Differential Distribution of Type II CRISPR-Cas Systems in Agricultural and Nonagricultural Campylobacter coli and Campylobacter jejuni Isolates Correlates with Lack of Shared Environments.
CRISPR (clustered regularly interspaced palindromic repeats)-Cas (CRISPR-associated) systems are sequence-specific adaptive defenses against phages and plasmids which are widespread in prokaryotes. Here we have studied whether phylogenetic relatedness or sharing of environmental niches affects the distribution and dissemination of Type II CRISPR-Cas systems, first in 132 bacterial genomes from 15 phylogenetic classes, ranging from Proteobacteria to Actinobacteria. There was clustering of distinct Type II CRISPR-Cas systems in phylogenetically distinct genera with varying G+C%, which share environmental niches. The distribution of CRISPR-Cas within a genus was studied using a large collection of genome sequences of the closely related Campylobacter species Campylobacter jejuni (N = 3,746) and Campylobacter coli (N = 486). The Cas gene cas9 and CRISPR-repeat are almost universally present in C. jejuni genomes (98.0% positive) but relatively rare in C. coli genomes (9.6% positive). Campylobacter jejuni and agricultural C. coli isolates share the C. jejuni CRISPR-Cas system, which is closely related to, but distinct from the C. coli CRISPR-Cas system found in C. coli isolates from nonagricultural sources. Analysis of the genomic position of CRISPR-Cas insertion suggests that the C. jejuni-type CRISPR-Cas has been transferred to agricultural C. coli. Conversely, the absence of the C. coli-type CRISPR-Cas in agricultural C. coli isolates may be due to these isolates not sharing the same environmental niche, and may be affected by farm hygiene and biosecurity practices in the agricultural sector. Finally, many CRISPR spacer alleles were linked with specific multilocus sequence types, suggesting that these can assist molecular epidemiology applications for C. jejuni and C. coli.
Institute of Food Research, Gut Health and Food Safety Programme, Norwich Research Park, Norwich, United Kingdom.
Bruce M
BM
Pearson
Department of Medical Microbiology and Infectious Diseases, Erasmus MC-University Medical Center Rotterdam, Rotterdam, The Netherlands.
Rogier
R
Louwen
Host-Microbe Interactomics Group, Department of Animal Sciences, Wageningen University, Wageningen, The Netherlands.
Peter
P
van Baarlen
Institute of Food Research, Gut Health and Food Safety Programme, Norwich Research Park, Norwich, United Kingdom arnoud.vanvliet@ifr.ac.uk.
Arnoud H M
AH
van Vliet
D000483:Alleles; D001419:Bacteria / Q000145:classification / Q000235:genetics; D064130:CRISPR-Associated Proteins / Q000235:genetics*; D064113:CRISPR-Cas Systems; D017000:Campylobacter coli / Q000235:genetics* / Q000302:isolation & purification; D016123:Campylobacter jejuni / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D064112:Clustered Regularly Interspaced Short Palindromic Repeats; D004783:Environmental Microbiology; D016680:Genome, Bacterial; D059372:Nucleotide Motifs; D010802:Phylogeny; D012329:RNA, Bacterial / Q000737:chemistry
D064130:CRISPR-Associated Proteins; D012329:RNA, Bacterial
CRISPR; Campylobacter; comparative genomics; horizontal gene transfer; mobile DNA; phage defense