Long-read metagenomics reveals a high burden of antimicrobial resistance, mobile genetic elements and bacterial diversity in hospital and community wastewater from Conakry, Guinea

Wastewater systems are increasingly recognized as important environmental reservoirs of antimicrobial resistance (AMR), acting as interfaces where resistant bacteria, antimicrobial resistance genes (ARGs), and mobile genetic elements (MGEs) converge and potentially disseminate. Wastewater samples were collected from hospital and community sites, including municipal medical centers, household wastewater outlets, and open drainage systems. Genomic DNA was extracted using the ZymoBIOMICS™ DNA/RNA Miniprep Kit and sequenced on the Oxford Nanopore Technologies MinION MK1D platform using the Native Barcoding Kit (SQK-NBD114.24, V14). Sequencing data were processed through a custom Snakemake workflow integrating quality control, taxonomic profiling, resistome characterization, mobilome analysis, and genome-resolved metagenomics. A total of 489 unique ARGs conferring resistance to 29 antibiotic classes were identified through metagenomic analysis. The resistome was dominated by genes conferring resistance to β-lactams (including cephalosporins and carbapenems), aminoglycosides, tetracyclines, macrolides, and fluoroquinolones. Clinically important resistance determinants, including bla OXA, bla TEM, bla GES, bla CARB, cfxA, tet, qnr, sul, dfrA, erm, msrE , and aminoglycoside-modifying enzyme genes such as aac(3) and ant(3’’) were detected across both hospital and community wastewater samples. Resistance mechanisms were predominantly driven by antibiotic inactivation, followed by efflux and target protection. Several priority bacterial pathogens were detected, including Escherichia coli, Klebsiella pneumoniae, Enterobacter cloacae, Pseudomonas aeruginosa, and Acinetobacter baumannii . Integration/excision elements were the predominant category of MGEs, followed by transfer-associated elements and replication/recombination/repair functions. Plasmid analysis further identified diverse incompatibility groups, predominantly IncP6, IncC, IncF, and IncR replicons, highlighting the widespread occurrence of plasmid-associated genetic mobility in both settings. Genome-resolved analysis reconstructed 103 dereplicated MAGs, of which 80 carried ARGs and 26 contained putative mobile resistance regions defined by ARG–MGE co-localizations within 10 kb. These findings reveal a substantial burden of clinically relevant ARGs, mobile genetic elements, and potential bacterial pathogens in hospital and community wastewater in Conakry. This study provides the first metagenomic baseline for environmental AMR surveillance in Guinea and highlights the urgent need for integrated One Health strategies to mitigate the environmental dissemination of antimicrobial resistance.