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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.

Implementation of European Reference Laboratories for public health

ECDC actively works to strengthen the capability and capacity of the EU public health microbiology system to provide the timely and reliable information that underpins infectious threat detection, assessment, and surveillance at Member State and EU level 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 [1]. 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 DG SANTE 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, with the first topics published within the EU4Health 2023 Annual Work Programme.

[1] Article 15 of the Regulation (EU) 2022/2371 on serious cross-border threats to health