Table_1_Identification of a Recently Dominant Sublineage in Salmonella 4,[5],12:i:- Sequence Type 34 Isolated From Food Animals in Japan.XLSX

Salmonella enterica subsp. enterica serovar Typhimurium sequence type 34 (ST34) and its monophasic variant (Salmonella 4,[5],12:i:-) are among the most frequently isolated clones from both humans and animals worldwide. Our previous study demonstrated that Salmonella Typhimurium/4,[5],12:i:- strains isolated in Japan could be classified into nine clades and that clade 9 consisted of ST34 strains. In Japan, ST34/clade 9 was first found in the 1990s and has become predominant among food animals in recent years. In the present study, we analyzed the whole genome-based phylogenetic relationships and temporal information of 214 Salmonella Typhimurium/4,[5],12:i:- ST34/clade 9 strains isolated from 1998 to 2017 in Japan. The 214 strains were classified into two sublineages: the newly identified clade 9–2 diverged from clade 9 in the early 2000s and has predominated in recent years. Clonally expanding subclades in clades 9–1 or 9–2 lacked Gifsy-1 or HP1 prophages, respectively, and some strains in these subclades acquired plasmids encoding antimicrobial resistance genes. Additional genome reduction around the fljB gene encoding the phase 2-H antigen was generated by an IS26-mediated deletion adjacent to the transposon in clade 9–2. Although most of the clade 9 strains were isolated from cattle in Japan, the clonally expanding subclades in clade 9–2 (i.e., all and 24% strains of subclades 9–2a and 9–2b, respectively) were isolated from swine. The spread of clade 9 in recent years among food animals in Japan was responsible for the emergence of multiple host-adapted sublineages involving the clonally expanding subclades generated by mobile genetic element-mediated microevolution.

肠炎沙门氏菌肠炎亚种鼠伤寒血清型序列型34（ST34）及其单相变种（沙门氏菌4,[5],12:i:-）是全球范围内从人类与动物中分离得到的最常见克隆株之一。我们既往研究表明，日本分离的鼠伤寒沙门氏菌/4,[5],12:i:-菌株可分为9个进化支，其中进化支9均由ST34菌株构成。在日本，ST34/进化支9最早于1990年代被发现，近年来已成为食用动物中的优势流行克隆株。本研究中，我们对1998年至2017年间日本分离的214株鼠伤寒沙门氏菌/4,[5],12:i:- ST34/进化支9菌株进行了全基因组系统发育关系与时序信息分析。该214株菌株被划分为两个亚谱系：新鉴定的进化支9–2于21世纪初从进化支9分化而来，近年来已成为优势流行株。进化支9–1与9–2中的克隆扩增亚支分别缺失了Gifsy-1前噬菌体和HP1前噬菌体，且这些亚支中的部分菌株获得了携带抗菌耐药基因的质粒。进化支9–2中，邻近转座子的IS26介导的缺失事件引发了编码2相H抗原的fljB基因区域的额外基因组缩减。尽管进化支9的多数菌株分离自日本的肉牛，但进化支9–2中的克隆扩增亚支（即亚支9–2a的全部菌株与亚支9–2b的24%菌株）均分离自猪只。近年来日本食用动物中进化支9的传播，催生了多个宿主适应性亚谱系，这些亚谱系包含了由移动遗传元件介导的微进化所产生的克隆扩增亚支。