Antimicrobial resistance (AMR) is a global, immediate and ongoing concern to human health. AMR occurs when microbes become resistant to clinical or veterinary drugs that are used to treat disease, and this has major consequences on how microbial diseases are managed and therefore how antimicrobial compounds are used.
AMR and antimicrobial usage (AMU) affects different aspects of our lives and environment, and this is reflected in ongoing research. Examples of the breadth of our work includes research on estimating the levels of resistance in sheep, surveillance of AMR genes in Scottish soils and understanding how resistance occurs in priority foodborne pathogens.
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Antimicrobial resistance (AMR) is one of the most important health challenges in the modern era, recognised internationally by the World Health Organisation (WHO) global action plan. The early success of antibiotics in disease control led to unprecedent improvements in human and veterinary healthcare. However, decades later, we are faced with the consequences of their universal and over-use, and the associated development of microbial resistance to antibiotics (and other antimicrobials). We know that AMR can be generated in agriculture by over-use of drugs, resulting in the emergence of resistant bacteria that can then be transferred to humans directly, via food or via the environment. Consequently, it is important to future human health to understand the occurrence of and selection for antimicrobial resistance in agriculture, and the transmission of resistant organisms to humans, putting AMR firmly into the ‘One Health’ agenda.
Across SEFARI our work includes research on antimicrobial and antibiotic resistance within rural agriculture and environmental settings. The work covers a wide range of topics from antimicrobial usage to the surveillance of microbes and development of resistance, and spans a range of agricultural environments to better understand the sources, reservoirs and transfers of antimicrobial genetic determinants, including farmed animals, wildlife, retail food, soil and water.
To help reduce the risk of evolution and transfer of antimicrobial resistance it is also vital we discuss our findings with key stakeholders, such as the Scottish Government and Food Standards Scotland. Consequently, in February 2020, SEFARI scientists organised a joint meeting to discuss AMR research and define the scope of research which is still needed. The event extends a previous open event on AMR hosted by SEFARI scientists. A key aim of the meeting (held February 2020), was to collate and coordinate our research and establish how findings fit within the wider context. By bringing together researchers and stakeholders from a range of different disciplines we sought to define the scope of the work (completed, on-going and still needed), identify synergies, and map onto established networks to enhance our efforts and impact. The meeting illustrated the strengths of our work in a wider, nationally relevant scale.
Key areas of work were identified and grouped into areas relevant to Scottish agriculture. These were then mapped onto established networks of antimicrobial transmission, (such as the one adopted by the Department of Health) to generate an ‘AMR systems map’ for Scottish AMR research.
The map illustrates the scope of our work and shows that most of the known transmission pathways are being researched, to at least some extent within SEFARI, with a focus on resistance in farmed animals, and in environmental habitats. The full map, complete with Strategic Research Programme (SRP) details (e.g. Research Deliverable (RD), Objective (O) and university partner numbers) and hyperlinks to further information can be accessed here.
Our four main research areas identified are in:
- Livestock Production,
- Transfer of AMR via Food,
- Responses to Infection and
- AMR in the Environment.
Some examples of our work are:
- Determining the level of AMR resistance in farmed animals is not straightforward because there are different ways to measure resistance levels. We found that AMR in sheep can be assessed either from individual bacteria isolated from a sheep faecal sample, or from the complex mixture of all bacteria within the sheep faecal sample, but the choice of method influences the apparent prevalence of AMR. Therefore, a new mathematical modelling method was developed to readily estimate the proportion of resistant bacteria. The information gained from the new method shows where the variation in AMR exists, e.g. between animals or farms. In turn this helps to determine how sampling can be carried out efficiently and also identifies likely predictors of resistance.
- Surveillance of AMR genes in environmental habitats has resulted in the production of a Scottish nationwide map of hundreds resistance gene abundances in rural soils. The data shows that while some forms of resistance are an endemic part of microbial ecology in soils, others are localised, and the genetic diversity is driven by environmental factors (e.g. heavy metals) and agricultural practices.