Development and application of single-tube multiplex real-time PCR for lineage classification of Mycobacterium tuberculosis based on large sequence polymorphism in Northeast Thailand

Faksri, Kiatichai; Hanchaina, Rattanavinan; Sangka, Arunnee; Namwat, Wises; Lulitanond, Viraphong

doi:10.1016/j.tube.2015.04.009

Cited by 5 publications

(3 citation statements)

References 31 publications

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“…Using these deleted fragments as genetic markers, this analysis can be performed by simple PCR-based methods 63 . A recent study performed in Northeast Thaliland by Faksri et al 64 showed the classification of Mtb based on LSP using multiplex real-time PCR which provided a simple, rapid and high performance tool for characterizing Mtb based on LSPs.…”

Section: Genetic Markers and Genotyping Methods Of M Tubermentioning

confidence: 99%

Genetic markers, genotyping methods & next generation sequencing in Mycobacterium tuberculosis

Desikan

Narayanan

2015

Indian J Med Res

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Molecular epidemiology (ME) is one of the main areas in tuberculosis research which is widely used to study the transmission epidemics and outbreaks of tubercle bacilli. It exploits the presence of various polymorphisms in the genome of the bacteria that can be widely used as genetic markers. Many DNA typing methods apply these genetic markers to differentiate various strains and to study the evolutionary relationships between them. The three widely used genotyping tools to differentiate Mycobacterium tuberculosis strains are IS6110 restriction fragment length polymorphism (RFLP), spacer oligotyping (Spoligotyping), and mycobacterial interspersed repeat units - variable number of tandem repeats (MIRU-VNTR). A new prospect towards ME was introduced with the development of whole genome sequencing (WGS) and the next generation sequencing (NGS) methods, where the entire genome is sequenced that not only helps in pointing out minute differences between the various sequences but also saves time and the cost. NGS is also found to be useful in identifying single nucleotide polymorphisms (SNPs), comparative genomics and also various aspects about transmission dynamics. These techniques enable the identification of mycobacterial strains and also facilitate the study of their phylogenetic and evolutionary traits.

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Section: Genetic Markers and Genotyping Methods Of M Tubermentioning

confidence: 99%

Genetic markers, genotyping methods & next generation sequencing in Mycobacterium tuberculosis

Desikan

Narayanan

2015

Indian J Med Res

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“…Yet, WHO has not endorsed the use of multiplex realtime PCR technique to be used to detect drug resistant MTB strains [12]. However, many countries including Thailand, have already used this technique to identify resistant TB in clinical practice [13].…”

Section: Introductionmentioning

confidence: 99%

Evaluation of Anyplex™ II MTB/MDR kit’s performance to rapidly detect isoniazid and rifampicin resistant Mycobacterium tuberculosis from various clinical specimens

et al. 2020

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To determine the accuracy of multiplex real-time PCR (Anyplex™ II MTB/MDR kit) in detecting Isoniazid (INH)-and Rifampin (RIF)-resistant Mycobacterium tuberculosis strains from various clinical specimens. The performance of Anyplex™ II MTB/MDR kit in detecting INH-and RIF-resistant M. tuberculosis compared to the conventional drug susceptibility tests by Mycobacterial Growth Indicator Tube (MGIT). A total of 430 clinical samples had positive results for M. tuberculosis from both Anyplex™ II MTB/MDR kit assay and mycobacterial cultures by MGIT method. When compared to MGITs, the sensitivity and specificity of Anyplex™ II MTB/MDR kit in detecting INH-resistant TB were 85.71% and 99.75%, respectively. For the detection of MDR-TB, the sensitivity and specificity of the test were 82.35% and 99.76%, respectively. The positive predictive values and negative predictive values to detect INH-resistant TB were 96.77% and 98.75%, respectively. Anyplex™ II MTB/MDR kit can be used to rapidly detect isoniazid and rifampicin resistances. It has a high sensitivity, specificity and PPV in detecting INH-resistant TB and MDR-TB. This test can be used as an alternative test to Xpert MTB/ RIF because it can rapidly detect both INH-resistant TB and RIF-resistant TB.

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“…Next generation sequencing and our understanding of the genetic basis of antibiotic resistance has led to the development of rapid genotypic TB tests ( Cole et al, 1998 ; Brossier et al, 2017 ). These methods can offer high sensitivity, even for paucibacillary samples, and do not require culture ( Garberi et al, 2011 ; Teo et al, 2011 ; Mboowa et al, 2014 ; Rufai et al, 2014 ; Faksri et al, 2015 ; Sales et al, 2015 ; Rahman et al, 2016 ). Xpert and MTBDR-plus allow detection of M. tuberculosis and determination of rifampicin resistance (RIF R ) directly in sputum samples within hours, and is recommended by the World Health Organization ( WHO, 2011 ; Ocheretina et al, 2014 ; Rahman et al, 2016 ).…”

Section: Introductionmentioning

confidence: 99%

Fluoromycobacteriophages Can Detect Viable Mycobacterium tuberculosis and Determine Phenotypic Rifampicin Resistance in 3–5 Days From Sputum Collection

et al. 2018

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The World Health Organization (WHO) estimates that 40% of tuberculosis (TB) cases are not diagnosed and treated correctly. Even though there are several diagnostic tests available in the market, rapid, easy, inexpensive detection, and drug susceptibility testing (DST) of Mycobacterium tuberculosis is still of critical importance specially in low and middle-income countries with high incidence of the disease. In this work, we have developed a microscopy-based methodology using the reporter mycobacteriophage mCherrybombϕ for detection of Mycobacterium spp. and phenotypic determination of rifampicin resistance within just days from sputum sample collection. Fluoromycobacteriophage methodology is compatible with regularly used protocols in clinical laboratories for TB diagnosis and paraformaldehyde fixation after infection reduces biohazard risks with sample analysis by fluorescence microscopy. We have also set up conditions for discrimination between M. tuberculosis complex (MTBC) and non-tuberculous mycobacteria (NTM) strains by addition of p-nitrobenzoic acid (PNB) during the assay. Using clinical isolates of pre-XDR and XDR-TB strains from this study, we tested mCherrybombΦ for extended DST and we compared the antibiotic resistance profile with those predicted by whole genome sequencing. Our results emphasize the utility of a phenotypic test for M. tuberculosis extended DST. The many attributes of mCherrybombΦ suggests this could be a useful component of clinical microbiological laboratories for TB diagnosis and since only viable cells are detected this could be a useful tool for monitoring patient response to treatment.

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Development and application of single-tube multiplex real-time PCR for lineage classification of Mycobacterium tuberculosis based on large sequence polymorphism in Northeast Thailand

Cited by 5 publications

References 31 publications

Genetic markers, genotyping methods & next generation sequencing in Mycobacterium tuberculosis

Genetic markers, genotyping methods & next generation sequencing in Mycobacterium tuberculosis

Evaluation of Anyplex™ II MTB/MDR kit’s performance to rapidly detect isoniazid and rifampicin resistant Mycobacterium tuberculosis from various clinical specimens

Fluoromycobacteriophages Can Detect Viable Mycobacterium tuberculosis and Determine Phenotypic Rifampicin Resistance in 3–5 Days From Sputum Collection

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