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Addressing knowledge gaps in the sources, epidemiology and genetic diversity of important foodborne pathogens

Addressing knowledge gaps in the sources, epidemiology and genetic diversity of important foodborne pathogens

  • Diet & Food Safety
  • 2022-2027
Sustainable Development icon: good health and wellbeing
Sustainable Development icon: responsible consumption and production
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There are significant gaps in our knowledge regarding the epidemiology and transmission of two foodborne pathogens: Campylobacter spp. and Toxoplasma gondii. These pathogens are some of the most important foodborne pathogens in Europe in terms of disease burden. Despite this, there remain gaps in our understanding, and have been identified as priorities for future research by food safety authorities:

  • How certain animal reservoirs contribute to the overall burden of disease
  • Information relating to the genetic diversity of strains circulating in livestock populations
  • The role of the environment in their transmission

Campylobacter is a versatile foodborne pathogen with the ability to evolve rapidly. Foodborne Campylobacter spp., which includes Campylobacter jejuni and Campylobacter coli, colonise the gut of a wide range of animal species and while some genotypes are associated with specific hosts, others have evolved to become more generalistic. While the major source of campylobacteriosis in Scotland is raw or undercooked poultry, studies have also highlighted livestock as an important reservoir. Furthermore, Campylobacter spp. may also play a role as a vehicle for antimicrobial resistance genes (ARGs) through the food supply chain. However, the role of antimicrobial selective pressure in the emergence of Campylobacter resistance in livestock is not well understood.

Toxoplasma gondii is a zoonotic parasite of global importance and can infect all warm-blooded animals, including humans. One of the most important transmission routes for people is through the consumption of undercooked meat from infected animals. Indeed, foodborne transmission is thought to be attributable to up to 50% of cases of toxoplasmosis. Despite this, there are still significant knowledge gaps surrounding the sources and epidemiology of foodborne toxoplasmosis. In particular, the role of livestock in transmission as well as the genetic diversity of strains circulating in food animals and the environment. Both the European Food Safety Authority and the UK Food Standards Agency have highlighted the urgent requirement for further studies to address these knowledge gaps.


  • What are the sources and epidemiology of foodborne disease in Scotland and what interventions can be introduced to reduce foodborne disease?


The aim of this project is to investigate the role of Scottish livestock and their environments in transmission of important foodborne pathogens, Toxoplasma gondii and Campylobacter spp., to humans. 


Circulation of Campylobacter within farmed ecosystems

We adopt two approaches to improve our understanding of how Campylobacter spp. circulating within sheep farms may contribute to the burden of human disease in Scotland. Firstly, we are applying comparative genomics of Campylobacter isolates from sheep, wildlife, and environmental samples to assess on-farm transmission. We are carrying out an intensive sampling campaign from a lowland sheep farm, which will include samples from farm animals as well as the wider ecosystem, including wildlife faecal samples and the environment. Samples from sheep, wild birds and rodents are being used to investigate host restriction of Campylobacter genotypes and the presence of generalist strains which may result in increased Campylobacter burden and dissemination of Campylobacter–associated ARGs. Water and soil samples are being used to investigate the role of the environment in the transmission of Campylobacter on-farm.

Secondly, we are focusing on host factors which may influence carriage and shedding by sheep, potentially identifying risk factors for increased transmission. We are monitoring the carriage of Campylobacter by a cohort of sheep through a longitudinal study over a year and successive lambing seasons. The health status of the animals will be recorded, their genetic background will be defined, and the farming practices will be well-controlled. This cohort will allow us to explore carriage association with several factors including age, season, and reproductive status.

Carriage of Campylobacter spp. by farmed deer in Scotland represents a further significant knowledge gap, with potential implications for the safety of venison meat and we are also investigating the presence and diversity of Campylobacter strains circulating in farmed deer populations.


The metabolic versatility in host association and clinical outcome

Metabolic versatility may influence the ability of Campylobacter subtypes to colonise multiple hosts by utilising different substrates within the host intestine, potentially increasing Campylobacter incidence on farms as well as the dissemination of ARGs. An improved understanding of substrate utilisation within the gut of animal reservoirs could also inform dietary interventions which decrease the bacterial load. We are conducting a survey of metabolic traits within 6000 Campylobacter genomes to investigate the distribution of metabolic traits within sequence types that are associated with human clinical disease and animal reservoirs, including poultry, livestock, and wild birds.


Genetic diversity of Toxoplasma gondii in Scotland

We are furthering our understanding of the sources and epidemiology of T. gondii in Scotland and identifying interventions to reduce disease. We are doing this by:

  • Investigating the genetic diversity of T. gondii in livestock, humans, and the environment (water)
  • Determining the seroprevalence of T. gondii in food animals
  • Exploring intervention strategies to reduce foodborne disease

Project Partners



2022 / 2023
2022 / 2023

Circulation of Campylobacter within farmed ecosystems

To assess the carriage of Campylobacter in different farmed ecosystems, a number of culture methods were initially compared to ensure maximum recovery of the pathogen from faecal and environmental samples. The optimum recovery method was then used to isolate and culture Campylobacter from sheep, wildlife and water from the same catchment. Samples were also collected from farmed deer at several different premises, with subsequent isolation and culturing of Campylobacter. Confirmation of isolates, and species identification will be conducted in Year 2 using Matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry (MS) analysis.

Genetic diversity of Toxoplasma gondii in Scotland

To assess genetic diversity of Toxoplasma, current methods rely on analysis of tissue samples which may not always be feasible, especially in humans. An alternative method utilises serum and offers a more accessible, and less invasive option for characterising infecting strains of the parasite in different hosts. In order to use this method for livestock, we first had to identify and source Toxoplasma strain-specific synthetic peptides as required for the assay, which required liaising and collaborating with international colleagues. Sera from different livestock species (cattle, sheep, pigs), and mice, were sourced and tested for antibodies to Toxoplasma to ensure their suitability for use in the serotyping assay. Synthetic peptides have been reconstituted, and optimisation of the Enzyme-Linked Immunosorbent Assay (ELISA) format is underway, and will continue in Year 2.

Project Impact

The research output on foodborne pathogens and antimicrobial resistance generated in this group has been presented to members of the Scottish Government Rural and Environment Science and Analytical Services Division, and Food Standards Scotland. Initiatives to reduce foodborne pathogen carriage and transmission may lower spread of antimicrobial resistance, potentially addressing National Action Plan commitments within the UK'S five-year national action plan on tackling antimicrobial resistance. Project Principal Investigators (PIs) also met with members of the Venison Advisory Service to discuss foodborne pathogens as well as sample collection in deer. Public engagement activities included the Royal Highland Show and Biggar Science Festival discussing foodborne pathogens and the spread of antimicrobial resistance on farms. A booklet has been produced, together with other researchers in Topic B6, providing information on antimicrobial resistance for the general public, which is available on the Microbe Safari website. Project PIs took part in the Annual Teachers' conference, highlighting the availability of digital educational resources on food safety and antimicrobial resistance relevant to the Scottish Biology curriculum. We have also presented our work at national and international meetings, and participated in workshops on food and waterborne Toxoplasmosis, and antimicrobial resistance. 

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