Table_5_Phylogenetic Analysis and Genome-Wide Association Study Applied to an Italian Listeria monocytogenes Outbreak.XLSX

From May 2015 to March 2016, a severe outbreak due to Listeria monocytogenes ST7 strain occurred in Central Italy and caused 24 confirmed clinical cases. The epidemic strain was deeply investigated using whole-genome sequencing (WGS) analysis. In the interested area, the foodborne outbreak investigation identified a meat food-producing plant contaminated by the outbreak strain, carried by pork-ready-to-eat products. In the same region, in March 2018, the epidemic strain reemerged causing one listeriosis case in a 10-month-old child. The aim of this study was to investigate the phylogeny of the epidemic and reemergent strains over time and to compare them with a closer ST7 clone, detected during the outbreak and with different pulsed-field gel electrophoresis (PFGE) profiles, in order to identify genomic features linked to the persistence and the reemergence of the outbreak. An approach combining phylogenetic analysis and genome-wide association study (GWAS) revealed that the epidemic and reemergent clones were genetically closer to the ST7 clone with different PFGE profiles and strictly associated with the pork production chain. The repeated detection of both clones was probably correlated with (i) the presence of truly persistent clones and the repeated introduction of new ones and (ii) the contribution of prophage genes in promoting the persistence of the epidemic clones. Despite that no significant genomic differences were detected between the outbreak and the reemergent strain, the two related clones detected during the outbreak can be differentiated by transcriptional factor and phage genes associated with the phage LP-114.

2015年5月至2016年3月，意大利中部暴发了由单核细胞增生李斯特菌ST7菌株（Listeria monocytogenes ST7）引发的严重疫情，累计确诊24例临床病例。研究人员通过全基因组测序（Whole-Genome Sequencing，WGS）技术对此次流行菌株开展了深度分析。在该疫情波及区域内，食源性疫情调查发现一家肉类生产加工厂被此次暴发菌株污染，该菌株定植于即食猪肉制品中。2018年3月，同一区域再次检出该流行菌株，导致一名10月龄幼儿罹患李斯特菌病。本研究旨在探究此次暴发及复现菌株的系统发育随时间的演化特征，并将其与疫情期间检出的、脉冲场凝胶电泳（Pulsed-Field Gel Electrophoresis，PFGE）图谱存在差异的亲缘ST7克隆株进行比对，以明确与该疫情持续存在及复现相关的基因组特征。本研究结合系统发育分析与全基因组关联研究（Genome-Wide Association Study，GWAS）开展分析，结果显示：此次暴发及复现的克隆株与PFGE图谱存在差异的ST7克隆株亲缘关系更近，且与猪肉生产链紧密相关。两次检出的克隆株的持续存在可能与两方面因素相关：（i）存在真正的持久性克隆株以及新克隆株的反复引入；（ii）前噬菌体基因在促进流行克隆株持续存在过程中发挥作用。尽管未检测到此次暴发菌株与复现菌株之间存在显著基因组差异，但疫情期间检出的两株相关克隆株可通过与LP-114噬菌体相关的转录因子及噬菌体基因进行区分。