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2014年，鼠伤寒沙门氏菌全基因组测序揭示了澳大利亚一起由地方流行的多位点可变数目串联重复序列分析型菌株引发的不同疫情。

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

作者信息

Phillips Anastasia, Sotomayor Cristina, Wang Qinning, Holmes Nadine, Furlong Catriona, Ward Kate, Howard Peter, Octavia Sophie, Lan Ruiting, Sintchenko Vitali

机构信息

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.

出版信息

BMC Microbiol. 2016 Sep 15;16:211. doi: 10.1186/s12866-016-0831-3.

DOI:10.1186/s12866-016-0831-3
PMID:27629541
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC5024487/
Abstract

BACKGROUND

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.

METHODS

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.

RESULTS

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.

CONCLUSIONS

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.

摘要

背景

鼠伤寒沙门氏菌（STM）是全球食源性疾病暴发的重要病因。STM的亚型分型对于暴发调查仍然至关重要，但目前的技术（如多位点可变数目串联重复序列分析，MLVA）可能提供的鉴别力不足。全基因组测序（WGS）为支持传染病监测提供了更大的鉴别力。

方法

我们对62株属于单一地方性MLVA型的STM分离株进行了WGS分析，这些分离株与2014年澳大利亚新南威尔士州两起流行病学上独立的食源性暴发以及散发病例相关。使用HiSeq（Illumina）对病例和环境分离株的基因组进行测序，并通过单核苷酸多态性（SNP）分析评估它们之间的遗传距离。将SNP分析结果与流行病学背景进行比较。

结果

WGS分析支持了流行病学证据，暴发内分离株的基因组几乎相同。散发病例与暴发病例存在少量SNP差异，尽管它们与暴发病例的密切关系可能代表了一个未确定的共同食物来源，可能需要进一步的公共卫生跟进。检测到了先前未识别的小聚类。

结论

STM的WGS可以区分单一地方性MLVA克隆内的食源性社区暴发。我们的研究结果支持将WGS应用于沙门氏菌病的公共卫生实验室监测。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e2c6/5024487/7e4fa6f88269/12866_2016_831_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e2c6/5024487/2ae05a57b2cf/12866_2016_831_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e2c6/5024487/9c8a0d3a0138/12866_2016_831_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e2c6/5024487/7e4fa6f88269/12866_2016_831_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e2c6/5024487/2ae05a57b2cf/12866_2016_831_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e2c6/5024487/9c8a0d3a0138/12866_2016_831_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e2c6/5024487/7e4fa6f88269/12866_2016_831_Fig3_HTML.jpg

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