Isolation of Antibiotic-resistant Soil Bacteria from a Detroit Urban Garden

Introduction: Environmental reservoirs, in particular soils, are widely believed to constitute an important source of antibiotic resistance. This is because many soil bacteria are capable of producing antibiotic substances and are naturally antibiotic resistant themselves. However, the nature and extent of this antibiotic resistance reservoir is yet to be determined, especially that associated with urban agriculture. 

Purpose: This study was to isolate antibiotic-resistant soil bacteria from a Detroit urban garden. 

Methods: A total of 21 soil samples were collected from an urban garden in Detroit in the summer of 2015. Soil bacteria were isolated using an R2A agar, supplemented with three antibiotics including ampicillin, streptomycin and tetracycline, individually, at a concentration of 15µg/ml. Bacteria were analyzed by Gram staining, 16S rRNA gene sequencing, followed by bacteria identification using 16S rRNA gene database (http://greengenes.lbl.gov). A disk diffusion test was then performed to measure the bacteria susceptibility to ampicillin, streptomycin, and tetracycline.

Results: A total of 270 soil bacteria were isolated, with the majority of isolates being Gram negative. The predominant soil bacteria identified by 16S rRNA gene sequencing were Chryseobacterium sp. (30.5%), Stenotrophomonas maltophilia (13.8%), Sphingobacterium faecium (8.3%), Flavobacterium sp.(8.3%), followed by Xanthomonas sp., and Sphingobacterium kitahiroense. Disk diffusion data showed that ampicillin resistance was common among the bacteria (90%). Streptomycin and tetracycline resistance was identified in 40% and 20% isolates, respectively. 

Significance: The data will add to our knowledge of the extent of soil bacteria serving as an environmental reservoir of antibiotic resistance in the context of urban agriculture.