Department of Biological Sciences, Old Dominion Universitygrid.261368.8, Norfolk, Virginia, USA.
Department of Infectious Diseases, University of Georgiagrid.213876.9, Athens, Georgia, USA.
Microbiol Spectr. 2022 Jun 29;10(3):e0115821. doi: 10.1128/spectrum.01158-21. Epub 2022 May 17.
Mycobacterium shottsii is a dysgonic, nonpigmented mycobacterium originally isolated from diseased striped bass (Morone saxatilis) in the Chesapeake Bay, USA. Genomic analysis reveals that M. shottsii is a Mycobacterium ulcerans/Mycobacterium marinum clade (MuMC) member, but unlike the superficially similar M. pseudoshottsii, also isolated from striped bass, it is not an M. ulcerans ecovar, instead belonging to a transitional group of strains basal to proposed "Aronson" and "M" lineages. Although phylogenetically distinct from the human pathogen M. ulcerans, the genome shows parallel but nonhomologous genomic degeneration, including massive accumulation of pseudogenes accompanied by proliferation of unique insertion sequences (IS01, IS03), large-scale deletions, and genomic reorganization relative to typical M. marinum strains. Coupled with its observed ecological characteristics and loss of chromogenicity, the genomic structure of is suggestive of evolution toward a state of obligate pathogenicity, as observed for other Mycobacterium spp., including M. ulcerans, M. tuberculosis, and M. leprae. Morone saxatilis (striped bass) is an ecologically and economically important finfish species on the United States east coast. Mycobacterium shottsii and Mycobacterium pseudoshottsii were originally described in the early 2000s as novel species from outbreaks of visceral and dermal mycobacteriosis in this species. Biochemical and genetic characterization place these species within the Mycobacterium ulcerans/M. marinum clade (MuMC), and has been proposed as an ecovar of M. ulcerans. Here, we describe the complete genome of , demonstrating that it is clearly not an M. ulcerans ecovar; however, it has undergone parallel genomic modification suggestive of a transition to obligate pathogenicity. As in M. ulcerans, the genome demonstrates widespread pseudogene formation driven by proliferation of insertion sequences, as well as genomic reorganization. This work clarifies the phylogenetic position of relative to other MuMC members and provides insight into processes shaping its genomic structure.
希氏分枝杆菌是一种非产色的、有异味的分枝杆菌，最初从美国切萨皮克湾患病的条纹鲈鱼（Morone saxatilis）中分离出来。基因组分析表明，M. shottsii 是分枝杆菌溃疡/分枝杆菌海鱼亚种（MuMC）成员，但与同样从条纹鲈鱼中分离出来的、表型相似的 M. pseudoshottsii 不同，它不是分枝杆菌溃疡亚种，而是属于“Aronson”和“M”谱系前过渡群菌株。虽然与人类病原体分枝杆菌溃疡在系统发育上有明显区别，但基因组显示出平行但非同源的基因组退化，包括大量假基因的积累，同时伴随着独特插入序列（IS01、IS03）的增殖、大规模缺失和与典型分枝杆菌海鱼亚种菌株相比的基因组重组。再加上观察到的生态特征和丧失色素沉着性，的基因组结构表明它向专性致病性状态进化，这与其他分枝杆菌属物种，包括分枝杆菌溃疡、结核分枝杆菌和麻风分枝杆菌的情况类似。条纹鲈鱼（条纹鲈）是美国东海岸具有重要生态和经济意义的一种鱼类。分枝杆菌 shottsii 和分枝杆菌 pseudoshottsii 最初是在 21 世纪初作为这种物种内脏和皮肤分枝杆菌病爆发的新物种描述的。生化和遗传特征将这些物种置于分枝杆菌溃疡/分枝杆菌海鱼亚种（MuMC）内，并且已经被提议为分枝杆菌溃疡的生态变种。在这里，我们描述了的完整基因组，表明它显然不是分枝杆菌溃疡的生态变种；然而，它经历了平行的基因组修饰，表明向专性致病性过渡。与分枝杆菌溃疡一样，的基因组显示出广泛的假基因形成，这是由插入序列的增殖驱动的，以及基因组的重组。这项工作澄清了相对于其他 MuMC 成员的系统发育地位，并提供了对塑造其基因组结构的过程的深入了解。
