ECDC programme in reference public health microbiology

Transcription

1 ECDC programme in reference public health microbiology Marc Struelens, Chief Microbiologist Microbiology Coordination Section Office of the Chief Scientist, ECDC 6 eme Seminaire des Centes Nationaux de Refrence Paris, 28 November 2013

2 ECDC mandate on microbiology Regulation (EC) 851/2004 By encouraging cooperation between expert and reference laboratories, the Centre shall foster the development of sufficient capacity within the Community for the diagnosis, detection, identification and characterization of infectious agents which may threaten public health. The Centre shall maintain and extend such cooperation and support the implementation of quality assurance schemes.

3 Goal of ECDC Public Health Microbiology Programme To strengthen the capacity of EU public health microbiology system to provide timely and reliable information for infectious disease prevention and control at Member State and EU level *ECDC Updated Public Health Microbiology Strategy

4 ECDC Microbiology Coordination A cross-cutting partnership ECDC EXTERNAL Microbiology Steering Committee European Commission Disease Programmes Support Sections (e.g. Epi methods, Epidemic Intelligence ) Microbiology Coordination Section Member State experts EU Agencies WHO Training (EUPHEM) Learned societies

5 Public health microbiology programme strategic priorities ( ) Strategy 1 Consolidate capacity Strategy 2 Monitor microbiology capabilities Strategy 3 Integration of molecular typing Strategy 4 Antimicrobial resistance surveillance integrated approach

6 Strategy 1: Consolidate capacity Activity Outputs 2012 Harmonisation EUCAST antimicrobial testing Training and IT tools European PHM programme (EUPHEM) Laboratory training courses Pilot TESSy Molecular service Outbreak investigations Salmonella Stanley Hepatitis A virus genotype 1b Diagnostic preparedness and response MERS CoV coronavirus Avian influenza A(H7N9)

7 Working through EU Disease Networks Disease networks = epidemiology + microbiology 15 EU Networks, 11 lab consortia or networks * European Network on Communicable Diseases (set up by European Parliament and Council decision 2119/98/EC) for surveillance, early warning and response, and preparedness)

8 * Extracted from the ECDC Microbiology Activities Reports between for 12 laboratory networks and 3 other projects under the ECDC PHM programme Laboratory network activities ECDC 2012 Type of work No. of Projects Technical laboratory guidance 14 Laboratory training courses 13 External quality assessment (EQA) 11 Technical capacity mapping 10 Cross-border testing services 8 Outbreak investigation support 7

9 Strategy 2: Monitor microbiology capabilities Middle East Respiratory Syndrome Coronavirus WHO and ECDC surveillance guidance: Any probable or confirmed case should be reported to national authorities and notified to IHR and EWRS. Network surveys by ECDC and WHO Europe MERS-CoV screening and confirmation by RT-PCR assay Survey I: Nov. 2012, Survey II: June 2013 NMFP (National Microbiology Focal Points) ENIVD (European Network for Imported Viral Diseases) ERLI-Net (European Network of Reference Laboratories for Surveillance of Human Influenza)

10 MERS CoV testing capability and testing practice, EU/EEA countries, Number of countries Nov-12 Jun Screening assays Confirmation assays Testing travel patients Testing contacts of cases Source: Palm et al EuroSurveillance, Dec 2012; Pereyaslov et al submitted

11 Strategy 3: Integration of molecular typing Which diseases first? Typing method? PH use of information? Sampling design implementation processes ECDC Road map for molecular surveillance implementation ( )

12 Criteria for molecular typing methods for EU level surveillance (Concept paper 2011) Methods should: Be driven by practical needs for surveillance Be discriminatory in a meaningful way Produce comparable data of high quality across laboratories Be cost-efficient Be interpreted and assessed by molecular typing experts of method/pathogen combination

13 ECDC support to Laboratory network molecular typing projects, Pathogen MRSA Methods Spa typing, MLVA C. difficile Capillary-electrophoresis-PCR ribotyping Salmonella, L. monocytogenes, STEC PFGE, MLVA L. pneumophila SBT vcjd Influenza A viruses Influenza B viruses Source: ECDC Microbiology Activity Reports 2012 PRNP genotyping N. gonorrhoeae NG-MAST N. meningitidis MLST, MAST, WGST Antiviral susceptibility, antigenic and genetic characterisation Lineage & antigenic characterisation, Antiviral susceptibility H. influenzae, S.pneumoniae PCR based capsule typing

14 EU Surveillance of foodborne infections collecting data for action timeliness for control measures Long term Annually: Trend monitoring Medium term Quarterly: Unusual increase (Salm, STEC) Short term Unusual increase at national level => EPIS Real time Real-time surveillance through molecular typing (PFGE, MLVA): cluster search Pilot in progress

15 Integration of epidemiology and microbiology data Data upload and access MS MS MS MS MS Molecular typing 27 EU 3 EEA Australia Canada MS MS MS MS MS MS MS MS TESSy The European Surveillance System Structured data: - Isolates - Notified cases Epidemic Intelligence Information System Discussion/assessment: - Microbiological clusters - Outbreaks Japan New Zealand South Africa Switzerland Turkey United States

16 100 EU multistate Salmonella Stanley outbreak, : multidisciplinary investigation PFGE_XbaI PFGE_XbaI PL BE BE /02/2012 3/02/2012 ANIMAL FOOD HUMAN farm environment turkey Turkey DE DE DE FR IT FOOD HUMAN ENVIRONMENT FOOD FOOD swab from fridge turkey meat frozen raw minced beef. turkey meat CZ CZ HU GR AT HUMAN FOOD HUMAN HUMAN HUMAN SVA CZ turkey SI ANIMAL turkey/fattening flock BE alert on 29 June 2012 on EPIS platform Joint investigation by EU and national agencies for public health, veterinary and food safety in 10 Member States Source: Kinross P et al, FWD network, EFSA and EU RL: in prep.

17 TESSy Molecular Surveillance Service (MSS) Management process for isolate type data Lab data generation Experiment Protocols Quality Control Submission Upload Validation Approval Cluster analysis Web interface Escalation ECDC supported process. Standard TESSy functionality. New MSS functionality. Curation Quality Control Nomenclature Cluster Detection Link with notified cases

18 Acknowledgements Voluntary participants in FWD molecular surveillance pilot project Institution Country Institution Country Österreichische Agentur für Gesundheit und Ernährungssicherheit Robert Koch Institute AT DE Istituto Superiore di Sanità, Dipartimento di Malattie Infettive, Parassitarie e Immunomediate Istituto Superiore di Sanità, Dipartimento di Sanità Pubblica Veterinaria e Sicurezza Alimentare Statens Serum Institut DK Laboratoire National de Santé LU Instituto de Salud Carlos III ES National Institute for Public Health and the Environment Terveyden ja Hyvinvoinnin Laitos FI Nasjonalt folkehelseinstitutt NO Institut Pasteur FR National Institute of Public Health RO IT IT NL Institut de veille sanitaire National School of Public Health - National Reference Centre for Salmonella FR National Institute of Research and Development for Microbiology and Immunology "Cantacuzino" GR Smittskyddsinstitutet SE RO Croatian National Institute of Public Health HR Institute of Public Health SI National Reference Centre for Listeria HR National Health Service Scotland, Scottish Salmonella Shigella and Clostridium difficile Reference Laboratory UK Health Service Executive IE Public Health England UK

19 Routine typing data submitted in 2013 Salmonella, STEC and Listeria A portion of the PFGE image data is rejected by curators on quality grounds. They also assign nomenclature, i.e. pattern names, and perform initial cluster detection.

20 Multi country cluster detection per month Apr-Oct 2013 Number of 10 clusters 8 Salmonella 6 Listeria Apr May June Jul Aug Sep Oct Number of resulting EPIS Urgent Inquiries: 2 Salmonella (1 started by Member State), 1 Listeria. Of 39 clusters, 30 involved two countries and 9 involved three or more countries.

21 Frequency of Neisseria gonorrhoeae MAST G-1407 genotype in EU/EEA countries Genotype G-1407 : strong association with decreased susceptibility to cefixime. ECDC Technical Report Molecular typing of N.gonorrhoeae 2012

22 Role of molecular typing in cross-border outbreak detection

23 Molecular surveillance roadmap Priority pathogens and methods Pathogens/AMR issue proposed for implementation Typing method EU public health objective/sampling design Surveillance continuous Surveillance prevalence surveys Multi-state outbreak investigations Influenza virus sequencing * Human Immunodeficiency Virus sequencing * (HIV) Neisseria meningitidis sequencing * * Legionella pneumophila sequencing * Neisseria gonorrhoeae/mdr sequencing * Enterobacteriaceae and Acinetobacter baumannii XDR/carbapenem-R PCR, sequencing * Staphylococcus aureus MDR/meticillin-R PCR, sequencing *

24 N. meningitidis possible objectives and benefits for molecular surveillance Public health need EU risk assessment Potential risk management Outbreak investigation Control-oriented surveillance Strategy-oriented surveillance Support to multicounty outbreak investigation Identify cross-border epidemic strains Monitoring of vaccine strain coverage and vaccine programme effectiveness Coordinated outbreak control measures including strain-targeted vaccination Coordinated epidemic control measures including strain-targeted vaccination Revision of vaccine composition or national immunisation programmes : Disease specific molecular surveillance strategy and business plan to be developed with IBD-LabNet consortium members

25 Molecular typing Roadmap: next steps in evaluation and implementation process Evaluation of pilot study: 2014 Disease Networks and Member States involvement in developing additional components Advisory Forum and Microbiology Focal Points review of strategic and technical proposals Molecular surveillance strategy Business case System implementation Routine use

26 Strategy 4: Antimicrobial resistance EU integrated approach

27 Implementation of EUCAST breakpoints, January 2013 % Laboratories >50% Iceland Finland 10-50% <10% Norway Sweden Estonia Russia No information Latvia Denmark Lithuania Ireland UK Netherlands Poland Belarus Belgium Luxembourg Germany Czech Republic Slovak Republic Moldova Ukraine France Switzerland Austria Slovenia Hungary Romania Portugal Spain Croatia Bosnia- Italy Herzegovina Serbia Montenegro Macedonia Albania Bulgaria Turkey Greece Malta

28 Conclusions: implementation of ECDC Public health microbiology strategy Continued EU networks support to laboratory capacity and quality to enhance integrated disease surveillance Jointly with WHO, rapid deployment and verification of MS detection capability for emerging pathogens by reference laboratories Jointly with EC, EFSA and ESCMID, progress comparability of surveillance data by harmonisation of microbiological methods and case definitions Assessment of improved resolution for detection and investigation of cross-border outbreaks by molecular typing Analysis of gaps in laboratory services at EU level jointly with the Commission and Member States

29 Acknowledgements ECDC Microbiology section and National Microbiology Focal Points ECDC Microbiology-enhanced Surveillance Coordination Group Karin Johansson, Daniel Palm, Ivo van Walle, Johanna Takkinen, Csaba Ködmön, Marieke van der Werf, Jaime Martinez Urtaza, Bruno Ciancio, Phillip Zucs, Andrew Amato, Denis Coulombier TESSy MSS Project Team and participants ECDC disease programmes and Disease networks experts ESGEM and ESCV Roadmap consultation experts

30 Please take a look at our web site! 1. Information ECDC PHM Programme 2. European Public Health Microbiology Training Programme (EUPHEM) 3. DG SANCO Laboratory Collaborations