Developing a 3rd generation sequencing based method for identification of bacteria without culturing
There are many instances in which we need to identify bacteria, but are unable to grow them in the laboratory, for example, urinary tract infections, wound infections and bacterial vaginosis.
Recently we have adopted molecular-based methods in order to overcome this culturing barrier and at the same time married these with next-generation sequencing platforms such as the Illumina MiSeq. However, such an approach is time consuming and expensive. In my laboratory we have just started using the new third-generation nanopore based systems, Minion, for sequencing amplicons. This project will undertake to develop this third-generation system and see whether it can be used to sequence long amplicons and if it is accurate enough to differentiate between species in a mixture. This is an exciting opportunity to start using the most state of the art sequencing platform which is currently only been beta tested in a handful of laboratories around the world.