Open AccessDiversity and microevolution of CRISPR loci in Helicobacter cinaedi
Author(s) -
Junko Tomida,
Yuji Morita,
Keigo Shibayama,
Ken Kikuchi,
Tomohiro Sawa,
Takaaki Akaike,
Yoshiaki Kawamura
Publication year - 2017
Publication title -
plos one
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.99
H-Index - 332
ISSN - 1932-6203
DOI - 10.1371/journal.pone.0186241
Subject(s) - crispr , biology , genotyping , genetics , genotype , multilocus sequence typing , typing , computational biology , gene
Helicobacter cinaedi is associated with nosocomial infections. The CRISPR-Cas system provides adaptive immunity against foreign genetic elements. We investigated the CRISPR-Cas system in H . cinaedi to assess the potential of the CRISPR-based microevolution of H . cinaedi strains. A genotyping method based on CRISPR spacer organization was carried out using 42 H . cinaedi strains. The results of sequence analysis showed that the H . cinaedi strains used in this study had two CRISPR loci (CRISPR1 and CRISPR2). The lengths of the consensus direct repeat sequences in CRISPR1 and CRISPR2 were both 36 bp-long, and 224 spacers were found in the 42 H . cinaedi strains. Analysis of the organization and sequence similarity of the spacers of the H . cinaedi strains showed that CRISPR arrays could be divided into 7 different genotypes. Each genotype had a different ancestral spacer, and spacer acquisition/deletion events occurred while isolates were spreading. Spacer polymorphisms of conserved arrays across the strains were instrumental for differentiating closely-related strains collected from the same hospital. MLST had little variability, while the CRISPR sequences showed remarkable diversity. Our data revealed the structural features of H . cinaedi CRISPR loci for the first time. CRISPR sequences constitute a valuable basis for genotyping, provide insights into the divergence and relatedness between closely-related strains, and reflect the microevolutionary process of H . cinaedi .