Do Antibiotic Resistance Genes From Cow-Calf Operations Move Through The Environment?

Background

Available evidence suggests that it’s very unlikely that an antimicrobial resistant (AMR) microbe will find its way directly from cattle to a human through beef because of all the food safety interventions the industry has in place. It’s also unlikely that an antibiotic resistant microbe will find its way from cattle to humans through the environment, because specific bacteria are often very specialized to live in their preferred environment, so they get outcompeted and die when they move from their natural environment into an unfamiliar environment (e.g. from the cow to soil, or from soil to water, or from running to standing water, etc.).

The real concern is that some bacteria are extremely good at trading their DNA and AMR genes back and forth. Although the bacteria themselves may not move too far from their original environment, they may be able to transfer their AMR genes through the environment like a bucket brigade.

Research has shown that the risk that either AMR pathogens or genes will escape the feedlot environment is relatively low due to the extensive use of runoff collection ponds, composting, incorporation of manure into soil, etc. These practices are much less common in cow-calf operations. So although AMR bacteria may be less prevalent in cow-calf environments, there are also fewer potential environmental barriers to their transmission. This study will examine compare E. coli from different sources to investigate the potential role of the environment as a reservoir for AMR bacteria, AMR genes and their transmission.

Objectives

• Determine the genetic relatedness of indicator bacteria (E. coli) isolated from numerous sources, using phylogenetic trees;
• Characterize the genetic basis of resistance in chromosomes and MGE of resistant isolates and describe the patterns and frequency of resistance determinants across the sources;
• Compare E. coli from enteric and naturalized environmental sources with respect to their ability to act as reservoirs in resistance transmission;
• Assess the associations between multidrug resistance, ARG and risk factors including AMU; and phenotype genotype comparisons; and
• Model the possible transmission of antimicrobial resistant E. coli along the beef production chain

What they will do

This team has a collection of E. coli isolates from six different environments (different animal species, well water, retail poultry and beef, humans, wastewater). From this collection they will study a total of 288 E. coli isolates (48 from each source), 16 of which are susceptible to all antibiotics, 16 that are resistant to one or two antibiotics, and 16 that are resistant to three or more antibiotics. They will compare the genetic relatedness of the different isolates, their AMR genes, virulence, and their ability to act as reservoirs (ability to survive in the environment, form biofilms, and conjugate with each other). They will also determine whether E. coli from chicken (A2C) and cattle (ESBL) trade AMR genes back and forth. Then they will build statistical models to identify how changing management and antimicrobial use practices could impact AMR in the environment and as well as animal and human health. The relationship between AMR results from genetic tests vs. culture-based tests will also be compared.

Implications

Antimicrobial resistance and use are important sustainability issues for the beef industry. Antimicrobial use, resistance and the potential for environmental transmission have been studied in detail in feedlot environments. This study will fill an important knowledge gap for the cow-calf sector.