Access Type

Open Access Dissertation

Date of Award

January 2018

Degree Type


Degree Name



Nutrition and Food Science

First Advisor

Yifan Zhang


Urban agricultural environment can be an important reservoir of antibiotic resistance and have great food safety and public health indications. This study was to investigate antibiotic-resistant bacteria and antibiotic resistance genes in urban agricultural environment using phenotypic, whole genome sequencing, and metagenomic tools. Three urban community gardens from metro Detroit were studied in two phases.

First phase of this study recovered a total of 207 soil bacteria from 41 soil samples collected from an urban agricultural garden. The most prevalent antibiotic resistance phenotypes demonstrated by Gram-negative bacteria was the resistance to ampicillin (94.2%), followed by chloramphenicol (80.0%), cefoxitin (79.5%), gentamicin (78.4%), and ceftriaxone (71.1%). Gram-positive bacteria were all resistant to gentamicin, kanamycin, and penicillin. Genes encoding resistance to quinolone, β-lactam, and tetracycline were the most prevalent and abundant in the soil. qepA and tetA, both encoding efflux pumps, predominated in 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.

Second phase of this study isolated a total of 226 bacteria from 15 soil samples and 45 vegetable samples from all three urban gardens. Multidrug resistance was identified. The percentages of resistant bacteria to some antibiotics (cefoxitin, amoxicillin/clavulanic acid, chloramphenicol, gentamicin, and tetracycline) were higher in vegetables than those in soil. Transfer of tetracycline resistance by conjugation was observed in bacteria of both soil and vegetable origin. Efflux pump genes were common in soil bacteria as identified by whole genome sequencing. For example, adeI, adeJ, adeK, mexB, mexK, and mexF were detected in antibiotic-resistant bacteria.

The concentrations of soil contaminants detected in this study were either below what would normally be needed to select antibiotic resistance (antibiotics) or below the EPA recommended level (metals). Although no significant correlation was observed between antibiotic resistance and heavy metals, the positive correlation between antibiotic resistance genes and metal resistance genes at the genomic level still suggests the need to explore the possible co-selection of antibiotic resistance by heavy metals.

The data demonstrated a diverse population of antibiotic resistance phenotypes and genotypes in urban agricultural soil and vegetables. Phenotypic determination together with soil metagenomics can be a valuable tool to study the nature and extent of antibiotic resistance in the environment. Due to the increasing evidence of the public health implication of naturally-occurring antibiotic resistance and the scarcity of environmental data in this regard, establishing ecological breakpoints for environmental antibiotic resistance interpretation and identifying environmental indicators to monitor antibiotic resistance appear to be important research areas to pursue.