AUTHOR=Li Hsin-Yu , Kao Cheng-Yen , Lin Wei-Hung , Zheng Po-Xing , Yan Jing-Jou , Wang Ming-Cheng , Teng Ching-Hao , Tseng Chin-Chung , Wu Jiunn-Jong 

TITLE=Characterization of CRISPR-Cas Systems in Clinical Klebsiella pneumoniae Isolates Uncovers Its Potential Association With Antibiotic Susceptibility

JOURNAL=Frontiers in Microbiology

VOLUME=9

YEAR=2018

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2018.01595

DOI=10.3389/fmicb.2018.01595

ISSN=1664-302X

ABSTRACT=<p>Prokaryotic CRISPR-Cas systems limit the acquisition of genetic elements and provide immunity against invasive bacteriophage. The characteristics of CRISPR-Cas systems in clinical <italic>Klebsiella pneumoniae</italic> isolates are still unknown. Here, 97 <italic>K. pneumoniae</italic> genomes retrieved from the Integrated Microbial Genomes &amp; Microbiomes genome database and 176 clinical isolates obtained from patients with bloodstream (BSI, <italic>n</italic> = 87) or urinary tract infections (UTI, <italic>n</italic> = 89) in Taiwan, were used for analysis. Forty out of ninety-seven genomes (41.2%) had CRISPR-Cas systems identified by the combination of CRISPRFinder and <italic>cas1</italic> gene sequence alignment. The phylogenetic trees revealed that CRISPR-Cas systems in <italic>K. pneumoniae</italic> were divided into two types (type I-E, 23; subtype I-E<sup>∗</sup>, 17) based on the sequences of Cas1 and Cas3 proteins and their location in the chromosome. The distribution of type I-E and I-E<sup>∗</sup> CRISPR-Cas systems was associated with the multilocus sequence typing and the pulsed-field gel electrophoresis results. Importantly, no CRISPR-Cas system was identified in published genomes of clonal complex 258 isolates (ST11 and ST258), which comprise the largest multi-drug resistant <italic>K. pneumoniae</italic> clonal group worldwide. PCR with <italic>cas</italic>-specific primers showed that 30.7% (54/176) of the clinical isolates had a CRISPR-Cas system. Among clinical isolates, more type I-E CRISPR-Cas systems were found in UTI isolates (BSI, 5.7%; UTI, 11.2%), and subtype I-E<sup>∗</sup> CRISPR-Cas systems were dominant in BSI isolates (BSI, 28.7%; UTI, 15.7%) (<italic>p</italic> = 0.042). Isolates which had subtype I-E<sup>∗</sup> CRISPR-Cas system were more susceptible to ampicillin-sulbactam (<italic>p</italic> = 0.009), cefazolin (<italic>p</italic> = 0.016), cefuroxime (<italic>p</italic> = 0.039), and gentamicin (<italic>p</italic> = 0.012), compared to the CRISPR-negative isolates. The strains containing subtype I-E<sup>∗</sup> CRISPR-Cas systems had decreased numbers of plasmids, prophage regions, and acquired antibiotic resistance genes in their published genomes. Here, we first revealed subtype I-E<sup>∗</sup> CRISPR-Cas system in <italic>K. pneumoniae</italic> potentially interfering with the acquisition of phages and plasmids harboring antibiotic resistance determinants, and thus maintained these isolates susceptible to antibiotics.</p>