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首页> 外文期刊>Journal of Clinical Microbiology >Delineating Community Outbreaks of Salmonella enterica Serovar Typhimurium by Use of Whole-Genome Sequencing: Insights into Genomic Variability within an Outbreak
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Delineating Community Outbreaks of Salmonella enterica Serovar Typhimurium by Use of Whole-Genome Sequencing: Insights into Genomic Variability within an Outbreak

机译：通过使用全基因组测序来描述小肠沙门氏菌鼠伤寒沙门氏菌的社区暴发：对暴发中基因组变异的见解

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Whole-genome next-generation sequencing (NGS) was used to retrospectively examine 57 isolates from five epidemiologically confirmed community outbreaks (numbered 1 to 5) caused by Salmonella enterica serovar Typhimurium phage type DT170. Most of the human and environmental isolates confirmed epidemiologically to be involved in the outbreaks were either genomically identical or differed by one or two single nucleotide polymorphisms (SNPs), with the exception of those in outbreak 1. The isolates from outbreak 1 differed by up to 12 SNPs, which suggests that the food source of the outbreak was contaminated with more than one strain while each of the other four outbreaks was caused by a single strain. In addition, NGS analysis ruled in isolates that were initially not considered to be linked with the outbreak, which increased the total outbreak size by 107%. The mutation process was modeled by using known mutation rates to derive a cutoff value for the number of SNP difference to determine whether or not a case was part of an outbreak. For an outbreak with less than 1 month of ex vivo/in vivo evolution time, the maximum number of SNP differences between isolates is two or four using the lowest or highest mutation rate, respectively. NGS of S. Typhimurium significantly increases the resolution of investigations of community outbreaks. It can also inform a more targeted public health response by providing important supplementary evidence that cases of disease are or are not associated with food-borne outbreaks of S. Typhimurium.
机译：使用全基因组下一代测序（NGS）回顾性检查了5种由流行病学确认的由沙门氏菌肠型血清鼠伤寒噬菌体DT170引起的社区暴发（第1至5次）的57个分离株。在流行病学上确认与暴发有关的大多数人类和环境分离株，在基因组学上是相同的，或具有一个或两个单核苷酸多态性（SNP），但在暴发1中则不同。 12个SNP，这表明暴发的食物来源受到一种以上菌株的污染，而其他四次暴发中的每一种都是由一种菌株引起的。此外，NGS分析排除了最初不被认为与爆发有关的分离株，这使总爆发规模增加了107％。通过使用已知的突变率对突变过程进行建模，以得出SNP差异数的临界值，以确定病例是否属于暴发。对于少于1个月的体外 / 体内进化时间的暴发，使用最低或最高突变率，分离株之间的SNP差异最大为2或4个， 分别。 S 的NGS。鼠伤寒显着提高了社区暴发调查的分辨率。通过提供重要的补充证据，即疾病病例与食源性 S 暴发有关，它也可以为更具针对性的公共卫生应对提供信息。鼠伤寒

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