Salmonella Despite control efforts, it remains the second most frequently reported zoonotic pathogen in the EU/European Economic Area (EEA). Poultry and pork have long been recognized as major sources of infection, but new research leveraging machine learning and whole genome sequencing (WGS) data provides nuanced insight into the sources and countries of human salmonellosis cases. The findings highlight the importance of a Europe-wide coordinated management strategy.
the study, Published in infection journalwas carried out by an international team of researchers under the DISCOVER research project of the One Health European Collaborative Programme.
Pan-European genome analysis
Researchers analyzed more than 10,000 cases Salmonella Genomes were collected from human, animal, and environmental sources in Denmark, England and Wales, France, Ireland, the Netherlands, Poland, Portugal, Spain, and Sweden. A total of 3,548 isolates were collected and sequenced through routine surveillance activities conducted by national public health and veterinary institutions.
Using core genome multilocus sequence typing (cgMLST) and a random forest classifier machine learning model, the team estimated the relative contributions of five major sources of information. Salmonella Serotype: S. enteritis, S. Typhimurium, S. infantis, S. Newport and S. Derby.
This model achieved moderate accuracy, although slightly lower than previous studies using WGS. Still, the findings are consistent with previously established patterns. This means that while livestock remain the main source of infection for humans, pets and wild animals play a smaller role.
Insights into serotype-specific attribution
Researchers' analysis showed that the most important causes of salmonellosis cases in humans are:
- S. Typhimurium: The main source of infection was pigs (63.8 percent), followed by dogs (7.1 percent), horses (6 percent), and broiler chickens (4.9 percent). Denmark and Portugal showed a particularly strong association with pigs (81% and 64.1%, respectively), while cases in the Netherlands were biased towards broilers (66.7%).
- S. Enterocolitis: Two-thirds (68.8 per cent) of cases were traced to laying hens, with broilers accounting for a further 19.7 per cent. Many isolates across Europe originate from Poland and Spain.
- S. infant: Broilers were the most important source (56.1 percent), followed by pigs (14.4 percent), dogs (9.8 percent), layer hens (7.6 percent), cows (6.8 percent), and turkeys (4.5 percent). Most human clinical isolates were attributed to sources in Poland (37.9 percent) and the Netherlands (31.1 percent). Interestingly, 64.3 percent of Portuguese isolates originated from Poland, and none of them occurred within Portugal.
- S. Newport: Contrast with past trend links S. From Newport to poultry, current data shows reptiles (28.1 percent) and cattle (25.9 percent) as the main sources. This finding may have been influenced by the reptile isolates being a more homogeneous population. All Portuguese sequences were attributed to Poland, as were half of the Dutch sequences.
- S. Derby: Pigs contributed the most (62.9%), followed by turkeys (22.7%) and cattle (6.1%). Consecutive sources of human isolates were considered to be Poland (43.9 percent), England and Wales (37.9 percent), and Spain (18.2 percent).
Connections beyond borders
Attribution at the country level revealed that only one third (33.1%) of human salmonellosis cases were linked to a domestic source. Many isolates originate from countries other than those where the relevant salmonellosis cases were reported, highlighting the interconnectedness of Europe's food supply chain. For example, Poland is a frequent source of infections in other countries (32.2%), reflecting the country's long-standing role as the origin of multilateral states. S. Occurrence of enteritis. In addition, approximately 20% S. Human strains of Salmonella typhimurium isolated in England and Wales, Portugal, and Denmark were attributed to Poland.
At the same time, a significant proportion (39.5%) of non-clinical sequences in the dataset was provided by Poland, with only Poland, England and Wales submitting non-clinical sequences for each serotype. Therefore, attribute overrepresentation is not unexpected. However, attributes were not proportional to the number of sequences for all other countries and/or sources for each serotype, and this model performed well for country attributes.
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Impact on control Salmonella in europe
This study confirms what risk managers already know: poultry and pigs remain the main sources of salmonellosis in humans. National action plans for poultry are on the decline; S. Similar efforts for enterocolitis infections, pigs and pork, remain lacking in most EU countries.
The findings also highlight the need for internationally harmonized control measures and improved genomic surveillance to address cross-border transmission.
Usefulness of machine learning in foodborne pathogen surveillance
Machine learning offers a promising complement to traditional typing methods, especially in real-time monitoring. However, challenges remain, especially in predicting minor sources and accounting for non-clonal populations such as pets and wildlife.
Future work should focus on expanding datasets, refining genomic markers for host adaptation, and integrating attribution models into One Health strategies.
