Diarrheagenic Escherichia coli and Their Antibiotic Resistance Patterns in Dairy Farms and Their Microbial Ecosystems

Arpita Aditya; Zajeba Tabashsum; Zabdiel Alvarado Martinez; Chuan Wei Tung; Grace Suh; Phuong Nguyen; Debabrata Biswas

doi:10.1016/j.jfp.2023.100051

Diarrheagenic Escherichia coli and Their Antibiotic Resistance Patterns in Dairy Farms and Their Microbial Ecosystems

J Food Prot. 2023 Mar;86(3):100051. doi: 10.1016/j.jfp.2023.100051. Epub 2023 Jan 26.

Authors

Arpita Aditya¹, Zajeba Tabashsum², Zabdiel Alvarado Martinez², Chuan Wei Tung¹, Grace Suh², Phuong Nguyen¹, Debabrata Biswas³

Affiliations

¹ Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA.
² Biological Sciences Program, University of Maryland, College Park, MD 20742, USA.
³ Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA; Biological Sciences Program, University of Maryland, College Park, MD 20742, USA; Centre for Food Safety and Security Systems, University of Maryland, College Park, MD 20742, USA. Electronic address: dbiswas@umd.edu.

PMID: 36916558
DOI: 10.1016/j.jfp.2023.100051

Abstract

Ruminants are the largest reservoir for all types of Escherichia coli, including the pathogenic ones, which can potentially be transmitted to humans via the food chain and environment. A longitudinal study was performed to estimate the prevalence and antibiotic-resistant pattern of pathogenic E. coli (pE.coli) strains in dairy farm environments. A total of 846 environmental samples (water, lagoon slurry, bedding, feed, feces, soil, and compost) were collected in summer over two years from five dairy farms in Maryland, USA. An additional 40 soil samples were collected in winter and summer seasons for evaluating microbiome composition. Collected environmental samples were screened for the presence of pE.coli, which was isolated using a selective culture medium, for later confirmation and virotyping using PCR with specific primers. The overall prevalence of pE.coli in dairy farms was 8.93% (71/846), with the most common virotype identified in isolates being ETEC, followed by STEC. The highest pE.coli prevalence were recorded in lagoon slurry (21.57%) while the lowest was in compost heap (2.99%). Among isolates, 95.87% of the virotypes were resistant to 9 classes of antibiotics whereas only 4.12% were sensitive. The highest proportion (68.04%) of resistance was found for quinolones (e.g., ciprofloxacin). The resulting metagenomic analysis at the phylum and genus levels of the grazing land soil suggests that climatic conditions actively influence the abundance of bacteria. Proteobacteria, which contains many Gram-negative foodborne pathogens (including pE.coli), was the most predominant phylum, accounting for 26.70% and 24.93% of soil bacteria in summer and winter, respectively. In addition to relative abundance, there was no significant difference in species diversity between seasons when calculated via Simpson (D) and Shannon (H) index. This study suggests that antibiotic-resistant E. coli virotypes are present in the dairy farm environment, and proper steps are warranted to control its transmission irrespective of seasonality.

Keywords: Antibiotic resistance; Dairy farm; E. coli; Prevalence; Soil microbiome.

Publication types

Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Anti-Bacterial Agents / pharmacology
Bacteria
Dairying
Drug Resistance, Microbial
Ecosystem*
Escherichia coli*
Farms
Feces / microbiology
Humans
Longitudinal Studies
Soil

Substances

Anti-Bacterial Agents
Soil