PDF(Pubmed)
Abstract：
Recently emerged S. Infantis strains carrying resistance to several commonly used antimicrobials have been reported from different parts of the globe, causing human cases of salmonellosis and with occurrence reported predominantly in broiler chickens. Here, we performed phylogenetic and genetic clustering analyses to describe the population structure of 417 S. Infantis originating from multiple European countries and the Americas collected between 1985 and 2019. Of these, 171 were collected from 56 distinct premises located in England and Wales (E/W) between 2009 and 2019, including isolates linked to incursions of multidrug-resistant (MDR) strains from Europe associated with imported poultry meat. The analysis facilitated the comparison of isolates from different E/W sources with isolates originating from other countries. There was a high degree of congruency between the outputs of different types of population structure analyses revealing that the E/W and central European (Germany, Hungary, and Poland) isolates formed several disparate groups, which were distinct from the cluster relating to the United States (USA) and Ecuador/Peru, but that isolates from Brazil were closely related to the E/W and the central European isolates. Nearly half of the analysed strains/genomes (194/417) harboured the IncFIB(pN55391) replicon typical of the \"parasitic\" pESI-like megaplasmid found in diverse strains of S. Infantis. The isolates that contained the IncFIB(pN55391) replicon clustered together, despite originating from different parts of the globe. This outcome was corroborated by the time-measured phylogeny, which indicated that the initial acquisition of IncFIB(pN55391) likely occurred in Europe in the late 1980s, with a single introduction of IncFIB(pN55391)-carrying S. Infantis to the Americas several years later. Most of the antimicrobial resistance (AMR) genes were identified in isolates that harboured one or more different plasmids, but based on the short-read assemblies, only a minority of the resistance genes found in these isolates were identified as being associated with the detected plasmids, whereas the hybrid assemblies comprising the short and long reads demonstrated that the majority of the identified AMR genes were associated with IncFIB(pN55391) and other detected plasmid replicon types. This finding underlies the importance of applying appropriate methodologies to investigate associations of AMR genes with bacterial plasmids.
摘要：
最近出现的S.Infantis菌株对几种常用的抗菌药物具有耐药性，引起人类沙门氏菌病的病例，据报道主要发生在肉鸡中。这里,我们进行了系统发育和遗传聚类分析,以描述1985年至2019年收集的来自多个欧洲国家和美洲的417例婴儿的种群结构.其中,在2009年至2019年之间，从英格兰和威尔士（E/W）的56个不同场所收集了171个，其中包括与来自欧洲的多药耐药（MDR）菌株入侵有关的分离株与进口禽肉有关。该分析促进了来自不同E/W来源的分离株与来自其他国家的分离株的比较。不同类型的人口结构分析的输出之间存在高度的一致性，这表明E/W和中欧（德国，匈牙利,和波兰)分离形成了几个不同的群体，与美国(美国)和厄瓜多尔/秘鲁相关的集群不同，但是来自巴西的分离株与E/W和中欧分离株密切相关。近一半的分析菌株/基因组（194/417）含有IncFIB（pN55391）复制子，该复制子是在不同的S.Infantis菌株中发现的典型的“寄生”pESI样巨型质粒。含有IncFIB（pN55391）复制子的分离株聚集在一起，尽管来自全球不同地区。时间测量的系统发育证实了这一结果，这表明对IncFIB（pN55391）的最初收购可能发生在1980年代后期的欧洲，几年后，将IncFIB（pN55391）携带的婴儿链球菌引入美洲。大多数抗菌素耐药性（AMR）基因是在含有一种或多种不同质粒的分离株中鉴定的，但是基于短读程序集，在这些分离株中发现的抗性基因中只有少数被鉴定为与检测到的质粒相关，而包含短读段和长读段的杂合装配体表明，大多数鉴定的AMR基因与IncFIB（pN55391）和其他检测到的质粒复制子类型相关。这一发现是应用适当方法研究AMR基因与细菌质粒关联的重要性的基础。
