Understanding the dynamics antimicrobial resistance genes flux in the soil, animals and humans in different fertilisation practices in grasslands

Challenges

Antimicrobials used in human and veterinary medicine end up in the environment where they have important impacts on agricultural and environmental ecosystems and may lead to the emergence of antimicrobial-resistant (AMR) bacteria. Livestock farms may function as reservoirs where genetic material from environmental bacteria transfers to human- or animal-associated bacteria, including zoonotic pathogens. Antimicrobial resistance genes are often associated with mobile genetic elements (MGEs) which capture genetic material from the environment and transfer it between bacterial species. Horizontal gene transfer occurs frequently in the animal gut, but agricultural environments like soils can also function as hotspots for bacterial exchange of genetic material.

It has long been known that the use of low-dose antimicrobial drugs may drive the development of AMR. However, over the last decade, it has been shown that polluted environments with low levels of antimicrobials may contribute to the selection, enrichment, and maintenance of multidrug-resistant bacteria. Such selection pressure could be exerted by

• Antimicrobial residues from human sewage sludge
• Using antimicrobials in livestock selecting for antimicrobial-resistant bacteria in the animal’s intestinal microbiome
• The manure/slurry storage areas and when applied to land as fertiliser

Currently, our understanding of the spread of AMR is limited to small-scale environments, like the animal gut, wastewater treatment plant, manure storage, or soil in a field. Major gaps exist in our understanding of the spread of AMR from “farm to fork.” This includes surveillance and data sharing related to the emergence of AMR in foodborne bacteria and its potential impact on both animal and human health. Therefore, we need to understand and tackle antimicrobial resistance to include integrated studies on AMR bacteria, genes, and mobile genetic elements at the farm level, including livestock and surrounding farm environments. A detailed examination of farming practices in animal production could highlight optimal procedures and how they can be modified to minimise the enrichment and dissemination of antimicrobial resistance.

• The key challenges driving this research are:
• Lack of knowledge and understanding of how anti-microbial resistant bacteria and resistance genes flow in a farm environment
• To improve understanding of the whole ecosystem involved in the spread of AMR using larger- scale studies.
• To develop best farming practices to tackle AMR, and AMR spread on the farm level
• Limited data regarding antimicrobial and heavy metal residues in farming systems and the risk of AMR selection and co-selection.
• Gaining insight into the mechanisms of AMR and understanding short and long-term persistence, and successful transmission. This knowledge is fundamental to the development of novel strategies to tackle AMR.

Questions

Solutions

This project is determining which farming practices for pasture fertilization has the lowest/highest risk of spreading AMR into the environment, into the commensal gut microbiota, and onwards to animals and humans.

Understanding the risk of farming practices and the flow of antimicrobial resistance genes (ARGs)

We are analysing the transmission routes that different fertilisers (sludge pellets, sheep manure, mixed manure, and animal slurry­) have on ARGs and mobile genetic elements flow on different farm systems.

Understanding the impact of farming practices on AMR bacteria selection

The impact of Escherichia coli – the AMR indicator bacterium - on bacteria circulating in the farm environment is being evaluated. We are performing susceptibility testing against antimicrobials with relevance in veterinary and human medicine. The most promising E. coli isolates are being whole-Genome Sequenced (WGS). The information obtained from the WGS of all isolates enables an assessment of the impact of new farming systems strategies, as well as highlighting measures to be taken to mitigate the use of antimicrobials. WGS is being used to identify ARGs carried by Campylobacter isolates from corresponding samples and compared with a Campylobacter database.

Analysis of soil and animal for detection of antimicrobials and heavy metal residues

We are analysing concentrations of key antimicrobial agents in the soils of farms employing different pasture management practices. This analysis is identifying the concentrations of specific heavy metals that are implicated in increasing the transferability of AMR and shows which inorganic contaminants are present in the different organic fertilisers and soil contamination. It helps us understand the risk of co-selecting for antimicrobial resistance in soil pastures and in animals that graze on it. 

Statistical analysis to model the flow and spread of bacteria and ARGs through the environment

We are then modelling the flow and spread of bacteria and ARGs through the environment, particularly grasslands and arable soils at national level.

Overall, we are determining which farming practices for pasture fertilization have the lowest and highest risk of spreading AMR into the environment, into the commensal gut microbiota, and onwards to animals and humans. We are using mathematical models to improve our understanding of AMR spread through the farm ecosystem and into food animals and identifying key intervention points.