Genomic epidemiology of Salmonella from retail chicken meat in Japan: decline in pESI-like plasmid-harboring S. Infantis ST32 and predominance of S. Schwarzengrund ST241.

Salmonella is a major foodborne pathogen, and chicken meat is an important source of infection. This study investigated Salmonella prevalence, serovar distribution, antimicrobial resistance, and genomic characteristics in 150 retail chicken meat samples collected in Japan in 2023. The predominant serovar was S. Schwarzengrund (42.7%), followed by S. Infantis (7.3%), which has long been the predominant serovar in Japan. The globally expanding S. Infantis sequence type (ST) 32 harboring pESI-like plasmids has declined in Japan. In contrast, S. Schwarzengrund ST241 was isolated more frequently in winter (66%) than in summer (31%, P < 0.001) and more often from chicken meat produced in eastern Japan (47.1%) than in western Japan (29.4%, P = 0.042). Antimicrobial resistance was most common to tetracycline (50.6%) and streptomycin (45.7%), whereas kanamycin resistance (33.3%) had declined compared with 2015 to 2019, consistent with reduced use of this antimicrobial in broiler production. Moreover, the proportion of S. Schwarzengrund isolates lacking antimicrobial resistance genes (ARGs) increased markedly from summer (19.4%) to winter (45.5%). cgMLST analysis revealed that antimicrobial-susceptible S. Schwarzengrund isolates formed the largest clade and, notably, retained pESI-like plasmids despite apparent loss of ARG-containing regions from these plasmids. These findings demonstrate ongoing genomic shifts in Salmonella populations in Japan and underscore the need for continuous genomic surveillance to mitigate their public health impact.