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 increasing incidence and lethality of urinary tract infections.

Objective: To characterize uropathogenic E. coli isolates obtained from patients with urinary tract infections in two hospitals in Bucaramanga, Colombia. Specifically, we assessed the significance of CRISPR 2.1 locus elements as a target for genotyping.

Materials and methods: We combined phylotyping based on the Clermont classification, antimicrobial susceptibility testing approaches, and PCR amplification of the CRISPR 2.1 array.

Results: We found that the variation in the CRISPR 2.1 array, along with the presence of resistance and virulence genes, phylogroups, and antibiotic sensitivity patterns provide 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. The isolates also demonstrated the occurrence of blaCTX-M, blaTEM, and blaSHV genes in 54.55, 18.18, and 4.17% of the cases, 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: Our results emphasized the utility of CRISPR 2.1 array polymorphism in reliably identifying uropathogenic E. coli and enhancing distinction, which is a noteworthy advance in regional epidemiological monitoring systems.