Antimicrobial Resistance Genes in Animal Manure, Manure-Amended and Nonanthropogenically Impacted Soils in Spain

Environmental dissemination of antimicrobial resistance genes may occur through agricultural residues, such as animal manure. We studied the resistome of 16 pool samples of animal manure (pig slurry [n = 8] and poultry manure [n = 8]), and 16 soil samples (manure-amended [n = 8] and nonmanure-amended [n = 8]). All samples were collected in central Spain. Detection was based on 18 selected antimicrobial resistance genes (ARGs). The most commonly detected genes in animal manure were sul1 (16/16), sul2 (16/16), tet(A) (16/16), aadA (16/16), tet(B) (15/16), and str (15/16). Genes blaTEM (7/8), mecA (6/8), vanA (5/8) and qnrB (4/8) were more frequently detected in chicken manure, whereas pig slurry samples presented higher levels of tet(C) (8/8) and tet(M) (8/8). Out of the four genes selected for their clinical relevance, three—blaCTX-M, vanA, and mecA—were detected in animal manure. The blaCTX-M (1/8) and vanA (5/8) genes were only identified in chicken manure. To our knowledge, this is the first report of direct detection of mecA gene in poultry manure and pig slurry. Eleven out of 18 ARGs were detected in amended soil, while only genes sul2 (3/8) and str (2/8) were found in nonanthropogenically impacted soils (NAIS), supporting the hypothesis that ARGs may serve as indicators of “anthropogenic impact” on the environment.