Mycobacterium hainanense sp. nov. represents an emerging nontuberculous Mycobacterium associated with chronic pulmonary disease.

Nontuberculous mycobacteria (NTM) are increasingly recognized as important opportunistic pathogens, particularly in immunocompromised individuals. We discovered a newly identified NTM, initially misidentified as Mycobacterium paraffinicum, isolated from a 42-year-old female with an eight-year history of persistent pulmonary infection. The pathogen shares high molecular similarities with Mycobacterium paraffinicum, Mycobacterium nebraskense, and Mycobacterium scrofulaceum, exhibiting atypical acid-fast properties and slow growth. Phylogenetic analysis and pairwise comparisons based on digital DNA-DNA hybridization and average nucleotide identity suggest it as a new species, which we propose naming it Mycobacterium hainanense sp. nov.. Significant differences were also observed in the 16 S rRNA, hsp65, rpoB, and sodA gene sequences between Mycobacterium hainanense and closely related mycobacterial species, confirming it as a novel species. Clinical, radiological, and microbiological findings, along with the patient's response to a tailored antibiotic regimen, are analyzed to understand disease progression and evaluate treatment efficacy against this newly identified pathogen. Functional genomic analysis highlighted diverse metabolic pathways, including lipid and carbohydrate metabolism, indicating the strain's ability to adapt to varying nutrient conditions and environmental stress. This study highlights the need for accurate identification of Mycobacterium species and calls for further in-depth research on the pathogenic mechanisms of Mycobacterium hainanense.