Phylogenomics of the Mycobacterium tuberculosis Beijing genotype

Tuberculosis caused by Mycobacterium tuberculosis complex (MTBC) bacteria is a worldwide public health issue. Among MTBC, phylogenetic lineage 2 (~ Beijing genotype) is one of the most common and is characterized by increased transmissibility and drug resistance. Over time, its classification has undergone a number of changes, from the IS6110-based restriction fragment length polymorphism analysis and large sequence polymorphisms in regions of difference to differentiation based on single nucleotide polymorphisms. Here we have reviewed and correlated the main classifications of lineage 2 at different levels of genome organization. We also introduced a set of genomes and polymorphisms that can be used for further analysis of this lineage. The presented lineage 2 phylogeny can be used for further research on important epidemiological clusters and their ancestors, as well as unclassified strains.