Workshop title: Genotyping workshop

The workshop was held 4-5 February 2008, at the Institute of Veterinary Bacteriology, University of Bern, Switzerland. This event was organised by Peter Kuhnert (UBERN), Eva Møler Nielsen (SSI), and Stefan Emler (SMART).

The purpose of the workshop was to update and train BIOTRACER partners in the use of genotyping.

Background
Genotyping of pathogenic bacteria is an important tool for tracing bacteria in food. Genotyping is used for investigating and detecting transmission routes, cross-infections, and resevoirs of pathogenic bacteria. The choice of genotyping method should depend on the purpose and the organism studied.

Target group
BIOTRACER partners who are  interested in learning the basics about genotyping and get an introduction to the use of sequence-based methods, especially MLST. Industry partners who are inteested in using gentotyping in their production/process will be given preference.

Expected outcome
Participants should understand the basics of genotyping, its use and different principles. Participants will be able  to use the software analysis made by SmartGene for MLST.

Programme
Monday 13:00 – 18:00
13:00-13:30 Sandwiches and drinks
13:30-13:45 Welcome and introduction of participants
13:45-14:15 General introduction to genotyping methods (Eva Møller Nielsen, SSI)
14:15-14:45 Using typing for tracing the source of food-borne infections (Eva Møller Nielsen, SSI)
14:45-15:15 Sequence-based identification of bacteria (Peter Kuhnert, UBERN)
15:15-15:45 Coffee break
15:45-17:00 Microbial typing and tracing in the food industry (Bernard Berger, NESTEC)
17:00-18:00 General discussion on the need for tracing tools in the food sector and how he food industry and the research organisations can benefit the most from ach other (Chair: Jacques-Edouard Germond, NESTEC and Eva Møller Nielsen, SSI)
19:00 Walking tour of the old city of Bern
20:00 Dinner in the old city

Tuesday 8:30 – 13:00
08:30-09:15 Introduction to web-based data analysis and data sharing (Stefan Emler, SMART)
09:15-09:45 MLST of Campylobacter (Bozena Korczak, UBERN)
09:45-10:15 Coffee break
10:15-13:00 Demonstration and training on data analysis using the SmartGene MLST Campylobacter Module used in BIOTRACER (Marc Fehlmann, SMART and Bozena Korczak, UBERN)
13:00-14:00 Farewell, sandwiches and drinks