Introducing the pig barometer: A comprehensive pilot tool for mapping diagnostic test results and geolocation of swine endemic pathogens in Spain
Abstract
This work introduces the Pig Barometer, a pilot dashboard that visualizes PCR-based diagnostic data for three endemic swine pathogens—Mycoplasma hyopneumoniae, swine influenza virus (SIV), and Lawsonia intracellularis—from Spanish veterinary laboratories. Data from 23,249 cases (2020–2023) were cleaned in Python, converted to RDF, and structured with ontologies for interoperability. Visualization was implemented in Tableau, showing trends by time, specimen type, production stage, and geography. Positive detection rates were 24.1% for SIV, 27% for M. hyopneumoniae, and 41.8% for L. intracellularis. The tool supports disease surveillance and decision-making, with plans to expand to more pathogens and countries. This work was presented as a poster at the European Symposium of Porcine Health Management (ESPHM) 2025, held in Bern, Switzerland (Reference: HHM-PP-08).
Full text
Introducing the Pig Barometer: A comprehensive pilot tool for mapping diagnostic test results and geolocation of swine endemic pathogens in Spain Garcia-Morante, B1, Noor, S2, Hostens, M3, Ainoza, A4, Barrera, X5, Camón, S4, Chacón, G6, Del Caso, S6, Fernández, V7, Maldonado, J8, Martínez-Guinó, L5, Penalba, C9, Valls, L8, Sibila, M1, Vilalta, C1, Segalés, J1 1 Unitat mixta d’investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Catalonia, Spain. 2Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium. 3Department of Animal Science, Cornell University, Ithaca, NY 14853, United States. 4Eurofins Convet S.L.U., Corregidor Escofet 83-85, 25005 Lleida, Spain. 5 Biofar Labratoris S.L., Calle Forns 18, 08261 Cardona, Barcelona, Spain. 6Exopol S.L., Polígono Río Gállego, 50840 San Mateo de Gállego, Zaragoza, Spain. 7Zootecnia®, S.L.P., Calle Tierra de Campos 24-26, Pol. Ind. El Montalvo II, 37008 Salamanca, Spain. 8Laboratorios Hipra S.A., Avenida de la Selva 135, 17170 Amer, Girona, Spain. 9 Labopat Nuzoa, Carretera de Valladolid 28, 40196 La Lastrilla, Segovia, Spain. INTRODUCTION MATERIALS & METHODS The Pig Barometer is a pilot tool co-developed with veterinary diagnostic laboratories (VDLs) from Spain to share information on endemic and potentially emerging diseases affecting the swine population in the country, assisting veterinarians and producers to make informed decisions on disease prevention, detection, and management. OBJECTIVE This ongoing project has the goal to aggregate swine diagnostic data from Spain and report them in web dashboards, describing the dynamics of pathogen detection by PCR-based assays over time, specimen, age group, and geographical area. RESULTS The Pig Barometer was designed to visualize pathogen-specific laboratory test results from VDLs in Spain (Fig. 1.). •The pilot dashboard shows results of three endemic pathogens: Mycoplasma hyopneumoniae, swine influenza virus (SIV) and Lawsonia intracellularis. •Anonymized diagnostic data included PCR assay results, sample type, productive stage, and a proxy for province geolocation. •Data was aggregated by case (i.e., submission). •Heterogeneous data from VDLs was structured using ontologies and RDF to ensure interoperability (Fig. 2.). Figure 2. Ontology-based workflow for pig diagnostic data integration and analysis. Data from various Spanish VDLs were collected and cleaned using Python. Next, a species-specific ontology (LHO) was developed and used to map the data into RDF. This enabled the creation of knowledge graphs. SPARQL queries were run in Python to extract insights on pathogen trends, which were then visualized in Tableau DISCUSSION & CONCLUSIONS •The Pig Barometer holds the potential of showing historical trends, dynamics and current presence of specific pathogens per area, aiding in the control of infectious swine diseases. •We aim to expand the tool by including data from additional pathogens (and countries) with the long-term objective of helping the industry towards generating better swine health information. Acknowledgements: We would like to thank all the participating veterinary diagnostic laboratories for their valuable data contributions. For any comments or inquiries, please contact [email protected] This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 101000494. Go live and test out the Pig Barometer! Figure 1. The Pig Barometer. This interactive dashboard presents results either as the percentage of positive cases, as shown in this screenshot, or as the absolute number of positive cases. https://decide-projecteu.github.io/case-studieswebsite/case-studies/pigbarometer.html Six VDLs provided data from 23,249 anonymized diagnostic cases submitted between 02/01/2020 and 29/12/2023 Out of the samples tested for each pathogen, 3,306/13,748 (24%) tested positive for SIV, 2,014/7,448 (27%) for M. hyopneumoniae, and 859/2,053 (42%) for L. intracellularis Although tissue submissions were the most frequent (12,127), the highest proportion of positive cases was observed in bronchoalveolar lavage samples (50%) The finishing stage accounted for the highest number of reported cases (10,477); however, the proportion of positive cases was higher among weaning pigs Data from 49 provinces is represented in the dashboard