Genotypic Characterization and Detection of CTX-M Groups 1, 2, and 9, and Antibiotic Susceptibility Profiles in Clinical Escherichia coli Isolates from a Pediatric Hospital in Lima, Peru

An increasing frequency of CTX-M-type extended-spectrum β-lactamase (ESBL)-producing Escherichia coli has been documented among pediatric infections in recent decades. This study aimed to analyze the antibiotic susceptibility profiles of ESBL-producing and non-ESBL-producing E. coli isolates, to detect CTX-M groups 1, 2, and 9 among ESBL producers, and to assess the clonal relationships between both groups in pediatric patients. A total of 124 E. coli isolates were recovered from clinical specimens (urine, stool, peritoneal fluid, and tracheal aspirates) collected between April and September 2025 at the Pediatric Emergency Hospital (PEH), Lima, Peru. CTX-M groups were detected by multiplex Polymerase Chain Reaction (mPCR), and clonal relationships were assessed by BOX-PCR. ESBL production was identified in 27.4% of isolates, significantly more frequent in urine samples (p < 0.05) and associated with multidrug-resistant (MDR) or extensively drug-resistant (XDR) profiles (p < 0.001). CTX-M group 1 predominated among ESBL producers (91.3%), while groups 2 and 9 were sporadic (2.9% each). BOX-PCR revealed high genetic heterogeneity, resolving 113 patterns (Simpson’s Index of Discrimination = 0.9986) and 31 ESBL-associated clones. These findings indicate that ESBL-producing E. coli dissemination in this setting is driven by diverse lineages rather than a dominant clone, highlighting the need for continued resistance surveillance.