Scientific Reports (Jun 2021)

Phenotypic and genotypic features of the Mycobacterium tuberculosis lineage 1 subgroup in central Vietnam

  • Nguyen Thi Le Hang,
  • Minako Hijikata,
  • Shinji Maeda,
  • Akiko Miyabayashi,
  • Keiko Wakabayashi,
  • Shintaro Seto,
  • Nguyen Thi Kieu Diem,
  • Nguyen Thi Thanh Yen,
  • Le Van Duc,
  • Pham Huu Thuong,
  • Hoang Van Huan,
  • Nguyen Phuong Hoang,
  • Satoshi Mitarai,
  • Naoto Keicho,
  • Seiya Kato

DOI
https://doi.org/10.1038/s41598-021-92984-5
Journal volume & issue
Vol. 11, no. 1
pp. 1 – 12

Abstract

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Abstract Mycobacterium tuberculosis (Mtb) has different features depending on different geographic areas. We collected Mtb strains from patients with smear-positive pulmonary tuberculosis in Da Nang, central Vietnam. Using a whole genome sequencing platform, including genome assembly complemented by long-read-sequencing data, genomic characteristics were studied. Of 181 Mtb isolates, predominant Vietnamese EAI4_VNM and EAI4-like spoligotypes (31.5%), ZERO strains (5.0%), and part of EAI5 (11.1%) were included in a lineage-1 (L1) sublineage, i.e., L1.1.1.1. These strains were found less often in younger people, and they genetically clustered less frequently than other modern strains. Patients infected with ZERO strains demonstrated less lung infiltration. A region in RD2bcg spanning six loci, i.e., PE_PGRS35, cfp21, Rv1985c, Rv1986, Rv1987, and erm(37), was deleted in EAI4_VNM, EAI4-like, and ZERO strains, whereas another 118 bp deletion in furA was specific only to ZERO strains. L1.1.1.1-sublineage-specific deletions in PE_PGRS4 and PE_PGRS22 were also identified. RD900, seen in ancestral lineages, was present in majority of the L1 members. All strains without IS6110 (5.0%) had the ZERO spoligo-pattern. Distinctive features of the ancestral L1 strains provide a basis for investigation of the modern versus ancestral Mtb lineages and allow consideration of countermeasures against this heterogeneous pathogen.