The workshop is intended to introduce the emerging role of next-generation sequencing in clinical and public health microbiology and support the building of national and regional capacity in this area. Special focus will be placed on available sequencing technologies, their implementation in the microbiology laboratory settings, the use of various bioinformatics tools for analysing NGS outputs and clinical interpretation. Capacity building will take place using relevant exemplars such as surveillance of infection, outbreak investigation and control, antimicrobial resistance and food and water microbiology. Moreover, the course aims to create new networks between microbiologists, infectious disease specialists, bioinformaticians and other allied professions in the region in order to facilitate the application of NGS in the European neighbourhood.
60 – 100 microbiologists, epidemiologists, infectious disease specialists and bioinformaticians from hospital and public health settings from Middle Eastern, European, Balkan and African countries.
Joao Andre Carrico, Lisboa, Portugal
Alexander W. Friedrich, Groningen, Netherlands
Hajo Grundmann, Freiburg, Germany
Jacob Moran-Gilad, Beer Sheva, Israel
John W. A. Rossen, Groningen, Netherlands
No Option Selected
The event has been granted 15 European CME credits (ECMEC®s) by the European Accreditation Council for Continuing Medical Education (EACCME®).


Joao Andre Carrico, Lisboa, Portugal
Eric Claas, Leiden, Netherlands
Eddie Cytryn, Modiin, Israel
Amparo Fernández-Rodríguez, Madrid, Spain
Alexander W. Friedrich, Groningen, Netherlands
Dag Harmsen, NA, Country Not Specified
Colin R. MacKenzie, Düsseldorf, Germany
Jacob Moran-Gilad, Beer Sheva, Israel
Maria Luisa Ricci, Rome, Italy
John W. A. Rossen, Groningen, Netherlands
Paul Savelkoul, Maastricht, Netherlands
Ines Steffens, Solna, Sweden

Contact Person (Scientific Programme)

Jacob Moran-Gilad
Ben-Gurion University of the Negev
Faculty of Health Sciences
Rager Blvd
84101 Beer-Sheva
+972 50-624-3900

Administrative Secretariat

Reut Assor Zonens
Paragon Israel
Project Manager
15 Aba Even st
46851 Herzliya
+972 3-576-7708

Venue Info

Event Map
Venue Details
Daniel Herzliya Hotel
60 Ramat Yam, 46851 Herzliya
Phone: +972 9-952-8282
Fax: +972 9-952-8282

Monday, 30 October 2017

08:00 - 09:00
09:00 - 09:30
Welcome and introduction of the Study Groups and the ISID
Speaker(s): Alexander W. Friedrich
Speaker(s): Jacob Moran-Gilad
09:30 - 10:15
Overview of next-generation sequencing and new technologies in medical microbiology
Speaker(s): Alexander W. Friedrich
10:15 - 11:00
The basics of NGS I – overview of sequencing platforms and related equipment
Speaker(s): Eric Claas
11:00 - 11:30
Coffee break
11:30 - 12:15
The basics of NGS II – nucleic acid extraction and library preparation for microbial NGS
Speaker(s): John W. A. Rossen
12:15 - 13:00
Interactive discussion I – how to set up wet NGS in the hospital microlab? (Panel of faculty members)
Chairperson(s): Alexander W. Friedrich
13:00 - 14:00
14:00 - 14:45
Overview of molecular typing approaches for bacterial pathogens
Speaker(s): Joao Andre Carrico
14:45 - 15:30
Advanced NGS I – how to infer clinically relevant information from bacterial whole-genome sequences?
Speaker(s): Jacob Moran-Gilad
15:30 - 16:00
Coffee break
16:00 - 17:30
Advanced NGS II – bacterial typing applications using NGS
Speaker(s): Dag Harmsen

Tuesday, 31 October 2017

08:30 - 08:45
Summary of day 1
08:45 - 09:15
Case presentation I – NGS application for multi-resistant Gram-negative rods
Speaker(s): Colin R. MacKenzie
09:15 - 09:45
Case presentation II – NGS application for hospital outbreaks
Speaker(s): John W. A. Rossen
09:45 - 10:30
Metagenomics I – NGS application for microbiome analysis
Speaker(s): Paul Savelkoul
10:30 - 11:00
Coffee break
11:00 - 11:45
Metagenomics II – applications in water systems
Speaker(s): Maria Luisa Ricci
11:45 - 12:30
Metagenomics III – applications in environmental surveillance of resistance
Speaker(s): Eddie Cytryn
12:30 - 13:30
13:30 - 14:15
Metagenomics IV – application for forensic microbiology
Speaker(s): Amparo Fernández-Rodríguez
14:15 - 14:45
Case presentation III – NGS applications for One Health challenges
Speaker(s): Jacob Moran-Gilad
14:45 - 15:15
Coffee break
15:15 - 16:00
Interactive discussion II – interpretation of NGS findings – the clinical point of view (Panel of faculty members)
Speaker(s): Dag Harmsen
16:00 - 16:45
Interactive discussion III – quality issues in implementing new technology in the microlab (Panel of faculty members)
Speaker(s): Eric Claas
17:00 - 22:00
Social event and dinner

Wednesday, 1 November 2017

07:30 - 07:45
Summary of day 2
08:45 - 09:30
Bioinformatics I – international databases of genomes and genes, quality issues of bacterial genomes
Speaker(s): Joao Andre Carrico
09:30 - 10:30
Interactive discussion IV – I have sequenced a bacterial genome – what is next? (Panel of faculty members)
Speaker(s): Joao Andre Carrico
10:30 - 11:00
Coffee break
11:00 - 11:45
Bioinformatics II – graphical representation of WGS analysis
Speaker(s): Joao Andre Carrico
11:45 - 12:30
Considerations in publication of NGS-based studies – reflections from Eurosurveillance
Speaker(s): Ines Steffens
12:30 - 13:00
Concluding remarks & farewell

We can offer participants special hotel rates at the course venue (Daniel Herzliya Hotel):

For inquiries regarding accommodation kindly contact Mrs. Mira Tropp at

The fee includes the full scientific programme, coffee breaks, lunches, social activity and the conference dinner. Travel and accommodation are not included.
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