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Infect Genet Evol. 2019 Nov;75:103983. doi: 10.1016/j.meegid.2019.103983. Epub 2019 Jul 26.

Genome-based taxonomic revision detects a number of synonymous taxa in the genus Mycobacterium.

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Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milano, Italy. Electronic address:
BCCM/ITM Mycobacterial Culture Collection, Department of Biomedical Science, Institute of Tropical Medicine, Antwerp, Belgium.
Microbiology and Virology Unit, University Hospital Polyclinic, Modena, Italy.
Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milano, Italy.


The aim of this study was to clarify the taxonomic status of named species within the genus Mycobacterium. The analysis of genomes belonging to 174 taxa (species or subspecies) of the genus Mycobacterium was conducted using both the Average Nucleotide Identity and the Genome to Genome Distance. A number of synonymous taxa were detected. The list of synonyms includes: two subspecies of M. chelonae (M. chelonae subsp. bovis and M. chelonae subsp. gwanakae), two subspecies of M. fortuitum (M. fortuitum subsp. fortuitum and M. fortuitum subsp. acetamidolyticum), four subspecies of M. avium (M. avium subsp. avium, M. avium subsp. silvaticum, M. avium subsp. paratuberculosis and "M. avium subsp. hominissuis"), two couples of subspecies of M. intracellulare (M. intracellulare subsp. intracellulare/M. intracellulare subsp. paraintracellulare and M. intracellulare subsp. chimaera/M. intracellulare subsp. yongonense), the species M. austroafricanum and M. vanbaalenii, the species M. senegalense and M. conceptionense, the species M. talmoniae and M. eburneum and the species M. marinum, M. ulcerans and M. pseudoshottsii. Furthermore one species were reclassified as subspecies of another mycobacterium: M. lepraemurium was reclassified as a subspecies of M. avium (M. avium subsp. lepraemurium). The updates to nomenclature are proposed basing on the priority of names according the Code of nomenclature of prokaryotes. For two species (M. bouchedurhonense and M. marseillense) the loss of standing in nomenclature is proposed because of unavailability of respective type strains in culture collections.


Average nucleotide identity; Genome to genome distance; Mycobacterium; Synonymous taxa; Taxonomy

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