Diversity of CRISPR-Cas Systems Identified in Urological Escherichia coli Strains

The type I-E and I-F CRISPR-Cas systems were identified in 237 E. coli strains isolated from patients with urinary tract infections (UTIs) between 2004 and 2019. The strains were classified into nine distinct groups (I-IX) based on the presence or absence of cas genes and repeat regions (RRs). Within the type I-E systems, two sequence variants were identified, distinguished by polymorphisms in the casB, cas3, cas7, cas5, and cas6 genes. The direct repeats (DRs) also differed, with I-E-associated RRs ranging from 26–32 bp and I-F-associated RRs being a consistent 28 bp. We identified 762 unique spacers (29–35 bp in length) across the strain collection. The number of spacers per strain varied from 1 to 47, and potential DNA targets were determined for 83 spacers, targeting 56 bacteriophage genomes, 19 plasmids, and 8 cas genes of the I-F type. Multilocus sequence typing (MLST) revealed 68 sequence types and 24 clonal complexes (CCs), with ST131, CC10, CC69, CC405, CC14, CC38, CC73, and CC648 being the most prevalent. Significant correlations were observed between specific phylogroups/CCs, the type of CRISPR-Cas system present, and distinct profiles of virulence and antibiotic resistance genes.