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Microbiology

Bacteria in Petri dish. © Istock

Microbiology laboratories are a first line of defence against health threats from communicable diseases. Adequate laboratory capacity is a critical component of health system preparedness by allowing rapid detection of infectious diseases and identification of transmissible agents.

In the area of microbiology ECDC has a specific mandate to ‘strengthen the capacity within the Union to diagnose, detect, identify and characterise infectious agents which have the potential to threaten public health’ (Publications Office (europa.eu)(link is external) ECDC mandate).

 

ECDC works closely with the EU Member States to strengthen and assess laboratory capacity and to ensure that standardized and high-quality microbiology data are an integrated part of surveillance and cross-border outbreak investigation.

WGS and RT-PCR infrastructure support

Since 2021, in collaboration with the European Commission, ECDC has made substantial investments to increase the capacity of Member States’ public health laboratories to perform whole genome sequencing (WGS) and reverse transcription polymerase chain reaction (RT-PCR).

In 2021, in collaboration with DG SANTE, ECDC implemented a WGS and RT-PCR infrastructure support programme aimed at national public health authorities. This programme was funded under the HERA Incubator and provided support for 24 national projects that ran from September 2021 to January 2023.

As a follow-up to this 2021 programme, DG HERA, in collaboration with ECDC, implemented a second WGS and RT-PCR infrastructure support programme under the EU4Health 2022 Annual Work Programme.

Both infrastructure support programmes have the following objectives:

  • In the short term, contribution to the establishment of a sustainable, efficient and high capacity WGS and/or RT-PCR infrastructure for national public health microbiology;
  • In the short/medium term, contribution to early detection and enhanced monitoring of emergent and known SARS-CoV-2 variants at the national and the EU/EEA levels;
  • In the medium/long term, contribution to enhanced genomic-based infectious disease outbreak investigation capacities at regional, national, and/or EU/EEA levels;
  • In the medium/long term, contribution to enhanced routine genomic-based surveillance of infectious diseases at the regional, national, and/or EU/EEA levels, in accordance with ECDC’s strategic framework for the integration of molecular and genomic typing into European surveillance and multi-country outbreak investigations; and
  • In the long term, contribution to enhanced preparedness to promptly and efficiently address cross-border outbreaks of infectious diseases and pandemics in the future.

Training in genomic epidemiology and public health bioinformatics (GenEpi-BioTrain)

ECDC established this training course to ensure the efficient use of whole genome sequencing (WGS) infrastructure investments and further strengthen laboratory capacity, including training of in Member States. The course aims to strengthen capacity and collaboration within and between countries for applied genomic epidemiology in surveillance, preparedness and response.

The ‘GenEpi-BioTrain’ was initiated in January 2023 and will continue over the next four years.  

The overall objectives of the training courses are to support countries in building capacity in genomic epidemiology and bioinformatics for public health purposes; to increase the interdisciplinary collaboration between bioinformaticians, epidemiologists and microbiologists within a country; and to facilitate the routine use of genomic information for surveillance, preparedness, and outbreak response. Activities will also strengthen data-sharing and collaboration between public health institutions and ECDC,  while enhanced networking activities will foster cross-border collaboration.  

Training activities include face-to-face workshops of lengths and at varying levels, virtual workshops and webinars, and exchange visits. Each year, training activities will be dedicated to two pathogen groups (‘pathogen waves’) each lasting around six months. 

The planned pathogen waves are as follows: 

  • Respiratory viruses (concluded in early 2023) 

  • Antimicrobial resistant pathogens (concluded in late 2023) 

  • Food- and waterborne diseases (early 2024, ongoing) 

  • Vaccine-preventable diseases (late 2024) 

  • Tuberculosis (2025).

Depending on training needs and demand from Member States, the pathogen waves can be repeated in late 2025 and 2026 and/or additional pathogen waves added (e.g. sexually-transmitted diseases).

For more information, contact ECDC.Microbiology@ecdc.europa.eu.

Go to the online learning platform (EVA)

Implementation of European Reference Laboratories for public health

ECDC actively works to strengthen the capability and capacity of the European Union (EU) public health microbiology system to provide the timely and reliable information that underpins infectious disease threat detection, assessment and surveillance at Member State and EU levels for effective prevention and control of infectious diseases.

ECDC works closely with countries and coordinates a range of laboratory networks.

These contribute to EU-level surveillance and ECDC support network laboratories with activities to increase capacity and improve standardisation and comparability of data.

The European Commission may designate European Reference Laboratories (EURLs) in the area of public health or for specific public health areas relevant for the implementation of the regulation (article 5). These EURLs are expected to perform and coordinate work within the following areas:

  1. reference diagnostics, including test protocols;
  2. reference material resources;
  3. external quality assessments;
  4. scientific advice and technical assistance;
  5. collaboration and research;
  6. monitoring, alert notifications and support in outbreak response, including to emerging communicable diseases and pathogenic bacteria and viruses; and
  7. training.

ECDC is currently working closely with the Directorate-General for Health and Food Safety to define how such EURLs should be nominated and designated, and how they should work with the existing networks of microbiology laboratories in EU Member States.

Funding for EURLs will be provided through the EU4Health programme. The first round of calls for application was launched in 2023 and the first laboratories were designated as EURLs in March 2024. 

In April 2024, the European Commission issued three new calls for applications related to EURLs in public health. 

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