Pathogens-in-Foods database: a web application for assessing the occurrence data of microbiological hazards in foods marketed in Europe

Pathogens-in-Foods (PIF) is a dynamic database of systematically organized occurrence data (both prevalence and enumeration) of important pathogenic bacteria, parasites and virus in foods randomly surveyed across Europe, extracted from published peer-reviewed articles and reports.

The database is constructed upon systematic literature searches on several bibliographic engines for the most relevant pathogens, specifically Bacillus cereus, Campylobacter spp., Clostridium perfringens, Listeria monocytogenes, Salmonella spp., Shiga toxin-producing Escherichia coli, Staphylococcus aureus, Yersinia enterocolitica, Cryptosporidium spp., Giardia spp., Toxoplasma gondii, Hepatitis A virus, Hepatitis E virus and Norovirus, in foods surveyed from European farms, processing facilities, retail establishments and restauration.

After the filtered primary studies are screened for relevance and their methodological quality are assessed for inclusion, the data are extracted into the PIF database following a systematic categorization comprised of primary study characteristics, pathogen information, microbiological methods, food and food chain characteristics, and prevalence and/or enumeration results.

The database is accessible through a web application (https://fsqa.esa.ipb.pt/) that facilitates data access and retrieval according to microbiological hazard, country, food class, or other relevant variables, producing dynamic charts and summary statistics of incidence, and it is highly intuitive and easy to use.

The Pathogens-ln-Foods database presently includes 1172 primary studies and close to 5200 bacteria, virus, and parasite entries, spanning data published from 2000 onwards to the present day, and new data are continuously added. It presents solid scientific and computational basis for growth and is intended to be used by researchers and food authorities after meta-analysis, in microbiological risk assessment for establishing future food safety guidelines.