Abstract
BackgroundBacterial genomes are mosaic structures composed of genes present in every strain of the same species (core genome), and genes present in some but not all strains of a species (accessory genome). The aim of this study was to compare the genetic diversity of core and accessory genes of a Salmonella enterica subspecies enterica serovar Typhimurium (Typhimurium) population isolated from food-animal and human sources in four regions of Mexico. Multilocus sequence typing (MLST) and macrorestriction fingerprints by pulsed-field gel electrophoresis (PFGE) were used to address the core genetic variation, and genes involved in pathogenesis and antibiotic resistance were selected to evaluate the accessory genome.ResultsWe found a low genetic diversity for both housekeeping and accessory genes. Sequence type 19 (ST19) was supported as the founder genotype of STs 213, 302 and 429. We found a temporal pattern in which the derived ST213 is replacing the founder ST19 in the four geographic regions analyzed and a geographic trend in the number of resistance determinants. The distribution of the accessory genes was not random among chromosomal genotypes. We detected strong associations among the different accessory genes and the multilocus chromosomal genotypes (STs). First, the Salmonella virulence plasmid (pSTV) was found mostly in ST19 isolates. Second, the plasmid-borne betalactamase cmy-2 was found only in ST213 isolates. Third, the most abundant integron, IP-1 (dfrA12, orfF and aadA2), was found only in ST213 isolates. Fourth, the Salmonella genomic island (SGI1) was found mainly in a subgroup of ST19 isolates carrying pSTV. The mapping of accessory genes and multilocus genotypes on the dendrogram derived from macrorestiction fingerprints allowed the establishment of genetic subgroups within the population.ConclusionDespite the low levels of genetic diversity of core and accessory genes, the non-random distribution of the accessory genes across chromosomal backgrounds allowed us to discover genetic subgroups within the population. This study provides information about the importance of the accessory genome in generating genetic variability within a bacterial population.
Highlights
Bacterial genomes are mosaic structures composed of genes present in every strain of the same species, and genes present in some but not all strains of a species
Three novel alleles were identified: purE70, which consisted of a synonymous substitution, purE110, which contained one synonymous and one non-synonymous substitution, as compared with the purE5 allele present in most of the Typhimurium strains reported; and sucA144 which consisted of a synonymous substitution, as compared with the predominant sucA9 allele
Despite the limitations of an analysis based on only four substitutions, an eBURST analysis of clonal relatedness among the different sequence types (ST) was consistent with the notion of Sequence type 19 (ST19) as the founder genotype of the clonal complex, with the other three STs linked to ST19 as single-locus variants [see Additional file 1]
Summary
Bacterial genomes are mosaic structures composed of genes present in every strain of the same species (core genome), and genes present in some but not all strains of a species (accessory genome). The aim of this study was to compare the genetic diversity of core and accessory genes of a Salmonella enterica subspecies enterica serovar Typhimurium (Typhimurium) population isolated from food-animal and human sources in four regions of Mexico. Multilocus sequence typing (MLST) and macrorestriction fingerprints by pulsed-field gel electrophoresis (PFGE) were used to address the core genetic variation, and genes involved in pathogenesis and antibiotic resistance were selected to evaluate the accessory genome. Bacterial genomes are mosaic structures composed of genes present in every strain of the same species (core genome), and genes present in some but not all isolates of a species (accessory genome) [1,2,3]. Multilocus sequence typing (MLST) has become an important tool for the study of Salmonella strains [10,11,12,13]
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