4th Workshop Rapid NGS for Clinical, Public Health, and Food Microbiology

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1 Organizers 4th Workshop Rapid NGS for Clinical, Public Health, and Food Microbiology March 11th 13th, 2015; Univ. Münster Sponsors In co-operation with MMGC Flyer Version 2

2 Objectives and Organization Objectives It is our great pleasure to welcome you to the 4 th Workshop Rapid Next-Generation- Sequencing for Clinical, Public Health, and Food Microbiology in Münster. Next-Generation- Sequencing (NGS) technology has developed rapidly during the last years. Innovative benchtop NGS platforms broaden application opportunities, especially for diagnostic use and surveillance. The program highlights opportunities and challenges posed by this technology. The workshop has been designed to boost practical knowledge exchange as well as ample discussions with your colleagues from all over Europe. Fee and Registration No participation fees will be charged for members of BMBF MedVet-Staph, BMBF RESET, SeqNet.org, ESGEM, EU PathoNGenTrace, or DGHM Division of Population Genetics & Infectious Disease Epidemiology. However, a non-refundable service charge of 99 for beverages will be claimed from every participant. - Given the international scope of the initiative and the limited laboratory capacity available, the meeting organizers strive to select qualified participants from as many different European countries as possible. Only two participants form each organization are eligible. The Workshop language will be English. Registration is open via If your application has been approved please remember to bring a lab coat with you! Organization Dr. Dag Harmsen, Dr. Alexander Mellmann (Medical Faculty, University Münster, Germany), Dr. Stefan Albaum (CeBiTec, Bielefeld University, Germany) and Dr. Alexander Friedrich (Medical Microbiology, University Groningen) on behalf of the Society for Medical Microbial Genomics (SMMG) e.v. Workshop Tutors Dr. Karola Prior and Anja Schultes (Periodontology, University Münster) Dr. Stefan Bletz and Thomas Böking (Institute Hygiene, University Münster) Venue Department Periodontology, University Münster Waldeyerstr. 30, Münster, Germany Contact Heike Frieling-Braithwaite Department Periodontology University Münster, Germany [email protected] 2

3 Workshop: Wednesday - Friday, 11 th 13 th March 2015 (max. 28 participants) Wednesday, 11 th March Wet Laboratory Illumina MiSeq Whole Genome Shotgun (WGS) Next Generation Sequencing (NGS; Nextera XT libraries) of a Listeria monocytogenes Outbreak with Epi-Curve, Geo-coding, QC Consideration, and cgmlst/mlst+ Analysis Room: start in room ( Kleiner Hörsaal ) Thursday, 12 th March Scientific Talks Dag Harmsen and Alexander Mellmann (Univ. Münster, Münster, Germany), Sébastian Calvignac- Spencer (RKI, Berlin, Germany), Stefan Albaum (Bielefeld Univ., Bielefeld, Germany), Werner Ruppitsch (AGES, Vienna, Austria), Sylvain Brisse (Inst. Pasteur, Paris, France), and John Rossen (Univ. Groningen, Groningen, Netherlands). Room: ( Kleiner Hörsaal ) Thursday, 12 th March 2015 Social Event Evening Dinner (no extra fees; meal, softdrinks and beer included). Place: to be determined Friday, 13 th March Computer Class NGS WGS Data Analysis The following tools will be demonstrated or used in tutorials: Illumina Coverage Calculator, Illumina Sequence Analysis Viewer, Babraham Bioinformatics FastQC, ssgenefinder, PanSeq, Ridom SeqSphere+, and University Oxford BIGSdb. Room: ( CIP-Pool ) Luggage can be stored during Computer Class in room ( Demo-Raum ). 3

4 Scientific Talks - Thursday, 12th March :00-09:45 Overview of Software and Databases for Rapid High-throughput Sequence Analysis in Clinical & Public Health Microbiology Dag Harmsen, University of Münster, Münster, Germany 09:45-10:30 Klebsiella pneumoniae scgmlst, Virulence and Resistance Analysis Sylvain Brisse, Institut Pasteur, Paris, France 10:30-11:00 Coffee Break 11:00-11:45 WGS for (Inter)Regional Infection Prevention John Rossen, University of Groningen, Groningen, The Netherlands 11:45-12:30 Real-time Monitoring of Multi-resistant Bacteria in a University-Hospital by Whole Genome Sequencing Alexander Mellmann, University of Münster, Münster Germany 12:30-13:30 Lunch Break 13:30-14:15 MLST+ Analysis of Listeria monocytogenes Werner Ruppitsch, AGES, Vienna, Austria 14:15-15:00 cgmlst Analysis of Listeria monocytogenes Sylvain Brisse, Institut Pasteur, Paris, France 15:00-15:30 Coffee Break 15:30-16:30 Can t See the Forest for the Trees: What Phylogenetic Analyses (BEAST) Are Really About and What They Allow For Sébastian Calvignac-Spencer, Robert Koch Institute, Berlin, Germany 16:30-17:15 Tools for Metagenomic Analysis and Tools Stefan Albaum, Bielefeld University, Bielefeld, Germany 17:15-17:30 Wrap-up and Final Discussion Dag Harmsen, University of Münster, Münster, Germany 4

5 General Information Münster is a convention city in the German federal state of North Rhine-Westphalia with European tradition - envoys from Austria, France, Sweden, the Netherlands and Germany gathered there as early as In Münster City Hall they officially sealed the end of the Thirty Years War with the Treaty of Westphalia. Historical gabled buildings, baroque treasures, lots of green spaces and delightful surroundings all conspire to make visitors to Münster loath to say farewell years of University history, bikes, and a pulsating student community lend one of the largest German University Cities charm and character. How to get to Münster 1.) By plane Nearest airports: Münster/Osnabrück (IATA code: FMO) Airport is approx. 35 min by bus (line 51) Düsseldorf (IATA code: DUS) Airport is approx. 1.5 h by train (very convenient!) Hannover (IATA code: HAJ) Airport is approx. 2 h by train 2.) By train Münster is easy to reach by train via high-speed Inter-City Express trains. Choose Münster Central Station ( Hauptbahnhof ) as your destination ( 3.) By car Münster is situated in the North-West of Germany. It is located directly at the A1 and A43 Autobahn. Accommodation Hotel Mövenpick Kardinal-von Galen-Ring Münster, Germany Booking code: MM101A WWW: Hotel am Schlosspark Schmale Strasse Münster, Germany Booking code: Universität Münster WWW: There are many more hotels including cheaper ones available in Münster (WWW). The two above stated hotel are recommended, as they are close by to the venue and the University Münster has an arrangement with them. If you arrived in Münster, how do you find the Department of Periodontology? By bus/taxi The Department of Periodontology (named Zahnklinik on the following map) is located in the Waldeyer Street 30, Münster. From the Central Station: Busses leave every 10 min at the Central Station, i.e., line 11 (track C1), line 12 or 14 (both track B1). Suitable bus stops are Hüfferstiftung, Jungeblodtplatz, and Domagkstraße (takes about 12 min drive). A travel with a taxi from the Central Station takes about 10 min and costs about 10. From Mövenpick and Schlosspark Hotel: about 5 min by walking. 5

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