Exploring the co-occurrence of antibiotic, metal, and biocide resistance genes in the urban agricultural environment

Environmental reservoir of antibiotic and other resistance genes are an emerging public health concern, and especially so in food production sites. This study aimed to explore the co-occurrence of antibiotic resistance genes (ARG) and resistance genes to other compounds, including heavy metals and biocides, in urban vegetable garden soils. Total soil DNA was extracted and subjected to metagenomic analysis on ARG, metal resistance genes (MRG), biocide resistance genes (BRG), multi-compound resistance genes (MCRG), and mobile genetic elements (MGE). The relative abundance of ARGs and MRGs were 2.00–2.90 × 10−1 and 4.22–6.00 × 10−2 copies per 16S rRNA gene, respectively. The most abundant ARGs included multidrug, vancomycin, bacitracin, fosmidomycin, and macrolide-lincosamide-streptogramin (MLS) resistance genes. Common MRGs consisted of genes with resistance to copper (dnaK, copA, cueA), arsenic (arsM), multi-metal (recG_BAC0356, ruvB, cueA), iron (acn), and chromium (recG). BRGs identified were those conferring resistance to multi-biocide (smrA, mexW, tbtB, and emhB), peroxide (sodA, sodB), and phenolic compound (triC). MCRGs were found with resistance to biocide-metal (dpsA, ruvB, actP, ideR), drug-biocide-metal (mdtB), or drug-biocide (mexF, ceoB, sme, mexK, sdeB). Multidrug resistance genes (mexF, mexW, multidrug transporter gene), MLS resistance gene (macB), and MCRG (ruvB) showed most correlations with ARGs and resistance genes to other compounds. The data demonstrate extensive co-occurrence of ARGs, MRGs, BRGs, and MCRGs in urban agricultural environments and suggest the great potential of soil contaminants as co-selection agents for antibiotic resistance