Genomic surveillance of multidrug-resistant Escherichia coli and Klebsiella in clinical and wastewater isolates from a paediatric hospital in Lima, Peru

The environmental spread of antibiotic-resistant bacteria is a growing global health concern, particularly in low- and middle-income countries where limited wastewater treatment infrastructure may facilitate the dissemination of multidrug-resistant (MDR) organisms. Escherichia coli and Klebsiella spp. are clinically significant MDR pathogens commonly associated with healthcare-associated infections and known to carry diverse antimicrobial resistance genes (ARGs). In this study, we conducted genomic and phenotypic analyses of E. coli and Klebsiella spp. isolated from hospital wastewater and paediatric patient samples at a tertiary hospital in Lima, Peru, between 2017 and 2019. A total of 157 isolates were collected (E. coli, n=113; Klebsiella spp., n=44). Whole-genome sequencing was performed to identify ARGs and assess sequence types (STs). MDR phenotypes were more prevalent among wastewater isolates (73.5%) compared to clinical isolates (56.8%, P=0.014), while extended-spectrum β-lactamase production was more frequent in clinical isolates (52.9% vs. 13.9%, P<0.001). Carbapenemase-producing isolates were found only in wastewater, whereas colistin resistance was restricted to a subset of clinical E. coli isolates from urine. Genomic analysis revealed greater sequence type diversity among wastewater isolates, including high-risk STs such as ST10, ST131 and ST405. The Shannon diversity index was higher for wastewater-derived isolates (H=3.45) compared to clinical isolates (H=2.95), indicating a more heterogeneous resistance reservoir. In total, 1,302 resistance gene hits were identified, with clinical isolates carrying significantly more ARGs per genome than wastewater isolates. A small number of shared STs were detected in both sources, suggesting possible overlap in bacterial populations. Our findings highlight the potential role of hospital wastewater as a reservoir of antimicrobial resistance and support the value of integrating environmental and clinical genomic surveillance. Wastewater-based monitoring may inform infection control efforts and guide interventions to curb the spread of AMR within healthcare settings and their surrounding environments.