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Int J Antimicrob Agents. 2018 Aug;52(2):241-250. doi: 10.1016/j.ijantimicag.2018.05.016. Epub 2018 May 30.

Case study on the soil antibiotic resistome in an urban community garden.

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Department of Nutrition and Food Science, Wayne State University, Detroit, MI, USA.
Department of Food Science and Nutrition, Illinois Institute of Technology, Summit, IL, USA.
Department of Biological Sciences, Wayne State University, Detroit, MI, USA.
Department of Nutrition and Food Science, Wayne State University, Detroit, MI, USA. Electronic address:


Urban agricultural soils can be an important reservoir of antibiotic resistance, and have great food safety and public health indications. This study investigated antibiotic-resistant bacteria and antibiotic resistance genes in urban agricultural soils using phenotypic and metagenomic tools. In total, 207 soil bacteria were recovered from 41 soil samples collected from an urban agricultural garden in Detroit, MI, USA. The most prevalent antibiotic resistance phenotype demonstrated by Gram-negative bacteria was resistance to ampicillin (94.2%), followed by chloramphenicol (80.0%), cefoxitin (79.5%), gentamicin (78.4%) and ceftriaxone (71.1%). All Gram-positive bacteria were resistant to gentamicin, kanamycin and penicillin. Genes encoding resistance to quinolones, β-lactams and tetracyclines were the most prevalent and abundant in the soil. qepA and tetA, both encoding efflux pumps, predominated in the quinolone and tetracycline resistance genes tested, respectively. Positive correlation (P<0.05) was identified among groups of antibiotic resistance genes, and between antibiotic resistance genes and metal resistance genes. The data demonstrated a diverse population of antibiotic resistance in urban agricultural soils. Phenotypic determination together with soil metagenomics proved to be a valuable tool to study the nature and extent of antibiotic resistance in the environment.


Antibiotic resistance; Metagenomics; Soil; Urban agriculture

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