Infection and Drug Resistance (Sep 2023)

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

  • Yu X,
  • He Y,
  • Gu Y,
  • Zhang T,
  • Huo F,
  • Liang Q,
  • Wu J,
  • Hu Y,
  • Wang X,
  • Tang W,
  • Huang H,
  • Liu G

Journal volume & issue
Vol. Volume 16
pp. 6039 – 6052

Abstract

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Xia Yu,1,* Yingxia He,2,* Yuzhen Gu,1,* Tingting Zhang,1 Fengmin Huo,1 Qian Liang,1 Jing Wu,1 Yan Hu,2 Xuan Wang,2 Wei Tang,2 Hairong Huang,1 Guan Liu2 1National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory on Drug-Resistant Tuberculosis, Beijing Chest Hospital, Capital Medical University, Beijing, 101149, People’s Republic of China; 2Wuhan Pulmonary Hospital, Wuhan Institution of Tuberculosis Control, Wuhan, 430030, People’s Republic of China*These authors contributed equally to this workCorrespondence: Hairong Huang; Guan Liu, Email [email protected]; [email protected]: 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.Keywords: species identification, Mycobacterium, chromosomal virulence D, phylogenetic tree

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