Rooftop and Surface Garden Soils in Bangladesh Harbor Diverse Resistome Profiles

Despite the increasing prevalence of urban agriculture, the diversity, composition, and antimicrobial resistance (AMR) profiles ( i.e. , resistome) of microbial communities in rooftop and surface garden soils remain poorly characterized in Bangladesh, limiting our understanding of their role as reservoirs and disseminators of AMR. This study employed shotgun whole-metagenome sequencing (WMS) on 27 soil samples, comprising 7 Dhaka rooftop gardens (DRG), 6 Dhaka surface gardens (DSG), 8 Gazipur rooftop gardens (GRG), and 6 Gazipur surface gardens (GSG), to comprehensively profile resistomes. We identified 88 unique ARGs, with 19 (21.6%) shared across sites, and found significant differences by garden type (p = 0.04). Rooftop soils harbored more ARGs (DRG:50, GRG:48) than surface soils (DSG:40, GSG:41), and were dominated by glycopeptide resistance genes ( vanW , vanY , vanT ), collectively representing 62.43–74.07% of ARGs. Rooftop soils were also enriched in efflux pumps ( adeF , 45.21% of rooftop ARGs) and ribosomal protection mechanisms, exemplified by the oxazolidinone resistance gene O23S (62.13% in GRG). Surface soils featured higher abundances of enzymatic inactivation genes, including chloramphenicol acetyltransferase CATA (11.64% in DSG) and fosfomycin resistance gene FOSB , alongside co-selected biocide (e.g., qacG , 3.70% in DSG) and metal resistance genes. Key ARG carriers included Bacillus licheniformis , B. paralicheniformis , Pseudomonas sabulinigri , and Paenibacillus spp. Correlation analyses indicated showed strong positive correlations (r = 1.0) between specific taxa and resistance mechanisms, alongside co-occurrence of ARGs with biocide and metal resistance genes suggested co-selection and potential linkage on mobile genetic elements. These results highlight urban garden soils as critical reservoirs of ARGs, emphasizing the influence of garden type, location, and anthropogenic inputs, and underscore the importance of sustainable management and a One Health framework for monitoring environmental resistomes.