Presentation at the 20th NMFP meeting held on 4-5 June 2019 at ECDC in Stockholm, Sweden.

1. ECDC public health microbiology programme
… partnerships in action!
20th National Microbiology Focal Points meeting
Marc Struelens, Chief Microbiologist, on behalf of Microbiology Coordination Section
European Centre for Disease Prevention and Control, Solna, 4-5 June 2019

2. ECDC public health microbiology programme
… partnerships in action!
Update on implementing ECDC
• Public health microbiology strategy 2022
• External Quality Assessment strategy 2020
• Integration of genomics in EU surveillance and response,
Framework 2021
2

3. Vision for EU laboratory preparedness
By 2022 communicable disease and antimicrobial resistance
threat detection, risk assessment, public health surveillance and
response in the EU/EEA will be underpinned by reliable and
comparable microbiology laboratory data sharing by coordinated
networks supported by electronic communication systems

4. ECDC Public Health Microbiology Strategy
Strategic objectives
1. facilitating EU-wide use of WGS for outbreak and surveillance
2. benchmarking PHM practices in the EU and beyond
3. strengthening the EU microbiology capacity through networks
4. cross-sectorial and inter-agency integration of laboratory work
5. synergies with EU initiatives on innovative laboratory methods
and interoperability with public health information systems
“Microbiology laboratories provide a first line of defence against
communicable diseases and antimicrobial resistance.
“

5. Facilitating EU-wide use of WGS for outbreak and
surveillance
5

6. Whole Genome Sequencing: Vision 2020
• ECDC to establish standards and
manage systems
• EU wide use of whole genome
sequencing as the method of choice
for typing microbial pathogens
• Disease/AMR surveillance and
outbreak investigations
Expert opinion on whole genome sequencing for public health surveillance. Stockholm: ECDC; 2016.
Expert Opinion on whole genome sequencing for public health surveillance. Stockholm: ECDC; 2016 6

7. From the typing Roadmap to the Strategic framework
7

8. WGS typing Strategic Priorities by objective:
from the Roadmap 2018 to the Framework 2021
ECDC strategic framework for the integration of molecular and genomic typing into European surveillance and multi-country outbreak investigations –2019–2021. Stockholm: ECDC; 2019 8
Roadmap 2018 Strategic framework 2021
Investigation of cross-border outbreaks
• L. monocytogenes, Salmonella, STEC Any epidemic pathogen/MDR outbreak
EU-wide WGS- or sequence-based surveillance systems
• Listeria monocytogenes
• Neisseria meningitidis
• Listeria monocytogenes
• Neisseria meningitidis
• MDR TB
• Salmonella enterica
• STEC
• influenza virus
EU-wide WGS-based surveys
• Carbapenemase-producing Enterobacteriaceae
• Antibiotic-resistant Neisseria gonorrhoeae
• Carbapenem/ colistin-resistant Enterobacteriaceae
• Antibiotic-resistant Neisseria gonorrhoeae
• Carbapenem-resistant Acinetobacter baumannii
• Bordetella pertussis
• Streptococcus pneumoniae

9. 9

10. Genomic-based typing capability for national surveillance,
EU/EEA countries, 2013-2019
0
5
10
15
20
25
30
2013 2014 2015 2016 2017 2018 2019
Source: EULabCap and NMFP WGS surveys, 2013-17 (n=28-30 country respondents).
Numberofcountries

11. Use of WGS-based typing by EU/EEA countries for FWD
surveillance and/or outbreak investigations
(December 2016 for the food sector, July 2017 for the public health sector)
Fig 1. Use of WGS-based typing by EU/EEA countries for FWD surveillance and/or outbreak investigations, for at least one food-borne
pathogen L. monocytogenes, S. enterica and STEC; December 2016 for the food sector, July 2017 for the public health sector 11

12. ECDC-EFSA multi-country outbreak assessments and
notifications for foodborne diseases, 2011 – 2018
12
*As of November 2018
0
2
4
6
8
10
12
14
16
18
2011 2012 2013 2014 2015 2016 2017 2018*
Noofoutputs
Year
Salmonella Listeria E.coli Salmonella notification Listeria notification
WGS support
since November
2015

13. 2. Benchmarking PHM practices in the EU and beyond
• EULabCap 2016
EU Electronic laboratory reporting 2018
OECD Health at a Glance Europe 2018
• ENLabCap 2018
• EQA strategy impact indicators 2018
13

14. Health at a Glance: Europe 2018
14

15. NRL Core function 5: preparedness and response
capabilities, EULabCap 2013-2016
Target 3.3 Reference laboratory participation in
outbreak detection and response support
Target 3.4 Reference laboratory capabilities for
(re-)emerging diseases* preparedness
6.3
7.5
7.0
8.0
0
2
4
6
8
10
2013 2014 2015 2016
Target 3.3
7.5
7.0
8.0
8.9
0
2
4
6
8
10
2013 2014 2015 2016
Target 3.4
EU/EEA median EULabCap index (IQR)
* MERS, influenza A H5/7Nx, Ebola, chikungunya, dengue, hanta, TBE, West Nile, colistin resistance

16. Electronic laboratory reporting for automated national
surveillance national, EU/EEA 2018
Source: Leitmeyer K et al; NMFP survey, in prep. 16

17. ECDC EQA strategy, 2017-2020
ECDC mandate to provide quality
assurance and to foster laboratory
capacity building for surveillance
Aims to enhance:
• Quality and efficiency of the EQA
• EU-added value (new ECDC
strategic impact indicator from 2019
onwards)
https://ecdc.europa.eu/sites/portal/files/documents/EQA-strategy-2018.pdf
17

18. EQA Performance Indicator 4.1.1:
corrective measures and accreditation input
18
- By 2020, all ECDC EQA documents will be included in the Member States’ laboratory accreditation
dossiers, provided that the corrective measures were taken at the laboratory level, if required
20 (35%) of laboratories
(n=58) reported corrective
measures were taken based
on the EQA results
(n= 5 EQA, 2018).
0 2 4 6 8 10
No corrective actions for non-
conformities were taken.
Not applicable: all our EQA test results
conformed to expected results.
Yes, corrective actions were taken.
Number of laboratories
Listeria-WGS assembly Yellow fever
Salmonella-Campylobacter AST Influenza
n=20
n=26
n=12

19. EQA Performance Indicator 4.1.1:
corrective measures and accreditation input
Number of laboratories using ECDC EQAs as documentation for accreditation or licensing purposes, 2018
19
0 2 4 6 8 10 12 14
No
Not applicable
Yes
Number of laboratories
Listeria-WGS assembly Yellow fever
Salmonella-Campylobacter AST Influenza
n=38
n=4
n=16
38 (66%) laboratories using
ECDC EQA certificate as
documentation for
accreditation or licensing
purposes, (N = 5 EQA, 2018)

20. 3. Strengthening the EU microbiology capacity: networks
Network name Abbreviation
European Antimicrobial Resistance Surveillance Network EARS-Net
European antimicrobial resistance Genes surveillance Network EurGEN-Net
Emerging Viral Diseases expert Laboratory Network EVD-LabNet
European Food & Waterborne Diseases and Zoonoses Network FWD-Net
European Legionnaires’ Disease Surveillance Network ELDS-Net
Creutzfeldt–Jakob Disease International Surveillance Network EuroCJD
European Gonococcal Antimicrobial Surveillance Programme Euro-GASP
European Reference Laboratory Network for Human Influenza ERLI-Net
European Reference Laboratory Network for Tuberculosis ERLTB-Net
European Pertussis Laboratory Network EUPert-LabNet
Invasive Bacterial Disease Laboratory Network IBD-LabNet
Diphtheria Laboratory Network Diphtheria-Net
Healthcare-associated Clostridium difficile Infections Surveillance Network ECDIS-Net II
NMFP Forum

21. 3. Strengthening the EU microbiology capacity:
laboratory network support, 2018
• Source: ECDC Director Annual Report 2017
• * N=12 networks* and 5 pilot projects managed by ECDC Disease Programmes, NMFPs and advisory committees (EUCAST)
Support Activity No. of outputs
External quality assessment 13
Technical guidance/assessment 13
Laboratory training courses 8
Technical capacity mapping 7
Cross-border testing services 8
Outbreak investigation support 5
Pilot genomic surveillance & response 11

22. 4. Cross-sectorial collaboration and inter-agency
integration of laboratory work
22

23. Public health microbiology
Communication and dissemination

24. European Commission- ECDC collaboration on reference
laboratories, 2018-19
• EMERGE-SHARP Joint Actions for high threat pathogens
̶ ECDC Observer and Advisor
̶ Coordination and communication with EVD-LabNet
̶ Contribution of technical guidance for emerging pathogens
̶ Participation to simulation exercise
• In vitro diagnostic device Regulation 2017/746/EU
̶ ECDC technical advice to JRC technical work on risk classification of
diagnostic devices for infectious diseases

25. WHO collaborations 2018-2019
Polio containment exercise
Podgorica Workshop on
microbiology systems in EN
countries
WHO Draft Code of Conduct
Pathogen Genetic Sequence Data
Sharing
WHO Biosafety Manual
Laboratory leadership
25

26. Outreach to the clinical sector & surveillance interface

27. 5. Synergies with EU initiatives on innovative laboratory
methods and interoperability with public health
information systems
Observer to JRC – WGS-based AMR detection and monitoring
NMFP survey: electronic laboratory- based surveillance
Expert advice to laboratory R&D and translational projects
27
• PREPARE
• COMPARE
• One-Health EJP
• ENPEN
• TATFAR
• PulseNet
• GMI

28. Systematic review on WGS in surveillance for outbreak
detection: search strategy and PRISMA flow chart
28

29. Scientific advice on microbiology innovation projects
International conferences
• APHL- CDC Symposium, August 2018
• 29th ECCMID, April 2019
• GMI 12 Conference, June 219
• ASM Conference June 2019
• IMMEM XII, September 2019

30. 30
Progress May 2019
Three diseases in operation
90% of MS using WGS
typing (TBC 2019)
90% of MS medium/high
capabilities (2016)
77% of MS addressed gaps
(2016)
40 to 85% of MS (2016)
35-66% laboratories took
EQA- based corrective
action/ assay accreditation
(2018)
18 multi-country outbreaks
assessed by WGS-based
typing (2018)
43% of MS using
automated laboratory e-
notification (2018)

31. Europe’s microbiology preparedness for
infectious health threats: 2010-2019
• Strong and increasing microbiology capabilities in Europe
• Cooperation in EU reference laboratory networks
• Expansion of national capacities for WGS- based typing
• WGS data sharing on integrated European analysis platform
• Moving towards laboratory-integrated digital surveillance
• Cooperation with clinical, animal and international health

32. Epidemiology &
social sciences
Microbiology
& population biology
Clinical
pathology
Ecology and
biogeographic
modelling
Microbial
genetics and
phylogenomics
Human
genetics
Integrated Genomic Epidemiology for public health

33. Thank you
for 10 great years working together !
33