Detection of high-risk sequence type ST131 among multidrug-resistant Escherichia coli causing urinary tract infections in Cusco, Peru

Antimicrobial resistance in Escherichia coli represents a growing public health challenge, particularly in urinary tract infections (UTIs), where this pathogen remains the leading etiological agent. The emergence of multidrug-resistant strains producing extended-spectrum β-lactamases (ESBLs) and carbapenemases has markedly limited therapeutic options and promoted the persistence of high-risk lineages in hospital settings. In this study, phenotypic, molecular, and genomic characterization were conducted on 50 multidrug-resistant (MDR) E. coli isolates obtained from urine cultures of patients treated at the Regional Hospital of Cusco, Peru. ESBL and carbapenemase production were assessed using standardised phenotypic methods, while resistance genes were detected by endpoint PCR. For genomic characterization, MDR E. coli isolates (RUE 08 and RUE 29) were selected from the panel of 50 isolates. These were chosen as representative samples for whole-genome sequencing and comparative genomic analysis. All isolates were confirmed as ESBL producers, and 40% exhibited carbapenemase production. The detected genes were bla_CTX-M (94%), bla_TEM (36%), bla_SHV (2%), bla_NDM (26%), bla_OXA-48 (20%) and bla_KPC was not detected. The detection of bla_NDM and bla_OXA-48 represents the first documented report of these genes in multidrug-resistant E. coli in the city of Cusco. Genomic analysis identified the high-risk lineage ST131 in one sequenced isolate, characterised by an extensive repertoire of virulence and resistance genes associated with the ExPEC/UPEC pathotype, as well as a second isolate belonging to ST361, which harboured clinically relevant resistance genes but displayed a limited virulence profile. These findings demonstrate the circulation of clinically relevant multidrug-resistant E. coli in southern Peru and underscore the need to strengthen molecular surveillance through the incorporation of genomic tools to enable early detection of high-risk clones and support effective antimicrobial control strategies.