Genomic Comparison of the Closely-Related Salmonella enterica Serovars Enteritidis, Dublin and Gallinarum

Abstract

The Salmonella enterica serovars Enteritidis, Dublin, and Gallinarum are closely related but differ in virulence and host range. To identify the genetic elements responsible for these differences and to better understand how these serovars are evolving, we sequenced the genomes of Enteritidis strain LK5 and Dublin strain SARB12 and compared these genomes to the publicly available Enteritidis P125109, Dublin CT 02021853 and Dublin SD3246 genome sequences. We also compared the publicly available Gallinarum genome sequences from biotype Gallinarum 287/91 and Pullorum RKS5078. Using bioinformatic approaches, we identified single nucleotide polymorphisms, insertions, deletions, and differences in prophage and pseudogene content between strains belonging to the same serovar. Through our analysis we also identified several prophage cargo genes and pseudogenes that affect virulence and may contribute to a host-specific, systemic lifestyle. These results strongly argue that the Enteritidis, Dublin and Gallinarum serovars of Salmonella enterica evolve by acquiring new genes through horizontal gene transfer, followed by the formation of pseudogenes. The loss of genes necessary for a gastrointestinal lifestyle ultimately leads to a systemic lifestyle and niche exclusion in the host-specific serovars.

Salmonella enterica serovar Gallinarum: addressing fundamental questions in bacteriology sixty years on from the 9R vaccine

“…Estimates suggest that evolution of S. Gallinarum and S. Enteritidis from a common S. Dublin-like ancestor that possessed both T6SSs coincided with domestication of the chicken where vertical transmission to chicks would be advantageous to maintaining infection within a flock. Other recent studies are in agreement that loss of metabolic function is the key event in this process and that horizontal transfer of novel genes associated with virulence occurs prior to the loss of metabolic pathways that drive adapted serovars towards a niche of causing systemic infection in a single or narrow range of hosts (Matthews et al, 2015). Genomics are also providing new understanding of how and why S. Gallinarum and S. Pullorum cause such differing diseases.…”

Molecular‐based identification and detection ofSalmonellain food production systems: current perspectives

“…Matthews et al . () also reported evidence for horizontal gene transfer among S . Enteritidis, Dublin and Gallinarum serovars when they identified, via WGS, the presence of several prophage cargo genes and pseudogenes.…”

Diverse distribution of Toxin-Antitoxin II systems in Salmonella enterica serovars

“…Salmonella evolution has continued through the acquisition of pseudogenes, which also led to host adaptation of a number of Salmonella serovars 9 . These genetic differences contributed to variations in terms of host range and virulence among different serovars 46 and could explain the variation in pathogenicity among the serovars. As a model pathogen and worldwide cause of disease in both humans and animals, Salmonella is an important focus of novel research into myriad aspects of pathogenesis, including its capability to rapidly adapt to and survive ever-changing environments.…”