Foodborne illness and food hypersensitivity research

1. Estimating Quality Adjusted Life Years and Willingness to Pay Values for Microbiological Foodborne Disease 

   To provide the evidence for the impact of foodborne illness, we have co-funded research to quantify the burden associated with microbiological foodborne disease (FBD) caused by 10 important pathogens. 

   • Estimating Quality Adjusted Life Years and Willingness to Pay Values for Microbiological Foodborne Disease (Phase 2) (September 2017)

2. The second study of infectious intestinal disease in the community (IID2 Study)

   The infectious intestinal disease (IID) study 2 was carried out to estimate the prevalence of IID in the UK population. It follows on from IID1 which was carried out between 1993 and 1996. The study provided critical data to support the surveillance of key pathogens responsible for gastrointestinal disease in the community, capturing information on cases that otherwise remain unreported in national databases.

   • IID2 Study-The second study of infectious intestinal disease in the community (September 2011) 

3. Fridge recording over set time (FROST; 2025)

   A citizen science project was conducted by FSS between August 2023 and May 2024 with over 350 households to measure fridge temperatures in consumers’ homes across Scotland. The data revealed that, on average, fridge temperatures were too high and few consumers were correctly checking the temperature of their fridge, putting the public at increased risk of foodborne illness.

   • FROST: Fridge Recording Over Set Time | Food Standards Scotland

1. Quantifying the seasonality of E. coli O157 shedding (concentration and prevalence) in cattle and estimating its effect on the number of cases of food poisoning (2003)

   A quantitative study of the seasonal variation in the prevalence and concentration of E. coli O157 shedding in cattle and an assessment of its impact on human foodborne illness. The report compared faecal samples collected at a local abattoir during winter and summer months.

   • Quantifying the seasonality of E. coli O157 shedding (concentration and prevalence) in cattle and estimating its effect on the number of cases of food poisoning (April 2003)

2. Prevalence of Faecal Shedding on Scottish Beef Cattle Farms of Verocytotoxigenic Escherichia Coli Serotypes: O26, O103, O111, O145 (2004)

   A study of the frequency of shedding of key non-O157 verocytotoxigenic E. coli (VTEC) strains (O26, O103, O111, O145)  in the faeces of Scottish beef cattle close to sale or slaughter, and to estimate the proportion of farms affected. Researchers collected >6,000 faecal samples from 338 farms across Scotland, to detect and characterise VTEC strains, and evaluating seasonal and regional variation.

   • Prevalence of Faecal Shedding on Scottish Beef Cattle Farms of Verocytotoxigenic Escherichia Coli Serotypes: O26, O103, O111, O145 (June 2004)

3. Comparison of Human and Cattle E. coli O26 Isolates by Pulsed Field Gel Electrophoresis (2004)

   A study aimed at determining whether E. coli O26 strains isolated from humans and Scottish cattle share common genetic profiles and assessing the potential for cattle to act as a reservoir for human infection. Researchers analysed E. coli O26 isolates using pulsed-field gel electrophoresis (PFGE) and virulence gene profiling to compare genetic similarity and assess overlap between human and bovine populations.

   • Comparison of Human and Cattle E. coli O26 Isolates by Pulsed Field Gel Electrophoresis (PFGE) (May 2004) 

4. Prevalence and concentration of Escherichia coli serotype O157 and other VTEC in sheep presented for slaughter in Scotland (2007)

   A study examining the prevalence and concentration of Escherichia coli O157:H7 and other verocytotoxigenic E. coli (VTEC) in sheep presented for slaughter in Scotland. To assess seasonal and demographic factors influencing shedding, researchers collected faecal samples from slaughtered sheep across various abattoirs, testing for E. coli O157:H7 and non-O157 VTEC.

   • Prevalence and concentration of Escherichia coli serotype O157 and other VTEC in sheep presented for slaughter in Scotland (September 2007)

5. Feasibility of introducing methods, in the UK, for reducing shedding of E. coli O157 in cattle (2013)

   The study aimed to assess the feasibility of implementing existing methods to reduce E. coli O157 shedding in cattle on UK farms, thereby lowering risks to human health via food and environmental exposure. It employed a two-part approach: (1) reviewing published data on the cost, practicality, and effectiveness of on-farm controls, and (2) investigating the behavioural and external factors influencing farmers’ willingness to adopt these measures, followed by stakeholder engagement to discuss implementation.

   • Feasibility of introducing methods, in the UK, for reducing shedding of E. coli O157 in cattle (February 2013)

6. Whole genome molecular epidemiology of E. coli O157 isolates from humans, food and the environment (2014)

   The report aimed to explore how whole genome sequencing (WGS) could enhance understanding of the diversity and transmission of E. coli O157 strains in Scotland. The study sequenced 148 isolates using Next gen sequencing and phylogenetic analysis to investigate relationships between strains of E. coli O157 isolates from humans, animals, and the environment.

   • Whole genome molecular epidemiology of E.coli O157 isolates from humans, food and the environment | Food Standards Scotland 

7. The fate of surrogate verocytotoxic E. coli contaminating the rhizospheres of root vegetables during processing and retail and wholesale distribution (2016)

   The study assessed how E. coli survives on vegetables contaminated via soil, manure, or irrigation water, particularly during harvesting and processing. Using non-pathogenic E. coli O145 as a surrogate, the study simulated worst-case contamination scenarios and evaluated how commercial washing and handling practices affect bacterial survival and potential cross-contamination risks.

   • The fate of surrogate verocytotoxic E. coli contaminating the rhizospheres of root vegetables during processing and retail and wholesale distribution (March 2016). 

8. Use of treatments to prevent the growth of pathogens on sprouted seeds (2016)

   In addition to these studies strategies to minimize bacteria contamination in vegetable produce were investigated. This study specifically looked at methods that can be used by consumers to reduce E. coli and Salmonella in legumes for home sprouting. Treatment with hot water, citric and acetic acid were tested, with hot water being the most effective method for reducing bacteria levels on mung beans and alfalfa seeds.

   • Use of treatments to prevent the growth of pathogens on sprouted seeds (March 2016) 

9. The capacity and pathogenic potential of bacteria that internalise into plant tissue (2017)

   FSS co-funded the studies to investigate the capacity and pathogenic potential of bacteria that internalise into plant tissue. The study revealed some key factors surrounding internalised bacteria that has enabled the identification of areas for potential improvement of current practices and opportunities for further research.

   • Capacity and pathogenic potential of bacteria that internalise into plant tissue (March 2017).

10. E. coli O157 Super-shedding in Cattle and Mitigation of Human Risk (2018)

    This research report aimed to investigate the dynamics of E. coli O157 excretion in cattle, particularly focusing on potential "super-shedder" animals that excrete exceptionally high levels of the pathogen. It used farm surveys, genomic sequencing, and transmission modelling to understand prevalence, strain variation, and potential interventions to reduce human exposure through the food chain.

    • E. coli O157 Super-shedding in Cattle and Mitigation of Human Risk (November 2018) 

11. Whole Genome Sequence Typing and Analysis of Non-O157 STEC (2020)

    FSS has commissioned research into the molecular epidemiology of E. coli O157 and non-O157 in the Scottish population. One study was commissioned to carry out whole genome sequencing on Scottish National Culture Collection of non-O157 STEC with the aim of identifying strains of non-O157 STEC causing human clinical infection in Scotland over a 16 year period. The study also aimed to assess the potential of each strain to cause clinical disease based on the presence of virulence genes, and to provide a Scottish-wide genomic database of non-O157 to aid  future monitoring of outbreaks.

    • Whole Genome Sequence Typing and Analysis of Non-O157 STEC (February 2020)

12. The risk of STEC contamination in wild venison (2020)

    FSS work into understanding the risk of E. coli in the food chain extends beyond cattle and fresh produce. We have funded studies into investigating the risk of STEC contamination in wild venison.

    This report aimed to fill knowledge gaps about the presence and transmission of Shiga toxin-producing E. coli (STEC) in Scotland’s wild venison supply chain. It mapped the venison industry, assessed STEC prevalence in wild deer faeces, and evaluated cross-contamination risks during field dressing and processing.

    • The risk of STEC contamination in wild venison (November 2020)

13. Pathogen Surveillance in Agriculture, Food and the Environment (PATHSAFE; 2021 – 2025)

    As part of the PATHSAFE programme run by the FSA, FSS ran a pilot project focused on E. coli transmission from farm to fork throughout Scotland, sequencing isolates obtained from livestock, wild animals, wastewater, shellfish, food, private water supplies and clinical samples. As part of this, source attribution models for bovine, ovine, poultry, swine, deer and human hosts were developed, resulting in a tool that can be used for identifying potential routes of contamination of E. coli within the food chain. This collection of approximately 4,500 E. coli sequences also provides a wealth of information of the antimicrobial resistance (AMR) genes present throughout the food chain.

    • Pathogen Surveillance in Agriculture, Food and Environment (PATH-SAFE) Programme | Food Standards Agency

Reducing the risk of Campylobacter infection is a key priority for FSS, as it is the most common form of bacterial foodborne illness in Scotland and the rest of the UK. 

1. Factors associated with geographic and temporal variation in campylobacteriosis in humans (2011)

   As part of understanding the epidemiology of campylobacter in Scotland, we commissioned research into examining the factors associated with the distribution of campylobacter cases in Scotland using molecular typing and epidemiological data.

   • Factors associated with geographic and temporal variation in campylobacteriosis in humans (April 2011) 

2. Private water supplies as a risk factor for Campylobacter infection in Aberdeen City and Aberdeenshire (2011)

   The risk of campylobacter in water supply have been investigated. Private water supply presents a higher risk of infection to people compared to mains water supply.

   • Private water supplies as a risk factor for Campylobacter infection in Aberdeen City and Aberdeenshire (August 2011)

3. Campylobacter in wild game (2016) 

   We have also investigated campylobacter in wild game birds. This study was carried out to determine the prevalence of campylobacter species in wild game pheasants processed in Approved Game Handling Establishments (AGHE) in Scotland. Campylobacter strains found in pheasants were compared with those isolated from broilers and humans in Scotland.

   • Campylobacter wild game project - University of Edinburgh (January 2016)

4. Campylobacter: Estimating the burden of gastrointestinal infection in Scotland using data linkage (2020)

   Our most recent study of Campylobacter estimates the burden of gastrointestinal infection caused by Campylobacter spp using linkage data for laboratory confirmed cases in Scotland from 2013 -2017.

   • Campylobacter: Estimating the burden of gastrointestinal infection in Scotland using data linkage (March 2020) 

5. Campylobacter: Estimating the healthcare cost of gastrointestinal infection in Scotland (2020)

   A similar study explored the healthcare cost associated with campylobacter infection and identified groups where reductions in the incidence of infection would potentially have the greatest impact in terms of the costs incurred by the health service in Scotland.

   • Campylobacter: Estimating the healthcare cost of gastrointestinal infection in Scotland (March 2020)

6. Factors affecting variations in campylobacter disease rates in Scotland (2020)

   FSS commissioned this study to investigate differences in campylobacter incidence in relation to deprivation in Scotland. The study aimed to understand why there are differences in disease incidence between more and less deprived populations, and to obtain an up-to-date picture of campylobacter infection in Scotland.

   • Factors affecting variations in campylobacter disease rates in Scotland (March 2020)

7. Campylobacter source attribution studies (2009-2018)

   To enable an in-depth understanding of the sources of campylobacter infection in humans, a series of source attribution studies were commissioned to assess a variety of potential sources of campylobacter that may present a risk to the Scottish population. Samples and isolates from human clinical cases, livestock (cattle, sheep, pigs and poultry), wild birds, and companion animals were analysed to generate epidemiological and genomics data to which statistical modelling was applied infer sources of infection.

   • Campylobacter source attribution project in Scotland 2005-2007 (May 2009)
   • Campylobacter source attribution project in Scotland 2011-2012 (November 2012)
   • Campylobacter source attribution project in Scotland 2010-2011 (November 2011)
   • Campylobacter source attribution project in Scotland 2012-2015 (December 2016) 
   • Campylobacter source attribution project in Scotland 2015-2016 (February 2018) 

8. Reducing campylobacter in the older population (2022)

   People aged 65 and over are at greater risk of serious side effects from campylobacter poisoning as the body’s immune system weakens as we age. A campaign was launched in 2022 to raise awareness of the risks of campylobacter with people aged 65 and over and their supporters, with information packs distributed at supermarkets throughout Scotland, presentations given at assisted living premises and digital and physical information packs disseminated via partnerships with external organisations.

   • Campylobacter campaign partner toolkit

1. Review of current practices in the management of L. monocytogenes during smoked fish production in Scotland and N. England (2012)

   A review of current practices used by the smoked fish sector in the management of Listeria monocytogenes was carried out to identify key issues that may influence the prevalence of this bacteria in smoked fish.  A literature review was carried out along with a series of farm and industry visits. A cross-sectional survey of environmental health officers (EHOs) was also conducted. It was identified that typically, 15-20% of raw fish entering smoking factories can be contaminated with L. monocytogenes. Certain biotypes of the bacteria can colonise and persist in smoking plants and these biotypes are more likely to be present in the finished product. 

   The survey indicated that EHOs’ main concerns relate to plant cleaning and sanitation, the control of key hazardous microorganisms, product characteristic monitoring, post process handling and shelf life determinations. EHOs also felt that there is a lack of understanding regarding HACCP, particularly in smaller businesses.

   • Review of current practices in the management of L. monocytogenes during smoked fish production in Scotland and N. England (September 2012)

1. Survey of antimicrobial resistance bacteria in chicken and pork (2018)

   Food Standards Scotland funded research to investigate the prevalence of antimicrobial resistance (AMR) in British-produced food to fill an evidence gap and provide important data to support risk assessments and monitoring of AMR. The study provides a baseline of the prevalence, types and levels of AMR in poultry and pork. AMR was more prevalent in chicken than pork. However, the risk of acquiring resistant bacteria is very low if proper cooking and hygiene measures are adhered to. 

   • Survey of antimicrobial resistance bacteria in chicken and pork (September 2018)

1. Food allergies survey results

   Our ongoing work involves protecting the public from the detrimental effects of food allergens. The food allergy survey was commissioned to understand the experiences and perceptions of young people in relation to food allergies. The survey which was carried out in partnership with Young Scot included a campaign to encourage people to be open and talk about food allergies. The findings showed that more than 1 in 4 persons who completed the survey has a food allergy and calls for increased awareness about the seriousness of food allergies.

   • Food allergies survey results (February 2020)