Real-Time WGS for Routine Typing, Surveillance, and Outbreak Detection of VTEC. Katrine Grimstrup Joensen, Ph.d.student

Transcription

1 Real-Time WGS for Routine Typing, Surveillance, and Outbreak Detection of VTEC Katrine Grimstrup Joensen, Ph.d.student

2 Short about me DTU Food Division for Epidemiology and Microbial Genomics (Frank Møller Aarestrup and Henrik Hasman) Statens Serum Institut (SSI) Department of Microbiology and Infection Control (Eva Møller Nielsen) Ph.d project: Application of WGS for Diagnostics, Surveillance and Outbreak Detection of Foodborne Pathogens

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4 Overview VTEC Conventional typing WGS typing Study for 3 months or until reaching 40 isolates Fall 2012

5 Conventional Vs. WGS-Typing Conventional: Serotyping PCR, Hybridisation VCA Haemolysis PFGE Whole genome sequencing: Determination of the complete DNA sequence of the organism at once Employ CGE tools

6 Benchtop Sequencing IonTorrent PGM ~200bp reads, 1 Gb output ~18 hours from DNA to sequence data (2.5 normal working days) ~8 hours hands-on time 2-4 E.coli per chip

7 The sequencing workflow

8 Web-tools for WGS data User-friendly WGS tools Main Service Pipeline CGE (In development) Sequence Typing MLST (Works) pmlst (Works) Resistance - Virulence - Plasmids Pathogen ResFinder (Works) PlasmidFinder (Works) VirulenceFinder (Works) PathogenFinder (Works) Phylogenetic Tree snptree (Works) NDtree (Works) TreeViewer (Works) Species Finding KmerFinder (Works) SpeciesFinder (Works) TaxonomyFinder (This program is in development) Read2Type (This service is not implemented on the new server) Tapir (This service is not implemented on the new server) Genome Assembly Assembler (Works) Other PanFunPro (in development) MGmapper (in development) GeneticDiseaseProject (stalled indefinitely) NetFCM (in development) Restriction-ModificationFinder (in development) Center for Genomic Epidemiology (CGE)

9 Database based on Identibac scheme BLASTing all gene accessions Including all hits of 90% in size and %ID Getting rid of everything partial and containing non-atgc

10 Virulence Database 76 virulence genes stx1 (14A,18B variants) stx2 (114A,43B variants) eae (45 variants) >stx1_1_a_ab ATGAAAATAATTATTTTTAGAGTGCTAACTTTTTTCTTTGTTATCTTTTCAGTTAATGTGG TGGCGAAGGAATTTACCTTAGACTTCTCGACTGCAAAGACGTATGTAGATTCGCTGAAT GTCATTCGCTCTGCAATAGGTACTCCATTACAGACTATTTCATCAGGAGGTACGTCTTT ACTGATGATGATAGTGGCACAGGGGATAATTTGTTTGCAGTTGATGTCAGAGGGATAG ATCCAGAGGAAGGGCGGTTTAATAATCTACGGCTTATTGTTGAACGAAATAATTTATAT GTGACAGGATTTGTTAACAGGACAAATAATGTTTTTTATCGCTTTGCTGATTTTTCACAT GTTACCTTTCCAGGTAAACAGCGGTTACATTGTCTGGTGACAGTAGCTATACCACGTTA CAGCGTGTTGCAGGGATCAGTCGTACGGGGATGCAGATAAATCGCCATTCGTTGACTA CTTCTTATCTGGATTTAATGTCGCATAGTGGAACCTCACTGACGCAGTCTGTGGCAAGA GCGATGTTACGGTTTGTTACTGTAAGCTGAAGCTTTACGTTTTCGGCAAATACAGAGGG GATTTCGTACAACACTGGATGATCTCAGTGGGCGTTCTTATGTAATGACTGCTGAAGAT GTTGATCTTACATTGAACTGGGGAAGGTTGAGTAGCGTCCTGCCTGACTATCATGGAC AAGACTCTGTTCGTGTAGGAAGAATTTCTTTTGAAGCATTAATGCAATTCTGGGAAGCG TGGCATTAATACTGAATTGTCATCATCATGCATCGCGAGTTGCCAGAATGGCATCTGAT GAGTTTCCTTCTATGTGTCCGGCAGATGGAAGAGTCCGTGGGATTACGCACAATAAAA TATTGTGGGATTCATCCACTCTGGGGGCAATTCTGATGCCGAACTATTAGCAGTTGAG GGGGTAAAATGAAAAAAACATTATTAATAGCTGCATCGCTTTCATTTTTTTCAGCAAGT GCGCTGGCGACGCCTGATTGTGTAACTGGAAAGGTGGAGTATACAAAATATAATGATG ACGATACCTTTACAGTTAAAGTGGGTGATAAAGAATTATTTACCAACAGAGGAATCTTC AGTCTCTTCTTCTCAGTGCGCAAATTACGGGGATGACTGTAACCATTAAAACTAATGCC TGTCATAATGGAGGGGGATTCAGCGAAGTTATTTTTCGTTGA Gene Description Variants in database asta Heat-stable enterotoxin 1 11 bfpa Major subunit of bundle-forming pili 5 cba Colicin B 15 cci Cloacin 4 cdtb Cytolethal distending toxin B 14 celb Endonuclease colicin E2 10 cfa_c Colonisation factor antigen I 4 cif Type III secreted effector 4 cma Colicin M 19 cnf1 Cytotoxic necrotizing factor 7 cofa Longus type IV pilus subunit 1 eae Intimin 45 eata SPATE 3 efa1 EHEC factor for adherence 11 ehxa Enterohaemolysin 12 epea SPATE 1 espa Type III secretions system 23 espb Secreted protein B 14 espc SPATE 3 espf Type III secretion system 13 espi SPATE 2 espj Prophage-encoded t3ss effector 2 espp Putative exoprotein precursor 4 etpd Type II secretion protein 3 f17-a Subunit A of F17 fimbrial protein 7 f17-g Adhesin subunit of F17 fimbriae 9 fana Involved in biogenesis of K99/F5 fimbriae 1 fasa Fimbriae 987P/F6 subunit 1 feda Fimbrial protein F107 subunit A 3 fedf Fimbrial adhesin AC precursor 6 fim41a Mature Fim41a/F41 protein 2 gad Glutamate decarboxylase 70 hlye Avian E.coli haemolysin 1 iha Adherence protein 19 ipad Invasion protein Shigella flexneri 9 ipah9.8 Invasion plasmid antigen 8 irea Siderophore receptor 4 iron Enterobactin siderophore receptor 13

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12 Output example

13 Output example

14 Back to the study Total of 46 isolates (42 patients) + 2 replicate sequences Collection for 7 weeks VTEC outbreak during the study 1 Morganella morganii, not included

15 Comparing typing results Serotype Routine Typing VirulenceFinder MLST Isolate O5:H- vtx1c vtx1c ST-447 C O26:H11 eae, vtx1a eae, vtx1a ST-21 C O27:H30 vtx2b vtx2b ST-753 C (replicate) O36:H C O55:H12 vtx1a vtx1a ST-101 C O76:H- vtx1c vtx1c ST-675 C904-12A O103:H2 O103:H- O rough:h2 eae, vtx1a eae, vtx1a ST-17 ST-1967 ST-17 C C C O115:H- eae, vtx2a eae, vtx2a ST-333 C885-12B C896-12A O117:K1:H7 vtx1a vtx1a ST-504 C C C O121:H19 eae, vtx2a eae, vtx2a ST-655 C O128ab:H2 vtx2b vtx2b ST-25 C vtx1c, vtx2b vtx1c, vtx2b ST-811 C O128abc:H- eae, vtx2f eae, vtx2f ST-20 C C O145:H- eae, vtx2a eae, vtx2a ST-32 C C C C O146:H21 vtx1c, vtx2b vtx1c, vtx2b ST-442 C eae eae C896-12B C885-12A O157:H7 (O157:H-) eae, vtx1a, vtx2c eae, vtx1a, vtx2c ST-11 C C697-12A (replicate) C697-12B eae, vtx1a C eae, vtx1a, vtx2a eae, vtx1a, vtx2a C C C C C C eae, vtx2a eae, vtx2a C eae, vtx2c eae, vtx2c ST-2966 C O165:H- eae, vtx1a, vtx2a eae, vtx1a, vtx2a ST-119 C905-12

16 Comparing typing results Serotype Routine Typing VirulenceFinder MLST Isolate O180:Heae eae C641-12A ST-301 eae, vtx2a 1 eae C641-12B O181:H16 vtx1a 2 vtx1c - C OX187:H28 vtx2d 3 vtx2g ST-200 C O rough:- vtx2a vtx2a ST-678 C Re-typed to lack vtx2 at SSI 2 Re-typed to vtx1c at SSI 3 Re-typed to vtx2g at SSI

17 Phylogeny -SNPtree Epidemiologically related isolates are the same color

18 Phylogeny -NDtree

19 VTEC Outbreak Denmark faced an outbreak of verocytotoxin-producing E. coli (VTEC) O157:H7 infections in autumn Thirteen cases were diagnosed of which eight had haemolytic uraemic syndrome (HUS). Epidemiological investigations suggested ground beef as the vehicle of the outbreak. The outbreak strain had a rare toxin gene subtype profile: eae, vtx1a and vtx2a, and a high proportion of HUS (62%) among cases, a finding previously linked with the outbreak subtype profile. Toxin subtyping can be useful to identify high risk VTEC strains

20 VTEC Outbreak Serotype Routine Typing VirulenceFinder MLST Isolate O5:H- vtx1c vtx1c ST-447 C O26:H11 eae, vtx1a eae, vtx1a ST-21 C O27:H30 vtx2b vtx2b ST-753 C (replicate) O36:H C O55:H12 vtx1a vtx1a ST-101 C O76:H- vtx1c vtx1c ST-675 C904-12A O103:H2 eae, vtx1a eae, vtx1a ST-17 C O103:H- ST-1967 C O rough:h2 ST-17 C O115:H- eae, vtx2a eae, vtx2a ST-333 C885-12B C896-12A O117:K1:H7 vtx1a vtx1a ST-504 C C C O121:H19 eae, vtx2a eae, vtx2a ST-655 C O128ab:H2 vtx2b vtx2b ST-25 C vtx1c, vtx2b vtx1c, vtx2b ST-811 C O128abc:Heae, vtx2f eae, vtx2f ST-20 C C O145:H- eae, vtx2a eae, vtx2a ST-32 C C C C O146:H21 vtx1c, vtx2b vtx1c, vtx2b ST-442 C O157:H7 (O157:H-) eae eae C896-12B C885-12A eae, vtx1a, vtx2c eae, vtx1a, vtx2c ST-11 C C697-12A (replicate) C697-12B eae, vtx1a C eae, vtx1a, vtx2a eae, vtx1a, vtx2a C C C C C C eae, vtx2a eae, vtx2a C eae, vtx2c eae, vtx2c ST-2966 C O165:H- eae, vtx1a, vtx2a eae, vtx1a, vtx2a ST-119 C O180:H- eae eae C641-12A ST-301 eae, vtx2a a eae C641-12B O181:H16 vtx1a b vtx1c - C OX187:H28 vtx2d c vtx2g ST-200 C O rough:- vtx2a vtx2a ST-678 C a Re-typed to lack vtx2 at SSI b Re-typed to vtx1c at SSI c Re-typed to vtx2g at SSI

21 Comparing Time WGS-typing was faster Same Isolate Price: ~430

22 Conclusion WGS faster than Routine WGS gives more information e.g.: more virulence genes, resistance genes, MLST, phylogeny etc. Same price Will work for other pathogens as well Easy-to-use bioinformatic tools are necessary Epidemiology is always necessary

23 Acknowledgements Eva Møller Nielsen and Flemming Scheutz Department of Microbiology and Infection Control, SSI Frank Møller Aarestrup, Henrik Hasman, Ole Lund and Rolf Sommer Kaas

24 Real-Time Surveillance of VTEC using WGS Reviewer comment: It appears that VTEC serotype was determined solely by conventional agglutination methods. Could the investigators add "molecular serotyping" to the WGS output by using the flagellar and O-antigen associated genes?

25 Construction of the SerotypeFinder For user-friendly (O:H) serotype determination from WGS data CGE tools ( Flemming Scheutz Head of WHO Collaborating Centre for Reference and Research on Escherichia and Klebsiella Dep. of Microbiology & Infection Control, SSI Anna Maria Malberg Tetzschner Master student DTU/SSI

26 In Silico H-typing H-antigen 53 known H-types (H1-H56) flic (flagellin) flka, flna, flma, flla

27 In Silico O-typing 187 known E. coli O-antigens (O1-O187) wzx and wzy (O-antigen flippase and polymerase) wzm and wzt (ABC transporter)

28 SerotypeFinder construction Collection of genes with serotype information from NCBI O-antigen cluster sequences from Dr. Atsushi Iguchi Few E. coli reference isolates sequenced at SSI

29 H Database flic genes All 53 H-types represented

30 O Database wzx wzy

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32 Output SerotypeFinder

33 Validation of the SerotypeFinder Validation on more than 500 genomes: 249 PulseNet STEC genome reference library (PRJNA218110) 131 genome sequences from a previous study on comparative genome analysis of E. coli 44 E. coli genome assemblies from our own Real-Time typing and surveillance of VTEC 109 E. coli reference strains (Illumina 2x100bp) obtained from CDC (will be deposited in PRJNA186441) >85 E. coli sequences from SSI strain collection

34 Validation of the SerotypeFinder Number of genomes for validation with detected genes with consistent WGS -and conventional results O-typing a (~95%) 542 b (~99%) H-typing (100%) 483 c (~98,5%) a) In 59 genomes, genes were either found by reference mapping, or only one gene was used for prediction. b) 12 predictions were ambiguous between the two O-processing genes: O118/O151(7), O164/O124, O134/O46, O90/O127, O162/O101, O153/O178. c) CDC (3): H24-H49:transcript error, H18-H19 : non-motile, H28-H25: transcript error Pending: SSI (2): H51-H19, H17-H16 Other (2): H8-H45: difficult to type, H4-H17 flic same

35 Validation of the SerotypeFinder Number of validations covering O-groups and H-types O-groups H-types 1 2 O4, O5, O18, O21, O24, O28ac, O29, O35,O39, O42, O44, O48, O49, O54, O58, O60, O70, O76, O80, O83, O87, O89, O101, O105, O107, O109, O125ac, O130, O131, O132, O133, O134, O135, O138, O139, O143, O147, O149, O150, O151, O153, O155, O156, O158, O159, O160, O164, O167, O168, O172, O173, O175, O177, O181, O183, O185, O187 O1, O17, O20, O25, O27, O32, O40, O46, O51, O78, O79, O81, O88, O98, O114, O123, O126, O142, O161, O165, O166, O169, O171, O177, O180, O184, 3 O9, O16, O36*, O75, O99, O112*, O113, O115, O127,O148 H3, H5, H31, H46, H51, H54 H14, H17, H49 H12, H15, H20, H26, H27, H32,H36, H37, H38, H41, H44, H45, H48, H52, H53 4 O2, O3, O11, O69, O104, O174 H24, H29, H35, H39, H42, H47, H55 5 O6, O15, O91, O117, O119, O146 H1, H9, H23, H40, H43, H56 6 O7, O8, O86, O118 H18, H H28, H34 8 O45 10 O103(17), O55(22), O128 * (16),O145(20), O121(30), O26(42), O111(48), O157(122) H33(9), H10(10), H16(10), H25(10), H21(13), H4(15), H8(14), H6(17), H2(34), H19(37), H11(45), H7(127)

36 VTEC O-groups in Danmark ( ) 36

37 Conclusion When the SerotypeFinder is ready, SSI will start performing WGS ROUTINE surveillance of VTEC

38 Acknowledgements Flemming Scheutz Head of WHO Collaborating Centre for Reference and Research on Escherichia and Klebsiella Dep. of Microbiology & Infection Control, SSI Atsushi Iguchi Department of Animal and Grassland Sciences, Japan Rebecca L. Lindsey Centers for Disease Control and Prevention, Atlanta, Georgia, USA Anna Maria Malberg Tetzschner Master student DTU/SSI Center for Genomic Epidemiology (CGE)

39 Questions?