Addressing the Global Threat of Antimicrobial Resistance: A Comprehensive Approach Integrating Agriculture, Health, and Environment

Antimicrobial resistance (AMR) is one of the most challenging global health and food security problems. It is estimated to cost the EU €1.5 billion in healthcare and productivity losses and cause the death of 33,000 European citizens each year. Left untackled, AMR is predicted to cause more than 10 million deaths and an 11% decrease in livestock production annually by 2050 [1]. Such is this threat, that the World Health Organisation and Centre for Disease Control have published a list of bacteria for which new antibiotics are urgently needed [2, 3]. Considering the fast development of resistance to new drugs and antimicrobials, stewardship programmes that actively discourage overuse/misuse of antibiotics are needed. One of the largest users of antibiotics is the agricultural industry, consuming estimates of up to 240,000 tonnes per annum, predicted to rise by 67% by 2030. More than 50% of medically important antibiotics are used in animals for treating/preventing infections and as growth promotors in some parts of the world [4]. The largest group of antimicrobials used in Irish farm animals include tetracyclines, sulphonamides, macrolides, penicillins and cephalosporins [5]. Evolution of fungicide resistance in cropping systems also threatens global food security. Crops are treated with antimicrobials including azole-based antifungals to control disease that would otherwise reduce global yields by over 20% [6]. The same azoles are used in clinical practice. Many countries report rises in antifungal resistance in environmental and clinical settings [6, 7]. This is concerning as worldwide there are over 150 million cases of severe fungal infections and around 1.7 million deaths annually [8]. Ultimately, antimicrobials and communities of AMR microbes in effluent, animal waste and crops contaminate the environment via agricultural, pharmaceutical and healthcare practices, contributing to the spread of an ever-rising planet and human health threat (Figure 1). Without the safeguard of antimicrobial agents or the development of new antimicrobials and therapeutic approaches, the future of modern medicine and food production is under threat. This will disproportionately impact third world countries. Even closer to home, the Agri-Food sector is Ireland’s most important indigenous industry, playing a vital role in Ireland’s economy [9]. The sector employed over 164,400 people or 7.1% of total employment in 2019. 

The solutions to the world’s AMR disaster are only achievable by taking a One Health, systems thinking approach [8]. Despite microorganisms existing as complex communities or ‘microbiomes’ in synergy with the environment and human body, most current approaches to tackling resistance focus on single microorganisms. However, interactions between species within communities can influence antibiotic susceptibility or provide ‘passive’ resistance, in the clinical setting [10]. Thus, this project will analyse interactions within and between farm microbiomes, and develop novel models for studying resistance or transmission of a ‘resistome’ - the collection of AMR conferring genes in microbial communities. It will also survey the regulators and stakeholders to assess decision making around use of antimicrobials in farm practices. Taken together, this project will bridge the knowledge gap between agricultural practices and transmission of resistance from farm-to-farmer and farm-to-environment. Applying an interdisciplinary approach which brings together the natural sciences, microbiology, medicine, computer science, statistics, sociology and engineering disciplines, we will tackle AMR from an innovative perspective and to train a unique cohort of PhD students skilled to confront the AMR challenge in the future.