Characterization of katG, inhA, rpoB and pncA in Mycobacterium tuberculosis isolates from MDR-TB risk patients in Thailand

Suthum, Krairerk; Samosornsuk, Worada; Samosornsuk, Seksun

doi:10.3855/jidc.11974

Cited by 10 publications

(10 citation statements)

References 39 publications

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“…Our report showed that katG gene mutation was found at the rate of 79.7%, in which 95.7% had mutations in katG315 codon and 4.3% harbored mutation in katG365 codon. The percentage of 79.7% for the katG gene mutation was consistent with earlier studies in Thailand (Boonaiam et al 2010) (Suthum et al 2020) and other Southeast Asian Countries (Ismail et al 2016) (Caws et al 2006) (Valvatne et al 2009) (Liu et al 2018) (Cheng et al 2021). The prevalence of katG315 mutation varied according to the geographical region: Southeast Asia (78.4%) (Seifert et al 2015), Vietnam (85.3%) (Hang et al 2019), China (59.4%) (Wu et al 2006), the Netherlands (53%) (Van Soolingen et al 2000), Japan (22%) (Ando et al 2010) and Singapore (26%) (Lee et al 1999).…”

Section: Discussionsupporting

confidence: 91%

Novel mutations detected from drug resistant Mycobacterium tuberculosis isolated from North East of Thailand

Thwe

Namwat

Pinlaor

et al. 2021

World J Microbiol Biotechnol

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The emergence of drug-resistant tuberculosis is a major global public health threat. Thailand is one of the top 14 countries with high tuberculosis, tuberculosis co-infected with Human Immunodeficiency Virus (HIV) and multi-drug resistant tuberculosis rates. Immediate detection of drug-resistant tuberculosis is necessary to reduce mortality and morbidity by effectively providing treatment to ameliorate the formation of resistant strains. Limited data exist of mutation profiles in Northeastern Thailand. Here, 65 drug-resistant Mycobacterium tuberculosis isolates were used to detect mutations by polymerase chain reaction (PCR) and DNA sequencing. In the katG gene, mutations occurred in 47(79.7%) among 59 isoniazid resistant samples. For rpoB gene, 31 (96.9%) were observed as mutations in 32 rifampicin resistant isolates. Of 47 katG mutation samples, 45 (95.7%) had mutations in katG315 codon and 2 (4.3%) showed novel mutations at katG365 with amino acid substitution of CCG-CGG (Pro-Arg). Moreover, 18 (58.1%) mutations at rpoB531, 11 (35.5%) mutations at rpoB516, 10 (32.3%) mutations at rpoB526 and 1 (3.2%) mutation at rpoB533 were found between 31 rifampicin resistant samples. Common and novel mutations of the rpoB and katG genes in Northeastern Thailand were generated. DNA sequencing showed high accuracy, while conventional polymerase chain reaction could be applied as an initial marker for screening rifampicin and isoniazid drug-resistant Mycobacterium tuberculosis in Northeastern Thailand. Mutations reported here should be considered when developing new molecular diagnostic methods for implementation in Northeastern Thailand.

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Section: Discussionsupporting

confidence: 91%

Novel mutations detected from drug resistant Mycobacterium tuberculosis isolated from North East of Thailand

Thwe

Namwat

Pinlaor

et al. 2021

World J Microbiol Biotechnol

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“…This is similar to the study of Namratha W et al, and documented that among, 265 showed AFB positive, and 115 showed AFB negative. 26 In drug susceptibility testing, 7% isoniazid (INH) and 6.3% rifampicin (RIF) resistance which was similar to Krairerk Suthum et al 18 Of 183 (43%) culture positive, 20 RIF-resistant strains (by MGIT 960 array) and in them 25 (14%) isoniazidresistant strains were identified similar to Chao-Ju Chen et al 27 In 425 pulmonary samples (Sputum, Pleural fluid Bronchial alveolar lavage, Endotracheal aspirate samples -CBNAAT Gene Xpert), 158 samples were negative. This study found the rifampicin resistance rate 28%.…”

Section: Discussionmentioning

confidence: 65%

“…For MDRTB Line Probe Assay detection, specimens with smear positive, culture-positive, smearnegative sample were used. 17,18 Cartridge Based Nuclear Acid Amplification test (CBNAAt)…”

Section: Microscopic Examination Zeihl-neelsen Stainingmentioning

confidence: 99%

A Comparison Study of CBNAAT, Gene Xpert and Line Probe Assays in the Diagnosis of Tuberculosis in smear Negative Specimens

Vijay¹,

Meharaj²,

Jayanthi³

et al. 2022

J. Pure Appl. Microbiol.

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Tuberculosis (TB) is a serious and important public health issue to be addressed in India. Timely diagnosis of the drug resistance in tuberculosis is essential to ensure and initiate appropriate therapy. The detection of drug resistant Mycobacterium tuberculosis (MTB) in cases of smear-negative and clinical diagnosed pulmonary TB. A prospective case-control study was conducted on 473 pulmonary samples received at the tertiary care center from January 2019 to December 2019. All specimens were processed for microscopy and culture. CBNAAT- Gene Xpert and LPA Genotype MTBDRplus (VER 2.0) was used to confirm in smear-negative samples. Among the pulmonary samples, 52% smear-positive, and 48% smear-negative, 183 (43%) were found to be culture-positive by Lowenstein Jensen medium (LJ) and MGIT 960, 267 (63%) were positive CBNAAT and LPA n= 216 (51%) samples positive for the TUB band. The use of CBNAAT-Gene Xpert, Line Probe Assay Genotype MTBDR plus(VER 2.0) can be done from the samples directly and the diagnostic performance are more specific for detecting MTB in smear-negative specimens. This study suggests that LPA also helps in the diagnosis of MDR rapidly and in initiation of earlier treatment.

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“…The INH resistance of MTB isolates was frequently associated with a mutant katG gene, while inhA mutations were identified in a small number of INH resistant strains [ 8 ]. Results of custom alignment with the sequenced results using the EPI2ME desktop agent algorithm (ONT) showed more than 95% with over 200 × coverage to virtually cover the complete MTB genome (Fig.…”

Section: Resultsmentioning

confidence: 99%

Integrative utility of long read sequencing-based whole genome analysis and phenotypic assay on differentiating isoniazid-resistant signature of Mycobacterium tuberculosis

Hung

Huang

et al. 2021

J Biomed Sci

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Background With the advancement of next generation sequencing technologies (NGS), whole-genome sequencing (WGS) has been deployed to a wide range of clinical scenarios. Rapid and accurate classification of drug-resistant Mycobacterium tuberculosis (MTB) would be advantageous in reducing the amplification of additional drug resistance and disease transmission. Methods In this study, a long-read sequencing approach was subjected to the whole-genome sequencing of clinical MTB clones with susceptibility test profiles, including isoniazid (INH) susceptible clones (n = 10) and INH resistant clones (n = 42) isolated from clinical specimens. Non-synonymous variants within the katG or inhA gene associated with INH resistance was identified using Nanopore sequencing coupled with a corresponding analytical workflow. Results In total, 54 nucleotide variants within the katG gene and 39 variants within the inhA gene associated with INH resistance were identified. Consistency among the results of genotypic profiles, susceptibility test, and minimal inhibitory concentration, the high-INH resistance signature was estimated using the area under the receiver operating characteristic curve with the existence of Ser315Thr (AUC = 0.822) or Thr579Asn (AUC = 0.875). Conclusions Taken together, we curated lists of coding variants associated with differential INH resistance using Nanopore sequencing, which may constitute an emerging platform for rapid and accurate identification of drug-resistant MTB clones.

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Characterization of katG, inhA, rpoB and pncA in Mycobacterium tuberculosis isolates from MDR-TB risk patients in Thailand

Cited by 10 publications

References 39 publications

Novel mutations detected from drug resistant Mycobacterium tuberculosis isolated from North East of Thailand

Novel mutations detected from drug resistant Mycobacterium tuberculosis isolated from North East of Thailand

A Comparison Study of CBNAAT, Gene Xpert and Line Probe Assays in the Diagnosis of Tuberculosis in smear Negative Specimens

Integrative utility of long read sequencing-based whole genome analysis and phenotypic assay on differentiating isoniazid-resistant signature of Mycobacterium tuberculosis

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