Learning from the Past: What Can the Genome of Beef Feedlot Environments Tell Us About Antimicrobial Resistance?

Background

Globally and within Canada there have been many projects focused on using DNA sequencing to investigate the microbial communities in beef feedlots though analyzed with different methodology due to researcher preference, lack of access to technologies, software limitations or over-simplifications. With a recent push to publicly share raw and processed DNA data, this team had the opportunity to go back with current knowledge to potentially understand more about antimicrobial resistance (AMR) across feedlots in North America. For these DNA-sequence based methods to have value to producers, a common unit to quantify AMR genes (ARGs) is required to understand the levels of ARGs in the environment and how that is correlated to feedlot health. This study seeks to make the first step through a unified and retrospective dive of bacterial whole genome and metagenome data from animals and environments associated with North American beef cattle feedlots.

Objectives

• Generate a North American feedlot-specific list of ARGs
• Perform quantification and comparison of ARGs based on sample types.

What they Did

This team will use data publicly available through the National Centre for Biotechnology Information (NCBI) to achieve their objectives. This data set includes whole genomes of bacteria that has been collected historically from cattle, humans, and the environment. The team will determine a criteria for which sequences will be included in the study vs. removed which will include rules that make sure all samples are directly or in-directly associated with North American beef cattle production.

After the dataset has been acquired and appropriately filtered, the Ruzzini lab will perform an analysis. First, by reporting the prevalence of specific ARGs by the pathogen they are associated with, including a comparison of BRD pathogens from North American and around the world in the past two decades. A list of ARGs that were found in North American cattle were then used specifically to search metagenomic datasets. The identification of these key players for the industry were then used to search metagenomes from animals and feedlot environments. Detection of ARGs in these complex samples was relatively low for technical rather than biological reasons, suggesting that shotgun metagenomic approaches are not appropriate for targeted surveillance and epidemiology. Finally, they used data from two studies on antimicrobial use (AMU) to examine the link in abundance of ARGs with AMU, including both clinically relevant genes and those that are not currently found in BRD pathogens.

What They Learned

The team leaned that North American BRD pathogens have a distinct suite of ARGs than those from around world, reflecting different antimicrobial usage within and outside of North America. The analysis showed an association between 15 ARGs and both Mannheimia haemolytica and Pasteurella multocida. A number of these ARGs were not related to AMU at feedlots, highlighting the clustering of ARGs into bacterial hotspots of genetic exchange that pose a risk for increasing AMR. In the future, the reliable detection of industry-specific ARGs in metagenomes should employ a targeted DNA-enrichment step which involves isolating and sequencing specific regions of the genome prior to the analysis for a heightened focused on the areas of interest which would make the process more efficient. Finally, collective consideration of the data as well as comparison of datasets obtained from animals exposed or not to antibiotics, clearly demonstrated the positive correlation between AMU and relative ARG abundance meaning, more ARGs were observed in response to exposure to antimicrobials.

What It Means

The administration and effectiveness of antibiotics to control and treat bovine respiratory disease (BRD) in beef cattle feedlots is a growing concern. Antimicrobial resistance (AMR) among bacterial pathogens that contribute to BRD has been the subject of extensive surveillance in Canada and globally. This retrospective analysis delivers a beef industry-specific list of ARGs found in opportunistic pathogens that contribute to BRD. ARGs commonly observed in pathogens isolated in North America were not conserved across the globe, underscoring the relationship between regional AMU and AMR. A positive relationship was also observed between the relative abundance of ARGs in cattle-associated metagenomes with greater exposure to antibiotics. Overall, this analysis should help to guide future surveillance efforts and experimental designs to more directly evaluate the impacts of feedlot practices on AMR.