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European Public Health Microbiology Training Path (EUPHEM)

Scene in a microbiological laboratory. Source: RKI


The Robert Koch-Institute has been a training site of the European Public Health Microbiology Training path (EUPHEM) since September 2009. EUPHEM is a two-year postgraduate qualification programme that aims to provide training for scientists with experience in microbiology and a keen interest in public health in the core areas of public health microbiology (PHM):

  • PHM Management and Communication
  • Applied PHM research and laboratory investigations
  • Epidemiological investigations (Surveillance and Outbreak investigation)
  • Biorisk Management
  • Quality Management
  • Teaching and pedagogical skills

This PHM training path is coordinated and funded by the European Centre for Disease Prevention and Control (ECDC) and is closely linked to its sister programme EPIET for epidemiology training. The EUPHEM training consists mainly of learning by doing (projects) aimed at finding and implementing appropriate action as a public health microbiologist when working in a public health institution, e.g. reference diagnostics, surveillance, preparedness, response activities. The EUPHEM fellows work under the supervision of experienced laboratory specialists and epidemiologists of our institution, and will collaborate with fellows from the EPIET path and the Postgraduate Training for Applied Epidemiology (PAE), the national epidemiology training programme at RKI.

PHM is a cross-cutting area that spans the fields of human, animal, food, water, and environmental microbiology, with a focus on human health and disease. Public health microbiology laboratories play a central role in detecting and monitoring pathogenic organisms, in outbreak response, and are providing scientific evidence to prevent and control infectious diseases. European preparedness for responding to threats by new and known infectious diseases requires a sustainable infrastructure including design of prevention, treatment and infection control strategies. Public health microbiology is required to provide access to scientists with expertise/experience of the important communicable diseases at the regional, national and international level for mounting a rapid response to emerging health threats, planning appropriate strategies for prevention, assess existing prevention disciplines in place/use, develop or assist in development of microbiological guidelines, evaluate/develop new diagnostic tools, assess risks of microbes or their products and provide necessary information to policy makers related to above issues from a microbiology perspective.


EUPHEM fellowships have a duration of two years. During this period, EUPHEM fellows are employed by a Public Health Institution accredited by ECDC for providing all necessary competencies to successfully train a fellow. EU track fellows are funded by ECDC for two years, while Member State (MS) track fellows are recruited in national PHM institutions and remain employed at their institution during and after the fellowship.

The practice-oriented training (learning-by-doing) involves performing/supporting projects within the remit of the public health institution to obtain competencies in the above-mentioned PHM areas. The results of the projects will be presented in the form of reports, publications, or presentations at scientific conferences such as ESCAIDE (Annual European Scientific Conference on Applied Infectious Disease Epidemiology), ECCMID (European Congress of Clinical Microbiology and Infectious Diseases) or others.

In addition to the practice-oriented training, theoretical knowledge is communicated through different training modules and courses, of which some are compulsory, and others optional. Each fellow is obliged to participate in around 10 to 11 module weeks. Most of these modules are offered in cooperation with the EPIET programme and take place in different member states of the European Union.

Compulsory modules are:

  • Introduction to R
  • Introductory course
  • Research protocol & scientific wirting
  • Multivariable AnalysisPHM
  • Project review
  • Participation in the ESCAIDE conference (3x)
  • Whole genome sequencing & bioinformatics
  • Biorisk and quality management

Elective moduls are:

  • Basic phylogeny and AMR
  • Social and behavioural sciences
  • Vaccinology
  • Qualitative research
  • Rapid assessment and survey methods
  • Project review
  • One Health
  • Time-series analysis
  • Emergency preparedness & response

Eligibility requirements

The training is aimed at EU citizens with:

  • Post-secondary education attested by a diploma in medicine, biology, microbiology, veterinary medicine, pharmacology, bioinformatics or biomedicine, at the level of graduate diploma, Masters’ degree or equivalent; and
  • At least three (3) years of work experience in microbiology; or a PhD degree in microbiology or equivalent (e.g. clinical microbiology specialisation, veterinary medicine specialisations, or a specialisation in any microbiology field).

Fellows are selected from nationals of member states of the European Union and the EEA-countries. Selection is based on the mentioned above criteria considering professional and personal characteristics/interpersonal skills. The criteria are defined by the ECDC with advice from the EUPHEM Training Forum and included in the call for application. Candidates are invited through a yearly call for application advertised on the ECDC website.

Applicants are expected to work for the public health service nationwide in their home country or abroad after completing the qualification.

Date: 03.04.2024