A new nomenclature for the livestock-associated Mycobacterium tuberculosis complex based on phylogenomics

Figure 1 - Distribution of the raw pairwise SNP distances between and within main La1 groups.

Table 1 – Accession numbers and metadata associated with the 839 WGS used of La1, La2 and La3.

Table 2 - Accession numbers and metadata associated with the 1,226 WGS used as representatives of the whole MTBC.

Table 3 – Spoligotypes patterns inferred from the WGS and used to complement the geographic distribution of La1 sublineages.

Table 4 – Single nucleotide polymorphisms (SNPs) specific to livestock-associated MTBC lineages and sublineages. Coordinates based on the M. tuberculosis H37Rv annotation (NC_000962.3) are given (Position_ref), and the lineage and or sublineage classification (PhylogeneticSNP). Additionally, the gene-based position is indicated (Position_gene) as well as the kind of mutation based on SnpEff annotation [40]. SNPs used to create the new KvarQ testsuite are indicated.

Table 5 – KvarQ results of lineage and sublineage typing done with the new testsuite implemented.