ArticleJournal of clinical microbiology2015
Mycobacterial DNA extraction for whole-genome sequencing from early positive liquid (MGIT) cultures.
Article in Journal of clinical microbiology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers, 1 of them a synthesis that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
64 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Pooled it
- Transmission of rifampicin-resistant tuberculosis in Ho Chi Minh City, Viet Nam: a prospective genomic epidemiology study.The Lancet regional health. Western Pacific · 2026Article
- Evaluation of DNA extraction methods from clinical Mycobacterium tuberculosis primary liquid culture for whole-genome sequencing.BMC genomics · 2026Article
- Diagnostic algorithms for tuberculosis in Europe: insights from the European Reference Laboratory Network for Tuberculosis (ERLTB-Net).The Lancet regional health. Europe · 2026Review
- The public health utility of whole genome sequencing: Insights from a tuberculosis outbreak in Australia and perspectives of public health professionals.PLOS global public health · 2026Article
- Extensive Endemic Transmission of Multidrug-ResistantOpen forum infectious diseases · 2026Article
- Genomic characterisation of recurrent Mycobacterium avium isolates from chronically infected patients reveals patterns of within-host evolution.Genome medicine · 2025Article
- Subpopulations in clinical samples ofJAC-antimicrobial resistance · 2025Article
- Mycobacterial DNA Extraction using Bead Beating in Custom Buffer Followed by NGS Workflow.Journal of visualized experiments : JoVE · 2025Article
- Complete genome and transcriptome ofMicrobiology resource announcements · 2025Article
- The application status of sequencing technology in global respiratory infectious disease diagnosis.Infection · 2024Review
- Comparative Genomic Analysis ofTropical medicine and infectious disease · 2024Article
- Genomic characteristics of prospectively sequencediScience · 2024Article
- Targeted sequencing from cerebrospinal fluid for rapid identification of drug-resistant tuberculous meningitis.Journal of clinical microbiology · 2024Article
- Aerosolization of viableProceedings of the National Academy of Sciences of the United States of America · 2024Article
- Article
- Strain structure analysis of Mycobacterium tuberculosis circulating among HIV negative, positive and drug resistant TB patients attending chest clinics in Western Kenya.BMC pulmonary medicine · 2023Article
- Assessment and validation of enrichment and target capture approaches to improveJournal of clinical microbiology · 2023Article
- Microfluidic Capture of Mycobacterium tuberculosis from Clinical Samples for Culture-Free Whole-Genome Sequencing.Microbiology spectrum · 2023Article
- The Role of Next-Generation Sequencing (NGS) in the Management of Tuberculosis: Practical Review for Implementation in Routine.Pathogens (Basel, Switzerland) · 2023Review
4 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
13 authors.
Funding
Abstract
We developed a low-cost and reliable method of DNA extraction from as little as 1 ml of early positive mycobacterial growth indicator tube (MGIT) cultures that is suitable for whole-genome sequencing to identify mycobacterial species and predict antibiotic resistance in clinical samples. The DNA extraction method is based on ethanol precipitation supplemented by pretreatment steps with a MolYsis kit or saline wash for the removal of human DNA and a final DNA cleanup step with solid-phase reversible immobilization beads. The protocol yielded ≥0.2 ng/μl of DNA for 90% (MolYsis kit) and 83% (saline wash) of positive MGIT cultures. A total of 144 (94%) of the 154 samples sequenced on the MiSeq platform (Illumina) achieved the target of 1 million reads, with <5% of reads derived from human or nasopharyngeal flora for 88% and 91% of samples, respectively. A total of 59 (98%) of 60 samples that were identified by the national mycobacterial reference laboratory (NMRL) as Mycobacterium tuberculosis were successfully mapped to the H37Rv reference, with >90% coverage achieved. The DNA extraction protocol, therefore, will facilitate fast and accurate identification of mycobacterial species and resistance using a range of bioinformatics tools.
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