Genomic comparison of Salmonella enterica serovars and Salmonella bongori by use of an S. enterica serovar typhimurium DNA microarray

Abstract

The genus Salmonella consists of over 2,200 serovars that differ in their host range and ability to cause disease despite their close genetic relatedness. The genetic factors that influence each serovar's level of host adaptation, how they evolved or were acquired, their influence on the evolution of each serovar, and the phylogenic relationships between the serovars are of great interest as they provide insight into the mechanisms behind these differences in host range and disease progression. We have used an Salmonella enterica serovar Typhimurium spotted DNA microarray to perform genomic hybridizations of various serovars and strains of both S. enterica (subspecies I and IIIa) and Salmonella bongori to gain insight into the genetic organization of the serovars. Our results are generally consistent with previously published DNA association and multilocus enzyme electrophoresis data. Our findings also reveal novel information. We observe a more distant relationship of serovar Arizona (subspecies IIIa) from the subspecies I serovars than previously measured. We also observe variability in the Arizona SPI-2 pathogenicity island, indicating that it has evolved in a manner distinct from the other serovars. In addition, we identify shared genetic features of S. enterica serovars Typhi, Paratyphi A, and Sendai that parallel their unique ability to cause enteric fever in humans. Therefore, whereas the taxonomic organization of Salmonella into serogroups provides a good first approximation of genetic relatedness, we show that it does not account for genomic changes that contribute to a serovar's degree of host adaptation.

FIG.1.

Genome order analysis of the serovar microarray data. Multiple arrays for each serovar and strain have been averaged, analyzed with GACK, and organized with respect to the LT2 genome order. Each row corresponds to a specific spot on the array, whereas columns represent strains analyzed and are labeled according to the designations in Table 1. The color scheme is located at the bottom of the figure, with the brightest yellow corresponding to spots that are absent/divergent with high certainty, the brightest blue indicating spots that are present/conserved with the greatest certainty, black indicating spots are uncertain or slightly divergent, and gray indicating missing data. (A) The entire data set of 4,122 spots. Indicated are the pSLT virulence plasmid, the SPI-1 and SPI-2 pathogenicity islands, the Stf and Lpf fimbrial operons, and the Fels and Gifsy prophages. Enlargement of the regions corresponding to the pSLT virulence plasmid (B), the SPI-2 pathogenicity island (C), and the SPI-1 pathogenicity island (D) are also shown. Specified are the annotated genes within each region, where vertical bars indicate multiple spots on the array that correspond to the same gene. Not indicated are putative genes, unannotated ORFs, and intergenic regions. This data set is available online (http://falkow.stanford.edu/whatwedo/supplementarydata/, Appendix 1).

FIG.2.

Hierarchical cluster analysis of the microarray data by XCLUSTER. (A) Clustering of the entire data set by both serovar and gene. Shown at the top is the unrooted tree for the relationship of the serovars. (B) Clustering of the data set is as described in panel A except that the 2,244 core genes have been removed. (C) Enlargement of the tree generated in panel B. Color scheme is as described in Fig. 1. The data set in panel B is available elsewhere (http://falkow.stanford.edu/whatwedo/supplementarydata/, Appendix 5).

FIG. 3.

A cluster pattern showing genes that are absent in the serovars associated with human enteric fever and cold-blooded animals but present in the other warm-blooded disease-associated serovars. This cluster was pulled out from the larger image shown in Fig. 2B. Indicated is the annotation gene number (STM) and annotated gene information. The color scheme is as described in Fig. 1. Intergenic regions are not shown. Putative genes are indicated by the term “put.”

FIG. 4.

(A) A cluster indicating genes that are conserved only in group B serovars. This cluster was pulled out from the larger image shown in Fig. 2B. Indicated is the annotation information from the LT2 sequence including the gene number (STM number) and the gene name if available. Not indicated are intergenic regions. The color scheme is as described in Fig. 1.