This two-day course will provide participants both theory and hands-on practical exercises on bacterial strain nomenclatures using the core genome MLST concept. Focus will be put on the BIGSdb software tool and database and its interface with other molecular epidemiology software including BioNumerics. The cgMLST approach and in particular, cgMLST schemes for Listeria and Campylobacter public health surveillance, will be used in exercises.
The overall objective of the course is to create a distributed community of curators of cgMLST nomenclature databases that will be dedicated to implement genomic epidemiological surveillance of bacterial pathogens using a unified nomenclature of alleles and bacterial genotypes.
The priority focus of the course will be Listeria and Campylobacter, although the concepts and tools that will be presented may be applicable to other bacterial pathogens such as E. coli or Salmonella.