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

Tuberculosis affects humans and livestock species. Its etiological agents are different bacteria belonging to the Mycobacterium tuberculosis complex (MTBC). In recent years, whole-genome sequencing (WGS) has become essential in both basic and clinical Tuberculosis research. Based on WGS, different human-adapted MTBC genotypes have been classified into lineages and sublineages, which have been shown to differ in their geographic distribution and in virulence. Studies based on WGS start to emerge also for livestock-associated MTBC pathogens but a body of operational nomenclature covering systematically all known genetic diversity is missing. After gathering several thousands of WGS, we propose here a backbone of operational nomenclature to classify the genetic diversity uncovered by genomic studies of livestock-associated MTBC. Furthermore, a set of molecular markers were provided which can be used to identify the newly proposed lineages and sublineages.