Resistome of culturable soil bacteria and whole soil obtained from ecological and intense farming sites

The resistance of non-pathogenic soil microorganisms to modern day antibiotics has come into notice in the recent years. The ecology, evolution and development of natural resistome and its possible spread to humans and animals is an area of interest and concern. Objectives In this study we aimed to compare the resistomes of bacterial populations in various farming environments and distinguish the influence of human interference. This could help indicating the possible routes of antibiotic resistance gene dissemination. Methods MIC values of antibiotic resistant bacteria from ecological and intensive wheat farming fields (soil 1 and 2) were tested. Clinically important genes responsible for enzyme-mediated resistance to βlactams (including 3th and 4th generation of cephalosporins, carbapenems), quinolones, and transferable genetic determinants integrons were investigated in culturable bacteria and total DNA extracted from the same soils. Conclusions Antibiotic-resistant culturable bacteria from both soils were mostly comprised of Pseudomonas genus. Most of the isolates were highly resistant to antibiotics, on the average to 8 and 11 antibiotics for soils 1 and 2, respectively. None of the isolates tested were positive for clinically important resistance genes. Similar results were observed when total soil DNA was screened. The only resistance genes detected in total soil DNA were blaTEM and tetM. The mechanisms responsible for antibiotic resistance of soil bacteria differ from those observed in clinical settings and should be investigated as a potential source of new antibiotic resistance genes.