New preprint: comparing long- and short-read sequencing of Mycobacteria

In this preprint, we compare the differences when Mycobacterial samples are sequenced with either long- or short-read sequencing and show that long-read sequencing (as exemplified by Oxford Nanopore Technologies) is now comparable to short-read sequencing (e.g. Illumina). As we are focussed on clinical microbiological outputs, we compare the ability of both approaches to resolve the species and, if M. tuberculosis, to predict to which antibiotics the infection will be susceptible. A key part of this manuscript is the development of a lab protocol that combines rapid, semi-automated DNA extraction from MGIT cultures with PCR-based whole-genome amplification.