prevalence of antibiotic resistance genes and bacterial pathogens in longterm manured greenhouse soils as revealed by metagenomic survey antibiotic resistance genes args human pathogenic bacteria hpb and hpb carrying args pose a high risk to soil ecology and public health here we used a metagenomic approach to investigate their diversity and abundance in chicken manures and greenhouse soils collected from guli pulangke and hushu vegetable bases with different greenhouse planting years in nanjing eastern china there was a positive correlation between the levels of antibiotics args hpb and hpb carrying args in manures and greenhouse soils in total 156250014 gkg of antibiotic residues 22 classes of args 32 hpb species and 46 species of hpb carrying args were found the highest relative abundance was tetracycline resistance genes manures and multidrug resistance genes greenhouse soils the dominant hpb and hpb carrying args in the manures were bacillus anthracis bordetella pertussis and b anthracis sulfonamide resistance gene sul1 respectively the corresponding findings in greenhouse soils were mycobacterium tuberculosis and m ulcerans m tuberculosis macrolidelincosamidestreptogramin resistance protein mlsrp and b anthracis sul1 respectively our findings confirmed high levels of antibiotics args hpb and hpb carrying args in the manured greenhouse soils compared with those in the field soils and their relative abundance increased with the extension of greenhouse planting years