Identification of core and variable components of the Salmonella enterica subspecies I genome by microarray

Abstract

We have performed microarray hybridization studies on 40 clinical isolates from 12 common serovars within Salmonella enterica subspecies I to identify the conserved chromosomal gene pool. We were able to separate the core invariant portion of the genome by a novel mathematical approach using a decision tree based on genes ranked by increasing variance. All genes within the core component were confirmed using available sequence and microarray information for S. enterica subspecies I strains. The majority of genes within the core component had conserved homologues in Escherichia coli K-12 strain MG1655. However, many genes present in the conserved set which were absent or highly divergent in K-12 had close homologues in pathogenic bacteria such as Shigella flexneri and Pseudomonas aeruginosa. Genes within previously established virulence determinants such as SPI1 to SPI5 were conserved. In addition several genes within SPI6, all of SPI9, and three fimbrial operons (fim, bcf, and stb) were conserved within all S. enterica strains included in this study. Although many phage and insertion sequence elements were missing from the core component, approximately half the pseudogenes present in S. enterica serovar Typhi were conserved. Furthermore, approximately half the genes conserved in the core set encoded hypothetical proteins. Separation of the core and variant gene sets within S.enterica subspecies I has offered fundamental biological insight into the genetic basis of phenotypic similarity and diversity across S. enterica subspecies I and shown how the core genome of these pathogens differs from the closely related E. coli K-12 laboratory strain.

FIG.1.

Distribution of variance in gene presence level (μ) as a function of gene order. Distribution of variance in gene presence level over the 4,048 genes present in our data set was analyzed. The genes were ordered by increasing variance with the linear part of the curve to the left and the exponential part to the right. Regions of the graph used to form the various sets are indicated (a). Also shown schematically is a decision tree, which was used in the filtering process by which the genes were separated into the six sets (b). Sets A, C, and E formed the high-mean-low-variance gene group; sets B and D formed the low-mean and low-variance group, while set F formed the high-variance group.

FIG.1.

Distribution of variance in gene presence level (μ) as a function of gene order. Distribution of variance in gene presence level over the 4,048 genes present in our data set was analyzed. The genes were ordered by increasing variance with the linear part of the curve to the left and the exponential part to the right. Regions of the graph used to form the various sets are indicated (a). Also shown schematically is a decision tree, which was used in the filtering process by which the genes were separated into the six sets (b). Sets A, C, and E formed the high-mean-low-variance gene group; sets B and D formed the low-mean and low-variance group, while set F formed the high-variance group.

FIG.2.

Separation of the core from the variable component of genes within the 40 S. enterica subspecies I strains studied. (a) A comparative genomic index of 40 S. enterica subspecies I field and clinical isolates, using the serovar Typhi chromosome as baseline, was compiled in GeneSpring version 5.0 and shows the microarray data arranged with respect to the CT18 annotation. Mathematical filters were used to separate within all 40 strains the core component, representing the conserved core S. enterica serovar Typhi coding DNA sequence with high mean and low variance (b) and the noncore genes (c). The noncore genes were further divided into low-mean-low-variance (i) and high-variance (ii) groups, which were ordered with increasing variance. Strains can be identified according to their numbering. The color codes for high and low log intensity (Cy5/Cy3) ratioes are shown.

FIG.2.

Separation of the core from the variable component of genes within the 40 S. enterica subspecies I strains studied. (a) A comparative genomic index of 40 S. enterica subspecies I field and clinical isolates, using the serovar Typhi chromosome as baseline, was compiled in GeneSpring version 5.0 and shows the microarray data arranged with respect to the CT18 annotation. Mathematical filters were used to separate within all 40 strains the core component, representing the conserved core S. enterica serovar Typhi coding DNA sequence with high mean and low variance (b) and the noncore genes (c). The noncore genes were further divided into low-mean-low-variance (i) and high-variance (ii) groups, which were ordered with increasing variance. Strains can be identified according to their numbering. The color codes for high and low log intensity (Cy5/Cy3) ratioes are shown.