Access Type

Open Access Thesis

Date of Award

January 2017

Degree Type


Degree Name



Nutrition and Food Science

First Advisor

Yifan Zhang


Urban farming is gaining popularity around the world as a sustainable agricultural system for providing heatlhy and inexpensive food. However, there are limited data available on the microbial safety related to this sector of agriculture. The objective of the present study was to examine the prevalence and antimicrobial susceptibilities of E. coli and Enterococcus in soil and vegetables associated with urban agriculture.

A total of 19 soil samples and 48 vegetable samples, including 21 leafy greens and 27 root vegetables, were collected from three urban gardens in Detroit. E. coli and Enterococcus were isolated and identified by PCR. Enterococcus species were determined on unique isolates by PCR and 16S rDNA sequencing. The disc diffusion test was used to examine the antimicrobial susceptibility profile of all unique isolates of E. coli and Enterococcus. Pulsed-field gel electrophoresis (PFGE) was performed to distinguish the bacteria at the molecular level.

Out of 19 soil samples, 11 (57.9%) carried E. coli and 17 (89.5%) contained Enterococcus. Of 48 vegetable samples, 23 (48%) were positive for E. coli and 38 (79%) for Enterococcus. Enterococcus mundtii (29.4%) was the most abundant in soil, followed by Enterococcus casseliflavus (11.8%), Enterococcus durans (11.8%) and Enterococcus faecalis (11.8%). In contrast, the vast majority of Enterococcus from vegetables was identified as E. faecalis (81.6%).

E. coli showed resistance to ampicillin only in both soil and vegetables, with a prevalence rate of 23.5% and 36.8% respectively. Streptomycin resistance was observed in 64.7% of Enterococcus isolated from soil followed by 11.8% erythromycin. Antimicrobial-resistant phenotypes in Enterococcus in vegetables were more diverse than soil. Streptomycin resistance was the most prominent with a prevalence of 78.9%. Further, resistance to ampicillin (31.6%), ciprofloxacin (7.9%), erythromycin (7.9%) and tetracycline (7.9%) was observed in Enterococcus of vegetable origin. Two E. faecium strains (3.6%) showed multi-drug resistance and both were isolated from vegetables and E. faecalis (1.8%) isolated from soil also showed multidrug-resistant. No statistical difference was observed in antimicrobial resistance prevalence between isolates of soil and vegetable origin.

PFGE results demonstrate a diverse population of E. coli and no unique patterns identified in isolates from soil or vegetables. The identification of common PFGE patterns suggests the clonal distribution of E. coli in urban gardens.

In conclusion, common foodborne bacteria are prevalent in the urban agricultural system and may serve as a vital source of food contamination and antimicrobial resistance. Antimicrobial resistance also confers E. coli and Enterococcus a fitness advantage to persist in the environment.