Investigating the resistome, bacterial composition, and mobilome in hospital wastewaters in Metro Manila using a shotgun metagenomics approac

We employed shotgun metagenomics to profile the relative abundances of antibiotic resistance genes (ARGs), bacterial composition, and mobile genetic elements (MGEs) in untreated hospital wastewater (HWW) from three tertiary hospitals in Metro Manila, Philippines. A total of 18 HWW samples were collected biweekly over a three-month period (May to July 2023), between 8:00 and 11:00 AM, from three hospitals (Hospital A, Hospital B, and Hospital C) located in Metro Manila. These samples were processed and subjected to shotgun metagenomic sequencing and bioinformatics analysis. DNA was extracted from all 18 samples, and Nextera XT library preparation was performed, followed by shotgun metagenomic sequencing using the Illumina NovaSeq 6000 platform. The resulting sequence reads were analyzed to identify bacterial taxa, ARGs, and MGEs using a range of curated databases. The relative abundances of the resistome, bacterial community, and mobilome were profiled to compare the distinct hospital wastewater environments.