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.
Sandra Reuter, Freiburg, Germany
Hajo Grundmann, Freiburg, Germany
Alexander W. Friedrich, Groningen, Netherlands
Jacob Moran-Gilad, Beer Sheva, Israel
John W. A. Rossen, Groningen, Netherlands
ESCMID Study Group for Epidemiological Markers - ESGEM
ESCMID Study Group for Genomic and Molecular Diagnostics - ESGMD
University of Freiburg Medical Center, Freiburg, Germany
University Medical Center Groningen (UMCG), Groningen, Netherlands
The organizer(s) of the course will apply for European CME accreditation through EACCME.

Speakers


Jennifer Karin Bender, Wernigerode, Germany
Yvette Bisselink, Groningen, Netherlands
Stephan Fuchs, Wernigerode, Germany
Oliver Goldenberg, Berlin, Germany
Hajo Grundmann, Freiburg, Germany
Sarah Klassen, Freiburg, Germany
Axel Kola, Berlin, Germany
Jacob Moran-Gilad, Beer Sheva, Israel
Silke Peter, Tübingen, Germany
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
Sabine Weber, Freiburg, 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

Tuesday, 10 October 2017

13:30 - 14:00
Registration and coffee
14:00 - 14:05
Opening of the course, welcome
Speaker(s): Hajo Grundmann
14:05 - 14:30
Next-generation epidemiology and infection prevention
Speaker(s): Jacob Moran-Gilad
14:30 - 15:00
Introduction of Illumina sequencing – theory
Speaker(s): Oliver Goldenberg
15:00 - 15:30
Coffee break
15:30 - 16:00
Data QC: introduction to basespace tools
Speaker(s): Oliver Goldenberg
16:00 - 16:30
Introduction to Unix
Speaker(s): Stephan Fuchs
16:30 - 17:00
Coffee break
17:00 - 18:00
Workshop: introduction to Artemis sequence viewer
Speaker(s): Sandra Reuter
18:00 - 18:30
Wrap up – questions of the day
Speaker(s): Stephan Fuchs
Speaker(s): Sandra Reuter
18:30 - 19:15
Keynote: detection of resistance genes – application of WGS and metagenomics
Speaker(s): Silke Peter

Wednesday, 11 October 2017

08:30 - 09:30
Workshop: data QC – raw reads
Speaker(s): Stephan Fuchs
09:30 - 10:00
Coffee break
10:00 - 10:30
Aspects of library preparation
Speaker(s): Erwin Raangs
10:30 - 11:30
Workshop: DNA quantification
Speaker(s): Yvette Bisselink
Speaker(s): Sarah Klassen
Speaker(s): Erwin Raangs
Speaker(s): Sigrid Rosema
Speaker(s): Sabine Weber
11:30 - 12:30
Workshop: tagmentation & index PCR
Speaker(s): Yvette Bisselink
Speaker(s): Stephan Fuchs
Speaker(s): Sarah Klassen
Speaker(s): Erwin Raangs
Speaker(s): Sigrid Rosema
Speaker(s): Sabine Weber
12:30 - 13:30
Lunch
13:30 - 14:30
Workshop: PCR cleanup
Speaker(s): Yvette Bisselink
Speaker(s): Sarah Klassen
Speaker(s): Erwin Raangs
Speaker(s): Sigrid Rosema
Speaker(s): Sabine Weber
14:30 - 15:30
Workshop: library normalization & pooling
Speaker(s): Yvette Bisselink
Speaker(s): Sarah Klassen
Speaker(s): Erwin Raangs
Speaker(s): Sigrid Rosema
Speaker(s): Sabine Weber
15:30 - 16:00
Coffee break
16:00 - 16:30
Wrap up – questions of the day
Speaker(s): Yvette Bisselink
Speaker(s): Stephan Fuchs
Speaker(s): Sarah Klassen
Speaker(s): Erwin Raangs
Speaker(s): Sigrid Rosema
Speaker(s): Sabine Weber
16:30 - 17:15
Keynote: application of WGS in a routine diagnostic lab
Speaker(s): Axel Kola
17:15 - 18:30
Keynote: application of WGS in national health surveillance
Speaker(s): Birgit Strommenger
18:30 - 19:15
Keynote: studying the intestinal microbiota – recent insights and pitfalls to be avoided
Speaker(s): Alan Walker

Thursday, 12 October 2017

08:30 - 09:30
Workshop: data QC – assembly and species ID
Speaker(s): Stephan Fuchs
09:30 - 10:00
Coffee break
10:00 - 12:00
Workshop: data analysis – online typing tools: MLST and resistance
Speaker(s): Jennifer Karin Bender
Speaker(s): Sandra Reuter
Speaker(s): Birgit Strommenger
12:00 - 13:00
Lunch
13:00 - 15:00
Workshop: data analysis – mapping and phylogenetics
Speaker(s): Sandra Reuter
15:00 - 15:30
Coffee break
15:30 - 16:00
Wrap up – questions of the day
Speaker(s): Jennifer Karin Bender
Speaker(s): John W. A. Rossen
Speaker(s): Birgit Strommenger
16:00 - 17:30
Keynote: personalized microbiology during outbreaks – unique markers and in silico screening approaches
Speaker(s): John W. A. Rossen
17:30 - 22:00
Social activity and dinner

Friday, 13 October 2017

08:30 - 10:00
Workshop: data analysis – own run (Course participants)
10:00 - 11:00
Coffee break
11:00 - 12:30
Workshop: data analysis – own run (Course participants)
12:30 - 14:00
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