Mangat et al. 2016]
• Vibrio cholerae
• Canada
• LMB-1: class B carbapenemase [Lange et al. 26th ECCMID #EP0187]
• Enterobacter cloacae
• Austria
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Filling the gaps in carbapenem
resistance surveillance
• Need better understanding of patient-related risk factors
other than travel or hospitalisation abroad
• Who are ‘high-risk’ patients?
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ERS data collection
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Two-stage submission process
Summary
• CRO and CPE continue to be a problem
• Epidemiology of CPE diverse depending on carbapenemase family
• Clonal vs. plasmid spread
• Whole genome sequencing
• Limiting the impact of carbapenemases requires rapid detection
• Phenotypic vs. genotypic
• In-house vs. commercial
• But need to think beyond the “big 5”
• Enhance surveillance needed to improve our understanding of
local and national epidemiology
40 CRO and CPE: Epidemiology and diagnostic tests SMVN Meeting 2016 © Crown copyright