First achieved in 1998 by Cole et al., the complete genome sequence of Mycobacterium
tuberculosis continues to provide an invaluable resource to understand tuberculosis (TB) …

Background Bedaquiline is a core drug for the treatment of multidrug-resistant tuberculosis;
however, the understanding of resistance mechanisms is poor, which is hampering rapid …

Long diagnostic wait times hinder international efforts to address antibiotic resistance in M.
tuberculosis. Pathogen whole genome sequencing, coupled with statistical and machine …

There are many short-read variant-calling tools, with different strengths and weaknesses.
We present a tool, Minos, which combines outputs from arbitrary variant callers, increasing …

Background Clinical bedaquiline resistance predominantly involves mutations in mmpR5
(Rv0678). However, mmpR5 resistance-associated variants (RAVs) have a variable …

Background Mycobacterium tuberculosis whole-genome sequencing (WGS) using Illumina
technology has been widely adopted for genotypic drug susceptibility testing (DST) and …

A bacterial species' genetic content can be remarkably fluid. The collection of genes found
within a given species is called the pan-genome and is generally much larger than the gene …