The evolutionary history and diagnostic utility of the CRISPR-Cas system within Salmonella enterica ssp. enterica.

James B Pettengill,Magaly Toro,Errol Strain,Steven M Musser,Marc W Allard,Rodolphe Barrangou,Eric W Brown,Ruth E Timme

doi:10.7717/peerj.340

Abstract

Evolutionary studies of clustered regularly interspaced short palindromic repeats (CRISPRs) and their associated (cas) genes can provide insights into host-pathogen co-evolutionary dynamics and the frequency at which different genomic events (e.g., horizontal vs. vertical transmission) occur. Within this study, we used whole genome sequence (WGS) data to determine the evolutionary history and genetic diversity of CRISPR loci and cas genes among a diverse set of 427 Salmonella enterica ssp. enterica isolates representing 64 different serovars. We also evaluated the performance of CRISPR loci for typing when compared to whole genome and multilocus sequence typing (MLST) approaches. We found that there was high diversity in array length within both CRISPR1 (median = 22; min = 3; max = 79) and CRISPR2 (median = 27; min = 2; max = 221). There was also much diversity within serovars (e.g., arrays differed by as many as 50 repeat-spacer units among Salmonella ser. Senftenberg isolates). Interestingly, we found that there are two general cas gene profiles that do not track phylogenetic relationships, which suggests that non-vertical transmission events have occurred frequently throughout the evolutionary history of the sampled isolates. There is also considerable variation among the ranges of pairwise distances estimated within each cas gene, which may be indicative of the strength of natural selection acting on those genes. We developed a novel clustering approach based on CRISPR spacer content, but found that typing based on CRISPRs was less accurate than the MLST-based alternative; typing based on WGS data was the most accurate. Notwithstanding cost and accessibility, we anticipate that draft genome sequencing, due to its greater discriminatory power, will eventually become routine for traceback investigations.

Highlights

Clustered regularly interspaced short palindromic repeats (CRISPRs) represent a unique and peculiar genomic element within many Archaeal and Bacterial groups (Barrangou, 2013; Haft et al, 2005; Horvath & Barrangou, 2010)
Focusing on clustering patterns of isolates from the same serovar, we found that they formed monophyletic groups most often under the SNP dataset followed by the multilocus sequence typing (MLST) and CRISPR loci
The CRISPR-Cas system and the putative immunity it provides for bacteria represents a significant discovery within microbiology and evolutionary biology in general

Summary

Introduction

Clustered regularly interspaced short palindromic repeats (CRISPRs) represent a unique and peculiar genomic element within many Archaeal and Bacterial groups (Barrangou, 2013; Haft et al, 2005; Horvath & Barrangou, 2010). They are formed through the acquisition of exogenous nucleic acids (termed spacers) that are embedded between endogenous DNA sequences (termed repeats, that are usually 21 to 47 bp). Construction and maintenance of the CRISPR array occurs through the CRISPR-associated (Cas) proteins, which identify foreign phage nucleic elements (termed proto-spacers) and incorporate them into the CRISPR locus (Marraffini & Sontheimer, 2010). The proposed biological significance of the CRISPR system is that through the incorporation of spacer elements, which serves as a monitoring system, the bacterium gains some degree of immunity to the harmful foreign elements within its environment (Barrangou et al, 2007; Horvath & Barrangou, 2010; van der Oost et al, 2009)

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