The evolutionary history and diagnostic utility of the CRISPR-Cas system within Salmonella enterica ssp. enterica
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...
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| Format: | Article |
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PeerJ Inc.
2014-04-01
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| Online Access: | https://peerj.com/articles/340.pdf |
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| author | James B. Pettengill Ruth E. Timme Rodolphe Barrangou Magaly Toro Marc W. Allard Errol Strain Steven M. Musser Eric W. Brown |
| author_facet | James B. Pettengill Ruth E. Timme Rodolphe Barrangou Magaly Toro Marc W. Allard Errol Strain Steven M. Musser Eric W. Brown |
| author_sort | James B. Pettengill |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-09T08:20:54Z |
| format | Article |
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| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T08:20:54Z |
| publishDate | 2014-04-01 |
| publisher | PeerJ Inc. |
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| series | PeerJ |
| spelling | doaj.art-9573246b079f448b99d7c73172446ff32023-12-02T21:49:40ZengPeerJ Inc.PeerJ2167-83592014-04-012e34010.7717/peerj.340340The evolutionary history and diagnostic utility of the CRISPR-Cas system within Salmonella enterica ssp. entericaJames B. Pettengill0Ruth E. Timme1Rodolphe Barrangou2Magaly Toro3Marc W. Allard4Errol Strain5Steven M. Musser6Eric W. Brown7Center for Food Safety & Applied Nutrition, US Food & Drug Administration, College Park, MD, USACenter for Food Safety & Applied Nutrition, US Food & Drug Administration, College Park, MD, USADepartment of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, USADepartment of Nutrition and Food Science, University of Maryland, College Park, MD, USACenter for Food Safety & Applied Nutrition, US Food & Drug Administration, College Park, MD, USACenter for Food Safety & Applied Nutrition, US Food & Drug Administration, College Park, MD, USACenter for Food Safety & Applied Nutrition, US Food & Drug Administration, College Park, MD, USACenter for Food Safety & Applied Nutrition, US Food & Drug Administration, College Park, MD, USAEvolutionary 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.https://peerj.com/articles/340.pdf Salmonella Horizontal gene transferEvolutionCRISPROutbreakPhylogeny |
| spellingShingle | James B. Pettengill Ruth E. Timme Rodolphe Barrangou Magaly Toro Marc W. Allard Errol Strain Steven M. Musser Eric W. Brown The evolutionary history and diagnostic utility of the CRISPR-Cas system within Salmonella enterica ssp. enterica PeerJ Salmonella Horizontal gene transfer Evolution CRISPR Outbreak Phylogeny |
| title | The evolutionary history and diagnostic utility of the CRISPR-Cas system within Salmonella enterica ssp. enterica |
| title_full | The evolutionary history and diagnostic utility of the CRISPR-Cas system within Salmonella enterica ssp. enterica |
| title_fullStr | The evolutionary history and diagnostic utility of the CRISPR-Cas system within Salmonella enterica ssp. enterica |
| title_full_unstemmed | The evolutionary history and diagnostic utility of the CRISPR-Cas system within Salmonella enterica ssp. enterica |
| title_short | The evolutionary history and diagnostic utility of the CRISPR-Cas system within Salmonella enterica ssp. enterica |
| title_sort | evolutionary history and diagnostic utility of the crispr cas system within salmonella enterica ssp enterica |
| topic | Salmonella Horizontal gene transfer Evolution CRISPR Outbreak Phylogeny |
| url | https://peerj.com/articles/340.pdf |
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