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

• Published in: PloS one 2015-06, Vol.10 (6), p.e0126883-e0126883
• Main Authors: Matthews, T David, Schmieder, Robert, Silva, Genivaldo G Z, Busch, Julia, Cassman, Noriko, Dutilh, Bas E, Green, Dawn, Matlock, Brian, Heffernan, Brian, Olsen, Gary J, Farris Hanna, Leigh, Schifferli, Dieter M, Maloy, Stanley, Dinsdale, Elizabeth A, Edwards, Robert A
• Format: Article
• Language: English
• Subjects: animal genomics; Antigens; bacteriophages; BASIC BIOLOGICAL SCIENCES; Biological evolution; Biology; bird genomics; comparative genomics; Computer science; Disease; Food; Gene sequencing; Gene transfer; Genes; Genetic aspects; genome analysis; genome annotation; genome evolution; Genome, Bacterial; Genomes; Host range; Laboratories; Metabolism; Microbiota; Mutation; operons; Physiological aspects; Polymorphism, Single Nucleotide; Pseudogenes; Salmonella; Salmonella enterica; Salmonella enteritidis - genetics; Salmonella enteritidis - pathogenicity; Serogroup; Single nucleotide polymorphisms; Single-nucleotide polymorphism; Typhoid; Virulence; Virulence (Microbiology)
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0126883

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.