Whole-genome sequencing of bacterial pathogens is used by public health agencies to link cases of food poisoning caused by the same source of contamination. The vast majority of these appear to be sporadic cases associated with small contamination episodes and do not trigger investigations. A “contamination episode” refers to one or more contamination events from a single source over a period of time. We examine clusters of sequenced clinical isolates of Salmonella , Escherichia coli , Campylobacter , and Listeria that differ by only a small number of mutations (SNPs) to identify features of the underlying contamination episodes. These analyses provide additional evidence that the youngest age groups have greater susceptibility to infection by Salmonella , E. coli , and Campylobacter than older age groups. This age bias is weaker for the common Salmonella serovar Enteritidis than Salmonella in general. A large fraction of the contamination episodes causing sickness appear to have a long duration. For example, 50% of the Salmonella cases are in clusters that persist for almost 3 y. For all four pathogen species, the majority of the cases were part of genetic clusters with illnesses in multiple states and likely to be caused by contaminated commercially distributed foods. Salmonella infections in infants under 3 mo are predominantly acquired from the same contaminated food, pet food, or environmental sources as older individuals, rather than infant formula contaminated during production.

中文翻译：

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食源性疾病的基因组观点


公共卫生机构使用细菌病原体的全基因组测序来关联由同一污染源引起的食物中毒病例。其中绝大多数似乎是与小规模污染事件相关的零星病例，不会引发调查。“污染事件”是指在一段时间内来自单一来源的一个或多个污染事件。我们检查了沙门氏菌、大肠杆菌、弯曲杆菌和李斯特菌的测序临床分离株簇，这些分离株仅与少量突变 （SNP） 不同，以确定潜在污染事件的特征。这些分析提供了额外的证据，表明最年轻的年龄组比年龄较大的年龄组更容易感染沙门氏菌、大肠杆菌和弯曲杆菌。普通沙门氏菌血清型 Enteritidis 的这种年龄偏倚比一般沙门氏菌弱。导致疾病的污染事件的大部分似乎持续时间很长。例如，50% 的沙门氏菌病例呈集群，持续近 3 年。对于所有四种病原体物种，大多数病例是在多个州患病的遗传集群的一部分，可能是由受污染的商业分销食品引起的。3 个月以下婴儿的沙门氏菌感染主要来自与老年人相同的受污染食品、宠物食品或环境来源，而不是生产过程中受污染的婴儿配方奶粉。