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

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.

Figure 1

Phylogenetic tree of 181 Da Nang strains (a) and 332 Hanoi strains (the northern Vietnam data set) (b), constructed using variants after mapping with H37Rv. Phylogenetic trees were constructed with the maximum likelihood method using RAxML version 8.2.8 (https://github.com/stamatak/standard-RAxML) and visualized with plotTree for python v2.7 (https://github.com/katholt/plotTree). Regions of difference (RDs), deletions, and SNVs in correlation with Mtb clades are depicted. Mtb Mycobacterium tuberculosis, SNV single nucleotide variant, Del deletion, aBJ ancient Beijing, mBJ modern Beijing, NA not available.

Figure 2

Phylogenetic tree of 87 lineage-1 strains from the Da Nang cohort. AP018033.1 (EAI4_VNM) was used as a reference genome. Phylogenetic trees were constructed with the maximum likelihood method using RAxML version 8.2.8 (https://github.com/stamatak/standard-RAxML) and visualized with plotTree for python v2.7 (https://github.com/katholt/plotTree). RD239, RD2bcg, deletion in furA, and SNVs in correlation with Mtb clades are shown. Mtb Mycobacterium tuberculosis, SNV single nucleotide variant, Del deletion.