Characterisation of the phylogenetic relationship of Salmonella enterica subsp. enterica (Subspecies I) Serotype 4,[5],12:i:-

Microevolution associated with emergence and expansion of new epidemic clones of bacterial pathogens holds the key to epidemiologic success. To determine microevolution associated with monophasic Salmonella Typhimurium during an epidemic, we performed comparative whole-genome sequencing and phylogenomic analysis of isolates from the United Kingdom and Italy during 2005-2012. These isolates formed a single clade distinct from recent monophasic epidemic clones previously described from North America and Spain. The UK monophasic epidemic clones showed a novel genomic island encoding resistance to heavy metals and a composite transposon encoding antimicrobial drug resistance genes not present in other Salmonella Typhimurium isolates, which may have contributed to epidemiologic success. A remarkable amount of genotypic variation accumulated during clonal expansion that occurred during the epidemic, including multiple independent acquisitions of a novel prophage carrying the sopE gene and multiple deletion events affecting the phase II flagellin locus. This high level of microevolution may affect antigenicity, pathogenicity, and transmission. http://www.sanger.ac.uk/resources/downloads/bacteria/salmonella.html

与细菌病原体新型流行克隆株的出现及扩增相关的微进化，是其获得流行病学成功的核心基础。为解析本次流行期间单相鼠伤寒沙门菌（monophasic Salmonella Typhimurium）的微进化特征，本研究对2005至2012年间采自英国与意大利的分离株开展了全基因组比较测序（comparative whole-genome sequencing）与系统基因组学分析（phylogenomic analysis）。该批分离株构成一个独立进化枝，与此前北美及西班牙报道的近期单相流行克隆株存在显著分化。英国单相流行克隆株携带一种新型基因组岛（genomic island），可介导重金属抗性；同时携带一种复合转座子（composite transposon），其编码的抗菌药物耐药基因（antimicrobial drug resistance genes）未在其他鼠伤寒沙门菌分离株中检出，这可能是该克隆株获得流行病学优势的重要促成因素。在本次流行期间的克隆扩增过程中，积累了大量基因型变异，包括携带sopE基因的新型原噬菌体（prophage）的多起独立获得事件，以及影响II期鞭毛蛋白基因座（phase II flagellin locus）的多次缺失事件。这种高水平的微进化可能对抗原性、致病性与传播能力产生影响。相关数据集可通过以下链接获取：http://www.sanger.ac.uk/resources/downloads/bacteria/salmonella.html