Open AccessComparative Genomics of 28 Salmonella enterica Isolates: Evidence for CRISPR-Mediated Adaptive Sublineage Evolution
Author(s) -
W. Florian Fricke,
Mark K. Mammel,
Patrick F. McDermott,
Carmen Tartera,
David G. White,
J. Eugene LeClerc,
Jacques Ravel,
Thomas A. Cebula
Publication year - 2011
Publication title -
journal of bacteriology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.652
H-Index - 246
eISSN - 1067-8832
pISSN - 0021-9193
DOI - 10.1128/jb.00297-11
Subject(s) - salmonella enterica , biology , crispr , prophage , plasmid , genetics , virulence , comparative genomics , genome , context (archaeology) , genomics , salmonella , bacteriophage , gene , bacteria , escherichia coli , paleontology
Despite extensive surveillance, food-borneSalmonella enterica infections continue to be a significant burden on public health systems worldwide. As theS. enterica species comprises sublineages that differ greatly in antigenic representation, virulence, and antimicrobial resistance phenotypes, a better understanding of the species' evolution is critical for the prediction and prevention of future outbreaks. The roles that virulence and resistance phenotype acquisition, exchange, and loss play in the evolution ofS. enterica sublineages, which to a certain extent are represented by serotypes, remains mostly uncharacterized. Here, we compare 17 newly sequenced and phenotypically characterized nontyphoidalS. enterica strains to 11 previously sequencedS. enterica genomes to carry out the most comprehensive comparative analysis of this species so far. These phenotypic and genotypic data comparisons in the phylogenetic species context suggest that the evolution of knownS. enterica sublineages is mediated mostly by two mechanisms, (i) the loss of coding sequences with known metabolic functions, which leads to functional reduction, and (ii) the acquisition of horizontally transferred phage and plasmid DNA, which provides virulence and resistance functions and leads to increasing specialization. Matches betweenS. enterica clustered regularly interspaced short palindromic repeats (CRISPR), part of a defense mechanism against invading plasmid and phage DNA, and plasmid and prophage regions suggest that CRISPR-mediated immunity could control short-term phenotype changes and mediate long-term sublineage evolution. CRISPR analysis could therefore be critical in assessing the evolutionary potential ofS. enterica sublineages and aid in the prediction and prevention of futureS. enterica outbreaks.