Uncovering the Resistome of a Peruvian City through a Metagenomic Analysis of Sewage Samples

Background: Antibiotic resistance is a major public health concern globally. In this study, we aimed to evaluate the abundance and diversity of antibiotic resistance genes (ARGs) in sewage water samples from two hospitals and an adjacent community or urban setting in Huanuco, a Peruvian city located in the highlands. Methods: We collected samples from the community wastewater system and from sewage pipes from the two hospitals in Huanuco. DNA was extracted from 250 mL of sewage water samples (n = 6) and subjected to microbiome profiling using 16S rRNA short amplicon sequencing and shotgun metagenomics. We analyzed the taxonomic and functional content in all samples, including alpha and beta diversity metrics, and searched for ARGs. Results: Our results showed that samples taken from the community wastewater system were compositionally different and harbored greater bacterial taxonomic and functional diversity compared to samples collected from the hospitals’ wastewater system. We found a high abundance of bacteria associated with resistance to beta-lactams, macrolides, aminoglycosides, fluoroquinolones, and tetracyclines in all samples. However, there were no significant differences in the abundance or composition of ARGs between the community wastewater samples and those taken from the two hospitals. Conclusions: Our findings suggest that metagenomics analyses in wastewater sewage could be a useful tool for monitoring antibiotic resistance in urban settings. These data could be used to develop local public health policies, particularly in cities or countries with limited resources to establish large-scale One Health projects.