Salmonella Genomes in the Context of Lifestyle

Abstract

The Enterobacteriaceae encompass a large family of Gram‐negative gastrointestinal resident bacteria, including the Salmonella enterica species. Members of this family have persisted for millions of years, although there is diversity in terms of host range and disease phenotype. The core genome shared between all Enterobacteriaceae includes genes essential for colonising the host intestine, whereas the accessory genome that is specific to certain subspecies and serovars reflects the diversity in lifestyle. This is especially well illustrated in S. enterica , which has over 2,000 different serovars with a wide range of lifestyles, comprising generalists and host‐adapted serovars. Changes to the genome content drive this diversity and this frequently occurs via horizontal gene transfer, bacteriophage and transposon acquisition, plasmid movement and genome degradation. Many specific examples illustrate these evolutionary adaptations in Salmonella . Key Concepts Whole genome sequencing and comparative genomics have revealed a conserved ‘core genome’ common to enteric bacteria. Horizontal gene transfer, bacteriophages and plasmid acquisition generates a repertoire of ‘accessory genome’ features that provides diversification. Presence of certain Salmonella Pathogenicity Islands (SPIs) differentiates Salmonella from other Enterobacteriaceae and differentiates S . bongori from S . enterica : all Salmonella spp. have SPI‐1, implicated in host cell invasion, while only S . enterica has SPI‐2, which is required for survival within the host cell. S . enterica is an old and complex species with over 2000 serovars that differ in terms of host range and disease phenotype. S . Typhi is an example of a host‐adapted serovar that causes severe invasive disease and is restricted to humans. Host adaptation in S . Typhi is driven by genome degradation, the loss of genes not required for the systemic lifestyle in human hosts and gene acquisition, including the genes encoding the Vi capsule and typhoid toxin.