Implementing the CRISPR 2.1 array for genotyping enhances identification of uropathogenic Escherichia coli in Colombian pediatric patients

Abstract

Introduction. The emergence of antibiotic resistance in Escherichia coli has contributed to the growing occurrence and fatality of urinary tract infections (UTIs).
Objectives. To characterize uropathogenic E. coli isolates obtained from patients with urinary tract infections in various hospitals in Bucaramanga, Colombia. Specifically, we assessed the significance of CRISPR 2.1 locus elements as a target for genotyping.
Material and methods. This study combined phylotyping based on the Clermont classification, antimicrobial susceptibility testing approaches, and PCR amplification of the CRISPR 2.1 array.
Results. Our research indicates that the variation in the CRISPR 2.1 array, along with the presence of resistance and virulence genes, phylogroups, and antibiotic sensitivity patterns, provides significant and reliable data for epidemiological studies. The analysis of 72 isolates revealed considerable resistance to ampicillin and trimethoprim/sulfamethoxazole, with rates of 80% and 60%, respectively. In addition, the isolates demonstrated the occurrence of blaCTX-M, blaTEM, and blaSHV genes in 54.55%, 18.18%, and 4.17% of instances, respectively. According to the Clermont classification, groups D and B2 accounted for 65.2% of all isolates. The CRISPR 2.1 array was present in most isolates except those in group B2 and exhibited length polymorphism.
Conclusions. The results emphasize the utility of CRISPR 2.1 array polymorphism in reliably identifying UPEC bacteria, leading to enhanced distinction. This signifies a noteworthy advance in the establishment of regional epidemiological monitoring systems.