Profession & Career

ESCMID Panorama

Capacity-building Workshop: Rapid NGS for Characterization and Typing of Resistant Gram-Negative Bacilli, ESCMID Postgraduate Technical Workshop

7 - 9 October 2015, Groningen, Netherlands

Organizers
  • ESCMID Study Group for Epidemiological Markers (ESGEM)
  • ESCMID Study Group for Molecular Diagnostics (ESGMD)
  • University Medical Center Groningen, Department of Medical Microbiology
  • EurSafety Health-Net
Course Coordinators
  • Alexander Friedrich, Groningen, Netherlands
  • Hajo Grundmann, Groningen, Netherlands
  • Dag Harmsen, Münster, Germany
  • Jacob Moran-Gilad, Jerusalem, Israel
  • John Rossen, Groningen, Netherlands
Course Objectives

Next-Generation-Sequencing (NGS) technology has developed rapidly during the last years. Innovative bench-top NGS platforms broaden application opportunities, especially for diagnostic use and surveillance. The programme highlights opportunities and challenges posed by this technology. The workshop has been designed to boost practical knowledge exchange as well as ample discussions with colleagues fromall over Europe.

Course Venue

University Medical Center Groningen
Hanzeplein 1
9713 GZ Groningen
Netherlands

Target Audience

20 – 30 technicians, (molecular) biologists, medical microbiologists, bioinformaticians, veterinarians and public health workers involved in animal, human or food-related research (one-health principle) are identified as main target of this workshop.

Contact Person (Scientific Programme)

Dr John WA Rossen
Head Molecular Unit
Department of Medical Microbiology
University Medical Center Groningen
Mailcode: EB80
Hanzeplein 1
9713 GZ Groningen
Netherlands

Phone +31 503 613 480
Fax +31 503 619 105


Administrative Secretariat

Henna Holband
Department of Medical Microbiology
University Medical Center Groningen
Mailcode: EB80
Hanzeplein 1
9713 GZ Groningen
Netherlands

Phone +31 503 619 650
Fax +31 503 619 105

Course Programme

Presentations are availabe in the ESCMID Online Lecture Library.

Wednesday, 7 October 2015

Practical day: Wet laboratory
08:30 Welcome. John Rossen
08:35 Next generation epidemiology in modern infection prevention and control.            Alexander Friedrich
09:05 Introduction of the day. John Rossen
09:15 Microbial whole genome sequencing (sample and library preparation,                   sequencing) – Part I
10:45 Coffee break
11:15 Microbial whole genome sequencing (sample and library                                            preparation, sequencing) – Part II
12:45 Lunch
13:30 Microbial whole genome sequencing (sample and library                                           preparation, sequencing) – Part III
15:00 Coffee break
15:15 Microbial whole genome sequencing (sample and library preparation,                   sequencing) – Part IV

Thursday, 8 October 2015

09:00 General overview of transmission dynamics and bacterial                                            population structures. Hajo Grundmann
09:45 Analysis of the dissemination of cephalosporin resistance genes in                       Escherichia coli by whole genome sequencing. Willem van Schaik
10:30 Coffee break
11:00 Whole genome sequence analysis of population snapshots at                                  continental scale. Corinna Glasner
11:45 Real-time genome sequencing of multidrugresistant bacteria                                   enables cost-effective high-resolution detection and refutation of                               nosocomial transmissions. Dag Harmsen
12:30 Lunch
13:30 Application of WGS for characterization of Acinetobacter spp.
           Jacob Moran-Gilad
14:15 Whole genome and core genome MLST analysis from NGS data: from                   reads to trees. João André Carriço
15:00 Coffee break
15:30 Use of WGS in routine clinical microbiology – epi- and pathotyping.
           John Rossen
16:15 Late-breaking presentation
18:00 Dinner and social programme

Friday, 9 October 2015

Practical day: Computer analysis
08:30 – 16:30

  • Computational data analysis and bioinformatics pipelines
  • Web-based whole genome sequence analysis for pathogen genomics
  • Computational data analysis and bioinformatics pipelines: online tools
Faculty Members
  • João André Carriço, Lisbon, Portugal
  • Alexander Friedrich, Groningen, Netherlands
  • Corinna Glasner, Hinxton, United Kingdom
  • Hajo Grundmann, Groningen, Netherlands
  • Dag Harmsen, Münster, Germany
  • Jacob Moran-Gilad, Jerusalem, Israel
  • John Rossen, Groningen, Netherlands
  • Willem van Schaik, Utrecht, Netherlands


Tutors
  • Yvette Bisselink, Groningen, Netherlands
  • Ruud Deurenberg, Groningen, Netherlands
  • Erwin Raangs, Groningen, Netherlands
  • Sigrid Rosema, Groningen, Netherlands
Last update: 10 December 2015

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Get the Course Leaflet as pdf.

Leaflet