BSFM

K. Dierick

K. Marchal

N. Roosens

S. Bertrand

S. De Keersmaecker

S. Denayer

V. Wuyts

W. Mattheus

English

S.C.J. De Keersmaecker

Sciensano Publications Repository

User-friendly WGS analysis of Salmonella Enteritidis PT4 outbreaks

Wuyts, Véronique

Denayer, Sarah

Roosens, Nancy HC

Mattheus, Wesley

Bertrand, Sophie

Marchal, Kathleen

Dierick, Katelijne

De Keersmaecker, Sigrid CJ

Ghent University Academic Bibliography

WIV-ISP | Rue Juliette Wytsmanstraat 14 | 1050 Brussels | BelgiumT +32 2 642 53 60 | F +32 2 642 52 92 | e-mail: veronique.wuyts@wiv-isp.be | website: www.wiv-isp.beUser-friendly WGS analysis ofSalmonella Enteritidis PT4 outbreaksVéronique Wuyts1,2,3, Sarah Denayer4, Nancy H.C. Roosens3, Wesley Mattheus5,Sophie Bertrand5, Kathleen Marchal2,6, Katelijne Dierick4 and Sigrid C.J. De Keersmaecker31Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium, 2Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; 3Platform Biotechnology and Molecular Biology, Scientific Institute of Public Health (WIV-ISP), Brussels, Belgium; 4National Reference Laboratory of Foodborne Outbreaks (NRL-FBO), Scientific Institute of Public Health (WIV-ISP), Brussels, Belgium; 5National Reference Centre for Salmonella and Shigella (NRCSS), Scientific Institute of PublicHealth (WIV-ISP), Brussels, Belgium; 6Department of Information Technology, Ghent University, IMinds, Ghent, Belgium OUTBREAK FLANDERSMICROBIOLOGICAL INVESTIGATIONOUTBREAK WALLONIAWHOLE GENOME SEQUENCING DATA ANALYSISSocial event: food supplied by catering service → ± 220 guestsDisease onset: April 23rd 2014Outbreak: 45 cases with 5 hospitalised personsSocial event: bbq meal prepared by volunteers → ± 300 guestsDisease onset: May 1st 2014Outbreak: ± 40 cases with some people hospitalisedStandard questionnaire for epidemiological information + food samples NRL-FBOIsolates of human cases NRCSSOutbreak Isolate Origin Phage type MLVA Antimicrobial resistanceFlanders S14FP01640 Chocolate mousse a PT4 3-10-5-4-1 ColistinFlanders S14FP01642 Chocolate mousse a PT4 3-10-5-4-1 ColistinFlanders S14BD01605 Human PT4 3-10-5-4-1 ColistinFlanders S14BD01672 Human PT4a 3-10-5-4-1 Colistin - ampicillinWallonia S14FP01877 Raw egg b PT4 3-10-5-4-1 ColistinWallonia S14BD01753 Human PT4 3-10-5-4-1 ColistinAll outbreak isolates: serotyped as Salmonella enterica subsp. enterica serovar Enteritidisa Prepared with non-commercial eggs from privately kept laying hensb Non-commercial egg from privately kept laying hens, which were used to prepare tiramisuWGS:Illumina HiSeq 2000100 bp paired-end readsRawFASTQ readsCLC Genomics Workbench:1) quality trim2) de novo assembly3) read mapping on S. EnteritidisP125109 chromosome + de novoassembly of unmapped readsCenter for Genomic Epidemiology:CSI Phylogeny5Center for Genomic Epidemiology:MLST1 + ResFinder2 + PlasmidFinder3Contigs: chromosome + plasmidsContigs: plasmids BRIG4Outbreak Isolate MLST ResFinder PlasmidFinderFlanders S14FP01640 ST-11 - pSLA5Flanders S14FP01642 ST-11 - pSLA5Flanders S14BD01605 ST-11 - pSLA5Flanders S14BD01672 ST-11 blaTEM-1B pSLA5 – pSD107Wallonia S14FP01877 ST-11 - pSLA5Wallonia S14BD01753 ST-11 - pSLA5BRIG: pSD107 – S14BD01672CONCLUSIONSREFERENCESCSI PhylogenyThis work was published as: Wuyts et al. Whole genome sequence analysis of Salmonella Enteritidis PT4 outbreaks from a National Reference Laboratory’s viewpoint.PLOS Currents Outbreaks, 11 September 2015WGS: confirmation of link between food and human isolates= initial epidemiological and microbiological investigationSNP analysis: discrimination between both outbreaks> initial epidemiological and microbiological investigationExploration of plasmids: fine-tuning of SNP analysis results Added value of WGS for outbreak investigationWGS is feasible for an average NRL or NRCif user-friendly tools are availableNeed for database on circulating strainsto estimate background variability1Larsen MV et al. (2012) J Clin Microbiol 50(4):1355-1361; 2Zankari E et al. (2012) J Antimicrob Chemother 67(11):2640-2644; 3Carattoli A et al. (2014)Antimicrob Agents Chemother 58(7):3895-3903; 4Alikhan N-F et al. (2011) BMC Genomics 12:402; 5Kaas RS et al. (2014) PLoS ONE 9(8):e104984.blaTEMSame sourceor different sourcesfor the 2 outbreaks?AIM OF THE STUDYAdded value of whole genome sequencing (WGS) for outbreak investigation?WGS data analysis feasible for average NRL or NRC?

User‐friendly WGS analysis of Salmonella Enteritidis PT4 outbreaks

https://biblio.ugent.be/publication/7068007/file/7068022

User‐friendly WGS analysis of Salmonella Enteritidis PT4 outbreaks

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