Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milano, Italy.
BCCM/ITM Mycobacterial Culture Collection, Department of Biomedical Science, Institute of Tropical Medicine, Antwerp, Belgium.
Infect Genet Evol. 2019 Nov;75:103983. doi: 10.1016/j.meegid.2019.103983. Epub 2019 Jul 26.
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.
本研究旨在阐明分枝杆菌属中已命名种的分类地位。使用平均核苷酸同一性和基因组到基因组距离对属于分枝杆菌属的 174 个分类群（种或亚种）的基因组进行了分析。检测到一些同义词分类群。同义词列表包括：两种龟分枝杆菌亚种（龟分枝杆菌亚种牛型和龟分枝杆菌亚种脓肿亚种）、两种脓肿分枝杆菌亚种（脓肿分枝杆菌亚种脓肿和脓肿分枝杆菌亚种乙酰胺酶）、四种鸟分枝杆菌亚种（鸟分枝杆菌亚种鸟、鸟分枝杆菌亚种森林、鸟分枝杆菌亚种结核和“鸟分枝杆菌亚种同源亚种”）、两种细胞内分枝杆菌亚种对（细胞内分枝杆菌亚种细胞内/细胞内分枝杆菌亚种副细胞内和细胞内分枝杆菌亚种 chimaera/细胞内分枝杆菌亚种 yongonense）、非洲分枝杆菌和范巴伦分枝杆菌、塞内加尔分枝杆菌和 conceptionense 分枝杆菌、talmoniae 分枝杆菌和 eburneum 分枝杆菌以及 marinum 分枝杆菌、溃疡分枝杆菌和 pseudoshottsii 分枝杆菌。此外，一种物种被重新分类为另一种分枝杆菌的亚种：麻风分枝杆菌被重新分类为鸟分枝杆菌的亚种（鸟分枝杆菌亚种麻风分枝杆菌）。根据原核生物命名法规的优先命名原则，提出了命名法的更新建议。由于无法在培养物中获得相应的模式株，建议取消两种物种（M. bouchedurhonense 和 M. marseillense）的命名地位。
