Sequencing of bacteria: anytime & anywhere

New innovative methods to determine the DNA sequences of different bacterial species are rising. In the field of microbiology, these methods are very important since it is now possible to determine all the genetic characteristics of the bacterium in one step! This enables to define e.g. the species family, drug resistance or relatedness to other bacteria in outbreak evaluations which is necessary to efficiently treat the bacteria or target potential outbreaks. For many years, PCR-based methods have been the technique of choice to determine DNA sequences (including next-generation sequencing techniques). Recently, a new technique has been introduced to the market that is based on single molecule real-time sequencing (SMRT) with the possibility to determine the DNA sequence of a bacterium. This SMRT MinION sequencing technique is housed on an USB stick and is known for its user-friendliness and huge data output. However, before such a new technique can be implemented and presented in laboratories and used for educational purposes, methods should be harmonized and evaluated to proof its applicability. Harmonisation of the methodology regarding new laboratory techniques is very important to be able to compare results generated by different laboratories. A single consistent protocol, applied in each lab, is essential to obtain the best results in interlaboratory comparisons. During this KIEM-hbo project, we – i.e. Avans UAS, Maastricht University Medical Center and the company IS-diagnostics – will determine the DNA sequence of bacterial species and mixes thereof with a harmonized protocol for an interlaboratory comparison. We will compare this technique to the IS-PRO, an existing technology. Finally a workshop will be organized for medical technicians and other SMRT sequencing users to evaluate the protocols. This will, generate an up-to-date and harmonized sequencing protocol which can be expanded to future research and diagnostics in the different areas.