Inns T, Ashton P M, Herrera-Leon S, Lighthill J, Foulkes S, Jombart T, Rehman Y, Fox A, Dallman T, DE Pinna E, Browning L, Coia J E, Edeghere O, Vivancos R
Field Epidemiology Services, Public Health England, UK.
University of Liverpool, UK.
Epidemiol Infect. 2017 Jan;145(2):289-298. doi: 10.1017/S0950268816001941. Epub 2016 Oct 26.
Since April 2015, whole genome sequencing (WGS) has been the routine test for Salmonella identification, surveillance and outbreak investigation at the national reference laboratory in England and Wales. In May 2015, an outbreak of Salmonella Enteritidis cases was detected using WGS data and investigated. UK cases were interviewed to obtain a food history and links between suppliers were mapped to produce a food chain network for chicken eggs. The association between the food chain network and the phylogeny was explored using a network comparison approach. Food and environmental samples were taken from premises linked to cases and tested for Salmonella. Within the outbreak single nucleotide polymorphism defined cluster, 136 cases were identified in the UK and 18 in Spain. One isolate from a food containing chicken eggs was within the outbreak cluster. There was a significant association between the chicken egg food chain of UK cases and phylogeny of outbreak isolates. This is the first published Salmonella outbreak to be prospectively detected using WGS. This outbreak in the UK was linked with contemporaneous cases in Spain by WGS. We conclude that UK and Spanish cases were exposed to a common source of Salmonella-contaminated chicken eggs.
自2015年4月以来，全基因组测序（WGS）一直是英格兰和威尔士国家参考实验室用于沙门氏菌鉴定、监测和疫情调查的常规检测方法。2015年5月，利用WGS数据检测到一起肠炎沙门氏菌病例的疫情并展开调查。对英国的病例进行了访谈以获取饮食史，并绘制了供应商之间的联系，从而构建了一个鸡蛋的食物链网络。使用网络比较方法探讨了食物链网络与系统发育之间的关联。从与病例相关的场所采集了食品和环境样本，并检测其中是否含有沙门氏菌。在此次疫情单核苷酸多态性定义的聚类中，在英国确认了136例病例，在西班牙确认了18例。从一份含有鸡蛋的食品中分离出的一株菌株属于此次疫情聚类。英国病例的鸡蛋食物链与疫情分离株的系统发育之间存在显著关联。这是首次发表的使用WGS前瞻性检测到的沙门氏菌疫情。英国的此次疫情通过WGS与西班牙同期的病例相关联。我们得出结论，英国和西班牙的病例接触到了受沙门氏菌污染的鸡蛋这一共同来源。
