Taxonomic landscape of the <i>Mycobacterium</i> "<i>Fortuitum-Vaccae</i>" clade: a genome study

<h4>Introduction</h4>The <i>Mycobacterium</i> "<i>Fortuitum-Vaccae</i>" clade (FVC) contains many rapid-growing species and is increasingly reported in human infections globally. However, the clade's taxonomic composition and the exact association with human infections remain to be explored.<h4>Methods</h4>In this study, we conducted a comprehensive genome-based analysis of the FVC, aiming to update its taxonomy and identify new taxa. We compiled a dataset of 298 <i>Mycobacterium</i> species using public databases, ultimately including 222 type strain genomes for phylogenomic analysis.<h4>Results</h4>This revealed 106 species within the FVC. Subsequent curation of 11,534 public <i>Mycobacterium</i> identified 557 belonging to the FVC, from which we uncovered 86 new taxa (genomospecies) and resolved one new synonym pair. We reconstructed three core-protein phylogenomic trees and found the FVC comprising eight distinct subclades. Our analysis unveiled a remarkably complicated taxonomic landscape within the clade, encompassing 106 known species, among which 16 species, such as <i>M. syngnathidarum</i> and <i>M. yunnanensis</i>, have not previously been classified within the FVC. We detected a pair of synonyms: <i>M. murale</i> is a heterotypic synonym of <i>M. tokaiense</i>.<h4>Discussion</h4>These findings highlight the remarkable taxonomic diversity within the FVC. The updated taxonomy and the curated database of genomes allow precise species identification in diagnostics, clinical reporting, epidemiological surveillance, and future studies on the ecology and pathogenesis. Accurate identification may uncover the disease spectrum, clinical manifestation, and prognosis of infections by individual FVC species, guiding countermeasures.