Description of a Clinical Strain of Mycobacterium cambodiensis sp. nov., a New Member of the Mycobacterium simiae Complex

A bronchoalveolar lavage sample was collected by bronchoscopy from a 25-year-old Cambodian male patient with suspected clinical tuberculosis and was inoculated in Lowenstein-Jensen medium. Colonies of a rapidly growing, non-chromogenic Gram-positive and acid-fast bacterium were investigated. Scanning electron microscopy showed 1.2 ± 0.29 μm-long and 0.58 ± 0.07 μm-large bacilli that could not be identified using routine matrix-assisted laser desorption ionization-time of flight-mass spectrometry and phenotypic tests (API® ZYM, API® Coryne and Biolog® Phenotype MicroArray assays). In vitro, the isolate was susceptible to isoniazid, amikacin and trimethoprim- sulfamethoxazole. Whole-genome sequencing yielded a 5,703,981-bp draft genome that displayed 69.3% of GC content with 5,207 coding-protein genes and 56 predicted RNA genes, including 3 rRNAs. The rpoB sequence showed 93% sequence similarity with that of Mycobacterium parascrofulaceum in the Mycobacterium simiae complex. Genome sequence-derived DNA-DNA hybridization, OrthoANI and pan-genomic analyses confirmed that this isolate represented an undescribed species within the M. simiae complex. This species was named Mycobacterium cambodiensis after its source of isolation. The isolate was deposited in the Collection de Souches de l’Unite des Rickettsies (CSUR) with the number CSURP9652.