CRO and CPE: Epidemiology and diagnostic tests

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1 CRO and CPE: Epidemiology and diagnostic tests Scottish Microbiology and Virology Network Scientific Meeting 22 nd April 2016 Katie Hopkins PhD Clinical Scientist, Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit Public Health England Crown copyright

2 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 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 2 CRO and CPE: Epidemiology and diagnostic tests SMVN Meeting 2016 Crown copyright

3 Gram-negative resistance ad infinitum 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 5 of 7 ESKAPEEs are Gram-negative Increasing reliance on carbapenems detection of carbapenemases required for IPC and public health 2 CRO and CPE: Epidemiology and diagnostic tests SMVN Meeting 2016 Crown copyright

4 The nightmare bacteria Health Protection Report Vol 9 No January CRO and CPE: Epidemiology and diagnostic tests SMVN Meeting 2016 Crown copyright

5 The big 5 carbapenemases KPC (22 variants) NDM (14 variants) OXA-48-like (>10 variants) VIM (43 variants) IMP (48 variants) 5 CRO and CPE: Epidemiology and diagnostic tests SMVN Meeting 2016 Crown copyright

6 Global perspective: KPC-producers Nordmann & Poirel, CRO and CPE: Epidemiology and diagnostic tests SMVN Meeting 2016 Crown copyright

7 KPC: international strain epidemic of KPC +ve K. pneumoniae ST258 ST258 ST258 NW England KPC outbreak: K. pneumoniae STs 11, 25, 27, 248, (258 - Col-R), 321, 468, 490 and 491 plus Enterobacter, E. coli + others Nordmann et al. TLID 2009; 9:

8 Global perspective: OXA-48-producers Nordmann & Poirel, CRO and CPE: Epidemiology and diagnostic tests SMVN Meeting 2016 Crown copyright

9 OXA-48: international plasmid epidemic OXA-181 (c. 7kb) OXA-48 (c. 62 kb) OXA-48 OXA-48 found on related plasmids in clonally diverse isolates of E. coli, K. pneumoniae and E. cloacae. Dimou et al. JAC 2012 ; Poirel et al. AAC 2012

10 Global perspective: NDM-producers Multiple plasmid backbones in multiple clones of different genera Nordmann & Poirel, CRO and CPE: Epidemiology and diagnostic tests SMVN Meeting 2016 Crown copyright

11 NDM epidemiology is diverse Kumarasamy et al., 2010 Kumarasamy et al., 2010 Nordmann et al., CRO and CPE: Epidemiology and diagnostic tests SMVN Meeting 2016 Crown copyright

12 Global perspective: VIM- and IMP-producers Nordmann et al., CRO and CPE: Epidemiology and diagnostic tests SMVN Meeting 2016 Crown copyright

13 EARS-Net data: Proportion of carbapenem resistant (R+I) invasive E. coli and K. pneumoniae, 2014 E. coli K. pneumoniae 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 13 CRO and CPE: Epidemiology and diagnostic tests SMVN Meeting 2016 Crown copyright

14 Overall European situation regarding occurrence of CPE using an epidemiological scale of nationwide expansion 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 14 CRO and CPE: Epidemiology and diagnostic tests SMVN Meeting 2016 Crown copyright

15 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? Bioconnections CRO and CPE: Masterclass Epidemiology 14th and April diagnostic 2015 tests SMVN Meeting 2016 Crown copyright

16 The problem with spotting carbapenemase producers Wild-type Carbapenemase N ESBL / AmpC + porin loss or true carbapenemase? Carbapenem MIC Not all carbapenemase producers are resistant to the carbapenems ESBL/AmpC + porin loss = not transferable, may have fitness cost rarely cause outbreaks 16 CRO Phenotypic and CPE: detection Epidemiology of ESBLs and and diagnostic carbapenemases tests SMVN - BSAC Meeting workshop Crown Crown copyright copyright

17 Chromogenic screening media 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! CRO and CPE: Epidemiology and diagnostic tests SMVN Meeting 2016 Crown copyright

18 How can we identify a carbapenemase-producing organism? -lactamase inhibitor tests Detect carbapenem hydrolysis Detect carbapenemase antigens Detect carbapenemase genes Clinical specimen Bacterial isolate some assays some of the big 5 some of the big CRO and CPE: Epidemiology and diagnostic tests SMVN Meeting 2016 Crown copyright

19 EUCAST guidance for resistance mechanism detection 19 CRO and CPE: Epidemiology and diagnostic tests SMVN Meeting 2016 Crown copyright

20 How can we identify a carbapenemase-producing organism? -lactamase inhibitor tests Detect carbapenem hydrolysis Detect carbapenemase antigens Detect carbapenemase genes Clinical specimen Bacterial isolate some assays some of the big 5 some of the big CRO and CPE: Epidemiology and diagnostic tests SMVN Meeting 2016 Crown copyright

21 Cleavage of -lactam ring by carbapenemases hydrolysis decarboxylation +18 Da - 44 Da red ph change yellow 21 CRO and CPE: Epidemiology and diagnostic tests SMVN Meeting 2016 Crown copyright

22 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. 22 CPE CRO screening and CPE: Epidemiology where are we and now? diagnostic tests IBMS SMVN Congress Meeting Crown Crown copyright copyright

23 CarbaNP for direct detection of carbapenemase producers in blood cultures Identification of a carbapenemase producer reduced from hrs to 3-5 hrs Dortet et al Phenotypic detection of ESBLs and carbapenemases - BSAC workshop 2015 Crown 23 CRO and CPE: Epidemiology and diagnostic tests SMVN Meeting 2016 Crown copyright copyright

24 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 Phenotypic detection of ESBLs and carbapenemases - BSAC workshop 2015 Crown 24 CRO and CPE: Epidemiology and diagnostic tests SMVN Meeting 2016 Crown copyright copyright

25 MALDI-ToF for direct detection of carbapenemase producers in blood cultures Carvalhaes et al CRO and CPE: Epidemiology and diagnostic tests SMVN Meeting 2016 Crown copyright

26 Detecting carbapenemase antigens: immunochromatographic tests Coris RESIST K-SeT sets Currently only KPC and OXA % sensitivity/specificity from bacterial colonies (Meunier et al. in press) and spiked blood cultures (Wareham et al. 2016) 26 CPE CRO screening and CPE: Epidemiology where are we and now? diagnostic tests IBMS SMVN Congress Meeting Crown Crown copyright copyright

27 Detection of carbapenemase genes KPC OXA-48-like NDM VIM + internal positive control 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 27 ACB CRO ASM and CPE: 2015 Epidemiology - Antimicrobial and drug diagnostic resistance: tests current SMVN challenges Meeting and 2016 future threats Crown copyright

28 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 28 ACB CRO ACB ASM and ASM CPE: Epidemiology - - Antimicrobial and drug drug diagnostic resistance: tests current SMVN challenges Meeting and and 2016 future threats Crown Crown copyright copyright

29 Commercial molecular assays 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 * Coverage within OXA-48, VIM and IMP families varies between kits Proprietary <2 h 29 CRO and CPE: Epidemiology and diagnostic tests SMVN Meeting 2016 Crown copyright

30 AMRHAI commercial kit evaluation [Findlay et al. 2015] Amplex Eazyplex SuperBug Complete KPC, OXA-48*, NDM, VIM Cepheid GeneXpert Carba-R KPC, OXA-48*, NDM, VIM, IMP-1 Check-Points Check-Direct CPE on ABI 7500 KPC, OXA-48-like, NDM/VIM Check-Points Check-Direct CPE on BD MAX KPC, OXA-48-like, NDM, VIM Assay coverage 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 30 CRO and CPE: Epidemiology and diagnostic tests SMVN Meeting 2016 Crown copyright

31 The Equipment BD MAX (Check-Points) Cepheid GeneXpert Amplex Genie II 31 CRO and CPE: Epidemiology and diagnostic tests SMVN Meeting 2016 Crown copyright

32 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 2x NDM; 1x OXA- 2x NDM; 1x OXA- 2x NDM; 2x OXA- 2x NDM; 2x OXA- NDM+OXA-48-like (n=2) 48-like 48-like 48-like 48-like Non-carba (n=24) 0% 0% 0% 0% 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 32 CRO and CPE: Epidemiology and diagnostic tests SMVN Meeting 2016 Crown copyright

33 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 33 CRO and CPE: Epidemiology and diagnostic tests SMVN Meeting 2016 Crown copyright

34 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 34 CRO and CPE: Epidemiology and diagnostic tests SMVN Meeting 2016 Crown copyright

35 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 ( 16 th 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 35 CRO and CPE: Epidemiology and diagnostic tests SMVN Meeting 2016 Crown copyright

36 Carbapenemases come in many varieties 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 NMC A IMI A Carbapenems and aztreonam, but not 3rd/4th G cephalosporins GES A Imipenem and 3rd/4th cephalosporins IMP B (metallo-β-lactamases) All β-lactams except VIM monobactams (aztreonam) NDM AIM, GIM, SIM, (not detected in the UK yet) S. marcescens Enterobacter species P. aeruginosa and Enterobacteriaceae Pseudomonas species Acinetobacter species Enterobacteriaceae DIM, SPM OXA D Weakly active against carbapenems A. baumannii, Enterobacteriaceae and rarely P. aeruginosa 36 CRO and CPE: Epidemiology and diagnostic tests SMVN Meeting 2016 Crown copyright

37 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. 26 th ECCMID #EP0187] Enterobacter cloacae Austria 37 CRO and CPE: Epidemiology and diagnostic tests SMVN Meeting 2016 Crown copyright

38 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? 38 CRO and CPE: Epidemiology and diagnostic tests SMVN Meeting 2016 Crown copyright

39 Two-stage submission process ERS data collection CRO 39 and CPE: Epidemiology and diagnostic tests SMVN Meeting 2016 Crown copyright

40 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