Comparative Genomics of 28 Salmonella enterica Isolates: Evidence for CRISPR-Mediated Adaptive Sublineage Evolution

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.

CRISPR– cas Loci Profiling of Cronobacter Sakazakii Pathovars

“…CRISPR spacer array content has previously been strongly associated with sequence-based phylogeny and hence could be used as a rapid lineage-based detection method and as a discriminatory tool for epidemiological purposes [19,25,42].…”

“…CRISPR-cas systems are a known adaptive immune mechanism in Eubacteria and Archaea [19,25]. These are generally regarded as providing immunity against foreign genetic elements such as phages and plasmids by targeting nucleic www.futuremedicine.com acid in a sequence specific manner.…”

“…Many applications have been identified for the CRISPR-cas system including gene editing, evolutionary and phylogenetic studies, as well as genotyping for epidemiological investigations [19,25]. The degree of variability in the CRISPR-cas system is a useful marker for species diversity and evolution.…”

“…The degree of variability in the CRISPR-cas system is a useful marker for species diversity and evolution. This approach has been applied to Yersinia, Salmonella and E. coli in the Enterobacteriaceae family for phylogenetic, evolutionary and virulence-related analysis [25][26][27]. Since spacers are added sequentially at the leader proximal end and a given spacer is rarely acquired twice or duplicated, hierarchical relationships can be constructed between strains.…”

Salmonella Pathogenicity and Host Adaptation in Chicken-Associated Serovars

“…The clustered regularly interspaced short palindromic repeats (CRISPRs) may also play an important role in the defense of Salmonella against foreign DNA from incoming plasmids and phages. A comparative analysis of 28 sequenced Salmonella genomes demonstrated that CRISPR-mediated immunity among specific strains might control short-term phenotype changes and mediate long-term sublineage evolution (189). Thus, it is evident that bacteriophages reshape the Salmonella genome not only through their direct contributions to the host bacterium but also through indirect interactions with other mobile elements and cellular regulatory networks.…”