The emergence of anti-microbial resistance: A major problem at the intersection of food production, safety and public health by Issmat Kassem

Over reliance on antibiotics in human medicine and in agricultural practice has become prevalent due to the over-dependence and misuse of antibiotics in human and animal medicine and in agriculture (growing food). This has caused pathogens to rapidly evolve and acquire resistance to the antibiotics. Pathogens transmitted through the food chain have become increasingly resistant to antibiotics over time. Antimicrobial resistance has become a global issue that is predicted to result in 300 million people dying prematurely and in economic losses of 60-100 trillion US$ by 2050. 

In Lebanon, very few clinical studies address this issue, while community, agricultural, and environmental studies are severely lacking. Lebanon does not have a national system to observe antimicrobial resistance, leaving the status of resistance trends in the country largely unknown. Dr. Issmat Kassem, Assistant Professor of Food Microbiology/ Safety in FAFS, has researched the topic extensively in Lebanon and abroad. Central to and intersecting with food safety, public health, and medicine, is the issue of anti-microbial resistance, named by WHO as the major public health concern facing humanity this century. Dr. Kassem’s research: The emergence of anti-microbial resistance: The intersection between food production and public health, revolves around a specific type of anti-microbial resistance known as “last resort antibiotics”. These antibiotics are used to reduce pathogen infection in humans after other antibiotics have failed, causing Dr. Kassem to label it “the last line of defense". The loss of the efficacy of these antibiotics will result in severe consequences to human health.


Before Kassem embarked on this research, a gene on a plasmid, the Mobile Colistin Resistance (MCR) gene, was discovered in agricultural settings in China in 2016. Since its discovery, the MCR gene spread globally causing resistance to Colistin, a last resort antibiotic used to treat complicated infections with certain types of bacteria. The status of MCR in Lebanon is unknown, but its importance lies in the fact that it does not stick to a single bacterium but can jump between species, making it easily dispersed and transmitted. 

Kassem reviewed agricultural practices in Lebanon and surveyed veterinary drug stores to discover that Colistin is widely and readily available for animal use under twelve different brand names. Although Colistin is not accessible in community pharmacies and only available in hospital pharmacies for treating complicated infections in Lebanon, Dr. Issmat concluded that it is used in agriculture, perhaps heavily and definitely in unmonitored ways. Second, he inferred that contamination can also happen from medical practices: Lebanon’s poor infrastructure indicates that hospital waste contaminates the environment, creating a cross link between the environment, agriculture, and the medical practices. 

Kassem examined​ the amount of Colistin imported to Lebanon between 2010 to 2017, and noticed a fivefold increase in Colistin use, which might be indicative of an unprecedented increase in multi-drug resistant infections in hospitals requiring Colistin. Dr. Kassem also estimated that, in 2017, approximately three thousand Lebanese patients (0.05 % of the population) might have required intervention with Colistin: a significant and potentially catastrophic number if Colistin becomes ineffective.

After examining agricultural practices and the clinical uses of Colistin, Dr. Kassem began looking at farming practices, particularly in poultry, one of the most defined animal farming productions in the country. A national sample selected from multiple farms in both the north and the south used fecal matter to study occurrence of the Colistin resistance gene in those farms. Kassem relied on molecular microbiology techniques to study the genetic elements and mechanisms underlying the potential resistance.

The MCR gene was highly prevalent in Lebanese poultry: in over 90% of the sampled bacteria, E. coli specifically, the gene was present, indicating that MCR was widely available to be transmitted to human populations. Kassem also looked at the transmission of Colistin resistance gene (MCR) via irrigation: irrigation water can contaminate many other essential matrices, and bacteria that carry the marker can survive in water for at least 4 weeks based on Kassem’s data. Kassem’s published paper on irrigation water is among the first on Colistin resistance in irrigation water worldwide and the first in the MENA region. 

Kassem explained: “the markers were found in bacterial strains that are also multi drug resistant, so they are problematic on their own merit even without the consideration of Colistin.” If this spreads to human populations, it will be of great concern in countries like ours with a high proportion of infectious diseases, a debilitated infrastructure, and a high number of refugees”, continued Kassem.

This research carries regional and global implications: resistance does not stay in one location and, if this pace continues in Lebanon and globally, we will reach a 'pre-antibiotic' era in which simple infections could lead to severe consequences. Already stressed populations, such as refugees, are at particular risk. Kassem hopes that FAFS and the food safety program will pioneer the galvanization of the Ministry of Public Health, the Ministry of Agriculture and the Agro-industry industry, to make the use of Colistin illegal in farming practices, via either finding a substitute or phasing Colistin out. The Ministries should begin addressing the problem via an official mandate or a decree for to use Colistin wisely in medical and agricultural practices. If the efficacy of Colistin is lost, public health will be threatened at multidisciplinary scales.

Dr. Kassem would like to acknowledge the Deanship of FAFS (present and past), collaborators at FAFS, and his wonderful research team (RAs and students) for their support and efforts in addressing this important topic. 

Dr. Issmat I. Kassem is an Assistant Professor of Food Microbiology/ Safety and the Food Safety program leader at the American University of Beirut (AUB), and an adjunct Assistant Professor of Food Safety at the Department of Veterinary Preventive Medicine at Ohio State University. Dr. Kassem led the establishment of the ASHA-USAID funded Laboratory for the Detection and Control of Foodborne Pathogens (LDCP) at AUB. His research interests include 1) understanding the mechanisms that contribute to the survival and transmission of foodborne bacterial pathogens in the host-environment continuum with emphasis on the food production chain, 2) evaluating factors that impact the selection and emergence of antimicrobial resistant pathogens in food production, and 3) evaluating antibiotic-alternatives (probiotics, organic acids) to control foodborne pathogens and enhance production.  Kassem’s overall objective is to develop antibiotic-independent and cost-effective approaches to reduce the burden of foodborne bacterial pathogens and antimicrobial resistance on public health and the economy. He has published more than 50 peer-reviewed manuscripts and serves as an associate editor and reviewer for a number of professional journals.