New Technology Applications in the Fight Against Foodborne AMR

Scientists, medical experts, and researchers continue to sound the alarm on antimicrobial resistance (AMR). Is the world paying enough attention? We cannot afford to think of AMR as a "future problem." The proverbial wolf is no longer at the door; it has already crossed the threshold.

According to the World Health Organization (WHO), an estimated 1.27 million people die globally each year directly from AMR, and 4.95 million more deaths are associated with AMR.¹ In the food and agriculture sector, increasing multidrug resistance of foodborne pathogens make foodborne infections harder to successfully treat. The U.S. Centers for Disease Control and Prevention (CDC) has found that clinical outcomes in cases of foodborne salmonellosis are significantly worse when the pathogen exhibits AMR, for example. Nontyphoidal Salmonella accounts for an estimated 1.35 million infections in the U.S. annually, making it one of the most common illness-causing foodborne pathogens.² It is grim to imagine a significant percentage of those cases being complicated by resistance to the key antibiotics used to treat salmonellosis.

Across the pond, analyses by the European Food Safety Authority (EFSA) and the European Center for Disease Prevention and Control (ECDC) have found worrying levels of resistance to common antibiotics in Salmonella and Campylobacter.³ Furthermore, significant AMR (commonly to tetracyclines, fluoroquinolones, and sulfonamides) has been identified in Campylobacter jejuni and Campylobacter coli isolates from humans and poultry in East Africa.⁴ Foodborne AMR is a growing, worldwide problem that requires global—and increasingly higher-tech—solutions.

Emergence and Spread of AMR: A Review

So, how did we get to where we are today with AMR? Much of the cause can be traced to antibiotic overuse in animal agriculture. In low- and middle-income countries, overuse of antibiotics in food animals is contributing to the spread of AMR bacteria. Researchers warn that rising AMR in food animals in Africa and Asia, particularly Southeast Asia, could contribute to the likelihood of another global pandemic if the overuse of antibiotics in animal agriculture is not curbed.^4,5

Complex problems require complex solutions. The Food and Agriculture Organization of the United Nations (FAO) notes, "A current challenge is developing policies that consider the trade-offs between producers' financial investments in antimicrobial stewardship and the societal benefits of reduced antimicrobial resistance achieved by decreased antimicrobial usage."⁶ However, there is more than just a public health obligation to address AMR—there is business incentive, as well. The World Bank estimates a drop in global GDP, due to losses from AMR, of 1.1–3.8 percent by 2050, as well as a 7.5 decrease in the value of global livestock production and a 3.8 percent reduction in global exports.⁶ If realized, these projected losses will have profound effects on global commerce over the long term.

Dr. Issmat Kassem at the University of Georgia's Center for Food Safety wrote an extensive review in Food Safety Magazine of the complications caused by overuse of antibiotics in agriculture and the emergence of AMR in foodborne pathogens. Kassem recommends that investments be directed to support low- and middle-income countries to allow them to transition away from intensive antibiotic use in animal agriculture. He also stresses the importance of national and multinational investments in the discovery of new antibiotics and alternative interventions. You can read Dr. Kassem's article here.⁷

“Big data and AI technologies, such as machine learning, show promise for informing AMR surveillance and mitigation efforts.”

In Canada, where the overuse of antibiotics in food-producing animals and horses has been identified as an issue of concern, the country has established an action plan that provides a 5-year (2023–2027) blueprint for strengthening Canada's collective AMR preparedness and response across the One Health spectrum.⁸ Providing further evidence of increasing foodborne AMR, antibiotic-resistant Salmonella, C. jejuni, Listeria monocytogenes, E. coli, and Enterococci have been found in 50 percent of chicken samples taken from Lidl grocery stores in five European countries.⁹ Lidl is Europe's largest grocery chain and one of the biggest meat distributors on the continent. EFSA, ECDC, and the European Medicines Agency (EMA) stress that AMR trends can be reversed by reducing antibiotic use in humans and animals under a One Health approach.¹⁰

Furthermore, EFSA notes that resistance to critical antibiotics is increasing in some Vibrio species in response to coastal warming and extreme weather events, especially in brackish waters. The prevalence of the pathogen in seafood is expected to rise globally due to climate change. Maintaining cold chain integrity and properly applying process controls like high-pressure processing and irradiation are essential to reduce the spread of Vibrio in seafood.^11,12

AI Technologies to Tackle AMR

Big data and artificial intelligence (AI) technologies, such as machine learning (ML), show promise for informing AMR surveillance and mitigation efforts. In their review of the advances in ML techniques for predicting and identifying AMR in foodborne pathogens, Yun et al.¹³ noted that supervised ML models can be used to mine data to develop the best-fitting models to predict outcomes with high precision, while unsupervised ML models can analyze unlabeled data to identify patterns and trends in raw datasets.

ML applications that are currently being studied or used for the identification of AMR in foodborne pathogens include ML analysis of whole genome sequencing (WGS) datasets, containing hundreds or thousands of genomes, to identify and predict AMR. Machine learning can also assist in predicting and identifying bacterial virulence factors. When spectroscopy methods are combined with ML, larger datasets for a variety of microbial species can be used to establish AMR profiles. This area in particular is witnessing exciting technological progress, although Yun et al.¹³ cautioned that food industry researchers and engineers will need to cooperate with technology specialists to take full advantage of ML applications for AMR research. Data cleaning and standardization of methods are other concerns that food industry researchers will need to address to improve the precision and efficiency of ML algorithms.

In one example of ML applied to AMR surveillance and mitigation, a UK–China study led by researchers from academia, government, and industry analyzed antimicrobial use and antibiotic resistance genes in poultry production. Within the chicken gut microbiome, the researchers found a core subset of clinically relevant bacteria and antibiotic-resistance genes (ARGs) that correlated with AMR profiles of E. coli. The associations between environmental variables, and the species and genes associated with AMR, could provide opportunities for the development of novel AMR monitoring solutions.¹⁴

In another example, researchers from the EU, UK, Norway, and U.S. used ML to analyze genomic data on campylobacteriosis gathered from national and state laboratories in the U.S. in the 10-year period to 2019.¹⁵ Their findings were sobering. According to the researchers' analysis, the majority of campylobacteriosis cases in the U.S. can be attributed to poultry, and chicken is an increasing source of multidrug-resistant Campylobacter in human illness. Campylobacteriosis infections attributable to poultry rose from 22.8 percent in 2009 to 71 percent in 2018. Of even greater concern, the proportion of multidrug-resistant isolates rose from 12.3 percent in 2009 to 22.3 percent in 2018, driven by a rise in fluoroquinolone resistance for C. jejuni and C. coli. Additionally, isolates taken from poultry harbored the most AMR elements, leading the researchers to caution that rising campylobacteriosis infections attributable to poultry could increase AMR in human illnesses.¹⁶

“FAO has also been active in technology uptake for addressing AMR, such as developing its InFARM surveillance and data-gathering platform, which is currently being piloted at the country level.”

In other technology-assisted efforts to fight AMR, European project SPARE-SEA hopes to address AMR issues in oyster cultivation by combining biochemical, microbiological, and genetic analyses from four oyster-growing countries. You can read the Food Safety Magazine article on that project here.¹⁷ Meanwhile, Denmark and Sweden have formed a public health consortium to jointly establish an EU reference laboratory for AMR, which will contribute to diagnostics and infection preparedness.¹⁸

In the U.S., the National Antimicrobial Resistance Monitoring System (NARMS)—a joint project by the U.S. Department of Agriculture’s Food Safety and Inspection Service (USDA-FSIS), the U.S. Food and Drug Administration (FDA), CDC, and state and local public health departments—tracks changes in the antimicrobial susceptibility of specific foodborne pathogens isolated from clinical patients, retail meats, food-producing animals, and animal-derived foods. The most recent NARMS report, covering 2021, highlighted the decreasing susceptibility of Salmonella spp. to ciprofloxacin in humans, chickens, and retail chicken and turkey products. For E.coli, decreased susceptibility to ciprofloxacin was also noted for most retail food and animal samples, while fluoroquinolone resistance increased in Campylobacter human isolates, as well as in beef, chicken, and turkey samples. However, none of the Salmonella or E. coli isolates from animals, animal products, or retail meats showed any mobile colistin resistance genes.¹⁹

In November 2024, USDA’s Animal and Plant Health Inspection Service (USDA-APHIS) announced eight awards totaling nearly $5 million to maintain, expand, and utilize previously developed AMR dashboard tools to securely track the emergence, spread, and patterns of antimicrobial-resistant microbes in domesticated animals. The awards will help advance scientific knowledge around AMR through partnerships with five universities and the National Association of State Departments of Agriculture (NASDA). The dashboard tools will help APHIS better understand the relationships among antimicrobial use, animal health management practices, and AMR, complementing the AMR research already underway by APHIS' National Animal Health Monitoring System (NAHMS). The public-private partnerships will improve access to information on AMR in domesticated animals, including livestock, poultry, and companion animals.²⁰

IGO Efforts to Guide AMR Mitigation

Intergovernmental organizations, such as FAO and WHO, are very active in addressing AMR in the food and agriculture sector from a global perspective. In April of this year, FAO announced the launch of an initiative to reduce antimicrobial use on farms in over 100 countries. The initiative, dubbed RENOFARM (Reduce the Need for Antimicrobials on Farms for Sustainable Agrifood Systems Transformation), will work to mitigate the growing public health threat posed by AMR over the next 10 years. Following pilots in Indonesia, Uganda, and Nigeria, RENOFARM will work with governments, farmers, the private sector, and other stakeholders to provide more than 100 countries with policy support and technical assistance, while facilitating capacity-building and knowledge-sharing to help reduce the need for antibiotics in livestock production.²¹

FAO has also been active in technology uptake for addressing AMR, such as developing its International Antimicrobial Resistance Monitoring (InFARM) surveillance and data-gathering IT platform, which is currently being piloted at the country level.²² FAO also offers the FAO Assessment Tool for Laboratories and Antimicrobial Resistance Surveillance Systems (FAO-ATLASS), used in approximately 28 countries, in addition to international standards for foodborne AMR and antimicrobial management guidance.^23,24 Furthermore, FAO held a live technical webinar on November 6 on AI applications in food safety, including AMR mitigation.²⁵ FAO has directly supported AMR-related activities in the food and agriculture sector in at least 47 countries in Africa, Asia, Europe, Latin America, and the Caribbean.^23,24

Meanwhile, WHO has issued new guidance for food safety authorities in Europe regarding the prevention and control of AMR in the food supply chain. To effectively address foodborne AMR, WHO recommends that food safety authorities must first strengthen national policy and legal frameworks by regulating marketing authorization of antimicrobials. They must also study the risk of AMR, set maximum residue limits for antimicrobials and generate preclinical data, define the conditions of use of antimicrobials, and promote the rational prescription of antimicrobials.²⁶

WHO also leads a global campaign against AMR, World AMR Awareness Week, every year from November 18–24.²⁷ In honor of this year's recently held campaign—the theme of which was "Educate, Advocate, Act Now"—we need to keep expanding awareness on the threats posed by AMR, as well as the solutions available to mitigate its spread. Please consider sharing this Editorial Comment, and the excellent resources listed below, with your colleagues. And keep following Food Safety Magazine for more news and research in the fight against foodborne AMR!

References

1. World Health Organization (WHO). "Antimicrobial Resistance: Key Facts." November 21, 2023. https://www.who.int/news-room/fact-sheets/detail/antimicrobial-resistance.
2. Henderson, B. "Strain Factors May be as Important as AMR in Clinical Outcomes of Foodborne Salmonella Infections." Food Safety Magazine. October 18, 2023. https://www.food-safety.com/articles/8970-strain-factors-may-be-as-important-as-amr-in-clinical-outcomes-of-foodborne-salmonella-infections.
3. Food Safety Magazine Editorial Team. "European AMR Trends in Humans, Animals, Foods for 2021–2022." February 28, 2024. https://www.food-safety.com/articles/9275-european-amr-trends-in-humans-animals-foods-for-20212022.
4. Food Safety Magazine Editorial Team. "Significant AMR Found in Campylobacter From East African Poultry and Humans." Food Safety Magazine. October 4, 2024. https://www.food-safety.com/articles/9795-significant-amr-found-in-campylobacter-from-east-african-poultry-and-humans.
5. Food Safety Magazine Editorial Team. "Antibiotic Use in SE Asian Food Animals Must be Curbed to Protect Global Health, Say Researchers." Food Safety Magazine. August 27, 2024. https://www.food-safety.com/articles/9700-antibiotic-use-in-se-asian-food-animals-must-be-curbed-to-protect-global-health-say-researchers.
6. Food and Agriculture Organization of the United Nations (FAO), Division of Food Systems and Food Safety. "Foodborne Antimicrobial Resistance (AMR): An Economic Concern." September 2023. https://openknowledge.fao.org/server/api/core/bitstreams/1b8dd4ac-3c28-469c-9c52-8e490e87484e/content.
7. Kassem, I.I. "Paradise Lost: The Impact of the Emergence of Antimicrobial Resistance on Food Safety." Food Safety Magazine June/July 2023. https://www.food-safety.com/articles/8671-paradise-lost-the-impact-of-the-emergence-of-antimicrobial-resistance-on-food-safety.
8. Food Safety Magazine Editorial Team. "Canada Makes 5-Year Commitment to Tackling AMR Through One Health Approach." Food Safety Magazine. June 29, 2023. https://www.food-safety.com/articles/8707-canada-makes-5-year-commitment-to-tackling-amr-through-one-health-approach.
9. Food Safety Magazine Editorial Team. "Antibiotic-Resistant Bacteria Found in Half of Chicken Meat from Europe’s Biggest Grocery Chain." Food Safety Magazine. June 20, 2024. https://www.food-safety.com/articles/9554-antibiotic-resistant-bacteria-found-in-half-of-chicken-meat-from-europes-biggest-grocery-chain.
10. Food Safety Magazine Editorial Team. "AMR Trends can be Reversed by Decreasing Antimicrobial Use, EU Agencies Report." Food Safety Magazine. February 21, 2024. https://www.food-safety.com/articles/9262-amr-trends-can-be-reversed-by-decreasing-antimicrobial-use-eu-agencies-report.
11. Food Safety Magazine Editorial Team. "EFSA: Vibrio Becoming More Prevalent in Seafood Due to Climate Change; AMR Worsening." Food Safety Magazine. July 23, 2024. https://www.food-safety.com/articles/9625-efsa-vibrio-becoming-more-prevalent-in-seafood-due-to-climate-change-amr-worsening.
12. European Food Safety Authority (EFSA). "Climate Change and Vibrio Bacteria in Seafood." YouTube. July 23, 2024. https://www.youtube.com/watch?v=0QCh0-wAIA8.
13. Yun, B., X. Liao, J. Feng and T. Dian. "Machine Learning-Enabled Prediction of Antimicrobial Resistance in Foodborne Pathogens." CyTA—Journal of Food. March 15, 2024. https://www.tandfonline.com/doi/full/10.1080/19476337.2024.2324024#abstract.
14. Food Safety Magazine Editorial Team. "Study Shows Promise for AI-Powered AMR Surveillance, Mitigation in Livestock Production." Food Safety Magazine. August 25, 2023. https://www.food-safety.com/articles/8833-study-shows-promise-for-ai-powered-amr-surveillance-mitigation-in-livestock-production.
15. Pasco, B., G. Futcher, J. Pensar, et al. "Machine Learning to Attribute the Source of Campylobacter Infections in the United States: A Retrospective Analysis of National Surveillance Data." Journal of Infection. September 6, 2024. https://www.journalofinfection.com/article/S0163-4453(24)00199-3/fulltext.
16. Food Safety Magazine Editorial Team. "Rising Campylobacter Infections From Poultry May Lead to Increasing AMR in U.S., Study Suggests." Food Safety Magazine. October 18, 2024. https://www.food-safety.com/articles/9843-rising-campylobacter-infections-from-poultry-may-lead-to-increasing-amr-in-us-study-suggests.
17. Andree, K.B. "The Art of Bacterial Warfare: Know Thy Enemy." Food Safety Magazine April/May 2024. https://www.food-safety.com/articles/9405-the-art-of-bacterial-warfare-know-thy-enemy.
18. Food Safety Magazine Editorial Team. "Danish, Swedish Institutions Form Consortium to Establish EU Reference Laboratory for AMR." Food Safety Magazine. March 28, 2024. https://www.food-safety.com/articles/9348-danish-swedish-institutions-form-consortium-to-establish-eu-reference-laboratory-for-amr.
19. Food Safety Magazine Editorial Team. “Highlighting Most Recent U.S. AMR Trends in Foodborne Pathogens During World AMR Awareness Week.” Food Safety Magazine. November 18, 2024. https://www.food-safety.com/articles/9911-highlighting-most-recent-us-amr-trends-in-foodborne-pathogens-during-world-amr-awareness-week.
20. Food Safety Magazine Editorial Team. “USDA Invests $5 Million Into Development of AMR Monitoring Tools.” November 19, 2024. https://www.food-safety.com/articles/9914-usda-invests-5-million-into-development-of-amr-monitoring-tools.
21. Food Safety Magazine Editorial Team. "FAO Launches Initiative to Reduce Antimicrobial Use on Farms in More Than 100 Countries." Food Safety Magazine. April 30, 2024. https://www.food-safety.com/articles/9442-fao-launches-initiative-to-reduce-antimicrobial-use-on-farms-in-more-than-100-countries.
22. FAO. "Antimicrobial Resistance: InFARM System." 2024. https://www.fao.org/antimicrobial-resistance/resources/infarm-system/en/.
23. Food Safety Magazine Editorial Team. "FAO Publishes Summary of Work Against AMR in 2020–2022." Food Safety Magazine. February 12, 2024. https://www.food-safety.com/articles/9233-fao-publishes-summary-of-work-against-amr-in-20202022.
24. Food and Agriculture Organization of the United Nations (FAO). "Tackling Antimicrobial Resistance in Food and Agriculture." Rome, 2024. https://openknowledge.fao.org/server/api/core/bitstreams/f9194e44-eeb5-4210-bd00-a1b86b25c501/content.
25. Food Safety Magazine Editorial Team. "FAO to Livestream Technical Seminar on AI for Food Safety." Food Safety Magazine. October 15, 2024. https://www.food-safety.com/articles/9831-fao-to-livestream-technical-seminar-on-ai-for-food-safety.
26. WHO. "Prevention and Control of Antimicrobial Resistance in the Food Chain: Guidance for Food Safety Authorities in Europe." February 23, 2024. https://www.who.int/europe/publications/i/item/9789289058759.
27. World Health Organization (WHO). "World AMR Awareness Week." 2024. https://www.who.int/campaigns/world-amr-awareness-week.