Abstract
BackgroundSalmonella 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.MethodsWe 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.ResultsThe 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.ConclusionsWGS 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12866-016-0831-3) contains supplementary material, which is available to authorized users.
Highlights
IntroductionSubtyping of Salmonella Typhimurium (STM) remains critical to outbreak investigation, yet current techniques (e.g. multilocus variable number tandem repeat analysis, multi-locus variable number tandem repeat analysis (MLVA)) may provide insufficient discrimination
Salmonella Typhimurium (STM) is an important cause of foodborne outbreaks worldwide
Two case isolates from Outbreak A and two from Outbreak M were excluded from the analysis due to the poor quality of sequences
Summary
Subtyping of STM remains critical to outbreak investigation, yet current techniques (e.g. multilocus variable number tandem repeat analysis, MLVA) may provide insufficient discrimination. Salmonella gastroenteritis is responsible for considerable disease burden in both developed and developing countries, with an estimated 93.8 million cases and 155,000 deaths each year [1]. The majority of these cases are foodborne [1,2,3], transmission may occur directly from infected persons [4]. In New South Wales (NSW), Australia, where STM accounts for around half of all culture-confirmed cases of salmonellosis [7], multi-locus variable number tandem repeat analysis (MLVA) has been used since 2006 to prospectively subtype STM and identify potential clusters. Common or endemic MLVA types may cause multiple outbreaks along with sporadic cases and a few selected MLVA types may represent a large portion of isolates observed in a geographical location [9]
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