Journal: Journal of Clinical Microbiology

Title: Phylogenetic characterization of Salmonella enterica serovar Typhimurium and its monophasic variant isolated from food animals in Japan revealed replacement of major epidemic clones in the last four decades

Authors: Nobuo Arai, Tsuyoshi Sekizuka, Yukino Tamamura, Kiyoshi Tanaka, Lisa Barco, Hidemasa Izumiya, Masahiro Kusumoto, Atsushi Hinenoya, Shinji Yamasaki, Taketoshi Iwata, Ayako Watanabe, Makoto Kuroda, Ikuo Uchida, and Masato Akiba*

Abstract: Salmonella enterica serovar Typhimurium (Salmonella Typhimurium) and its monophasic variant (Salmonella 4,[5],12:i:-) are the major cause of gastroenteritis in both humans and animals. Pulsed-field gel electrophoresis and multilocus variable-number tandem-repeat analysis have been used widely as subtyping methods for these pathogens in molecular epidemiological analyses, but the results do not precisely reflect phylogenetic information. In this study, we performed a phylogenetic analysis of these serovars using whole-genome sequencing data and identified nine distinct genotypic clades. Then, we established an allele-specific PCR-based genotyping method detecting a clade-specific single nucleotide polymorphism to rapidly identify the clade of each isolate. Among a total of 815 isolates obtained from cattle in Japan between 1977 and 2017, clades 1, 7, and 9 contained 77% of isolates. Obvious replacement of the dominant clone was observed five times in this period, and clade 9, which mostly contains Salmonella 4,[5],12:i:-, is currently dominant. Among 140 isolates obtained from swine in Japan between 1976 and 2017, clades 3 and 9 contained 64% of isolates. Clade 9 is the latest clone as is the case in cattle isolates. Clade 9 is similar to an epidemic clone from Europe, which is characterized by ST34, chromosomal Salmonella genomic island 3 and a composite transposon containing antimicrobial resistance genes. The increased prevalence of clade 9 among food animals in Japan might be a part of the pandemic of the European Salmonella 4,[5],12:i:- clone.