Next-generation sequencing (NGS) technology has developed rapidly during the last years. Innovative bench-top NGS platforms broaden application opportunities, especially for diagnostic use, epidemiological inference, and surveillance. 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 Europe.
20 – 30 technicians, (molecular) biologists, medical microbiologists, bioinformaticians, hospital infections control experts, infectious disease epidemiologists and public health specialists with an interest in transmission dynamics are the target groups which would benefi t most from this workshop.
Alexander W. Friedrich, Groningen, Netherlands
Hajo Grundmann, Freiburg, Germany
Jacob Moran-Gilad, Beit Kama, Israel
Sandra Reuter, Freiburg, Germany
John W. A. Rossen, Groningen, Netherlands
ESCMID Study Group for Epidemiological Markers - ESGEM
ESCMID Study Group for Genomic and Molecular Diagnostics - ESGMD
The organizer(s) of the course will apply for European CME accreditation through EACCME.

Speakers


Jennifer Karin Bender, Wernigerode, Germany
Hajo Grundmann, Freiburg, Germany
Axel Kola, Berlin, Germany
Jacob Moran-Gilad, Beit Kama, Israel
Erwin Raangs, Groningen, Netherlands
Sandra Reuter, Freiburg, Germany
Sigrid Rosema, Groningen, Netherlands
John W. A. Rossen, Groningen, Netherlands
Birgit Strommenger, Wernigerode, Germany
Alan Walker, Aberdeen, United Kingdom
Guido Werner, Wernigerode, Germany

Contact Person (Scientific Programme)

Sandra Reuter
Medical Center, University of Freiburg
Infection Prevention and Hospital Hygiene
Breisacher Strasse 115b
79106 Freiburg
Germany
+49 761 27082350
sandra.reuter@uniklinik-freiburg.de

Administrative Secretariat

Deborah Lawrie-Blum
Medical Center, University of Freiburg
Infection Prevention and Hospital Hygiene
Breisacher Strasse 115b
79106 Freiburg
Germany
+49 761 27082060
deborah.lawrie-blum@uniklinik-freiburg.de

Venue Info

Event Map
Venue Details
Medical Center, University of Freiburg
Breisacher Strasse 115b, 79106 Freiburg
Germany
Phone: +49 761 27082060
Fax: +49 761 27082060
Email: deborah.lawrie-blum@uniklinik-freiburg.de

Course Programme



  1. 13:30 - 14:00
    Social Activity
    Registration and coffee


  2. 14:00 - 14:05
    Presentation
    Opening of the course, welcome
    Speaker(s): Hajo Grundmann



  3. 14:05 - 14:30
    Presentation
    Next-generation epidemiology and infection prevention
    Speaker(s): Jacob Moran-Gilad



  4. 14:30 - 14:35
    Presentation
    Introduction of Illumina sequencing – theory


  5. 15:00 - 15:30
    Coffee Break
    Coffee break


  6. 15:30 - 16:00
    Presentation
    Data QC: introduction to basespace tools


  7. 16:00 - 16:30
    Workshop
    Workshop: data QC – raw reads


  8. 16:30 - 17:00
    Coffee Break
    Coffee break


  9. 17:00 - 18:00
    Workshop
    Workshop: introduction to Artemis sequence viewer
    Speaker(s): Sandra Reuter



  10. 18:00 - 18:30
    Presentation
    Wrap up – questions of the day
    Speaker(s): Sandra Reuter



  11. 18:30 - 19:15
    Presentation
    Keynote: detection of resistance genes – application of WGS and metagenomics


  1. 08:30 - 09:30
    Workshop
    Workshop: data QC – assembly


  2. 09:30 - 10:00
    Coffee Break
    Coffee break


  3. 10:00 - 10:30
    Presentation
    Aspects of library preparation
    Speaker(s): Erwin Raangs



  4. 10:30 - 11:30
    Workshop
    Workshop: DNA quantification
    Speaker(s): Erwin Raangs, Sigrid Rosema



  5. 11:30 - 12:30
    Workshop
    Workshop: tagmentation & index PCR
    Speaker(s): Erwin Raangs, Sigrid Rosema



  6. 12:30 - 13:30
    Lunch
    Lunch


  7. 13:30 - 14:30
    Workshop
    Workshop: PCR cleanup
    Speaker(s): Erwin Raangs, Sigrid Rosema



  8. 14:30 - 15:30
    Workshop
    Workshop: library normalization & pooling
    Speaker(s): Erwin Raangs, Sigrid Rosema



  9. 15:30 - 16:00
    Coffee Break
    Coffee break


  10. 16:00 - 16:30
    Presentation
    Wrap up – questions of the day
    Speaker(s): Erwin Raangs, Sigrid Rosema



  11. 16:30 - 17:15
    Presentation
    Keynote: application of WGS in a routine diagnostic lab
    Speaker(s): Axel Kola



  12. 17:15 - 18:30
    Presentation
    Keynote: application of WGS in national health surveillance
    Speaker(s): Guido Werner



  13. 18:30 - 19:15
    Presentation
    Keynote: studying the intestinal microbiota – recent insights and pitfalls to be avoided
    Speaker(s): Alan Walker



  1. 08:30 - 09:30
    Workshop
    Workshop: data QC – species ID


  2. 09:30 - 10:00
    Coffee Break
    Coffee break


  3. 10:00 - 11:00
    Workshop
    Workshop: data analysis – MLST
    Speaker(s): Jennifer Karin Bender, Birgit Strommenger



  4. 11:00 - 12:00
    Workshop
    Workshop: data analysis – resistance
    Speaker(s): Sandra Reuter



  5. 12:00 - 13:00
    Lunch
    Lunch


  6. 13:00 - 15:00
    Workshop
    Workshop: data analysis – cgMLST and phylogenetics
    Speaker(s): John W. A. Rossen



  7. 15:00 - 15:30
    Coffee Break
    Coffee break


  8. 15:30 - 16:00
    Presentation
    Wrap up – questions of the day
    Speaker(s): Jennifer Karin Bender, John W. A. Rossen, Birgit Strommenger



  9. 16:00 - 17:30
    Presentation
    Keynote: personalized microbiology during outbreaks – unique markers and in silico screening approaches
    Speaker(s): John W. A. Rossen



  10. 17:30 - 22:00
    Social Activity
    Social activity and dinner


  1. 08:30 - 10:00
    Workshop
    Workshop: data analysis – own run (Course participants)


  2. 10:00 - 11:00
    Coffee Break
    Coffee break


  3. 11:00 - 12:30
    Workshop
    Workshop: data analysis – own run (Course participants)


  4. 12:30 - 14:00
    Lunch
    Lunch break, departures

08-Sep-2017
500
600
The fee includes the course, coffee, lunches and the social dinner. Travel and accommodation are not included.
18-Aug-2017
01-Sep-2017