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Koentjoro MP, Donastin A, Prasetyo EN. A SIMPLE METHOD OF DNA EXTRACTION OF MYCOBACTERIUM TUBERCULOSIS FROM SPUTUM CULTURES FOR SEQUENCING ANALYSIS. Afr J Infect Dis 2021; 15:19-22. [PMID: 34595382 PMCID: PMC8457349 DOI: 10.21010/ajidv15i2s:2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 06/23/2021] [Accepted: 06/29/2021] [Indexed: 11/29/2022] Open
Abstract
Background: Concern has been raised about DNA extraction from Mycobacterium tuberculosis due to its complex procedure. This study demonstrates a simple and fast DNA extraction method of mycobacterial genome to subsequent molecular investigation, such as Polymerization Chain Reaction (PCR) amplification, with species-specific primers and sequencing. Materials and Methods: Total DNA was isolated from M. tuberculosis cultured by using boil method. DNA was evaluated via measures of DNA quantity and quality (absorbance at 230, 260 and 280 nm), DNA integrity (electrophoresis). Molecular tests were tested namely PCR and sequencing. Conclusions: The quality of DNA obtained is acceptable for PCR and sequencing analysis. These findings demonstrate that the method used is inexpensive and suitable for minimum infrastructure facilities.
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Affiliation(s)
- Maharani Pertiwi Koentjoro
- Medical Laboratory Technology, Faculty of Health, Universitas Nahdlatul Ulama Surabaya, Jl. Jemursari No. 57, Surabaya, Indonesia
| | - Adyan Donastin
- Faculty of Medicine, Universitas Nahdlatul Ulama Surabaya, Jl. Jemursari No. 57, Surabaya, Indonesia
| | - Endry Nugroho Prasetyo
- Departement of Biology, Faculty of Science and Data Analytics, Institut Teknologi Sepuluh Nopember, Gedung H, Kampus ITS Sukolilo, Surabaya, Indonesia
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Aung HL, Tun T, Moradigaravand D, Köser CU, Nyunt WW, Aung ST, Lwin T, Thinn KK, Crump JA, Parkhill J, Peacock SJ, Cook GM, Hill PC. Whole-genome sequencing of multidrug-resistant Mycobacterium tuberculosis isolates from Myanmar. J Glob Antimicrob Resist 2016; 6:113-117. [PMID: 27530852 PMCID: PMC5010037 DOI: 10.1016/j.jgar.2016.04.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 04/27/2016] [Indexed: 11/28/2022] Open
Abstract
Drug-resistant tuberculosis (TB) is a major health threat in Myanmar. An initial study was conducted to explore the potential utility of whole-genome sequencing (WGS) for the diagnosis and management of drug-resistant TB in Myanmar. Fourteen multidrug-resistant Mycobacterium tuberculosis isolates were sequenced. Known resistance genes for a total of nine antibiotics commonly used in the treatment of drug-susceptible and multidrug-resistant TB (MDR-TB) in Myanmar were interrogated through WGS. All 14 isolates were MDR-TB, consistent with the results of phenotypic drug susceptibility testing (DST), and the Beijing lineage predominated. Based on the results of WGS, 9 of the 14 isolates were potentially resistant to at least one of the drugs used in the standard MDR-TB regimen but for which phenotypic DST is not conducted in Myanmar. This study highlights a need for the introduction of second-line DST as part of routine TB diagnosis in Myanmar as well as new classes of TB drugs to construct effective regimens.
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Affiliation(s)
- Htin Lin Aung
- Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago, Dunedin, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand.
| | - Thanda Tun
- National Health Laboratory, Ministry of Health, Yangon, Myanmar
| | | | - Claudio U Köser
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Wint Wint Nyunt
- National TB Programme (NTP), Ministry of Health, Naypyidaw, Myanmar
| | - Si Thu Aung
- National TB Programme (NTP), Ministry of Health, Naypyidaw, Myanmar
| | - Thandar Lwin
- National TB Programme (NTP), Ministry of Health, Naypyidaw, Myanmar
| | - Kyi Kyi Thinn
- Department of Microbiology, University of Medicine 1, Yangon, Myanmar
| | - John A Crump
- Centre for International Health, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Sharon J Peacock
- Department of Medicine, University of Cambridge, Cambridge, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK; London School of Hygiene and Tropical Medicine, London, UK
| | - Gregory M Cook
- Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago, Dunedin, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
| | - Philip C Hill
- Centre for International Health, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
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