1. CRE/CPE/CRO: Demystifying the microbiology and opportunities for whole genome sequencing Jon Otter, PhD FRCPath Imperial College Healthcare NHS Trust  jon.otter@imperial.nhs.ukjon.otter@imperial.nhs.uk @jonotter Blog: www.ReflectionsIPC.comwww.ReflectionsIPC.com You can download these slides from www.jonotter.netwww.jonotter.net

2. MRSA bacteraemia, England 2001-2013 1.Mandatory reporting, 2001 2.‘Gettting ahead of the curve’, 2002 3.‘Winning ways’, 2003 4.‘Towards cleaner hospitals’, 2004 5.‘Cleanyourhands’, 2004 6.Targets introduced, 2004 7.Cleanliness improvement, 2005 8.‘Going further faster’, 2006 9.Root cause analysis, 2006 10.Revised national guidelines, 2006 11.Deep clean, 2007 12.Screening elective admissions, 2008 13.Universal screening, 2010 12 3 456456 7 8 9 10 11 12 13

3. CDI cases, 2004-2013 C. difficile infection (CDI), England 2004-2013 1.Mandatory reporting, 2004 2.Targets, 2007 3.Revised guidelines, 2009 1 2 3

4. THE END OF ANTIBIOTICS IS NIGH

5. “CPE are nightmare bacteria.” Dr Tom Frieden, CDC Director “If we don't take action, then we may all be back in an almost 19th Century environment where infections kill us as a result of routine operations.” Dame Sally Davies, Chief Medical Officer “If we fail to act, we are looking at an almost unthinkable scenario where antibiotics no longer work and we are cast back into the dark ages of medicine where treatable infections and injuries will kill once again.” David Cameron, Prime Minister, UK “The rise of antibiotic-resistant bacteria, however, represents a serious threat to public health and the economy.” Barack Obama, President USA What’s the problem?

6. Rising threat from MDR-GNR % of all HAI caused by GNRs. Hidron et al. Infect Control Hosp Epidemiol 2008;29:966-1011. Peleg & Hooper. N Engl J Med 2010;362:1804-1813. % of ICU HAI caused by GNRs. Non-fermentersAcinetobacter baumannii Pseudomonas aeruginosa Stenotrophomonas maltophilia EnterobacteriaceaeKlebsiella pneumoniae Escherichia coli Enterobacter cloacae CPE CPO

7. Poll: would you be comfortable explaining the difference between ‘carbapenem-resistant Enterobacteriaceae (CRE)’ and ‘carbapenemase producing Enterobacteriaceae (CPE)’ to a colleague? A) Yes B) No

8. Gimme a “C” (TLA overdose) CCarbapenem or Carbapenemase R or PResistant or Producing E or OEnterobacteriaceae or Organism CRO > CPO CRE > CPE > >

9. CRE or CPE (or possibly CP-CRE)?! Carbapenem-resistant Enterobacteriaceae (CRE) – Enterobacteriaceae that are resistant to carbapenems by any mechanism. Carbapenemase-producing Enterobacteriaceae (CPE) – Enterobacteriaceae that are resistant to carbapenems by means of an acquired carbapenemase. CRE CPE

10. When CRE is not CPE Courtesy of Dr Katie Hopkins, PHE. Carbapenem MIC N 0.5 16 Wild-type Carbapenemase ESBL / AmpC + porin loss or true carbapenemase ?

11. Enterobacteriaceae ESBLs CPE Creating a monster Extended-spectrum beta-lactams Carbapenems

12. ShareDiffer Gram stain reactionRisk factors & at-risk population Concerning AMRPotential for epidemic spread Infection profile & mortality Prevalence Colonisation site & duration Transmission routes Resistance profile & mechanisms Enterobacteriaceae vs. non-fermenters

13. What’s the problem? Resistance Courtesy of Pat Cattini

14. EnterobacteriaceaeNon fermenters OrganismAmpC / ESBLCPEA. baumannii Attributable mortality ModerateMassive (>50%)Minimal Shorr et al. Crit Care Med 2009;37:1463-1469. Patel et al. Iinfect Control Hosp Epidemiol 2008;29:1099-1106. What’s the problem? Mortality

15. What’s the problem? Rapid spread Rapid spread Clonal expansion GI carriage Horizontal gene transfer

17. Acronym minefield MDR-GNR MDR-GNB CRO CPE CRE NDM CPC CRC CRAB ESBL KPC

18. Understanding the enemy PathogenCPE 1 CPAB 2 MRSAVREC. difficile Resistance+++ +++/- Resistance genes Multiple Single n/a SpeciesMultipleSingle HA vs CAHA & CAHA (ICU)HA At-risk ptsAllICUUnwell Old Virulence++++/-+++/-+ Environment+/-+++++++++ 1.Carbapenemase-producing Enterobacteriaceae. 2.Carbapenemase-producing Acinetobacter baumannii.

19. Poll: How much CPE have you seen in your hospital? A) None B) One or two cases C) One or two outbreaks D) Regularly (not related to known outbreaks)

20. NHSN / NNIS data; MMWR 2013;62:165-170. CRE in the USA

21. Colistin resistance in Italy Monaco et al. 2014; Euro Surveill 2014;19:pii=20939. Survey of 191 CPE from 21 labs across Italy. 43% Colistin resistant K. pneumoniae. Range = 10-80% for the 21 labs.

22. Emergence of CPE in the UK PHE.

23. CPE in the UK and US

24. Evidence-free zone

25. CPE prevention & control Hand hygiene Cleaning / disinfection SDD?Topical CHX?Education? Contact precautions Active screening Antibiotic stewardship Otter et al. Clin Microbiol Infect 2015;21:1057-1066.

27. Rectal swab Agar plate AST MADLDI- TOF MS WGS NAAT (PCR) NAAT (PCR) How do I screen? NAAT = nucleic acid amplification techniques AST = antimicrobial susceptibility testing MALDI-TOF = Matrix-assisted laser desorption /ionization – time of flight mass spectrometry WGS = whole genome sequencing

28. NAAT direct from clinical specimens PCR Rapid real-time PCR kits available to detect resistance genes direct from clinical specimens; point of care tests coming Rapid sequencing kits Kits available for rapid sequence-based simultaneous detection of common organisms and resistance genes

29. WGS & enhanced epidemiology Possible transmissions links using conventional epidemiology only (left, aka “Plate of Spaghetti”) or supplemented with WGS data (right). Snitkin et al. Sci Transl Med 2012;4:148ra16.

30. Summary 1.MDR-GNR are emerging worldwide and represent a unique threat. 2.CPE in particular combine resistance, virulence and the potential for rapid spread. 3.Prevalence in the US and Europe appears to be patchy, but increasing; rates in parts of S. Europe are high. 4.We do not yet know what is effective in terms of prevention and control, but screening and isolation of carriers seems prudent. 5.Whole genome sequencing presents exciting opportunities to enhance the surveillance of CPE.

31. CRE/CPE/CRO: Demystifying the microbiology and opportunities for whole genome sequencing Jon Otter, PhD FRCPath Imperial College Healthcare NHS Trust  jon.otter@imperial.nhs.ukjon.otter@imperial.nhs.uk @jonotter Blog: www.ReflectionsIPC.comwww.ReflectionsIPC.com You can download these slides from www.jonotter.netwww.jonotter.net