Short-term signatures of evolutionary change in the Salmonella enterica serovar typhimurium 14028 genome

Abstract

Salmonella enterica serovar Typhimurium is a Gram-negative pathogen that causes gastroenteritis in humans and a typhoid-like disease in mice and is often used as a model for the disease promoted by the human-adapted S. enterica serovar Typhi. Despite its health importance, the only S. Typhimurium strain for which the complete genomic sequence has been determined is the avirulent LT2 strain, which is extensively used in genetic and physiologic studies. Here, we report the complete genomic sequence of the S. Typhimurium strain 14028s, as well as those of its progenitor and two additional derivatives. Comparison of these S. Typhimurium genomes revealed differences in the patterns of sequence evolution and the complete inventory of genetic alterations incurred in virulent and avirulent strains, as well as the sequence changes accumulated during laboratory passage of pathogenic organisms.

FIG. 1.

Genealogy of S. Typhimurium strains (see Materials and Methods for source and storage conditions). Wherever possible, isolation dates are noted, and the divergence time between the LT2 and the 14028 lineages is estimated based on sequence data generated in the current study. ya, years ago.

FIG. 2.

Alignment of the S. Typhimurium 14028s and LT2 genomes. Differences in genome organization and gene contents and the distribution of substitutions (point mutations and 1-bp indels) are shown.

FIG. 3.

Relative frequencies of each type of base substitution detected at synonymous and nonsynonymous sites and in intergenic regions. The frequencies are adjusted for the base composition of the particular class of sites.