Molecular and genomic typing

Molecular and genomic typing. © Istock

Molecular typing of pathogens that cause infectious diseases complements the traditional epidemiological surveillance by providing appropriate discriminatory analyses to foster the rapid and early detection of widespread international outbreaks, to detect and investigate transmission chains and the relatedness of strains, and to detect the emergence of antimicrobial resistance and new evolving pathogenic strains.

It also supports studies to trace-back the source of an outbreak and identify new risk factors, as strains can be linked more accurately to epidemiological and clinical data.

The analysis of molecular typing data can also aid the study of pathogen characteristics and the pathogen’s behaviour in a community of hosts, for example its spread over time and space, its disease transmission dynamics, its genetic factors (including mutations which influence the recurrence or virulence of infections), antigenic drifts/shifts of strains over time, and the development of drug resistance across multiple generations of strains.

This information offers help in understanding the disease mechanisms and can be applied towards improving and better targeting existing infectious disease prevention and control measures and thus presents a clear benefit for public health and public health policies.

Based on the input of Member State experts ECDC has developed a Roadmap for integration of molecular and genomic typing into European surveillance and epidemic preparedness.

Whole genome sequencing 

Whole Genome Sequencing (WGS) has become the reference microbial typing method in outbreak studies and is increasingly applied to national surveillance of infectious diseases in EU/EEA countries and beyond.

Based on the input of the Member State experts, ECDC has developed a Expert opinion on whole genome sequencing for public health surveillance - Strategy to harness whole genome sequencing for strengthening EU cross-border outbreak investigation and public health surveillance.

The strategy envisages that within five years ECDC will have contributed to the establishment of standards and systems enabling the EU-wide use of WGS as the method of choice for typing of microbial pathogens, replacing other methods. This will improve the accuracy and effectiveness of disease surveillance, outbreak investigation and evaluation of prevention policies by enhanced assessment of disease and drug resistance transmission dynamics.

To support Member States in the transition to WGS from earlier technologies, and to ensure that WGS is adopted without compromising continuity of national and EU-level surveillance, ECDC proposes to:

  • Map other WGS-based public health initiatives and engage partnerships;
  • Lead on the integrated analysis of microbiological data and epidemiological data;
  • Provide guidance on and validation of WGS-based methods for surveillance and;
  • Develop, run and evaluate selected pilot

Latest news


Whole genome sequencing empowers disease surveillance and outbreak investigation

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Moving towards better global foodborne disease surveillance

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Peer-Reviewed Publication

WGS analysis and molecular resistance mechanisms of azithromycin-resistant (MIC >2 mg/L) Neisseria gonorrhoeae isolates in Europe from 2009 to 2014


Peer-Reviewed Publication

Update of Clostridium difficile-associated disease due to PCR ribotype 027 in Europe.


Peer-Reviewed Publication

The dynamic changes of dominant clones of Staphylococcus aureus causing bloodstream infections in the European region: Results of a second structured survey


Peer-Reviewed Publication

Survey of diagnostic and typing capacity for Clostridium difficile infection in Europe, 2011 and 2014


Peer-Reviewed Publication

Surveillance of extensively drug-resistant tuberculosis in Europe, 2003-2007


Peer-Reviewed Publication

Surveillance of congenital rubella and rubella infections in pregnancy in EU/EEA countries, 2012: Current status and future perspective to monitor elimination



Surveillance of communicable diseases in Europe – a concept to integrate molecular typing data into EU-level surveillance

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Eurosurveillance articles

12 January 2017 - A joint cross-border investigation of a cluster of multidrug-resistant tuberculosis in Austria, Romania and Germany in 2014 using classic, genotyping and whole genome sequencing methods: lessons learnt
22 September 2016 - Community-wide outbreak of haemolytic uraemic syndrome associated with Shiga toxin 2-producing Escherichia coli O26:H11 in southern Italy, summer 2013
15 September 2016 - Towards a consensus on genotyping schemes for surveillance and outbreak investigations of Cryptosporidium, Berlin, June 2016
28 February 2013 - Letter to the editor: Application of Bayesian methods to the inference of phylogeny for enterovirus surveillance
28 February 2013 - Authors' reply: Application of Bayesian methods to the inference of phylogeny for enterovirus surveillance
24 January 2013 - From molecular to genomic epidemiology: transforming surveillance and control of infectious diseases
24 January 2013 - Use of multilocus variable-number tandem repeat analysis (MLVA) in eight European countries, 2012
24 January 2013 - Overview of molecular typing methods for outbreak detection and epidemiological surveillance