by Shivaprasad Doddabematti Prakash, Ph.D. Candidate, Department of Grain Science and Industry, Kansas State University, Manhattan, Kansas (CAST Student Member and 2024 CAST Science Communication Scholarship winner)

For decades, low-moisture foods such as wheat, flour, nuts, and spices were regarded as “microbiologically safe” because of their low moisture content. This attribute has led to a general confidence that these products are low-risk foods (Jung & Harris, 2022). However, recent outbreaks and recalls, which were previously unexpected, tell a different story: low does not mean no.

Today, regulators and consumers are seeing that dry goods, including wheat flour, can act as unsuspected vehicles for enteric pathogens like Salmonella and Shiga-toxin producing Escherichia coli (STEC). In fact, in the past decade, wheat and flour have been repeatedly linked to foodborne illness outbreaks in the United States (Rivera et al., 2025). These incidents are reshaping how the agricultural and milling sectors think about food safety, highlighting the urgent need to address microbial risks even in products traditionally considered low-risk.

Where Do the Pathogens Come From?

Wheat grains and their derived products can harbor harmful pathogens introduced at various stages of the supply chain. It explores the primary sources of microbial contamination that impact the safety of wheat-based foods, highlighting both pre-harvest and post-harvest factors that contribute to the presence and persistence of pathogens (Shivaprasad et al., 2025).

• Pre-harvest contamination:
  Wheat grains are vulnerable to microbial contamination in the field due to exposure to soils, water, manure, and animal activity. Pathogens such as  coliand Salmonella can persist in soils for extended periods, especially when amended with manure, and may even internalize into plant tissues. Irrigation with contaminated surface or groundwater further increases the risk, as bacteria can survive on or within developing plants. Environmental factors like temperature, precipitation, soil type, and farming practices (e.g., use of untreated manure near livestock operations) strongly influence the survivability and spread of pathogens. Collectively, these factors make the pre-harvest stage a critical period for the introduction of enteric pathogens into wheat grains.
• Post-harvest contamination:
  After harvest, wheat grains can be exposed to additional contamination risks during transportation, storage, cleaning, tempering, and milling. Dust accumulation, insects, rodents, and birds in storage facilities can act as reservoirs and vectors of pathogens. Equipment surfaces and residual grain deposits also facilitate cross-contamination, especially during tempering and milling, where moisture and residues create niches for microbial growth. Additionally, the physical nature of the milling process redistributes the pathogens into flour fractions. Further, inadequate cleaning of transport vehicles, bins, or milling equipment increases the hazard. Thus, post-harvest handling practices and facility hygiene play a decisive role in determining the microbial safety of wheat flour and derived products.

Interventions to Improve the Safety of Wheat-Based Foods

Efforts to reduce pathogen contamination in wheat and flour can be grouped into three broad strategies: antimicrobial tempering, thermal treatments, and non-thermal technologies.

• Antimicrobial tempering integrates acids, oxidizers, or biological agents into the water used during wheat conditioning before milling. This approach takes advantage of the natural resting period in tempering to allow antimicrobials to act against pathogens, achieving up to 6 log reductions in Salmonella and STEC under research conditions. Options tested include lactic acid, sodium bisulfate, peracetic acid, ethanol-water blends, chlorinated water, and bacteriophages (Shivaprasad et al., 2023b; 2024; Rivera et al., 2025). The method is attractive because it fits into existing milling operations with minimal disruption, though its effectiveness depends on contact time, moisture level, and the agent used.
• Thermal treatments rely on heat delivered through steam, heated air, vacuum systems, or radiofrequency heating. Studies show these methods can achieve reductions up to 7 logs in pathogens while preserving flour quality. Combinations of mild heat with acids during tempering have also proven effective, shortening treatment times and increasing reductions. However, equipment costs, energy requirements, and challenges related to low water activity in wheat remain barriers to widespread commercial adoption (Rivera et al., 2025).
• Non-thermal treatments such as pulsed light and atmospheric cold plasma are emerging technologies that have gained attention as alternatives that inactivate pathogens without the drawbacks of intensive heat. These approaches produce 6 log reductions in pathogens under controlled conditions. Their advantage lies in flexibility; they can be applied to grains, flour, or dough. Still, they also require specialized equipment, and more work is needed to validate performance at commercial scale and assess impacts on flour functionality (Shivaprasad et al., 2023a).

Together, these interventions represent promising advances in flour safety, though scaling them to industry use will depend on optimizing cost, feasibility, and consistency across different wheat types and processing conditions.

Building a Safety Culture for Low-Moisture Foods

• The role of regulators: Currently, there are no mandated performance guidelines for pathogen reduction in wheat milling. The pathogen reduction performance of these mitigation strategies discussed above is still manufacturer-specific. However, in general, millers usually prefer at least a 3 log CFU/g reduction for interventions used on wheat or wheat flour (Rivera et al., 2021). Therefore, concerted efforts of regulators, researchers, and industry leaders are needed to establish benchmark pathogen reduction standards to ensure the safety of low-moisture foods.
• The role of consumer education: Currently, there is a lack of consumer knowledge about the food safety risks of wheat-based products, and the common risk behavior of consuming raw cookie dough and batter. This behavior can contribute to the occurrence of foodborne outbreaks. It is crucial that we, as a collective of public health officials, food safety regulators, policymakers, and food industry stakeholders, work together to increase awareness regarding the food safety issue of wheat-based products through educational campaigns.
• The role of collaborative research: An integrated research partnership between academia, industry, and government agencies is crucial. This collaboration provides scientific knowledge, practical industry needs, and regulatory oversight, which helps in developing novel intervention strategies to improve the safety of low-moisture foods. This integrated approach will also help validate and implement the novel strategies across the wheat supply chain, ensuring that they are both aligned with the food safety goals and economically feasible.

Conclusion:

Foodborne outbreaks and recalls involving wheat flour and wheat flour-based products have shown that the wheat-based foods should not be considered “microbiologically safe” foods and that improvements in the existing manufacturing process for wheat-based foods are needed in the future to prevent the occurrence of recalls and illness outbreaks. Implementing novel intervention strategies from the pre-harvest and post-harvest stages can provide a holistic approach to combating pathogen contamination.

References

Jung, J., & Harris, L. J. (2022). Survival of Salmonella and Shiga toxin–producing Escherichia coli during tempering of wheat berries. Food Control, 109343. https://doi.org/10.1016/j.foodcont.2022.109343

Rivera, J., Deliephan, A., Dhakal, J., Aldrich, C. G., & Siliveru, K. (2021). Significance of sodium bisulfate (SBS) tempering in reducing the Escherichia coli O121 and O26 load of wheat and its effects on wheat flour quality. Foods, 10(7). https://doi.org/10.3390/foods10071479

Rivera, J., Shivaprasad, D. P., Sabillón, L., & Siliveru, K. (2024). Enteric pathogen survival, food safety incidents, and potential mitigation strategies to address microbial contamination in wheat-based foods: a review. Critical Reviews in Food Science and Nutrition, 0(0), 1–12. https://doi.org/10.1080/10408398.2024.2387766

Shivaprasad, D. P., Siliveru, K., & Zheng, Y. (2023a). Emerging applications of cold plasma technology in cereal grains and products. Trends in Food Science and Technology, 141(September), 104177. https://doi.org/10.1016/j.tifs.2023.104177

Shivaprasad, D. P., Rivera, J., & Siliveru, K. (2023b). Control of Salmonella in wheat grains with sodium bisulfate tempering and its impact on flour quality. Cereal Chemistry, November. https://doi.org/10.1002/cche.10737

Shivaprasad, D. P., Rivera, J., & Siliveru, K. (2024). Acidic water tempering and heat treatment, a hurdle approach to reduce wheat Salmonella load during tempering and its effects on flour quality. Food Research International, 176(November 2023), 113723. https://doi.org/10.1016/j.foodres.2023.113723

Shivaprasad, D. P., Rivera, J., Sabillón, L., & Siliveru, K. (2025). From wheat grain to flour: a review of potential sources of enteric pathogen contamination in wheat milled products. Critical Reviews in Food Science and Nutrition, 65(15), 2965–2975. https://doi.org/10.1080/10408398.2024.2353892