title: Phylogenetic and population genetic analysis of Salmonella enterica subsp. enterica serovar Infantis strains isolated in Japan using whole genome sequence data.
abstract: Salmonella enterica subsp. enterica serovar Infantis has been reported to be carried asymptomatically in chickens and isolated from some human patients with diarrhea. The aim of this study was to investigate the phylogeny of S. Infantis strains isolated in Japan from chicken meat, chicken egg shells, environmental samples from a grading and packing center for chicken eggs (GP center), diarrhea patients, and asymptomatic carriers based on whole genome sequence data. The S. Infantis strains were in five clusters in a phylogenetic tree reconstructed by the maximum likelihood method. The five clusters were confirmed by neighbor-net and Bayesian cluster analyses. Two of the five clusters formed a group containing all of the strains isolated from chicken meat and some of the strains isolated from diarrhea patients and asymptomatic carriers. The median-joining network reconstructed in this study showed that strains in one of these two clusters diverged from one node with similar relatively short branches, suggesting clonal dissemination of these strains. The other three clusters formed a group containing all of the strains isolated from chicken egg shells and the GP center, and the remaining strains from diarrhea patients and asymptomatic carriers. Interestingly, strains isolated from patients did not cluster in only one group, indicating that none of the S. Infantis strains in this study had significantly higher human pathogenicity. The population genetic analyses in this study showed the separation of the five clusters into two groups was concordant with the sources where the strains in the clusters were isolated. These results suggested that evolutionary groups with higher hierarchy than the clusters identified in this study may be present, although such groups could not be determined by phylogenetic, neighbor-net, and Bayesian analyses in this study. Determination of higher level S. Infantis evolutionary groups should be investigated using other types of genetic markers.
authors.affiliation: Division of Bacteriology, Chiba Prefectural Institute of Public Health, Chiba, Japan. Electronic address: e.ykym@pref.chiba.lg.jp.
authors.forename: Eiji
authors.initials: E
authors.lastname: Yokoyama
authors.affiliation: Division of Pathology and Bacteriology, Fukuoka Institute of Health and Environmental Sciences, Fukuoka, Japan.
authors.forename: Koichi
authors.initials: K
authors.lastname: Murakami
authors.affiliation: Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, Tokyo, Japan.
authors.forename: Yuh
authors.initials: Y
authors.lastname: Shiwa
authors.affiliation: Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, Tokyo, Japan.
authors.forename: Taichiro
authors.initials: T
authors.lastname: Ishige
authors.affiliation: Division of Bacteriology, Chiba Prefectural Institute of Public Health, Chiba, Japan.
authors.forename: Naoshi
authors.initials: N
authors.lastname: Ando
authors.affiliation: Division of Bacteriology, Chiba Prefectural Institute of Public Health, Chiba, Japan.
authors.forename: Takashi
authors.initials: T
authors.lastname: Kikuchi
authors.affiliation: Laboratory of Animal Hygiene, Department of Animal Science, Tokyo University of Agriculture, Kanagawa, Japan.
authors.forename: Satoshi
authors.initials: S
authors.lastname: Murakami
mesh_terms: D000818:Animals; D002645:Chickens; D016000:Cluster Analysis; D005516:Food Microbiology; D005828:Genetics, Population; D016680:Genome, Bacterial; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D007564:Japan; D008460:Meat; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D011201:Poultry Diseases / Q000382:microbiology; D012480:Salmonella Infections / Q000382:microbiology; D012481:Salmonella Infections, Animal / Q000382:microbiology; D019779:Salmonella enterica / Q000145:classification* / Q000235:genetics*
keywords: Phylogeny; SNPs; Salmonella enterica subsp. enterica serovar Infantis; Whole genome sequencing