Survey on automated laboratory information reporting practices in the EU/EEA, 2018
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This document summarizes the results of a 2018 survey on automated laboratory reporting practices in EU/EEA countries. The survey found that nearly half of countries use automated reporting for some national infectious disease and antibiotic resistance surveillance. Automated reporting allows for early detection of outbreak clusters in most countries. However, challenges remain around lack of standards, incentives and legal obligations for laboratories to automate reporting. Next steps include publishing the results with national representatives as co-authors.
Survey on automated laboratory information reporting practices in the EU/EEA, 2018
- 1. Survey on automated laboratory information reporting practices in the EU/EEA, 2018 20th National Microbiology Focal Points meeting Katrin Leitmeyer, Senior Expert Virology, Office of the Chief Scientist European Centre for Disease Prevention and Control, Solna, 4-5 June 2019
- 2. Background ECDC Public health microbiology strategy foresees that ECDC in synergy with • relevant Commission supported eHealth initiatives and as part of the • Long-Term Surveillance Strategy 2014-2020 undertakes projects to identify and disseminate solutions for automated machine-to-machine transfer of microbiology data between laboratory and surveillance information systems from the local to national and EU surveillance levels. 2
- 3. Aims of the survey • To investigate the modalities and scope of clinical laboratory data reporting for national surveillance of EU notifiable diseases and antimicrobial resistance across Europe. • To assess the public health utility of and perceived obstacles to implementing automated laboratory data reporting for potential future real-time EU wide laboratory based surveillance. 3
- 4. Methods • Pilot tested draft online questionnaire (EU survey tool) • Survey sent to 30 NMFP and NFS • Open October-December 2018 • 21 questions Use of LIMS for reporting to clinicians Proportion of laboratories reporting automated (machine-to-machine; M2M) Modes of reporting for EU notifiable diseases and indicator AMR pathogens* to national level Type of data reported on automated basis Use of/data • Bilateral follow-up to clarify/validate some received answers *EU One Health Action Plan against AMR http://ww.ema.Europa.eu/docs/en/GB/document_libary/Report/2017/10/WC5002237745.pdf)
- 5. Definitions used - Manual versus automated electronic reporting Manual laboratory data reporting included paper-based reporting by mail and FAX; manual electronic reporting by e-mail messaging; manual reporting into web-based questionnaire forms and manual file upload via internet to a central webpage or online database. Automated laboratory data reporting is the direct, automated messaging of laboratory information from clinical LIMS machine-to-machine (M2M) to the appropriate public health jurisdictions’ communicable disease reporting system. 5
- 6. Results Response rate • 30 countries participated • 29 countries responded to the follow-up/validation/were included in this analysis Data completeness • all questions were answered • only 3 questions with “I do not know” answers
- 7. Laboratory Information System (LIMS) use for reporting of data from clinical diagnostic laboratories to clinicians 9 countries all clinical laboratories 13 countries most of the clinical laboratories 27/29 countries 5 countries some of the clinical laboratories 2 countries none of the clinical laboratories (Bulgaria, Latvia)
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- 9. Number of EU/EEA countries with clinical laboratories reporting M2M to national surveillance by disease 9
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- 11. Automated reporting of AST results to national database(s) by format 9/13 countries report automated AST results to the national level -> 9 in a qualitative format (R-I-S categories) according to EUCAST 2018 definitions and breakpoints • Austria, Denmark, Finland, Hungary, Ireland, Netherlands, Slovak Republic, Sweden, and the UK ->5 countries report in addition in a quantitative format (disk diffusion zone size, MIC value) • Denmark, Finland, Hungary, Slovak Republic and the UK
- 12. Modes of clinical diagnostic laboratories’ reporting of indicator AMR pathogens* to the national surveillance database(s)
- 13. Use of data for cluster detection and early warning in 12/13 countries ! • 5 countries analyse the data for all pathogens reported to the national level • 7 for selected diseases 13 countries can de-duplicate positive samples per patient
- 14. Type of data reported on automated basis to national surveillance database(s)
- 15. Type of data reported on automated basis to national surveillance database(s)
- 16. Data semantic coding and data cross-linkage 5 countries use a standard health care vocabulary/terminology • ICD-10; n=2 • SNOMED-CT; n=1 • National microbiological diagnostic codes comparable to LOINC; n=1 • Unknown; n=1 7 countries laboratory data are automatically linked to case-based notified epidemiological data 5 countries can link their laboratory data on automated basis to other databases
- 17. Validation of laboratory data for surveillance • 6 countries validated the laboratory-based automated surveillance methods against the standard epidemiological surveillance method(s) e.g. the conventional notification-based data collection. • 5 countries automated reporting systems have replaced case- based reporting using standard epidemiological surveillance protocols.
- 18. Main reasons why diagnostic laboratories with a LIMS do not report on automated basis to National surveillance system database(s) • No technical support (n=16) • Lack of financial incentive to cover extra cost (n=14) • Lack of legal base/obligation (n=7) • Data protection issues (n=4) • Diversity of LIMS, dictionaries, computer systems …
- 19. Conclusions • Automated laboratory data reporting was used for national public health and alert purposes in almost half of the EU/EEA countries in 2018. • Reported data on EU-notifiable diseases and AMR varied in extent and disease coverage across countries and laboratories. • Reported laboratory data are used for cluster detection and early warning in almost all countries, real or close to real-time. • Challenges to overcome are lack of financial incentives or statutory mandate, diversity of clinical LIMS software, coding dictionaries and communicating systems among labs within and between countries in order to reach the ECDC proposed 2022 target to enable EU surveillance. 19
- 20. Next steps towards our joint publication Proposal: NMFPs and NFPs that participated in the survey to be co- authors as survey participants NMFP to validate the survey data and complete the missing data (deadline 21 June) Clearance and approval of the revised draft to be submitted for publication Suggested Journal – Eurosurveillance 20
- 21. Thank you 21