Genome sequencing reveals how Salmonella carves out a niche in pork production.

05 May 2021

A new study into common variants of Salmonella present in pigs has found that they can have very different effects on the health in pigs and also on the risks they pose to food safety.

Variants of concern (VOCs) and variants of interest (VOIs) have become familiar terms due to the current pandemic, but variants of familiar pathogens such as Salmonella also present a threat to human and animal health.

To better understand the different threats these variants pose, a collaboration led by Professor Rob Kingsley from the Quadram Institute and Professor Mark Stevens from the Roslin Institute working with scientists from the Earlham Institute has focused on common variants of Salmonella present in pigs in the UK. 

Their findings, published recently in the journal Nature Communications, has shown that despite being extremely closely related, variants can have very different effects on the health of the pig and also on the risks they pose to food safety.

Salmonella Typhimurium is one of the most common types of Salmonella. It is a major cause of human gastroenteritis, notably from consuming undercooked pork products or as a result of cross-contamination of foods consumed raw. This bacterial pathogen is also a concern to the pork industry due the health and welfare of pigs and potential effects on productivity. Salmonella Typhimurium is relatively common in pig herds globally, and processes implemented in abattoirs are designed to prevent contamination of meat destined for the food chain. 

Bacterial pathogens continually evolve to exploit new ecological niches. Human activity, including agricultural practices and how we use medicines and antimicrobials may drive the emergence of new variants. Understanding exactly how this happens is crucial to countering the consequences of new variants on human and animal health, and the answers lie in the bacteria’s genes. Genome sequencing can read all of an organism’s genes and can help unlock those answers by resolving relationship of variants, identifying variants that are evolving as they enter a new niche, and pinpointing potential functional changes that affect their ability to cause disease or survive in the food chain.

The team worked with Public Health England and the Animal and Plant Health Agency and to examine Salmonella isolates from human clinical infections during routine diagnostics or from animals during routine surveillance, with funding from the Biotechnology and Biological Sciences Research Council, part of UKRI.

Using whole genome sequencing the research team found that two types of S. Typhimurium, dubbed U288 and ST34 have been circulating in UK pigs since 2003. Surprisingly, U288 are rarely associated with human infection, while ST34 account for over half of all S. Typhimurium infections from all sources, not just pigs. What is more, the two types of Salmonella infected pigs differently, resulting in distinct levels of colonisation of the intestine and surrounding tissue, and disease severity in the first days of infection. The U288 variant grew more slowly in the lab and was more sensitive to stress associated with desiccation. These characteristics may affect its ability to survive in the food chain.

Inspection of changes in the genome sequence of U288 indicated that this variant emerged by a unique set of changes that occurred within a short period of time, probably between the years 1980 and 2000. The researchers believe that these changes hold the key to understanding how this variant interacts differently with pigs during infections, in the lab, and potentially the food chain.

"We have seen these types of changes before in variants of Salmonella that have become adapted to specific host species and cause a more invasive disease, including the type of Salmonella that specifically causes typhoid fever in people, but is never found in livestock or wild animals’ said Prof. Rob Kingsley, a group leader at the Quadram Institute and Professor of Microbiology at the University of East Anglia. 

‘One of the interesting findings is just how rapidly pathogens can adapt, and how even a few genomic changes can lead to very different disease outcomes,” said Dr Matt Bawn a researcher involved in the study based at both the Earlham Institute and Quadram Institute.

Understanding how variants of Salmonella emerge and pinpointing the genetic signatures responsible provide opportunities to improve diagnostics and surveillance that will help predict the risk that Salmonella poses to animal health and the risk to food safety.


Notes to editors.

Notes to Editor


For further information, please contact:

Hayley London

Marketing & Communications Officer, Earlham Institute (EI)

  • +44 (0)1603 450 107


About Earlham Institute

The Earlham Institute (EI) is a world-leading research Institute focusing on the development of genomics and computational biology. EI is based within the Norwich Research Park and is one of eight institutes that receive strategic funding from Biotechnology and Biological Science Research Council (BBSRC) - £5.43m in 2017/18 - as well as support from other research funders. - as well as support from other research funders. EI operates a National Capability to promote the application of genomics and bioinformatics to advance bioscience research and innovation.

EI offers a state of the art DNA sequencing facility, unique by its operation of multiple complementary technologies for data generation. The Institute is a UK hub for innovative bioinformatics through research, analysis and interpretation of multiple, complex data sets. It hosts one of the largest computing hardware facilities dedicated to life science research in Europe. It is also actively involved in developing novel platforms to provide access to computational tools and processing capacity for multiple academic and industrial users and promoting applications of computational Bioscience. Additionally, the Institute offers a training programme through courses and workshops, and an outreach programme targeting key stakeholders, and wider public audiences through dialogue and science communication activities. / @EarlhamInst

About University of East Anglia (UEA)

The University of East Anglia (UEA) is a UK Top 25 university and is ranked in the top 50 globally for research citations. Known for its world-leading research and good student experience, it was awarded Gold in the Teaching Excellence Framework and is a leading member of Norwich Research Park, one of Europe’s biggest concentrations of researchers in the fields of environment, health and plant science. / @uniofeastanglia

About Quadram Institute

The Quadram Institute ( is an interdisciplinary research centre at the forefront of a new era of food and health research.  It brings together researchers and clinicians under one roof and houses one of Europe’s largest endoscopy units and a clinical trial facility.  It focuses on lifelong health – from birth and throughout the lifecourse, increasing healthspan as well as lifespan.  It undertakes both fundamental and translational research working with industry to accelerate innovation and bring novel therapeutics and new food products to patients and consumers.  

Based on the Norwich Research Park, The Quadram Institute is a partnership between Quadram Institute Bioscience, the Norfolk and Norwich University Hospitals NHS Foundation Trust, the University of East Anglia and the Biotechnology and Biological Sciences Research Council (BBSRC).

Four interconnected interdisciplinary research themes in Quadram Institute Bioscience deliver a pipeline of research in plants, microbes, food and health: microbes in the food chain; the gut and the microbiome; food innovation and population health.

About Norwich Research Park

Norwich Research Park is home to over 12,000 people including 80 companies and 3,000 researchers and clinicians.

Norwich Research Park is a partnership between the University of East Anglia, the Norfolk and Norwich University Hospitals NHS Foundation Trust, four independent world-renowned research institutes namely the John Innes Centre, the Quadram Institute and the Earlham Institute (all strategically funded by the Biotechnical & Biological Sciences Research Council (BBSRC) as part of United Kingdom Research & Innovation (UKRI)) and The Sainsbury Laboratory linked to the Gatsby Charitable Foundation. The BBSRC - UKRI and the John Innes Foundation are also partners. 

The main strength of Norwich Research Park is the concentration of world-leading scientists, entrepreneurs and business. We continue to attract new partners and businesses to the Park as part of this innovation cluster.

An Enterprise Zone location providing business rates benefits, the Park includes 52 hectares of development land, ideal for expanding companies needing bespoke office space and research facilities.