ArticleScientific reports2022
Whole-genome single nucleotide variant phylogenetic analysis of Mycobacterium tuberculosis Lineage 1 in endemic regions of Asia and Africa.
Article in Scientific reports, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 28 citations in OpenAlex.
- Association between human genomes and mycobacterial genomes contributes to severity and transmissibility of pulmonary tuberculosis.iScience · 2026Article
- Reference-free clustering as an epidemiological tool forMicrobial genomics · 2026Article
- Evaluation of thermal desorption-electrospray ionization mass spectrometry for characterization ofJournal of mass spectrometry and advances in the clinical lab · 2025Article
- Mycobacterium tuberculosis complex Lineage 1: A neglected cause of tuberculosis.PLoS neglected tropical diseases · 2025Review
- Dissecting rifampicin heteroresistance inJournal of medical microbiology · 2025Article
- Analysis of complete genomes of Mycobacterium tuberculosis sublineage 2.1 (Proto-Beijing) revealed the presence of three pe_pgrs3-pe_pgrs4-like genes.Scientific reports · 2024Article
- Whole-genome sequencing ofMicrobiology resource announcements · 2024Article
- Case Report: Disseminated Tuberculosis After Kidney Transplantation.The American journal of tropical medicine and hygiene · 2024Article
- fastlin: an ultra-fast program for Mycobacterium tuberculosis complex lineage typing.Bioinformatics (Oxford, England) · 2023Article
- Lineage classification and antitubercular drug resistance surveillance ofMicrobiology spectrum · 2023Article
- Parallel signatures of Mycobacterium tuberculosis and human Y-chromosome phylogeography support the Two Layer model of East Asian population history.Communications biology · 2023Article
- A revised SNP-based barcoding scheme for typingmSphere · 2023Article
- Analysis of whiB7 in Mycobacterium tuberculosis reveals novel AT-hook deletion mutations.Scientific reports · 2023Article
- Genomic Sequencing Profiles ofTropical medicine and infectious disease · 2023Article
- Distribution ofTropical medicine and infectious disease · 2022Article
- Whole-genome sequencing of Mycobacterium tuberculosis from Cambodia.Scientific reports · 2022Article
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Authors and funding
7 authors at 7 institutions in 4 countries.
Funding
Abstract
Mycobacterium tuberculosis (Mtb) lineage 1 (L1) contributes considerably to the disease morbidity. While whole genome sequencing (WGS) is increasingly used for studying Mtb, our understanding of genetic diversity of L1 remains limited. Using phylogenetic analysis of WGS data from endemic range in Asia and Africa, we provide an improved genotyping scheme for L1. Mapping deletion patterns of the 68 direct variable repeats (DVRs) in the CRISPR region of the genome onto the phylogeny provided supporting evidence that the CRISPR region evolves primarily by deletion, and hinted at a possible Southeast Asian origin of L1. Both phylogeny and DVR patterns clarified some relationships between different spoligotypes, and highlighted the limited resolution of spoligotyping. We identified a diverse repertoire of drug resistance mutations. Altogether, this study demonstrates the usefulness of WGS data for understanding the genetic diversity of L1, with implications for public health surveillance and TB control. It also highlights the need for more WGS studies in high-burden but underexplored regions.
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