Whole genome sequencing of Salmonella Typhimurium illuminates distinct outbreaks caused by an endemic multi-locus variable number tandem repeat analysis type in Australia, 2014

BMC Microbiology

Research Article

Anastasia Phillips¹  Nadine Holmes²  Cristina Sotomayor²  Vitali Sintchenko³  Qinning Wang³  Peter Howard⁴  Kate Ward⁵  Catriona Furlong⁵  Sophie Octavia⁶  Ruiting Lan⁶ 

[1] Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Sydney, NSW, Australia;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;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;NSW Enteric Reference Laboratory, Centre for Infectious Diseases and Microbiology Laboratory Services, Pathology West, Sydney, NSW, Australia;OzFood Net, Communicable Disease Branch, Health Protection, NSW Ministry of Health, Sydney, NSW, Australia;School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia;

关键词: Salmonella;    Molecular epidemiology;    Foodborne outbreaks;    Whole genome sequencing;    Public health surveillance;   

DOI  :  10.1186/s12866-016-0831-3

 received in 2016-01-23, accepted in 2016-09-06,  发布年份 2016

来源: Springer

【 摘 要 】

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.

【 授权许可】

CC BY   
© The Author(s). 2016