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TITLE:  Comparative genomics of 28 Salmonella enterica isolates: evidence for CRISPR-mediated adaptive sublineage evolution
 
AUTHORS:  Fricke WF;Mammel MK;McDermott PF;Tartera C;White DG;Leclerc JE;Ravel J;Cebula TA;
 
YEAR:  2011
 
JOURNAL ABBREV:  J Bacteriol
 
MONTH:  Jul
 
TYPE:  JOUR
 
REFMAN INDEX:  607
 
JOURNAL FULL:  Journal of bacteriology
 
VOLUME:  193
 
ISSUE:  14
 
START PAGE:  3556
 
END PAGE:  3568
 
KEYWORDS:  analysis;antimicrobial;ANTIMICROBIAL RESISTANCE;BURDEN;classification;control;Dna;Evolution,Molecular;genetics;Genome,Bacterial;Genomics;Humans;Immunity;INFECTION;INFECTIONS;Inverted Repeat Sequences;Maryland;microbiology;OUTBREAKS;Phenotype;Phylogeny;PLASMID;Public Health;Research;Salmonella;Salmonella enterica;Salmonella Infections;SEROTYPES;STRAIN;STRAINS;SURVEILLANCE;SYSTEM;Virulence;
 
ABSTRACT:  Despite extensive surveillance, food-borne Salmonella enterica infections continue to be a significant burden on public health systems worldwide. As the S. 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 of S. enterica sublineages, which to a certain extent are represented by serotypes, remains mostly uncharacterized. Here, we compare 17 newly sequenced and phenotypically characterized nontyphoidal S. enterica strains to 11 previously sequenced S. 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 known S. 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 between S. 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 of S. enterica sublineages and aid in the prediction and prevention of future S. enterica outbreaks
 
AFFILIATIONS:  Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA. wffricke@som.umaryland.edu
 
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