Molecular Typing Methods for Pathogens, ESCMID Postgraduate Education Course

30 June - 4 July 2014, Lyon, France

  • ESCMID Study Group for Epidemiological Markers (ESGEM)
  • Lyon East Medical School
  • ESCMID Study Group for Legionella Infections (ESGLI)
  • ESCMID Study Group for Molecular Diagnostics (ESGMD)
  • ESCMID Study Group for Staphylococci and Staphylococcal Diseases (ESGS)
Course Coordinators
  • Alex Friedrich, Groningen, The Netherlands
  • Frédéric Laurent, Lyon, France
Course Objectives
  • Provide young microbiologists with basic knowledge in bacteriology and virology with an updated overview of molecular typing methods for pathogens
  • Give participants the opportunity to get insights and technical experience of the most common methods (including NGS approaches) in the daily infection control practice
Course Venue

Lyon East Medical School-Laennec
Bacteriology Department
7, rue Guillaume Paradin
69372 Lyon, Cedex 08

Directions & Hotel
Subway Map

Target Audience
15 – 20 young microbiologists with basic knowledge in bacteriology and virology who want to get an updated overview of the theoretical and practical use of molecular typing methods and epidemiological markers for pathogens.

Contact Person

Dr Frédéric Laurent
Hospices Civils de Lyon
Centre de Biologie Nord
Laboratoire de Bactériologie
Hôpital de la Croix-Rousse
103, Grande Rue de la Croix-Rousse
69004 Lyon

Phone +33 472 07 18 37

Administrative Secretariat

Hélène Meugnier
Institut de Microbiologie
Laboratoire de Bactériologie
Centre national
de référence des staphylocoques
59, Boulevard Pinel
69677 Bron Cedex

Phone +33 472 12 95 80
Fax +33 472 12 96 26

Course Programme

Presentations are availabe in the ESCMID Online Lecture Library.

Monday, 30 June 2014

  • Welcome introduction. Jérôme Etienne (Dean of the Lyon East Medical School)


  • Molecular typing: an overview. Alex Friedrich & Hajo Grundmann
  • How to validate a new typing method? Raquel Sá-Leão & Richard Goering
  • PFGE/SBT/Spoligotyping: principles and applications.
    Sophie Jarraud & Christophe Ginevra
  • SLST, MLST, MLVA, DNA microarrays: principles and tools for data analysis. Anne Tristan & Frédéric Laurent
  • Typing at different geographic levels. Hajo Grundmann


  • DNA extraction, PCR, PFGE preparation. Hélène Meugnier, Michèle Bes,
    Anne Tristan, Christophe Ginevra & Raquel Sá-Leão

Tuesday, 1 July 2014


  • How rapid molecular diagnosis helps in the management of outbreaks.
    Paul Savelkoul
  • Making sense out of molecular typing data: current gold standards and issues in data interpretation. Richard Goering
  • Use of typing methods in the daily infection control practice. Alex Friedrich
  • Limitations of molecular typing and how to integrate typing results into a comprehensive epidemiological investigation in highly endemic nosocomial situations. Hajo Grundmann


  • Gel, migration, sequence analysis and interpretation (SLT, MLST, MLVA), microarray. Hélène Meugnier, Michèle Bes, Anne Tristan, Christophe Ginevra & Raquel Sá-Leão

Wednesday, 2 July 2014


Epidemiological use of Next Generation Sequencing data

  • NGS: principles and methods. Patricia Simoes-Martins
  • Overview of bioinformatics and software for rapid high-throughput sequence analysis in clinical and public health microbiology. Dag Harmsen
  • Outbreak analysis by using whole genome sequencing. John Rossen
  • Evolution and phylogeny of S. aureus using NGS in practice. David Aanensen


  • PFGE analysis and interpretation, phylogenetic tree, WG sequencing, Legionella SBT. Alex Friedrich, John Rossen, Dag Harmsen &
    Sophie Jarraud

Thursday, 3 July 2014


  • Typing of ESBL and VRE. Guido Werner & Sylvain Brisse

Pivotal role of typing: the legionellosis example

  • From application of typing methods including whole genome sequencing to epidemiology of Legionella infections. Valeria Gaia & Tim Harrisson
  • Practical added value of the network for national and European cross-border molecular surveillance of Legionella. Sophie Jarraud
  • Molecular typing and whole genome sequencing in public health.
    Tim Harrisson


  • WGS sequence analysis (part 1). Alex Friedrich, Hajo Grundmann &
    David Aanensen

Friday, 4 July 2014


Epidemiological markers: to infinity and beyond

  • Bacterial typing: from animal to human and reverse - ST398 S. aureus.
    Robert Skov & Anders Rhod Larsen
  • Coalescence analysis and demogenetical analysis based on full genome data. Thierry Wirth
  • Phylogeographic reconstruction and visualisation of S. aureus ST80 spread through time and space. François Vandenesch
  • Influenza virus: phylodynamics/phylogenomics and public health impact. Maude Bouscambert


  • WGS sequence analysis (part 2). Alex Friedrich, Hajo Grundmann &
    David Aanensen
Confirmed Faculty Members
  • David Aanensen, London, United Kingdom
  • Michèle Bes, Lyon, France
  • Maude Bouscambert, Lyon, France
  • Sylvain Brisse, Paris, France
  • Alex Friedrich, Groningen, The Netherlands
  • Valeria Gaia, Bellinzona, Switzerland
  • Christophe Ginevra, Lyon, France
  • Richard Goering, Omaha, United States
  • Hajo Grundmann, Groningen, The Netherlands
  • Dag Harmsen, Münster, Germany
  • Tim Harrisson, London, United Kingdom
  • Sophie Jarraud, Lyon, France
  • Anders Rhod Larsen, Copenhagen, Denmark
  • Frédéric Laurent, Lyon, France
  • Hélène Meugnier, Lyon, France
  • John Rossen, Groningen, The Netherlands
  • Raquel Sá-Leão, Lisbon, Portugal
  • Paul Savelkoul, Maastricht, The Netherlands
  • Patricia Simoes-Martins, Lyon, France
  • Robert Skov, Copenhagen, Denmark
  • Anne Tristan, Lyon, France
  • François Vandenesch, Lyon, France
  • Guido Werner, Wernigerode, Germany
  • Thierry Wirth, Paris, France