GENOMIC SURVEILLANCE OF FOOD AND WATERBORNE BACTERIA: DIFFERENT LABORATORIES, A SHARED INTERPRETATION

Understanding where an infection begins and how it spreads is key to protecting public health. Some microorganisms can affect humans, animals or both, and may be transmitted either directly between hosts or via contaminated food or water. Tracing the links between cases, even across time and distance, requires increasingly sophisticated tools. Genomics is transforming the game: by examining the entire genetic makeup of bacteria, scientists can spot connections that traditional methods might miss. When combined with epidemiological investigations — the study of how infections move through populations over time and space — it enables more accurate and rapid outbreak investigations.

The new study, part of the European BeONE project, examined how reliable and comparable different genomic approaches are across a wide range of European public health laboratories. Eleven research institutes, including the Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, took part in a large-scale comparison, working on the same strains of food and waterborne bacteria: Listeria monocytogenes, Salmonella enterica, Escherichia coli, and Campylobacter jejuni.

To ensure a fair assessment, the laboratories worked with real datasets but were not told in advance which samples were epidemiologically linked. This allowed researchers to see whether different analytical methods, despite using distinct procedures, could still group the samples in similar ways. The results showed a high level of consistency across the board.

“We worked as if we were part of a real international surveillance network, each using our own method but all analysing the same data - says Nicolas Radomski, IZS Teramo - The goal was to understand the similarities and differences between the various approaches, and to see how well we were speaking the same analytical language.”

At the heart of the study is Whole Genome Sequencing (WGS), a technique that decodes the full genome of a microorganism. Unlike traditional methods, which focus only on certain regions of DNA, WGS provides a complete picture, detailed enough to tell apart even closely related strains. That kind of resolution enable researchers, for example, to understand whether infection cases in different countries might share a common source.

IZSAM played a key role in the project, contributing both to data analysis and to the development of digital tools for comparing results across laboratories. Thanks to its long-standing experience in genomics applied to food and environmental safety, the Institute was also able to address some of the more technical aspects, such as evaluating the impact of software updates on analytical outcomes.

The findings were encouraging: in most cases, different laboratories produced highly similar results. Some differences did emerge with Campylobacter jejuni, a bacterium known for its high genetic variability.

One of the key challenges lies in setting thresholds to decide when two bacterial strains are considered genetically "close". It’s a bit like reading a map: two cities might seem near or far depending on the scale you are using. Similarly, in genome comparisons, small tweaks to the criteria can shift the outcome. The study showed that with well-calibrated flexibility, it is possible to align different approaches and improve the ability to detect connections between cases.

“There is no need to force everyone to use a single method. What matters is finding ways for different methods to work together - says Andrea de Ruvo, IZS Teramo - It’s about interoperability, not rigid standardisation”.

“This is a good example of how collaboration between human, animal, and environmental health sectors across Europe can lead to better tools for protecting public health - comments Adriano Di Pasquale, IZS Teramo - And how genomics, when combined with epidemiology, can become a practical resource for laboratories in their everyday work".