Use of GenoType® MTBDRplus assay to assess drug resistance and mutation patterns of multidrug-resistant tuberculosis isolates in northern India

Maurya, Anand Kumar; Singh, Amresh Kumar; Kant, Surya; Umrao, Jyoti; Kumar, Madhu; Kushwaha, Ramesh Kumar; Nag, Vijaya Lakshmi; Dhole, Tapan N.

doi:10.4103/0255-0857.115625

Cited by 17 publications

(15 citation statements)

References 25 publications

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“…The most common katG, inhA, and ahpC promoter mutations in our study were identified at frequencies similar to those reported previously (11,23,24). However, our finding of 315ACC mutations among INH s specimens (2.8%) was unexpected.…”

Section: Discussionsupporting

confidence: 89%

Frequency and Distribution of Tuberculosis Resistance-Associated Mutations between Mumbai, Moldova, and Eastern Cape

Georghiou

Seifert

Catanzaro

et al. 2016

Antimicrob Agents Chemother

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f Molecular diagnostic assays, with their ability to rapidly detect resistance-associated mutations in bacterial genes, are promising technologies to control the spread of drug-resistant tuberculosis (DR-TB). Sequencing assays provide detailed information for specific gene regions and can help diagnostic assay developers prioritize mutations for inclusion in their assays. We performed pyrosequencing of seven Mycobacterium tuberculosis gene regions (katG, inhA, ahpC, rpoB, gyrA, rrs, and eis) for 1,128 clinical specimens from India, Moldova, and South Africa. We determined the frequencies of each mutation among drug-resistant and -susceptible specimens based on phenotypic drug susceptibility testing results and examined mutation distributions by country. The most common mutation among isoniazid-resistant (INH r ) specimens was the katG 315ACC mutation (87%). However, in the Eastern Cape, INH r specimens had a lower frequency of katG mutations (44%) and higher frequencies of inhA (47%) and ahpC (10%) promoter mutations. The most common mutation among rifampin-resistant (RIF r ) specimens was the rpoB 531TTG mutation (80%). The mutation was common in RIF r specimens in Mumbai (83%) and Moldova (84%) but not the Eastern Cape (17%), where the 516GTC mutation appeared more frequently (57%). The most common mutation among fluoroquinolone-resistant specimens was the gyrA 94GGC mutation (44%). The rrs 1401G mutation was found in 84%, 84%, and 50% of amikacin-resistant, capreomycin-resistant, and kanamycin (KAN)-resistant (KAN r ) specimens, respectively. The eis promoter mutation ؊12T was found in 26% of KAN r and 4% of KAN-susceptible (KAN s ) specimens. Inclusion of the ahpC and eis promoter gene regions was critical for optimal test sensitivity for the detection of INH resistance in the Eastern Cape and KAN resistance in Moldova. (This study has been registered at ClinicalTrials.gov under registration number NCT02170441.) I n 2014, an estimated 9.6 million people developed tuberculosis (TB), and 1.5 million people died of their infection (1). Although global TB incidence rates have fallen an average of 1.5% per year since 2000, the rise of drug-resistant TB (DR-TB) globally has complicated TB control efforts (1). The World Health Organization (WHO) estimates that as many as 1 in every 20 new, active TB infections is now drug resistant (1). One of the major roadblocks in combating this growing problem has been the lack of diagnostic technology for DR-TB. Current growth-based culture and drug susceptibility testing (DST) methods can take several weeks to months to yield results (2). While waiting on culture results, physicians are forced to treat their patients empirically, adjusting treatment regimens only once DST results become available. As a result, many undiagnosed DR-TB patients are being given medications that are ineffective, which amplifies resistance, increases the risk of mortality, and increases the risk of transmitting DR-TB infections in the community.Rapid molecular diagnostic assays for DR-TB have the p...

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Section: Discussionsupporting

confidence: 89%

Frequency and Distribution of Tuberculosis Resistance-Associated Mutations between Mumbai, Moldova, and Eastern Cape

Georghiou

Seifert

Catanzaro

et al. 2016

Antimicrob Agents Chemother

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“…Twenty-four (96%) of the 25 isolates, which were determined to be rifampicin-resistant with the BACTEC 460 TB method, were found to be rifampicin-resistant with GenoType MTBDRplus. Our result was similar to other reports from India, France, Germany and Ethiopia (16, [23][24][25]. One isolate (4%) was susceptible to rifampicin.…”

Section: Discussionsupporting

confidence: 92%

“…In 2018, in the study by Kamiri et al, among the 35 specimens identified as RIF-resistant using the Geno-TypeMTBDRplus assay, 23 (65%) carried the S531L, eight isolates (22%) showed mutation in codon H526Y and four isolates (11%) in D516V codon (32). In 2013, in the study by Maurya et al, the frequency of rpoB mutation was 28 in S531L (62.3%), eight in D516V (17.7%), six in H526Y (11.1%), one in the H526D (2.2%) region and nine (20%) unknown mutations (absence of one or more wild-type) among a total of 45 MDR-TB strains (23). In 2017, in the study by Abanda et al, among the 48 isolates determined as RIF-resistant using the GenoTypeMTBDRplus assay, 41 (85%) had the S531L mutation and three isolates (6%) showed mutation in codon H526Y.…”

Section: Discussionmentioning

confidence: 95%

Gene Mutation Patterns of Rifampicin in Multidrug Resistant Mycobacterium Tuberculosis Complex Strains

Servi¹,

Uzun²

2022

jmed

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Bu çalışmada, çoğul ilaca dirençli (ÇİD) Mycobacterium tuberculosis kompleks suşlarında rifampisin (RIF) direncinin saptanmasında GenoType ® MTBDRplus testinin değerlendirilmesi amaçlanmıştır. Gereç ve Yöntem: Yirmi beş ÇİD Mycobacterium tuberculosis klinik suşu kullanılmış, RIF direncine neden olan gen mutasyonları GenoType ® MTBDRplus ile araştırılmış ve sonuçlar BACTEC 460 TB sistemi sonuçları ile karşılaştırılmıştır. Eğer mutasyon veya Vahşi Tip (VT) bandı yoksa suş sekanslanmıştır. Kalite kontrol (QC) suşu olarak Mycobacterium tuberculosis ATCC 35838 kullanılmıştır.Bulgular: Rifampisin direncinin saptanmasında GenoType ® MTBD-Rplus ve BACTEC 460 TB sistemi arasında %96 uyum bulunmuştur. ÇİD suşlarda mutasyonun en sık rpoB S531L promotor bölgede (13 suş, %52) olduğu görülmüştür. Diğer rpoB gen mutasyonları H526Y (üç suş, %12) ve H526D (üç suş, %12) bölgesinde iken, beş suşta (%20) vahşi tip problarında Δ2-Δ5 mutasyonları saptanmıştır. Bir suşta (%4) GenoType ® MTBDRplus ile mutasyon bulunamamış, ancak BACTEC 460 TB sistemi ile rifampisine dirençli olduğu belirlenmiştir. Bu suş sekanslanmış, 489, 493 ve 503 kodonlarında üçlü mutasyona sahip olduğu tespit edilmiştir.Sonuç: Rifampisin direncinin saptanmasında GenoType ® MTBD-Rplus, BACTEC 460 TB sistemi ile iyi uyum göstermiştir ve ÇİD-TB hastalarında RIF duyarlılık testi için GenoType ® MTBDRplus'ın etkili ve güvenilir bir test olabileceği ve bunun teknik zaman açısından da önemli bir avantaj sağlayacağı düşünülmüştür.

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“…Further studies are required to fully characterize the molecular epidemiology of these isolates in Uganda, especially studies employing high throughput sequencing approaches to uncover all the potential resistance conferring mutations. Since the commercial rapid molecular assays for TB target only high confidence mutations to swiftly detect resistance to anti-TB drugs [ 31 , 32 , 42 , 50 ], absence of targets is troublesome as it makes it nearly impossible to employ rapid molecular assays to detect certain resistant strains in clinical samples. On the other hand, strains that lacked mutations could harbour resistance conferring mutations in other genes e.g.…”

Section: Discussionmentioning

confidence: 99%

Prevalence and patterns of rifampicin and isoniazid resistance conferring mutations in Mycobacterium tuberculosis isolates from Uganda

et al. 2018

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BackgroundAccurate diagnosis of tuberculosis, especially by using rapid molecular assays, can reduce transmission of drug resistant tuberculosis in communities. However, the frequency of resistance conferring mutations varies with geographic location of Mycobacterium tuberculosis, and this affects the efficiency of rapid molecular assays in detecting resistance. This has created need for characterizing drug resistant isolates from different settings to investigate frequencies of resistance conferring mutations. Here, we describe the prevalence and patterns of rifampicin- and isoniazid- resistance conferring mutations in isolates from Uganda, which could be useful in the management of MDR-TB patients in Uganda and other countries in sub-Saharan Africa.ResultsNinety seven M. tuberculosis isolates were characterized, of which 38 were MDR, seven rifampicin-resistant, 12 isoniazid-mono-resistant, and 40 susceptible to rifampicin and isoniazid. Sequence analysis of the rpoB rifampicin-resistance determining region (rpoB/RRDR) revealed mutations in six codons: 588, 531, 526, 516, 513, and 511, of which Ser531Leu was the most frequent (40%, 18/45). Overall, the three mutations (Ser531Leu, His526Tyr, Asp516Tyr) frequently associated with rifampicin-resistance occurred in 76% of the rifampicin resistant isolates while 18% (8/45) of the rifampicin-resistant isolates lacked mutations in rpoB/RRDR. Furthermore, sequence analysis of katG and inhA gene promoter revealed mainly the Ser315Thr (76%, 38/50) and C(-15)T (8%, 4/50) mutations, respectively. These two mutations combined, which are frequently associated with isoniazid-resistance, occurred in 88% of the isoniazid resistant isolates. However, 20% (10/50) of the isoniazid-resistant isolates lacked mutations both in katG and inhA gene promoter. The sensitivity of sequence analysis of rpoB/RRDR for rifampicin-resistance via detection of high confidence mutations (Ser531Leu, His526Tyr, Asp516Tyr) was 81%, while it was 77% for analysis of katG and inhA gene promoter to detect isoniazid-resistance via detection of high confidence mutations (Ser315Thr, C(-15)T, T(-8)C). Furthermore, considering the circulating TB genotypes in Uganda, the isoniazid-resistance conferring mutations were more frequent in M. tuberculosis lineage 4/sub-lineage Uganda, perhaps explaining why this genotype is weakly associated with MDR-TB.ConclusionSequence analysis of rpoB/RRDR, katG and inhA gene promoter is useful in detecting rifampicin/isoniazid resistant M. tuberculosis isolates in Uganda however, about ≤20% of the resistant isolates lack known resistance-conferring mutations hence rapid molecular assays may not detect them as resistant.

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Use of GenoType® MTBDRplus assay to assess drug resistance and mutation patterns of multidrug-resistant tuberculosis isolates in northern India

Abstract: The GenoType® MTBDRplus assay is highly sensitive with short turnaround times and a rapid test for the detection of the most common mutations conferring resistance in MDR-TB strains that can readily be included in a routine laboratory workflow.

Cited by 17 publications

References 25 publications

Frequency and Distribution of Tuberculosis Resistance-Associated Mutations between Mumbai, Moldova, and Eastern Cape

Frequency and Distribution of Tuberculosis Resistance-Associated Mutations between Mumbai, Moldova, and Eastern Cape

Gene Mutation Patterns of Rifampicin in Multidrug Resistant Mycobacterium Tuberculosis Complex Strains

Prevalence and patterns of rifampicin and isoniazid resistance conferring mutations in Mycobacterium tuberculosis isolates from Uganda

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