title: Whole genome sequencing of Salmonella Typhimurium illuminates distinct outbreaks caused by an endemic multi-locus variable number tandem repeat analysis type in Australia, 2014.
abstract: Salmonella Typhimurium (STM) is an important cause of foodborne outbreaks worldwide. Subtyping of STM remains critical to outbreak investigation, yet current techniques (e.g. multilocus variable number tandem repeat analysis, MLVA) may provide insufficient discrimination. Whole genome sequencing (WGS) offers potentially greater discriminatory power to support infectious disease surveillance.
  
  
  
  We performed WGS on 62 STM isolates of a single, endemic MLVA type associated with two epidemiologically independent, food-borne outbreaks along with sporadic cases in New South Wales, Australia, during 2014. Genomes of case and environmental isolates were sequenced using HiSeq (Illumina) and the genetic distance between them was assessed by single nucleotide polymorphism (SNP) analysis. SNP analysis was compared to the epidemiological context.
  
  
  
  The WGS analysis supported epidemiological evidence and genomes of within-outbreak isolates were nearly identical. Sporadic cases differed from outbreak cases by a small number of SNPs, although their close relationship to outbreak cases may represent an unidentified common food source that may warrant further public health follow up. Previously unrecognised mini-clusters were detected.
  
  
  
  WGS of STM can discriminate foodborne community outbreaks within a single endemic MLVA clone. Our findings support the translation of WGS into public health laboratory surveillance of salmonellosis.
authors.affiliation: Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Sydney, NSW, Australia. Anastasia.Phillips@health.nsw.gov.au.
authors.forename: Anastasia
authors.initials: A
authors.lastname: Phillips
authors.affiliation: Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Sydney, NSW, Australia.|Marie Bashir Institute for Emerging Infectious Diseases and Biosecurity and Sydney Medical School, The University of Sydney, Sydney, NSW, Australia.
authors.forename: Cristina
authors.initials: C
authors.lastname: Sotomayor
authors.affiliation: Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Sydney, NSW, Australia.|Marie Bashir Institute for Emerging Infectious Diseases and Biosecurity and Sydney Medical School, The University of Sydney, Sydney, NSW, Australia.|NSW Enteric Reference Laboratory, Centre for Infectious Diseases and Microbiology Laboratory Services, Pathology West, Sydney, NSW, Australia.
authors.forename: Qinning
authors.initials: Q
authors.lastname: Wang
authors.affiliation: Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Sydney, NSW, Australia.|Marie Bashir Institute for Emerging Infectious Diseases and Biosecurity and Sydney Medical School, The University of Sydney, Sydney, NSW, Australia.
authors.forename: Nadine
authors.initials: N
authors.lastname: Holmes
authors.affiliation: OzFood Net, Communicable Disease Branch, Health Protection, NSW Ministry of Health, Sydney, NSW, Australia.
authors.forename: Catriona
authors.initials: C
authors.lastname: Furlong
authors.affiliation: OzFood Net, Communicable Disease Branch, Health Protection, NSW Ministry of Health, Sydney, NSW, Australia.
authors.forename: Kate
authors.initials: K
authors.lastname: Ward
authors.affiliation: NSW Enteric Reference Laboratory, Centre for Infectious Diseases and Microbiology Laboratory Services, Pathology West, Sydney, NSW, Australia.
authors.forename: Peter
authors.initials: P
authors.lastname: Howard
authors.affiliation: School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.
authors.forename: Sophie
authors.initials: S
authors.lastname: Octavia
authors.affiliation: School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.
authors.forename: Ruiting
authors.initials: R
authors.lastname: Lan
authors.affiliation: Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Sydney, NSW, Australia.|Marie Bashir Institute for Emerging Infectious Diseases and Biosecurity and Sydney Medical School, The University of Sydney, Sydney, NSW, Australia.|NSW Enteric Reference Laboratory, Centre for Infectious Diseases and Microbiology Laboratory Services, Pathology West, Sydney, NSW, Australia.
authors.forename: Vitali
authors.initials: V
authors.lastname: Sintchenko
mesh_terms: D001483:Base Sequence; D016000:Cluster Analysis; D004269:DNA, Bacterial / Q000032:analysis / Q000235:genetics; D004196:Disease Outbreaks; D019353:Endemic Diseases; D004783:Environmental Microbiology; D005517:Foodborne Diseases / Q000453:epidemiology / Q000382:microbiology; D016680:Genome, Bacterial / Q000235:genetics*; D006801:Humans; D018598:Minisatellite Repeats / Q000235:genetics*; D017720:Molecular Epidemiology; D058889:Molecular Typing / Q000379:methods; D009517:New South Wales / Q000453:epidemiology; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D011634:Public Health; D012478:Salmonella Food Poisoning / Q000453:epidemiology; D012480:Salmonella Infections / Q000453:epidemiology*; D012486:Salmonella typhimurium / Q000235:genetics* / Q000302:isolation & purification / Q000472:pathogenicity*; D017422:Sequence Analysis, DNA
chemical_list: D004269:DNA, Bacterial
keywords: Foodborne outbreaks; Molecular epidemiology; Public health surveillance; Salmonella Typhimurium; Whole genome sequencing