Research & Projects

ESCMID Panorama

ESCMID Study Group for Genomic and Molecular Diagnostics - ESGMD

News & Activities

Clinical bioinformatics for microbial genomics and metagenomics

Co-organised by ESGMD, ESCMID, Lausanne University Hospital (CHUV) and the Swiss Institute of Bioinformatics (SIB)

Lausanne, Switzerland, 9 – 12 September 2019

Next generation sequencing (NGS) is being increasingly used and implemented at clinical microbiology laboratories, heavily relying on bioinformatics for data processing, analysis and interpretation. This course aims at providing participants with the essential tools to understand the output of bioinformatics analysis pipelines, interpret the results for making better-informed clinical recommendations, recognise the main challenges and limitations when using NGS bioinformatics analysis pipelines in clinical settings, and acquire a common language to foster multidisciplinary discussions of results with clinical bioinformaticians in their team. It will cover the essential bioinformatics concepts on NGS data management and processing for typing and phylogenetics, resistance and virulence prediction, and metagenomics-based taxonomic classification.

Programme

Course material in the ESCMID eLibrary

ESCMID Postgraduate Education Course

Phenotypic and Molecular approaches for Detection and Control of Carbapenem- and Colistinresistant Gram-negatives

Co-organised by ESGARS, ESGMD and ESCMID

Volos, Greece, 23 – 24 May 2019

Gram-negative pathogens currently represent a very significant public health issue in most countries worldwide. Particularly challenging are the diagnostic and treatment aspects of carbapenem- and/or colistin-resistant infections. In that respect, the prompt diagnosis of infections due to such pathogens and the accurate detection of their antibiotic resistance status are very important for the clinical microbiological laboratories. This Postgraduate Educational Course will comprise state-of-the-art lectures dealing with phenotypic and molecular diagnostic approaches of multi-resistant nosocomial bugs, emphasizing on carbapenemand colistin-resistant Gram-negatives, such as Acinetobacter baumannii, Klebsiella pneumoniae and Pseudomonas aeruginosa.

Programme

Course material in the ESCMID eLibrary

ESCMID Postgraduate Technical Workshop

Emerging infections for clinicians and the WHO Emerging Diseases Clinical Assessment and Response Network

Co-organised by ESGMD, ESGMYC, ESGITM and ESGPHM

Florence, Italy, 13 – 15 May 2019

This workshop aims to bridge the gap between advanced diagnostics (such as metagenomics and whole genome sequencing) and clinical practice. The program will include presentation of diagnostic methods and diagnostic strategies, as well as case stories presented by clinicians. The last day is focused on the emergency teams deployed by the WHO in collaboration with the WHO Emerging Diseases Clinical Assessment and Response Network (EDCARN).

Programme

Course material in the ESCMID eLibrary

15 April 2019

New Executive Committee takes office

ESGMD has a new executive committee composed of:

  • Chair: Prof. John W. A. Rossen, Netherlands
  • Secretary: Prof. Gilbert Greub, Switzerland
  • Treasurer: Dr Hege Vangstein Aamot, Norway
  • Science Officer: Prof. Frederic Laurent, France
  • Education Officer: Amel Renaud Bidias, Cameroon

Natacha Couto and Silke Peter as members of the election committee invited the membership to nominate candidates and vote. The results of the elections are the following:

  • Number of members with voting right: 193
  • Number of voters: 72 (37.3%)

Candidates:

  • John W. A. Rossen, The Netherlands        61, elected
  • Gilbert Greub, Switzerland        37, elected
  • Hege V. Aamot, Norway        32, elected
  • Frédéric Laurent, France        26, elected
  • Amel R. Bidas, Cameroon        6, elected
  • No preference        1

The new executive committee is elected for two years.

ESCMID Postgraduate Education Course

3rd Course on Principles of Molecular Microbiological Diagnostics

Co-organised by ESGEM, ESGMD and ESCMID

17 – 19 January 2018, Maastricht, Netherlands

Course Objectives: Basic information on microbiological molecular diagnostics and set-up; Advanced education (interactive workshops) on technical items (participants can discuss their own questions with experts); Advantages and pitfalls of specific techniques; Setting up molecular diagnostic laboratory (low resource settings); Typing approaches for infection control; New MDx techniques (NGS, automation, multiplex, mass spectrometry); Emerging fields in MDx (microbioma diagnostic applications; electronic nose expectations, etc.); Future perspectives of MDx in the clinical microbiological laboratory

Programme

Course material in the ESCMID eLibrary

ESCMID Postgraduate Technical Workshop

Capacity-Building Workshop: Metagenomics in the Diagnostic Laboratory

Co-organised by ESGMD, ESGEM and the University Medical Center Groningen

21 – 24 October 2018, Groningen, Netherlands

After the successful introduction of Next-Generation Sequencing (NGS) technology for epidemiological inference and surveillance in routine microbiology, laboratories face a new challenge as metagenomics for identification of pathogens and antimicrobial resistance genes is about to enter the laboratory. The programme highlights opportunities and challenges posed by this technology. The workshop has been designed to boost practical knowledge exchange (with respect to both “wet-lab” and “e-lab”) as well as ample discussions with colleagues from all over the world.

Programme

Course material in the ESCMID eLibrary

ESCMID Postgraduate Technical Workshop

Diagnostic Microbiology: MALDI-TOF, Bacterial Genomics, Metagenomics, Automation and Molecular Microbiology

Co-organised by ESGMD, ESGEM, the University and the University Hospital of Lausanne

25 – 28 September 2018, Lausanne,Switzerland

To further improve patients care, it is crucial to continue to develop new tools providing faster results, with a broader diversity of pathogenic agents with very high sensivity and specificity. To reach these goals, it is important to be aware of the new innovative methods that have recently been developed and to exchange knowledge and ideas on the future of diagnostic microbiology, including the emerging indications of metagenomics for non-infectious diseases such as obesity and asthma. This course thus aims to provide a unique platform to learn about the strengths and limitations of new diagnostic tools including Maldi-TOF, molecular diagnosis, genomics and metagenomics, as well as novel innovative technics such as nanoplasmonic sensors and atomic force microscopy. The course also offers a unique opportunity for participants to gain practical experience during the twelve different practicals led by local microbiologists.

Programme

Course material in the ESCMID eLibrary

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