Recent evolution in invasive Salmonellosis

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1 Recent evolution in invasive Salmonellosis Professor Gordon Dougan Wellcome Trust Sanger Institute and Cambridge University

2 How does evolution deal with dogma Statements that have launched a thousand grant applications and thesis introductions:- Salmonella typhimurium is a cause of gastroenteritis in humans whereas Salmonella typhi is responsible for the systemic disease typhoid.

3 Comparison of pathogenesis of infection associated with Salmonella typhimurium versus typhi Typhimurium Typhi Human Restricted Nature Immunology 3, (2002) Chronic bacterial infections: living with unwanted guests. Douglas Young, Tracy Hussell & Gordon Dougan

4 Genome diversity in different microbes Some pathogens are genetically monophyletic and cannot be differentiated by MLST H. pylori mean H ratio E. coli S. aureus S. pneumoniae S. enterica C jejuni N. meningitidis Y. pestis, S. typhi B. anthracis M. tuberculosis C. trachomatis V. cholerae 0 Shigella sonnei B. pertussis -0.2 Y. enterocolitica mean D s Mark Achtman

5 Comparison of the Salmonella Typhi genomes of Ty2 (92) and CT8 (992) illustrates a conserved genome PAI MLST Diversity Ty2 P4 phage 4,700 Genes Although variation in Typhi is limited it can be defined and the consequences assessed a paradigm for other human restricted pathogens?

6 What is the evidence for vertical and horizontal accumulation of mutation and diversity in S. Typhi? Progenitor IncH plasmids Ab-R Time ~30,000 yrs strain strain 2 strain 3 strain 4

7 Variation discovery in Typhi using sequencing of 200 genes and over 00 strains Found only 88 SNPs! In ~ 2% of the genome

8 Population structure SNP analysis of Salmonella Typhi Ancestral root Any new isolate can be unequivocally assigned to a position in the tree The position in the tree is irrefutable Roumagnac et al (2006) Science 34 30

9 SNP analysis of Salmonella Typhi linked to gyrase SNPs Root Nalidixic acid resistant point mutations SNPs Expanding SE Asian Naladixic acid resistant clones are H58 Nal R - gyra mutations

10 Selection of strains for resequencing S. Typhi Published sequence 454 resequencing Solexa resequencing A0 AV AZ Because we have a phylogenetic Tree we can truly sample diversity H58 SE Asia Expansion Roumagnac et al., Science.

11 New tech re-sequencing of Salmonella Typhi Kathryn Holt

12 S. Typhi phylogenetic tree after sequence analysis SNP scale 2736 SNPs identified; 85 SNPs used Variation landscape in typhoid Typhi is genetically isolated with no evidence for antigenic variation

13 Accumulation of plasmids and mutation on the tree Plasmids entering the tree We have different typhoid disease severity in our part of the world, is this due to the host or the pathogen genetics??? The differential accumulation of ~92 pseudogenes in different arms of the tree is giving rise to different pathotypes? 80 ~200

14 Typhi genotyping Typhi chromosome SNPs deletions resistance plasmid Can SNPs framework be used for association style genetics as in mammals?

15 Haplotypes circulating in the Jatinegara district of Jakarta over a two year period 500 SNPs assayed at once for each sample (ugs) on Illumina GoldenGate genotyping platform

16 Distribution of invasive salmonellosis disease Non-typhoidal Salmonellosis

17 Reports from tropical Africa of NTS as a major cause of pediatric bacteraemia Egypt Ethiopia The Gambia 980s and 2005 Ghana 990s Nigeria 970s CAR 2002 DRC 990s Uganda 2006 Kenya 980s Kenya 2000s Rwanda 980s Malawi Mozambique

18 NTS are the commonest cause of bacteraemia in Malawi: Blood isolates 0-4 years, Typhimurium Enteritidis,873 NTS S.pneumoniae H.influenzae S.aureus N.meningitidis Gp B strep S.typhi Other strep Other GNR Other

19 NTS in HIV-positive adults Death AIDS 2002, 6: /78 HIV-infected 47% inpatient mortality 77% dead at year 43% recurrence rate Recrudescence not reinfection Recurrence

20 NTS in HIV-negative children A diagnostic conundrum: 97% fever, 67% cough, 48% diarrhoea, 72% tachypnoea just ~8% of cases are associated with HIV infection 3% malaria slide positive 27% Anaemia 5% <60% weight-for-age, 5% 60-80% weight-for-age No diagnosis without blood culture facility Overall mortality 23%

21 Age (months) a Age of serum donor (months) b Cases of Salmonella Bacteraemia log0 change in Salmonella (cfu/ml) anti-salmonella IgG titer Age of serum donor (months) Cal MacLennan

22 In vitro models of Salmonella Bacteraemia Whole blood assay 8 salmonella Strains Healthy adult donor blood Washed Blood cells resuspended in RMPI Whole blood Serum Heat-inactivated serum Serum + C C9 deficient serum C9 deficient serum + purified C9

23 Complement-mediated killing of salmonella is dependent on classical pathway activity CLASSICAL (IgG, IgM) MANNOSE BINDING LECTIN ALTERNATIVE C3b C5b-9 Membrane Attack Complex

24 The emergence of drug resistant invasive salmonellosis in Malawi as monitored by Wellcome Trust Laboratories, Blantyre Number Isolated % Resistant Jan-June'96 July-Dec'96 Jan-June'97 June-Dec'97 Jan-June'98 July-Dec'98 Jan-June'99 July-Dec'99 Jan-June'00 July-Dec'00 Jan-June'0 July- Dec'0 Jan-June'02 July-Dec'02 Total S typhimurium Total S enteritidis % amp resistant SEN % chl resistant SEN % gent resistant SEN % cotrim resistant SEN

25 Many NTS strains circulating in Africa (Kenya/Malawi) have a novel MLST type ST33 NTS Classic gastroenteritis (DT04, LT2, SL344) Root

26 Plasmid, Pulse Field Gel Electrophoresis and Multi Locus Sequence Typing Profiles MDR, Cm-S MDR, Cm-R Chloramphenicol treatment Fluoroquinolone treatment

27 Complete sequence of a Malawian MDR NTS S. Typhimurium ST33 Rob Kingsley and Nick Thomson

28 S. Typhimurium D23580 has a unique phage repertoire compared to other sequenced strains DT04 D23580

29 Most S. Typhimurium NTS isolates from Malawi between have identical pulse field and plasmid pattern to D23580 V57 D/G L D/G D/G chr Indistinguishable strains of S. typhimurium NTS in HIV-positive adults and HIV-negative children

30 Antibiotic resistance genes located on an integron situated in the virulence plasmid of S. Typhimurium D23580 Kingsley et al, Figure 3

31 The invasion associated plasmid harbours a sophisticated mobile cassette encoding antibiotic and disinfect resistance 2004 sulphonamide trimethoprim streptomycin chloramphenicol β-lactamase aminoglycoside quaternary ammonium

32 Plasmid, Pulse Field Gel Electrophoresis and Multi Locus Sequence Typing Profiles MDR, Cm-S MDR, Cm-R Chloramphenicol treatment Fluoroquinolone treatment

33 Salmonella typhimurium isolated before 2004 have a different element encoding MDR D SL344, DT2, E. coli K2 aminoglycoside quartenary ammonium sulphonamide Mercury B-lactam tna CDS orf2 inti blao aada qace sul sul3 istb ista tnib tnia CDS Mer E Mer D MerA MerC MerP Mer T Mer R 3 4 2

34 The pressure for the use of prophylactic antibiotics in HIV positive children Lancet Infectious Disease2007, 7:686-93

35 Acknowledgements Julian Parkhill Nick Thomson Many in the PSU Stephen Baker Kathryn Holt Tim Perkins Robert Kingsley Derek Pickard Others in Team 5 Jeremy Farrar Christiane Dolecek Duncan Maskell Bruce Stocker Sam Kariuki Chisomo Msefula Malcolm Molyneux Melita Gordon Robert Heyderman Cal MacLennan

36 The Non-typhoidal Salmonellosis problem Multi-drug resistance (chloramphenicol, ampicillin, cotrimoxazole) >90% in Malawi Diagnostic difficulty. Non-specific presentation 23% case fatality rate with blood-culturing facility and appropriate antibiotic therapy Rapid progression of clinical course Currently no vaccine against non-typhoidal salmonella Clinical Infectious Diseases 2008; 46:963 9