New design of multilocus sequence analysis of rpoB, ssrA, tuf, atpE, ku, and dnaK for identification of Mycobacterium species

Phylogenetic analysis of prevalent Mycobacterium species in Northeastern Iran based on hsp65 and tuf genes

Phylogenetic analysis of Mycobacterium species can provide valuable insights into their evolutionary relationships and help to identify species and strains. In this study, two genetic markers, including the heat shock protein 65 (hsp65) gene and the elongation factor (EF)-Tu (tuf) gene were used for phylogenetic analysis of Mycobacterium species. Clinical samples were collected from patients suspected of tuberculosis. Bacterial isolates were obtained from sputum samples and cultured on Löwenstein-Jensen medium. Thirty Mycobacterium isolates (acid-fast +, culture +), were included in our study. After DNA extraction, hsp65 (441 bp) and tuf (741 bp) genes were PCR-amplified and sequenced. The Neighbor-Joining method was employed to infer the evolutionary history of the isolates and the analyses were conducted with MEGA X software. The phylogenetic trees were validated using bootstrap analysis with 1000 replicates. Bootstrap values above 70 % considered indicative of well support for the branches. The phylogenetic trees revealed the overall natural relationships among Mycobacterium species. Our results demonstrated that the tuf gene provides superior resolution for identifying distinct mycobacterial species, closely aligning its phylogenetic profile with the hsp65 gene. However, neither of the markers was effective in distinguishing members of the Mycobacterium tuberculosis complex (MTBC). This study highlights the high discriminatory power of the tuf gene, recommending its use as a primary genomic marker for phylogenetic analysis.

Advances in diagnosis and treatment of non-tuberculous mycobacterial lung disease

The prevalence of Non-tuberculous Mycobacterial Pulmonary Disease (NTM-PD) is increasing worldwide. The advancement in molecular diagnostic technology has greatly promoted the rapid diagnosis of NTM-PD clinically, and the pathogenic strains can be identified to the species level through molecular typing, which provides a reliable basis for treatment. In addition to the well-known PCR and mNGS methods, there are numerous alternative methods to identify NTM to the species level. The treatment of NTM-PD remains a challenging problem. Although clinical guidelines outline several treatment options for common NTM species infections, in most cases, the therapeutic outcomes of these drugs for NTM-PD often fall short of expectations. At present, the focus of research is to find more effective and more tolerable NTM-PD therapeutic drugs and regimens. In this paper, the latest diagnostic techniques, therapeutic drugs and methods, and prevention of NTM-PD are reviewed.

The Homologous Gene of Chromosomal Virulence D (chvD) Presents High Resolution as a Novel Biomarker in Mycobacterium Species Identification

Objective

To evaluate the resolution of chromosomal virulence D (chvD) as a novel marker for mycobacterial species identification.

Methods

A segment of chvD (652 bp) was amplified by PCR from 63 mycobacterial reference strains, 163 nontuberculous mycobacterial clinical isolates, and 16 M. tuberculosis complex (MTBC) clinical isolates. A phylogenetic tree based on the reference strains was constructed by the neighbor-joining and IQ-tree methods. Comparative sequence analysis of the homologous chvD gene efficiently differentiated the species within the genus Mycobacterium. Slowly growing Mycobacterium (SGM) and rapidly growing Mycobacterium (RGM) were separated in the phylogenetic tree based on the chvD gene.

Results

The sequence discrepancies were obvious between M. kansasii and M. gastri, M. chelonae and M. abscessus, and M. avium and M. intracellulare, none of which could be achieved by 16S ribosomal RNA (rRNA) homologous gene alignment. Furthermore, chvD manifested larger intraspecies diversity among members of M. intracellulare subspecies. A total of 174 of the 179 (97.21%) clinical isolates, consisting of 12 mycobacterial species, were identified correctly by chvD blast. Four M. abscessus subsp. abscessus were identified as M. abscessus subsp. bolletii by chvD. MTBC isolates were indistinguishable, because they showed 99.84%-100% homology.

Conclusion

Homologous chvD is a promising gene marker for identifying mycobacterial species, and could be used for highly accurate species identification among mycobacteria.