Tracking global foodborne bacterial diseases

Using bacterial genomes to trace disease outbreaks in food

Each year, foodborne bacterial diseases such as those caused by Salmonella are estimated to cause millions of infections across the world in both animals and humans.

In our international societies, increasingly dependent on global food chains, it is important for public safety that scientists are able to identify and track bacterial strains that can be transferred through the food we consume.

In response to this challenge, Professor Mark Achtman and his team developed EnteroBase, a world-class genome website and database for bacterial pathogens, including as Salmonella. This provided a standardised typing method that has accelerated the investigation and tracking of foodborne disease outbreaks and supported the adoption of whole genome multilocus sequence typing and bioinformatics by public health scientists.

The challenge

The huge diversity of bacterial pathogens has presented challenges for public health scientists and microbiologists, making it difficult to recognise and classify strain types.

Foodborne bacterial disease outbreaks are often multi-country, but inconsistencies in identification method and the names given to different bacterial strains across countries impede attempts to track and identify disease outbreaks. EnteroBase is a huge intervention in this field, improving and accelerating the identification and tracking of outbreaks. Similar problems affect higher order population groupings, which also need a uniform nomenclature that has previously been lacking.

Our approach

EnteroBase is a unique, web-based platform and database that enables the rapid analysis of bacterial genomic information combined with a common nomenclature for the identification of bacterial strains. It has been publicly accessible since 2016, enabling scientists across the world to share knowledge and effectively track outbreaks. Microbiologists can access the user-friendly software platform to:

• Upload sequenced DNA fragments (short reads)

• Assemble and genotype genomes

• Investigate genomic relationships and population structures

The database contains more than 450,000 genomes for the genera Salmonella, Escherichia, Yersinia, Clostridiodes, Helicobacter, and Vibrio. EnteroBase enables comparisons of genomes from diverse, distinct geographical sources and over extended time scales, helping to more effectively identify new bacterial outbreaks, and also to reconstruct the long term evolutionary history of bacterial pathogens.

Our impact

EnteroBase now has more than 3,500 users in public health organisations and industrial and allied research laboratories globally, including national reference laboratories in the UK, France, Denmark, Canada, China and South Africa responsible for investigating foodborne bacterial disease outbreaks. EnteroBase’s tools enable users to characterise bacterial isolates and use a common nomenclature, particularly helpful in the investigation of multi-national outbreaks.

This enables prompt public health decision making and rapid recall of contaminated products; in France in 2019, EnteroBase facilitated the discovery of the link between a salmonellosis outbreak in infants and contaminated infant formula, resulting in rapid product recall and investigation. Professor Achtman and his team have created a publicly accessible resource that addresses the complexity of public health concerns in an increasingly global world.