title: Genetic distance in the whole-genome perspective on Listeria monocytogenes strains F2-382 and NIHS-28 that show similar subtyping results.
abstract: BACKGROUND
  Genome subtyping approaches could provide useful epidemiological information regarding food pathogens. However, the full genomic diversity of strains that show similar subtyping results has not yet been completely explored. Most subtyping methods are based on the differences of only a portion of the genome. We investigated two draft genome sequences of Listeria monocytogenes strain F2-382 and NIHS-28, which have been identified as closely related strains by subtyping (identical multi-virulence-locus sequence typing and multiple-locus variable number tandem repeat analysis sequence types and very similar pulsed-field gel electrophoresis patterns), despite their different sources.
  
  
  RESULTS
  Two closely related strains were compared by genome structure analysis, recombination analysis, and single nucleotide polymorphism (SNP) analysis. Both genome structure analysis and recombination analysis showed that these two strains are more closely related than other strains, from a whole-genome perspective. However, the analysis of SNPs indicated that the two strains differ at the single nucleotide level.
  
  
  CONCLUSIONS
  We show the relationship between the results of genome subtyping and whole-genome sequencing. It appears that the relationships among strains indicated by genome subtyping methods are in accord with the relationships indicated by whole-genome analysis. However, our results also indicate that the genetic distance between the closely related strains is greater than that between clonal strains. Our results demonstrate that subtyping methods using a part of the genome are reliable in assessing the genetic distance of the strains. Furthermore, the genetic differences in the same subtype strains may provide useful information to distinguish the bacterial strains.
authors.affiliation: Department of Food Science and Technology, Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato, Tokyo, 108-8477, Japan. d131006@kaiyodai.ac.jp.
authors.forename: Daisuke
authors.initials: D
authors.lastname: Kyoui
authors.affiliation: Department of Food Science and Technology, Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato, Tokyo, 108-8477, Japan. hajime@kaiyodai.ac.jp.
authors.forename: Hajime
authors.initials: H
authors.lastname: Takahashi
authors.affiliation: Department of Food Science and Technology, Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato, Tokyo, 108-8477, Japan. s-miya@kaiyodai.ac.jp.
authors.forename: Satoko
authors.initials: S
authors.lastname: Miya
authors.affiliation: Department of Food Science and Technology, Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato, Tokyo, 108-8477, Japan. kuda@kaiyodai.ac.jp.
authors.forename: Takashi
authors.initials: T
authors.lastname: Kuda
authors.affiliation: Division of Biomedical Food Research, National Institute of Health Science, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo, 158-8501, Japan. igimi@nihs.go.jp.
authors.forename: Shizunobu
authors.initials: S
authors.lastname: Igimi
authors.affiliation: Department of Food Science and Technology, Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato, Tokyo, 108-8477, Japan. kimubo@kaiyodai.ac.jp.
authors.forename: Bon
authors.initials: B
authors.lastname: Kimura
mesh_terms: D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D023061:Gene Order; D014644:Genetic Variation; D005838:Genotype; D006801:Humans; D007564:Japan; D008089:Listeria monocytogenes / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D008088:Listeriosis / Q000382:microbiology; D008969:Molecular Sequence Data; D058889:Molecular Typing; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D014481:United States
chemical_list: D004269:DNA, Bacterial