This document outlines ECDC's strategic framework for integrating molecular and genomic epidemiology data into public health operations from 2019-2021. It demonstrates new features for molecular surveillance in the TESSy database and a prototype web interface for genomic analysis. Priority diseases are identified for whole genome sequencing-based typing, including carbapenem-resistant Enterobacteriaceae, Listeria monocytogenes, Salmonella enterica, and Neisseria meningitidis. Improved tools will provide automated quality control feedback and detection of matches to outbreak clusters when sequence data is uploaded.

1. Demonstration of ECDC web interface
platform for molecular and genomic
epidemiology analysis
Erik Alm, Senior Expert Applied Molecular Epidemiology
ECDC, 4 June 2019

2. Outline
Strategic framework for EU integration of disease-specific molecular and genomic
typing data into public health operations, 2019–2021
New and improved features for molecular surveillance in TESSy
Demonstration of current prototype
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3. Strategic framework
3
This document is now available through
ECDC:s web page
It describes the priority diseases for
implementation of WGS-based typing at
ECDC for 2019-2021
It categorizes surveillance into:
• Outbreak investigations
• Control-oriented surveillance
• Strategy-oriented surveillance

4. 4
Pathogen Outbreak investigation Control-oriented Strategy-oriented
Carbapenem resistant
Enterobacteriaceae (CRE) and
Acinetobacter baumannii (CRAB)
X X
Clostridium difficile X
MRSA X
Emerging multidrug resistant
clones/plasmids
X
Outbreaks of newly emerging
pathogens/ new modes of
transmission of known healthcare-
associated pathogens
X
Antimicrobial Resistance and Healthcare-Associated
Infections
Structured WGS surveys on CRE and CRAB. Outbreak analysis support in the case of multi-country events.

5. 5
Pathogen Outbreak investigation Control-oriented Strategy-oriented
West Nile virus X
Emerging and Vector-Borne Diseases
The technical solution envisioned for West Nile virus can be applied to outbreak analysis for any RNA virus

6. 6
Pathogen Outbreak investigation Control-oriented Strategy-oriented
Campylobacter jejuni/C. coli X
Hepatitis A virus X
Legionella spp. X
Listeria monocytogenes X X X
Salmonella enterica X X X
Shiga toxin-producing E. coli
(STEC)
X X X
Food- and Waterborne Diseases and Zoonoses
Comprehensive Listeria WGS data collection has been initiated. When it has been tweaked to a suitable format,
Salmonella and STEC will follow.

7. 7
Pathogen Outbreak investigation Control-oriented Strategy-oriented
Antibiotic-resistant
Neisseria gonorrhoeae
X X
HIV transmitted drug resistance X
HIV, AIDS, STIs and Viral Hepatitis
Structured WGS survey on Antibiotic-resistant N. gonorrhoeae. HIV surveillance will not be performed by
collecting the sequence data at ECDC.

8. 8
Pathogen Outbreak investigation Control-oriented Strategy-oriented
Influenza virus X X
Influenza and other Respiratory Viruses
Influenza surveillance continues as usual, but will be improved using:
• Automatic detection of resistance mutations and genetic clade from sequence
• Visualisation of phylogenetic data available in TESSy

9. 9
Pathogen Outbreak investigation Control-oriented Strategy-oriented
Multidrug-resistant tuberculosis X X X
Tuberculosis
After an ongoing WGS surveillance pilot, ECDC will start performing surveillance in 2020

10. 10
Pathogen Outbreak investigation Control-oriented Strategy-oriented
Bordetella pertussis X
Neisseria meningitidis X X X
Streptococcus pneumoniae X
Vaccine-Preventable Diseases (VPD)
Comprehensive surveillance of N. meningitidis. WGS-based surveys will be performed for S. pneumoniae and B.
pertussis.

11. New and improved features in TESSy for molecular
surveillance
• There will be automated feedback after uploading WGS data to TESSy
• QC metrics
• Any matches with clusters or isolates from other countries
• There will be an improved tool for exploring WGS-based surveillance data
(demonstration of prototype)
• Data from several calculation systems will be gathered in an ECDC
Surveillance data warehouse for visualisation and download
• Upload options will be improved continously
• ECDC upload app for WGS-data (existing)
• Plugins for Bionumerics (existing) and SeqSphere+ (new)
• Support to countries for machine-to-machine upload
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12. Intended user experience (simplified)
12
• sequence
• dateUsedForStastics
• country
• age
• gender
• isolationSource
The user uploads their sequence data and epi data
through a single interface, or through an API
The user can
continue to explore
other data and
discuss with others
using the ETMS
platform (new EPIS)
ETMS
The raw data can be sent to long term
storage and eventually become public
TESSy
WGS
analysis
The epi data is sent to TESSy while WGS data is
automatically processed in Bionumerics or other
software, depending on the pathogen
recordId 1234
QC: pass
Your isolate matches
cluster UI-987
associated with dried fruits
http://.....
The user recieves an email with QC results and any
cluster hits
The user can log
into MyECDC
surveillance portal
to look at the
cluster and
associated epi
data

13. Technical solutions for upload
13
Member State
ENA/SRASFTP/file store
(provided by ECDC)
TESSy and WGS
systems
Basic epidemiological
data
WGS assembly
WGS reads
ECDC upload app or API
Bionumerics plugin or csv

14. Technical solution for download/visualisation
14
Bionumerics
Other WGS
systems
TESSy
WGS data warehouse
WGS web service
WGS web page
Cluster
detection and
notification
functionalities
ETMS
Surveillance portal
Raw data store
(ENA/cloud)
Notification

15. Demonstration of prototype visualisation
Rember that it is a prototype and we are open to suggestions for
improvements
http://zbiodev1.idmdevdmz.local
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16. Strategic Framework development
This report was drafted by Eeva Broberg, Joana Revez, Erik Alm, Ivo Van Walle, Daniel Palm and
Marc Struelens.
The following experts contributed to the disease specific proposals: Andrew Amato, Tamas Bakonyi,
Birgitta de Jong, Tarik Derrough, Karin Johansson, Ole Heuer, Liselotte Diaz Högberg, Pete Kinross,
Anke Kohlenberg, Saara Kotila, Csaba Ködmön, Katrin Leitmeyer, Angeliki Melidou, Dominique
Monnet, Lara Payne Hallström, Pasi Penttinen, Diamantis Plachouras, Ettore Severi, Gianfranco
Spiteri, Carl Suetens, Johanna Takkinen, Marieke J. Van der Werf and Therese Westrell.
Contributors: Mike Catchpole, Bruno Ciancio, Piotr Kramarz, Vicky Lefevre
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17. Thank you for your attention!
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