Clinical characteristics and species distribution of Mycobacterium fortuitum complex isolates

The Mycobacterium fortuitum complex (MFC) comprises multiple species associated with a wide range of human infections. However, accurate species-level identification of clinical MFC isolates and its clinical significance remain incompletely characterized. Species identification of 71 clinical MFC isolates was performed using ONT-based rpoB sequencing and MALDI-TOF MS. Long (3,325-bp) and partial (732-bp) rpoB sequences were analyzed by reference mapping and phylogenetic analysis. The 71 isolates were recovered from 61 patients with MFC colonization (83.6%), pulmonary disease (13.1%), or extrapulmonary disease (3.3%). Long rpoB sequencing identified M. fortuitum (50.7%), M. mageritense (18.3%), M. farcinogenes (15.5%), M. houstonense (5.6%), M. boenickei (1.4%), and M. peregrinum (1.4%); five isolates (7.0%) were classified as MFC. Partial rpoB sequencing yielded the same species distribution, except that M. boenickei and M. peregrinum were classified only as MFC, whereas one MFC isolate was classified as Mycobacterium sp. MALDI-TOF MS identified M. fortuitum (54.9%), M. mageritense (18.3%), M. peregrinum (1.4%), and MFC (19.7%), while four isolates (5.6%) remained unidentified. Concordance between long rpoB sequencing and MALDI-TOF MS was 69.0% at the species level and 94.4% at the complex level. M. mageritense was associated with pulmonary disease, bronchiectasis, and reduced amikacin susceptibility, whereas M. fortuitum was associated with non-pulmonary comorbidities. No significant associations were observed between other MFC species and susceptibility to amikacin, clarithromycin, or doxycycline. Multiple MFC species were identified among clinical isolates. Long rpoB sequencing provided greater species-level resolution than partial rpoB sequencing, whereas MALDI-TOF MS showed limited discriminatory power for closely related MFC species.