Investigating the resistome, taxonomic composition, and mobilome of bacterial communities in hospital wastewaters of Metro Manila using a shotgun metagenomics approach

We profiled antibiotic resistance genes, antibiotic-resistant bacteria, and mobile genetic elements in untreated hospital wastewater from three tertiary hospitals in Metro Manila using shotgun metagenomic sequencing. The resistome profiles revealed high abundances of resistance genes against sulfonamides (sul1, sul2), aminoglycosides (aadS), and macrolides/streptogramins (msrE, mphE). To the best of our knowledge, this study provides the first report of antiseptic resistance genes (qacEΔ1, qacL) in hospital wastewater in the Philippines. Resistance genes of critical concern were also detected, including those conferring resistance to β-lactams (bla _OXA, bla _TEM, bla _GES, bla _NDM, bla _KPC), colistins (mcr-5), and tetracyclines (tet(C), tet(A), tet(L), tet(M)). Bacterial composition was dominated by the phylum Pseudomonadota, with high abundances of the genera Stenotrophomonas, Rhodococcus, and Pseudomonas, while ESKAPEE pathogens were detected at lower levels. A wide diversity of mobile genetic elements associated with multiple drug classes, including antiseptic and disinfectant resistance genes was observed. Overall, this study demonstrates the utility of shotgun metagenomics for comprehensive profiling of the resistome, bacterial composition, and mobilome in hospital wastewaters and provides supplemental data to support AMR surveillance and mitigation in the Philippine healthcare system.