Distribution of CRISPR-Cas Systems in Clinical Carbapenem-Resistant Klebsiella pneumoniae Strains in a Chinese Tertiary Hospital and Its Potential Relationship with Virulence

Aim: In this study, we aimed to characterize the CRISPR-Cas systems in clinical carbapenem-resistant Klebsiella pneumoniae (CRKP) isolates and to investigate the potential association of CRISPR-Cas systems with bacterial virulence. Methods: A total of 168 CRKP strains were collected from inpatients in a teaching hospital in Jiangxi Province. Five common carbapenemase genes, subtype genes of the CRISPR-Cas system, and 13 virulence genes were amplified by PCR using specific primers. The potential virulence of all the clinical CRKP strains was tested in a Galleria mellonella infection model. Results: PCR analysis of five common carbapenemase genes revealed the frequency of carbapenemase gene KPC-2 was the highest in the CRISPR-negative strains, compared to CRISPR type I-E* strains or CRISPR type I-E strains (p < 0.01). Isolates having the subtype I-E* CRISPR-Cas system tended to have more virulence genes such as magA, kfu, wcaG, and allS, compared to CRISPR-negative isolates and type I-E CRISPR-Cas isolates (p < 0.01). The average survival time of the larvae infected with the isolates having the subtype I-E* CRISPR-Cas system was significantly shorter than the other two group isolates (p < 0.05). Conclusion: The CRKP strains, which had the subtype I-E CRISPR-Cas system or the subtype I-E* CRISPR-Cas system, showed reduced acquisition of carbapenemase genes compared to CRISPR-negative isolates. Importantly, we first found that a small portion of “CR-hvKP” strains were selected from the CRKP clones, which had the type I-E* CRISPR-Cas systems.