Abstract
A 59-year-old tobacco smoker male with chronic bronchitis living in Taravao, French Polynesia, Pacific, presented with a two-year growing nodule in the middle lobe of the right lung. A guided bronchoalveolar lavage inoculated onto Löwenstein-Jensen medium yielded colonies of a rapidly-growing non-chromogenic mycobacterium designed as isolate P7213. The isolate could not be identified using routine matrix-assisted laser desorption ionization-time of flight-mass spectrometry and phenotypic and probe-hybridization techniques and yielded 100% and 97% sequence similarity with the respective 16S rRNA and rpoB gene sequences of Mycobacterium virginiense in the Mycobacterium terrae complex. Electron microscopy showed a 1.15 µm long and 0.38 µm large bacillus which was in vitro susceptible to rifampicin, rifabutin, ethambutol, isoniazid, doxycycline and kanamycin. Its 4,511,948-bp draft genome exhibited a 67.6% G + C content with 4,153 coding-protein genes and 87 predicted RNA genes. Genome sequence-derived DNA-DNA hybridization, OrthoANI and pangenome analysis confirmed isolate P7213 was representative of a new species in the M. terrae complex. We named this species “Mycobacterium mephinesia”.
Highlights
The International Working Group on Mycobacterial Taxonomy delineated the Mycobacterium terrae complex in 19981
Tuberculosis due to M. tuberculosis is highly endemic in French Polynesia, the incidence of non-tuberculous mycobacterium (NTM) infections is unknown[13]
In the clinical case reported, the large opacity found on chest computed tomography (CT)-scanner and the isolation of a NTM from a bronchoalveolar lavage was considered as clinically relevant according the American Thoracic Society criteria for NTM lung infection[14]: compatible clinical presentation and symptoms, one NTM isolate from a BAL and radiological patterns that are compatible with NTM lung infection
Summary
The GC % content of isolate P7213 is lower than that M. hiberniae, M. kumamotonense, M. algericum, M. engabaekii, M. terrae, M. longobardum, M. heraklinonense, M. nonchromogenicum, M. senuense and “M. sinense” and higher than that of M. virginiense, M. icosiumassiliensis, M. arupense and M. minnesotense (Table 3). Type strains M. mephinesia M. heraklionense M. arupense M. hiberniae M. longobardum M. terrae M. engbaekii M. virginiense M. nonchromogenicum M. algericum M. icosiumassiliensis M. kumamotonense M. senuense M. tuberculosis H37Rv « M. sinense » M. minnesotense. Within the complex M. terrae, in silico DNA-DNA hybridization (DDH) analysis yielded 44.5 ± 5.2% identity with M. virginiense, 39.4 ± 5% with M. icosiumassiliensis, 39.1 ± 5% with M. heraklionense, 35.4 ± 4.8% with M. nonchromogenicum, 31.1 ± 4.9% with M. longobardum, 30.9 ± 4.8% with M. engbaekii, 30.2 ± 4.8% with M. arupense, 29.5 ± 4.8% with M. minnesotense, 29.4 ± 4.9% with M. hiberniae, 27.4 ± 4.9% with M. kumamotonense, 27 ± 4.8% with M. terrae, 26.6 ± 4.9% with “M. sinense”, 26.5 ± 4.9% with M. senuense and 26.4 ± 4.8% with M. algericum (Table 5).
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