Purpose: This study was conducted to examine the extent of antibiotic resistance and metal resistance in urban agricultural soils.
Methods: Soil bacteria were isolated from 41 soil samples collected from an urban garden in Detroit. Antibiotic resistance profiles were determined using the Sensititre Antimicrobial Susceptibility System. Ten multidrug-resistant soil bacteria were selected for whole genome sequencing. Deep HISeq Illumina sequencing was performed on 21 soil samples. The load of antibiotic and metal resistance genes was expressed as number of open reading frames (ORF). Common antibiotic and metal resistance genes were identified via automated BLAST search.
Results: A total of 207 soil bacteria were isolated. Gram-negative bacteria (n=190) demonstrated resistance to ampicillin (94.2%), chloramphenicol (80.0%), and cefoxitin (79.5%). All gram-positive bacteria (n=17) were resistant to penicillin, gentamicin, and kanamycin. Whole genome sequencing showed the abundance of antibiotic and metal resistance genes. All soil samples (100%) carried resistance genes to quinolones, followed by β-lactam (95%), and tetracyclines (85.7%). The highest number of identified ORF was found in resistance genes to β-lactams (37.3%), macrolides (36.0%), and tetracyclines (18.4%). Antibiotic resistance genes, especially tetracycline resistance genes, in soil correlated positively with the MIC of soil bacteria. Arsenic, copper, and zinc resistance genes were present in all 21 samples. A strong positive correlation was found between total antibiotic resistance genes and total metal resistance genes (P=0.00). Zinc resistance genes were positively correlated with resistance genes to aminoglycosides (P=0.02), β-lactams (P=0.05), quinolones (P=0.03), and tetracyclines (P=0.00).
Significance: The data adds to our knowledge regarding extent of the environmental reservoir of antibiotic resistance and the possible co-selection of antibiotic resistance by metals in the environment.