Rooftop and surface garden soils in Bangladesh harbor diverse resistome profiles
Hoque MN, Rana ML, Gilman MAA, Pramanik PK, Islam MS, Punom SA, Rahman R, Hassan J, Rahman MS, Ramasamy S, Schreinemachers P, Oliva R, Rahman MT
Environmental Monitoring and Assessment
Urban Farm DB summary
A shotgun metagenomic study motivated by how little is known about the microbial communities and antimicrobial resistance (AMR) profiles of rooftop and surface garden soils in Bangladesh, and their potential role as reservoirs and disseminators of AMR, despite the growing expansion of urban agriculture. Twenty-seven soil samples were sequenced — 7 from Dhaka rooftop gardens, 6 from Dhaka surface gardens, 8 from Gazipur rooftop gardens and 6 from Gazipur surface gardens. The work identified 88 antibiotic resistance genes (ARGs), of which 19 (21.6%) were shared across all sites, and found significant differences in resistome composition by garden type (p = 0.04). Rooftop soils harboured more ARGs (Dhaka 50, Gazipur 48) than surface soils (Dhaka 40, Gazipur 41) and were dominated by glycopeptide resistance genes, collectively 62.43-74.07% of ARGs; rooftop soils were also enriched in efflux pumps (adeF, 45.21% of rooftop ARGs) and the ribosomal-protection oxazolidinone resistance gene O23S (62.13% in Gazipur rooftops). Surface soils instead featured more genes mediating antibiotic inactivation, such as CATA (11.64% in Dhaka surface gardens) and fosBx1 (5.94% of surface ARGs).