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Bouyer F, Thiongane O, Hobeika A, Arsevska E, Binot A, Corrèges D, Dub T, Mäkelä H, van Kleef E, Jori F, Lancelot R, Mercier A, Fagandini F, Valentin S, Van Bortel W, Ruault C. Epidemic intelligence in Europe: a user needs perspective to foster innovation in digital health surveillance. BMC Public Health 2024; 24:973. [PMID: 38582850 PMCID: PMC10999084 DOI: 10.1186/s12889-024-18466-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 03/27/2024] [Indexed: 04/08/2024] Open
Abstract
BACKGROUND European epidemic intelligence (EI) systems receive vast amounts of information and data on disease outbreaks and potential health threats. The quantity and variety of available data sources for EI, as well as the available methods to manage and analyse these data sources, are constantly increasing. Our aim was to identify the difficulties encountered in this context and which innovations, according to EI practitioners, could improve the detection, monitoring and analysis of disease outbreaks and the emergence of new pathogens. METHODS We conducted a qualitative study to identify the need for innovation expressed by 33 EI practitioners of national public health and animal health agencies in five European countries and at the European Centre for Disease Prevention and Control (ECDC). We adopted a stepwise approach to identify the EI stakeholders, to understand the problems they faced concerning their EI activities, and to validate and further define with practitioners the problems to address and the most adapted solutions to their work conditions. We characterized their EI activities, professional logics, and desired changes in their activities using NvivoⓇ software. RESULTS Our analysis highlights that EI practitioners wished to collectively review their EI strategy to enhance their preparedness for emerging infectious diseases, adapt their routines to manage an increasing amount of data and have methodological support for cross-sectoral analysis. Practitioners were in demand of timely, validated and standardized data acquisition processes by text mining of various sources; better validated dataflows respecting the data protection rules; and more interoperable data with homogeneous quality levels and standardized covariate sets for epidemiological assessments of national EI. The set of solutions identified to facilitate risk detection and risk assessment included visualization, text mining, and predefined analytical tools combined with methodological guidance. Practitioners also highlighted their preference for partial rather than full automation of analyses to maintain control over the data and inputs and to adapt parameters to versatile objectives and characteristics. CONCLUSIONS The study showed that the set of solutions needed by practitioners had to be based on holistic and integrated approaches for monitoring zoonosis and antimicrobial resistance and on harmonization between agencies and sectors while maintaining flexibility in the choice of tools and methods. The technical requirements should be defined in detail by iterative exchanges with EI practitioners and decision-makers.
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Affiliation(s)
- Fanny Bouyer
- Groupe d'Expérimentation et de Recherche: Développement et Actions Locales (GERDAL), Angers, France.
| | - Oumy Thiongane
- Joint Research Unit Animal, Health, Territories, Risks, Ecosystems (UMR ASTRE), French Agricultural Research Centre for International Development (CIRAD), National Research Institute for Agriculture, Food and Environment (INRAE), Montpellier, France
| | - Alexandre Hobeika
- UMR MOISA, French Agricultural Research Centre for International Development (CIRAD), 34398, Montpellier, France
- MOISA, University Montpellier, CIHEAM-IAMM, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Elena Arsevska
- Joint Research Unit Animal, Health, Territories, Risks, Ecosystems (UMR ASTRE), French Agricultural Research Centre for International Development (CIRAD), National Research Institute for Agriculture, Food and Environment (INRAE), Montpellier, France
| | - Aurélie Binot
- Joint Research Unit Animal, Health, Territories, Risks, Ecosystems (UMR ASTRE), French Agricultural Research Centre for International Development (CIRAD), National Research Institute for Agriculture, Food and Environment (INRAE), Montpellier, France
| | - Déborah Corrèges
- Joint Research Unit EPIdemiological On Animal and Zoonotic Diseases (UMR EPIA), National School of Veterinary Services (VetAgro Sup), National Research Institute for Agriculture, Food and Environment (INRAE), Marcy L'Etoile, France
| | - Timothée Dub
- Department of Health Security, Finish Institute for Health and Welfare, Helsinki, Finland
| | - Henna Mäkelä
- Department of Health Security, Finish Institute for Health and Welfare, Helsinki, Finland
| | - Esther van Kleef
- Institute of Tropical Medicine, Department of Biomedical Sciences, Outbreak Research Team, Antwerp, Belgium
| | - Ferran Jori
- Joint Research Unit Animal, Health, Territories, Risks, Ecosystems (UMR ASTRE), French Agricultural Research Centre for International Development (CIRAD), National Research Institute for Agriculture, Food and Environment (INRAE), Montpellier, France
| | - Renaud Lancelot
- Joint Research Unit Animal, Health, Territories, Risks, Ecosystems (UMR ASTRE), French Agricultural Research Centre for International Development (CIRAD), National Research Institute for Agriculture, Food and Environment (INRAE), Montpellier, France
| | - Alize Mercier
- Joint Research Unit Animal, Health, Territories, Risks, Ecosystems (UMR ASTRE), French Agricultural Research Centre for International Development (CIRAD), National Research Institute for Agriculture, Food and Environment (INRAE), Montpellier, France
| | - Francesca Fagandini
- Joint Research Unit Land, Remote Sensing and Spatial Information (UMR TETIS), French Agricultural Research Centre for International Development (CIRAD), Montpellier, France
| | - Sarah Valentin
- Joint Research Unit Land, Remote Sensing and Spatial Information (UMR TETIS), French Agricultural Research Centre for International Development (CIRAD), Montpellier, France
| | - Wim Van Bortel
- Institute of Tropical Medicine, Department of Biomedical Sciences, Outbreak Research Team, Antwerp, Belgium
- Institute of Tropical Medicine, Department of Biomedical Sciences, Unit of Entomology, Antwerp, Belgium
| | - Claire Ruault
- Groupe d'Expérimentation et de Recherche: Développement et Actions Locales (GERDAL), Angers, France
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Divi N, Mantero J, Libel M, Leal Neto O, Schultheiss M, Sewalk K, Brownstein J, Smolinski M. Using EpiCore to Enable Rapid Verification of Potential Health Threats: Illustrated Use Cases and Summary Statistics. JMIR Public Health Surveill 2024; 10:e52093. [PMID: 38488832 PMCID: PMC10980988 DOI: 10.2196/52093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/26/2023] [Accepted: 01/31/2024] [Indexed: 03/19/2024] Open
Abstract
BACKGROUND The proliferation of digital disease-detection systems has led to an increase in earlier warning signals, which subsequently have resulted in swifter responses to emerging threats. Such highly sensitive systems can also produce weak signals needing additional information for action. The delays in the response to a genuine health threat are often due to the time it takes to verify a health event. It was the delay in outbreak verification that was the main impetus for creating EpiCore. OBJECTIVE This paper describes the potential of crowdsourcing information through EpiCore, a network of voluntary human, animal, and environmental health professionals supporting the verification of early warning signals of potential outbreaks and informing risk assessments by monitoring ongoing threats. METHODS This paper uses summary statistics to assess whether EpiCore is meeting its goal to accelerate the time to verification of identified potential health events for epidemic and pandemic intelligence purposes from around the world. Data from the EpiCore platform from January 2018 to December 2022 were analyzed to capture request for information response rates and verification rates. Illustrated use cases are provided to describe how EpiCore members provide information to facilitate the verification of early warning signals of potential outbreaks and for the monitoring and risk assessment of ongoing threats through EpiCore and its utilities. RESULTS Since its launch in 2016, EpiCore network membership grew to over 3300 individuals during the first 2 years, consisting of professionals in human, animal, and environmental health, spanning 161 countries. The overall EpiCore response rate to requests for information increased by year between 2018 and 2022 from 65.4% to 68.8% with an initial response typically received within 24 hours (in 2022, 94% of responded requests received a first contribution within 24 h). Five illustrated use cases highlight the various uses of EpiCore. CONCLUSIONS As the global demand for data to facilitate disease prevention and control continues to grow, it will be crucial for traditional and nontraditional methods of disease surveillance to work together to ensure health threats are captured earlier. EpiCore is an innovative approach that can support health authorities in decision-making when used complementarily with official early detection and verification systems. EpiCore can shorten the time to verification by confirming early detection signals, informing risk-assessment activities, and monitoring ongoing events.
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Affiliation(s)
- Nomita Divi
- Ending Pandemics, San Francisco, CA, United States
| | - Jaś Mantero
- Ending Pandemics, San Francisco, CA, United States
| | - Marlo Libel
- Ending Pandemics, San Francisco, CA, United States
| | - Onicio Leal Neto
- Ending Pandemics, San Francisco, CA, United States
- Department of Epidemiology and Biostatistics, Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ, United States
| | | | - Kara Sewalk
- Computational Epidemiology Lab, Boston Children's Hospital, Boston, MA, United States
| | - John Brownstein
- Computational Epidemiology Lab, Boston Children's Hospital, Boston, MA, United States
- Harvard Medical School, Harvard University, Boston, MA, United States
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Chang YC, Chiu YW, Chuang TW. Linguistic Pattern-infused Dual-channel BiLSTM with Attention for Dengue Case Summary Generation from ProMED-mail database (Preprint). JMIR Public Health Surveill 2021; 8:e34583. [PMID: 35830225 PMCID: PMC9491834 DOI: 10.2196/34583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 04/15/2022] [Accepted: 05/27/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Yung-Chun Chang
- Graduate Institute of Data Science, Taipei Medical University, Taipei, Taiwan
- Clinical Big Data Research Center, Taipei Medical University Hospital, Taipei, Taiwan
| | - Yu-Wen Chiu
- Graduate Institute of Data Science, Taipei Medical University, Taipei, Taiwan
- Department of Molecular Parasitology and Tropical Diseases, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Ting-Wu Chuang
- Department of Molecular Parasitology and Tropical Diseases, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
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Romero-Alvarez D, Peterson AT, Salzer JS, Pittiglio C, Shadomy S, Traxler R, Vieira AR, Bower WA, Walke H, Campbell LP. Potential distributions of Bacillus anthracis and Bacillus cereus biovar anthracis causing anthrax in Africa. PLoS Negl Trop Dis 2020; 14:e0008131. [PMID: 32150557 PMCID: PMC7082064 DOI: 10.1371/journal.pntd.0008131] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 03/19/2020] [Accepted: 02/11/2020] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Bacillus cereus biovar anthracis (Bcbva) is an emergent bacterium closely related to Bacillus anthracis, the etiological agent of anthrax. The latter has a worldwide distribution and usually causes infectious disease in mammals associated with savanna ecosystems. Bcbva was identified in humid tropical forests of Côte d'Ivoire in 2001. Here, we characterize the potential geographic distributions of Bcbva in West Africa and B. anthracis in sub-Saharan Africa using an ecological niche modeling approach. METHODOLOGY/PRINCIPAL FINDINGS Georeferenced occurrence data for B. anthracis and Bcbva were obtained from public data repositories and the scientific literature. Combinations of temperature, humidity, vegetation greenness, and soils values served as environmental variables in model calibrations. To predict the potential distribution of suitable environments for each pathogen across the study region, parameter values derived from the median of 10 replicates of the best-performing model for each pathogen were used. We found suitable environments predicted for B. anthracis across areas of confirmed and suspected anthrax activity in sub-Saharan Africa, including an east-west corridor from Ethiopia to Sierra Leone in the Sahel region and multiple areas in eastern, central, and southern Africa. The study area for Bcbva was restricted to West and Central Africa to reflect areas that have likely been accessible to Bcbva by dispersal. Model predicted values indicated potential suitable environments within humid forested environments. Background similarity tests in geographic space indicated statistical support to reject the null hypothesis of similarity when comparing environments associated with B. anthracis to those of Bcbva and when comparing humidity values and soils values individually. We failed to reject the null hypothesis of similarity when comparing environments associated with Bcbva to those of B. anthracis, suggesting that additional investigation is needed to provide a more robust characterization of the Bcbva niche. CONCLUSIONS/SIGNIFICANCE This study represents the first time that the environmental and geographic distribution of Bcbva has been mapped. We document likely differences in ecological niche-and consequently in geographic distribution-between Bcbva and typical B. anthracis, and areas of possible co-occurrence between the two. We provide information crucial to guiding and improving monitoring efforts focused on these pathogens.
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Affiliation(s)
- Daniel Romero-Alvarez
- Department of Ecology & Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, Kansas, United States of America
| | - A. Townsend Peterson
- Department of Ecology & Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, Kansas, United States of America
| | - Johanna S. Salzer
- Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Claudia Pittiglio
- Food and Agriculture Organization of the United Nations, Animal Health Service, Animal Production and Health Division, Rome, Italy
| | - Sean Shadomy
- Food and Agriculture Organization of the United Nations, Animal Health Service, Animal Production and Health Division, Rome, Italy
- One Health Office, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Rita Traxler
- Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Antonio R. Vieira
- Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - William A. Bower
- Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Henry Walke
- Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Lindsay P. Campbell
- Florida Medical Entomology Laboratory, Department of Entomology and Nematology, IFAS | University of Florida, Vero Beach, Florida, United States of America
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