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

Abstract

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.

The temporal dynamics of antimicrobial-resistant Salmonella enterica and predominant serovars in China

“…To further explore the genetic relationship of S. I 1,4, [5],12: i:—ST34 isolates collected from China and other geographical regions, we performed phylogenetic analysis of 157 Chinese isolates and 96 publicly available genomes from different sources, a random subset of isolates that was representative of lineages in recent reports [ 36 , 37 ] (Fig. 6 ).…”

Comparative genomics between Colombian clinical isolates of Monophasic VariantSalmonellaTyphimurium and international clonal lineages

“…Interestingly, these isolates possess the IncI1 plasmid, which shares 82% similarity to a previously reported MDR clinical isolate recovered in Italy (49).In contrast to the Colombian clones, Chinese isolates predominantly carry IncHI2-IncHI2A plasmids, as observed in previous studies. The Australian lineage is characterized by the predominance of IncA/C, IncI, and IncHI2 plasmids, while the Japanese isolates are associated with the pYT1 plasmid, a hybrid virus-resistance plasmid (39,50).…”

Multidrug resistance plasmids underlie clonal expansions and international spread ofSalmonella entericaserotype 4,[5],12,i:- ST34 in Southeast Asia

“…The evolution and epidemiology of ST34 has been investigated extensively in high income settings, including the UK, USA, Japan and Australia 9–12 . These showed that ST34 has likely diverged from the ancestral ST19 in the mid 1990s 10,13 , and it is characterized by several genetic features: (a) frequent deletion(s) of fljB and the IncFII S .…”