Abstract
BackgroundGenome 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.ResultsTwo 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.ConclusionWe 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12866-014-0309-0) contains supplementary material, which is available to authorized users.
Highlights
Genome subtyping approaches could provide useful epidemiological information regarding food pathogens
General properties of the draft genome sequence Using the shotgun sequencing method, a total of 46,603,422 bp and 107,127 reads with an average read length of 435.0 bp were obtained for the F2-382 strain
Differences in genome structure We examined the differences between the draft genome sequences of strains showing similar genome subtyping results by using Next-generation sequencing (NGS) technology
Summary
Genome subtyping approaches could provide useful epidemiological information regarding food pathogens. The full genomic diversity of strains that show similar subtyping results has not yet been completely explored. 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. Using NGS, some studies have already reported the relationships between molecular subtyping results and whole-genome sequences for Salmonella enterica and Escherichia coli, and presented useful information on phylogeny and virulence [14,15,16,17,18]. The relationship between the results of genome subtyping and wholegenome sequencing in L. monocytogenes has not yet been fully explored
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