Mittali Tyagi, a PhD student at Manav Rachna International Institute of Research & Studies in Faridabad, Haryana, is an environment enthusiast who works towards the promotion of sustainability. Her passion for nature has turned into a strong commitment to addressing environmental challenges and spurring change in the way we interact with the planet. As part of her PhD studies on pathogen-plant interactions, she came across fascinating research on enteric pathogen survival on plants and their implications for food safety — an observation that prompted her to author this article.
Over the past years there has been a consistent increase in the production of fresh fruits and vegetables worldwide. As production has steadily grown, exports have also expanded in tandem with the global market. Fresh fruits and vegetables are the cornerstone of a wholesome and balanced diet, offering protection against chronic ailments like heart diseases, cancer, diabetes, and obesity, as well as numerous micronutrient deficiencies — particularly in developing nations. However, raw vegetables are must now be recognised as crucial vectors for the spread of enteric pathogens. Since fresh greens are consumed raw or with minimal cooking to preserve their flavour and nutrients, they can become breeding grounds for various foodborne illnesses and outbreaks. Despite the rise in demand for fresh produce, this trend is under significant threat due to increasing microbial contamination.
Foodborne illness outbreaks can be caused by a variety of microbiological agents, including bacteria, parasites, viruses, fungi and mycotoxins. Among these, enteric pathogens — microorganisms that reside in the intestines of livestock, wild animals, and humans — pose a growing concern. Most reports involve pathogens such as E.coli, Salmonella, and Listeria. Bacterial contaminants can enter the fresh produce supply chain either during pre-harvest or post-harvest stages. Soil is one of the primary sources of contamination, particularly in fields that were previously used for animal farming, waste disposal, or manure-based fertilization. Another significant route is irrigation; water drawn from rivers or lakes may carry enteric pathogens due to runoff from sewage, soil or animal waste. Once in the plant phyllosphere or rhizosphere, these microbes nestle onto plant surfaces or are even absorbed into tissues.
What is concerning is that even disinfectants or simple water rinses are often ineffective at eliminating these pathogens.
If the microbial load on certain types of produce is sufficiently high, it can lead to gastrointestinal illnesses or other symptoms of intestinal diseases.
Standard sanitation techniques for produce are largely superficial, designed to reduce microbial load without altering texture or flavour. Yet multiple outbreak investigations have shown that even washing with chemical sanitizers often fails to eliminate harmful pathogens. The root of the problem lies in the biology of the pathogens and the complex surface structure of fresh produce — especially leafy greens — where microbes can hide in microscopic crevices.
Enteric pathogens have evolved sophisticated survival strategies. Chief among them is biofilm formation, in which bacterial communities encase themselves in protective matrices that resist disinfectants. This not only shields the microbes but also enhances their persistence on plant surfaces and equipment. Additionally, sub lethal exposure to sanitizers — due to improper dosing or short contact time — can trigger responses in pathogens, activating genes that increase tolerance. Over time, repeated low-level exposure may lead to genetic adaptation, with resistant strains emerging that survive standard cleaning procedures.
Farming practices: A double-edged sword
Modern agricultural methods may inadvertently be contributing to pathogen resistance.
The use of contaminated irrigated water, manure-based compost, and mechanical harvesting tools can introduce and spread resistant microbes across large areas.
Moreover, plants under environmental stress — be it drought, heat, or nutrient deficiency — may undergo physiological changes that make them more vulnerable to colonisation.
In high-input systems that prioritise yield and efficiency, microbial ecology is often overlooked. Could we be setting the stage for the evolution of ‘sanitizer-hardened’ pathogens? As global temperatures rise and fresh produce consumption increases, the urgency to rethink pathogen control becomes more pressing. In my view, to truly protect our food systems, it’s time to shift from a ‘kill-all’ mindset to strategies that work with — rather than against — the natural microbial communities on our farms.
The potential emergence of disinfectant-resistant enteric pathogens challenges the very foundation of current food safety systems. If the pathogens on our spinach and tomatoes are learning to survive post wash, what’s our next line of defense? Perhaps, the future of produce safety may lie beyond chemicals. Promising alternatives include biocontrol agents like beneficial bacteria or bacteriophages that outcompete or kill pathogens, plant microbiome engineering to strengthen natural defense and smart farming tools including biosensors and AI assisted hygiene systems that optimise disinfection precisely where it is needed.