Bacterial whole genome sequencing in clinical microbiology, infection control and public health. Julian Parkhill. FIS, Birmingham, November 2013

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1 Bacterial whole genome sequencing in clinical microbiology, infection control and public health Julian Parkhill FIS, Birmingham, November 2013

2 Falling costs of genomics 2003 Cost/genome Throughput 60,000 1 genome / 20 days ,000 genomes / 10 days genomes / 1 day Disclaimer: Illustrative figures only. Other sequencing machines are available

3 Genomics in public health microbiology Rapid high throughput sequencing will benefit in 3 areas: Epidemiology: Phenotyping: Diagnosis Rapid, unambiguous, high-resolution typing Single technique to replace multiple organism-specific schemes Common digital data can be shared globally Phylogenetic analysis allows temporal and directional inference (rather than simple same/different cutoffs) Can be used now Drug resistance/sensitivity Virulence, Transmissibility Will require further research and continuous updates Possible now in limited circumstances Widespread use will require further falls in cost and throughput

Staphylococcus aureus Widespread Gram +ve bacteria Natural biota of the skin ~40% carriage Versatile pathogen associated with a wide range of diseases Minor wound infections Food poisoning Toxic

4 Staphylococcus aureus Widespread Gram +ve bacteria Natural biota of the skin ~40% carriage Versatile pathogen associated with a wide range of diseases Minor wound infections Food poisoning Toxic shock syndrome Endocarditis Haemolytic pneumonia Complex pathology Drug resistance Methicillin-resistant S. aureus (MRSA) Vancomycin insensitive/resistant Image kindly provided by Sharon Peacock, Cambridge University

5 Staphylococcus aureus population structure by MLST CC1 CC51 CC8 CC22 CC39 CC45 CC5 CC30 CC25 CC12 CC15 CC9

6 Methicillin-resistant Staphylococcus aureus DoH reduction targets Identification of EMRSA15+16 Livermore (2012) Int J Antimicrob Agents. 39:283-94

7 Addenbrooke s Special Care Baby Unit outbreak Harris et al Lancet Infect Dis. 13:130

8 SCBU outbreak Harris et al Lancet Infect Dis. 13:130

9 SCBU outbreak Harris et al Lancet Infect Dis. 13:130

10 SCBU outbreak Harris et al Lancet Infect Dis. 13:130

11 SCBU outbreak Harris et al Lancet Infect Dis. 13:130

12 SCBU outbreak Harris et al Lancet Infect Dis. 13:130

13 SCBU outbreak Harris et al Lancet Infect Dis. 13:130

14 SCBU outbreak Harris et al Lancet Infect Dis. 13:130

15 SCBU outbreak Harris et al Lancet Infect Dis. 13:130

16 SCBU outbreak: consequences Harris et al Lancet Infect Dis. 13:130

17 Mycobacterium abscessus in Cystic Fibrosis Prior to 1990 M abscessus was rarely isolated from CF sputum. Now one of the top NTMs infecting CF patients Estimated to affect 5 10% of CF population Naturally high antibiotic resistance resistant to all frontline TB antibiotics (isoniazid, rifampin, pyrazinamide and ethambutol) Associated with decline in lung function (only less than 10% have no clinical deterioration) Thought to be environmentally acquired clinical guidelines based on this Tested in Papworth - Sequenced 168 isolates collected from 31 CF patients Bryant et al Lancet 381:1551

Loosely patient isolates Clustered isolates 1. 3.

18 Mycobacterium abscessus phylogeny 2. Deep divergences between different 4. Loosely patient isolates Clustered isolates Three Tightly subspecies Clustered isolates M.a. massiliense Maximum likelihood tree of 200 isolates M.a. abscessus M.a. bolletii Bryant et al Lancet 381:1551

19 Pairwise similarities Pairwise SNP distance between all isolates of same subspecies Bryant et al Lancet 381:1551

20 Epidemiology of possible patient contact Bryant et al Lancet 381:1551

21 Dating of possible transmission events Bryant et al Lancet 381:1551

22 Transmission of drug resistance Bryant et al Lancet 381:1551

23 Pairwise similarities Pairwise SNP distance between all isolates of same subspecies Bryant et al Lancet 381:1551

24 Epidemiology of possible patient contact Bryant et al Lancet 381:1551

25 Dating of possible transmission events Bryant et al Lancet 381:1551

26 M. a. massiliense circulating clone? Bryant et al Lancet 381:1551

27 Mycobacterium abscessus transmission routes 1. Independent acquisition from the environment 2. Between patient transmission 3. Dominant circulating clones Bryant et al Lancet 381:1551

28 Mycobacterium abscessus in Cystic Fibrosis Most typing techniques allow only identical/not-identical discrimination Use of whole genome sequencing and phylogenetic reconstruction allows dating of relationships between isolates Combining this with epidemiological information gives unambiguous demonstration of transmission events Accurate dating of deeper relationships allows identification of circulating (emerging) clones Bryant et al Lancet 381:1551

29 WTSI: Gordon Dougan Josephine Bryant Simon Harris Nick Thomson Stephen Bentley Matthew Holden Nick Croucher Ankur Mutreja Thomas Connor Cambridge: Sharon Peacock Estee Torok Nicholas Brown Claudio Köser Matt Ellington Ed Cartwright Amanda Ogilvy-Stuart M. abscessus: Andres Floto Sharon Peacock Dorothy M Grogono Daniel Greaves Juliet Foweraker Iain Roddick Thomas Inns, Mark Reacher Charles Haworth Martin Curran

30 Resistance prediction Current accuracy Antibiotic class False negative False positive Gentamicin 0.39% 0.20% Penicillin 0.0% 0.0% Oxacillin 2.36% 0.0% Fusidic acid 4.43% 0.10% Teicoplanin 1.38% 0.0% Vancomycin 0.20% 0.0% Erythromycin 3.05% 0.49% Mupirocin 1.38% 0.0% Linezolid 0.0% 0.0% Fluoroquinolone 0.99% 0.49% Rifampicin 0.39% 0.0% Tetracycline 0.89% 0.10% Minocycline 0.0% 0.0% Trimethoprim 2.86% 0.20%

31 M. a. massiliense adaption? Mammalian cell entry cluster Bryant et al Lancet 381:1551

32 Origin of ST22 (EMRSA15) 193 isolates, 15 countries, 20 years Holden et al Genome Res.

33 Origin of ST22 (EMRSA15) Fluoroquinolone resistance Holden et al Genome Res.

34 Origin of ST22 (EMRSA15) Holden et al Genome Res.

35 Origin of ST22 (EMRSA15) What was happening in the West Midlands in the mid 80s? 1986

Antimicrobial susceptibility

Antimicrobial susceptibility PATTERNS Microbiology Department Canterbury ealth Laboratories and Clinical Pharmacology Department Canterbury District ealth Board March 2011 Contents Preface... Page 1 ANTIMICROBIAL