GENOMIC SURVEILLANCE OF MULTIDRUG-RESISTANT E. COLI AND KLEBSIELLA IN CLINICAL AND WASTEWATER ISOLATES FROM A PEDIATRIC HOSPITAL IN LIMA, PERU

The increasing prevalence of antibiotic-resistant bacteria presents a major global public health concern, particularly in low- and middle-income countries (LMICs), where inadequate wastewater treatment may contribute to the dissemination of multidrug-resistant (MDR) organisms. Escherichia coli and Klebsiella spp. are among the most clinically significant MDR pathogens, frequently implicated in nosocomial infections and capable of harboring diverse antibiotic resistance genes (ARGs). This study investigated the genomic diversity and resistance profiles of E. coli and Klebsiella spp. isolated from hospital wastewater and clinical samples in Lima, Peru. A total of 157 isolates (E. coli, n=113; Klebsiella spp., n=44) were collected from hospital wastewater and pediatric patient samples between 2017 and 2019. Whole-genome sequencing (WGS) was performed to identify ARGs and assess phylogenetic relationships. MDR E. coli phenotypes were significantly more common in wastewater isolates (73.5%) compared to clinical isolates (56.8%, p=0.014), while extended-spectrum β-lactamase (ESBL) production was more frequent in clinical isolates (52.9% vs. 13.9%, p<0.001). Carbapenemase production was detected exclusively in wastewater isolates, whereas colistin resistance was found only in clinical urine isolates. Genomic analysis revealed a higher diversity of sequence types (STs) in wastewater isolates, with ST-10, ST-131, and ST-405 frequently detected. ARG analysis identified 1,302 resistance gene hits, with clinical E. coli and Klebsiella isolates carrying significantly more resistance genes than wastewater isolates. The presence of shared STs between clinical and wastewater isolates suggests a potential link between hospital settings and wastewater as reservoirs of resistance. These findings underscore the role of hospital wastewater in disseminating MDR bacteria and ARGs, emphasizing the need for genomic surveillance to monitor emerging resistance threats. Implementing wastewater-based monitoring programs could inform infection control strategies and targeted interventions to mitigate the spread of antimicrobial resistance in hospitals and surrounding communities, highlighting the urgent need for wastewater-based AMR surveillance, particularly in LMICs with limited treatment infrastructure.