6.2 Genome sequencing techniques

Whole genome sequencing (WGS) can also be used to look at the bacterial genome and its associated plasmids. WGS is primarily a research tool. It might be used for instance to study a newly identified mechanism of resistance or to study the different genes found in a particular setting. It could be used to understand how the resistant organisms had spread in an institution by constructing a phylogenetic tree of the bacteria in a particular species and seeing how this related to the different plasmids and resistance genes. It is also possible to sequence just the resistance genes, which is a little faster and less complex.

However, for now sequencing is still very expensive and time consuming. It also needs bioinformatics expertise to interpret the results, so even a reference laboratory is unlikely to be doing this routinely at present.