Understanding the diversity of Shiga toxin-producing E. coli and its relationship with human pathogenic potential

Challenges

Escherichia coli (E. coli) normally occur in the gut of animals, including humans. Most are harmless but some types of E coli cause illness in animals, some in humans, and some in both. Some are harmless to animals that carry them but cause a range of symptoms and clinical signs when they infect humans. These disease-causing E. coli often carry various genes that cause them to produce Shiga toxins. They are referred to as Shiga toxin-producing E. coli (STECs). Different strains of STEC are associated with different degrees of disease in humans, ranging from mild diarrhoea to long-term illness or, in extreme cases, death.

Scotland has more human cases per head of population than any other part of the United Kingdom. We now know a lot about the strains of STEC in Scotland due to the introduction of Whole-Genome Sequencing (WGS). This gives us lots of detailed information about each specific bacterial isolate. WGS is used to look at STEC bacteria isolated from different sources to determine if they are the same, or different. This enables us to tell if they are linked/ For instance, if a human clinical case can be attributed to a specific source, such as another human, animals, the environment, water, or food products. If we can make these links, we can begin to understand how the chain of transmission works. If we understand the chain of transmission, we can target our intervention actions to the point where they are most effective, so breaking the chain. This way we can reduce the burden of disease in the Scottish human population, reduce health service costs and save lives.

Questions

Solutions

We know how variable Shiga toxin-producing E. coli (STECs) from cattle entering the food chain for meat production, from wild deer and fresh retail beef mince in Scotland, and we know how they relate to Scottish human clinical cases. This project is finding out: 1) what types of STEC strains exist in two other important Scottish livestock ruminant sectors (dairy cattle and sheep) and the emerging sector of farmed deer; and 2) the relationships between different species within their ecosystems and with human cases. Whole-Genome Sequencing (WGS) of human outbreak isolates provides the opportunity to start to explore the One Health aspects of transmission and to investigate why the Phage-type of a STEC may influence its ability to colonise specific hosts and environmental habitats.

Isolating STEC from Scottish sheep, dairy cattle, and farmed deer

We are improving our understanding of the genetic profiles in STECs across a range of Scottish ecosystems. To do this, we are collecting faecal samples from a representative coverage of the Scottish sheep population, dairy farms, and deer farms. We are reviewing and mapping existing STEC research and surveillance activities that could contribute to the identification of circulating STEC strains in Scottish ecosystems. We are identifying where information is available, optimising the use of samples and sequences obtained for other purposes, and highlighting where important gaps exist. We are working with partners to prioritise where to focus resources to generate new ecosystem samples and data with case studies.

Whole-genome sequencing of STEC isolates 

We are whole genome sequencing STEC isolates to identify virulence gene profiles and enable phylogenetic analysis. We are investigating the relationship between the STEC strains from the different ruminant hosts and Scottish human clinical isolates. This is completing an important part of the overall picture. We are also establishing links with public health data concerning one specific strain of STEC E. coli PT 8. This is beginning to become important as a strain of interest found on leafy food produce.

Developing more rapid or simplified testing for non-O157 STEC

We are using non-O157 STEC strains (E. coli O157 is the most common strain) isolated in this project and from previous studies to improve current methods for isolation and characterisation of non-O157 STEC. This is currently a labour-intensive and time-consuming process for diagnostic laboratories.

Overall, this project is helping to understand the STEC strains in circulation within Scotland. This understanding is improving source attribution of STEC during clinical outbreak investigations and informing targeted interventions aimed at reducing human STEC infections.