title: 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.
authors.affiliation: Department of Biology, San Diego State University, San Diego, California, 92182, United States of America.
authors.forename: T David
authors.initials: TD
authors.lastname: Matthews
authors.affiliation: Department of Computer Science, San Diego State University, San Diego, California, 92182, United States of America.
authors.forename: Robert
authors.initials: R
authors.lastname: Schmieder
authors.affiliation: Computational Science Research Center, San Diego State University, San Diego, California, 92182, United States of America.
authors.forename: Genivaldo G Z
authors.initials: GG
authors.lastname: Silva
authors.affiliation: Department of Biology, San Diego State University, San Diego, California, 92182, United States of America.
authors.forename: Julia
authors.initials: J
authors.lastname: Busch
authors.affiliation: Department of Biology, San Diego State University, San Diego, California, 92182, United States of America.
authors.forename: Noriko
authors.initials: N
authors.lastname: Cassman
authors.affiliation: Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands; Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands.
authors.forename: Bas E
authors.initials: BE
authors.lastname: Dutilh
authors.affiliation: Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America.
authors.forename: Dawn
authors.initials: D
authors.lastname: Green
authors.affiliation: Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America.
authors.forename: Brian
authors.initials: B
authors.lastname: Matlock
authors.affiliation: Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America.
authors.forename: Brian
authors.initials: B
authors.lastname: Heffernan
authors.affiliation: Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America.
authors.forename: Gary J
authors.initials: GJ
authors.lastname: Olsen
authors.affiliation: Molecular Sciences Department, University of Tennessee Health Sciences Center, 858 Madison Ave, Memphis, Tennessee, United States of America.
authors.forename: Leigh
authors.initials: L
authors.lastname: Farris Hanna
authors.affiliation: University of Pennsylvania School of Veterinary Medicine, 3800 Spruce St, Philadelphia, Pennsylvania, 19104, United States of America.
authors.forename: Dieter M
authors.initials: DM
authors.lastname: Schifferli
authors.affiliation: Department of Biology, San Diego State University, San Diego, California, 92182, United States of America.
authors.forename: Stanley
authors.initials: S
authors.lastname: Maloy
authors.affiliation: Department of Biology, San Diego State University, San Diego, California, 92182, United States of America.
authors.forename: Elizabeth A
authors.initials: EA
authors.lastname: Dinsdale
authors.affiliation: Department of Biology, San Diego State University, San Diego, California, 92182, United States of America; Department of Computer Science, San Diego State University, San Diego, California, 92182, United States of America; Department of Marine Biology, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; Argonne National Laboratory, 9700 S. Cass Ave, Argonne, Illinois, 60349, United States of America.
authors.forename: Robert A
authors.initials: RA
authors.lastname: Edwards
mesh_terms: D016680:Genome, Bacterial; D009154:Mutation; D020641:Polymorphism, Single Nucleotide; D012477:Salmonella enteritidis / Q000235:genetics* / Q000472:pathogenicity*; D065288:Serogroup