Lecture on bacterial typing and whole genome data

A week ago, I was at a workshop in Denmark. This was for a Nordic Working Group for Microbiology and Animal Health and Welfare (NMDD) meeting on Source attribution of Campylobacter in the Nordic countries. We were around 12 people or thereabouts, mostly from the modelling side of the source attribution table.

Since starting my new job at the Norwegian Veterinary Institute in July, I have finally had time to focus something that I have found quite fascinating for some time, and that is how to use whole genome data for tracing bacterial infections. The Campylobacter source attribution project has as its goal to figure out how to use MLST data gathered from the Nordic countries to elucidate which reservoirs the human Campylobacter cases in these countries stem from. This merges very nicely with my interest in using whole genome data for such purposes.  My contribution to this workshop was a presentation concerning how whole genome sequencing is making its way into bacterial typing. I am including the slides from this meeting in this post.

[gview file=”https://blog.karinlag.no/wp-content/uploads/2015/12/2015-12-09_NMDD.pdf”]

Through this meeting I got a very useful insight into how the modelling side of these issues work. However, I also discovered that not everybody present were necessarily completely aware of the “shifty” nature of the bacterial genome, and by extension the characteristics of the MLST data the modelling within the project is done on. To alleviate that, I added more about what a bacterial genome actually is in the beginning, and also added more about horizontal gene transfer towards the end. In working with these things on the eve of lecturing, I was very happy to have the assistance of the twitter community, which helped me dig out details such as the rate of horizontal gene transfer in Campylobacter (heck, it apparently even happens with core genes, can’t we trust anything anymore?), which proved very useful in the discussions.

Comments and thoughts are very welcome!