UK Health Security Agency (UKHSA) data indicate that cases of illness caused by major foodborne pathogens like Shiga toxin–producing Escherichia coli (STEC), Listeria monocytogenes, Salmonella, and Campylobacter continue to increase, with year‑over‑year growth ranging from 14–26 percent. These trends underscore the need for stronger surveillance and improved microbial control tools across the food sector.

Addressing this need, a report produced by the UK Food Safety Research Network (FSRN), led by the Quadram Institute, has identified emerging defenses against microbiological risks in food production environments (FPEs).

The paper, published in Nature Antimicrobials and Resistance, draws upon insights informally shared by UK food safety professionals—including microbiologists, quality managers, and technical managers—who have discussed the practical challenges, evolving strategies, and knowledge that are foundational to day-to-day operations for managing microbial risks in FPEs.

In general, emerging genomics tools, improved environmental monitoring, and more realistic disinfectant validation methods are now driving a shift toward science‑driven strategies designed to mitigate microbiological contamination. Additionally, elements of a strong food safety culture, such as cross-team collaboration and enterprise-wide awareness of microbial risks, were identified as important.

Core Lines of Defense Against Persistent Microbial Communities

Resident microbiota, including environmental, spoilage, and pathogenic microorganisms, continually enter FPEs via raw ingredients, personnel, equipment, water, or air handling systems. Over time, selective pressures create highly adapted microbial communities. These microbes commonly form complex, multi-species biofilms that resist routine cleaning and can lead to contamination.

The report outlines four core lines of defense against microbial risks, as identified by industry stakeholders:

1. Preventing entry: Food businesses are tightening supplier controls and emphasizing microbiological awareness of personnel, relying on relevant standards as key resources. Stakeholders highlighted the need for ongoing training and mentorship to help employees fully understand the importance of controls and foster a strong food safety culture.
2. Preventing harborage: Aging infrastructure, worn surfaces, cracked floors, and poorly designed equipment represent problematic microbial niches. Hygienic design principles remain critical, including the use of smooth, non-absorbent materials in facilities and equipment, robust engineering standards, and maintaining dry conditions. Stakeholders also cited the value of tighter collaboration between engineering and hygiene teams to ensure maintenance decisions reflect microbiological risks.
3. Preventing spread: Facilities are working to integrate rapid, easy-to-use environmental monitoring tools; for example, chromogenic sprays or hydrogen peroxide–based color indicators. These tools help identify areas where biofilms may be forming and enable timely interventions, even when more advanced diagnostics are unavailable.
4. Seek and destroy: Effective cleaning remains the cornerstone of microbial risk control, removing up to 99.8 percent of microbes even before disinfection. Businesses continue to use a range of disinfectants, including quaternary ammonium compounds (QAC), chlorine-based agents, peracetic acid, and hydrogen peroxide, while also exploring enzyme-based cleaners and oxidizing agents for enhanced biofilm penetration. Many companies are supplementing traditional agents with ultraviolet (UV) light-enhanced air systems, high-efficiency particulate air (HEPA) filtration, or antimicrobial surfaces in high-risk zones.

Scientific and Technological Advancements to Improve Microbial Control Programs

As microbial communities evolve and resist conventional approaches, food businesses are turning toward scientific collaboration and advanced analytics to strengthen hygiene, sanitation, and microbial control programs.

• Surface engineering and antimicrobial materials: Newly developed surface coatings, such as silver- or copper-infused materials, photocatalytic films, and antimicrobial polymers, are being explored to prevent microbial attachment. While high costs remain a barrier, stakeholders view such passive antimicrobial designs as promising long‑term investments, especially in hard-to-clean areas.
• Genomics and metagenomics: Whole genome sequencing (WGS) and shotgun metagenomics are emerging as transformative tools for understanding how microbes persist, spread, and adapt within FPEs. Stakeholders report that sequencing resident isolates helps distinguish transient contamination from persistent strains and supports more precise root-cause investigations. Although cost limits widespread use, strategic metagenomic surveys can establish a baseline microbial profile and guide targeted monitoring for high-risk species.
• More realistic disinfectant validation: Stakeholders stressed that many standard laboratory assays—such as minimum inhibitory concentration (MIC)/minimum bactericidal concentration (MBC) tests or European Norms (EN)-series disinfectant validations—do not reflect real-world FPE conditions. Biofilm-related tolerance, soil loads, temperature, contact time, and surface wear all influence outcomes yet are poorly replicated in standard validation tests.

Researchers and businesses are now developing multi-species biofilm models, facility-specific challenge trials, and new tools to measure biofilm resilience and metabolic recovery. These approaches aim to replace single-strain, ideal-surface testing with models that better reflect real-world FPEs.

Improved Microbial Control Enabled by Science-Based Strategies, Strong Culture

Based on stakeholder insight, the report highlights several key priorities to advance hygiene strategies and microbial control:

• Strengthening collaboration between industry and research partners to develop practical, scalable tools
• Advancing detection and monitoring with rapid tests, genomics, and improved environmental mapping
• Adopting biofilm-relevant testing models that mirror real facility conditions
• Evaluating new antimicrobials and materials based on practical performance and environmental impact
• Incorporating product quality indicators, including recall rates and consumer complaints, into hygiene performance metrics.

Overall, the researchers highlight that improving food safety must go beyond the application of stronger chemicals or more frequent testing. It demands a systems-level approach grounded in microbiology, infrastructure design, workforce knowledge, and data-driven decision-making.