Characterization of Mutations Conferring Extensive Drug Resistance to Mycobacterium tuberculosis Isolates in Pakistan

Ali, Asho; Hasan, Rumina; Jabeen, Kauser; Jabeen, Nusrat; Qadeer, Ejaz; Hasan, Zahra

doi:10.1128/aac.05101-11

Cited by 43 publications

(28 citation statements)

References 50 publications

(69 reference statements)

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“…These results supported the notion that resistance to fluoroquinolones in M. tuberculosis was predominantly attributed to gyrA mutations [8,24]. The most frequent mutations were found at codons 94 (D94G, D94A, D94Y, D94N and D94H), 90 (A90V) and 91 (S91P) of gyrA, similar to data from India [15], Pakistan [25], Germany [24] and the USA [13]. The mutation at codon 95 (AGC → ACC) was observed in all clinical isolates, which was a natural polymorphism and unrelated to fluoroquinolone resistance in M. tuberculosis [5].…”

Section: Discussionsupporting

confidence: 91%

Molecular characterisation of extensively drug-resistant Mycobacterium tuberculosis isolates in China

Zhao

Sun

Zeng

et al. 2015

International Journal of Antimicrobial Agents

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Section: Discussionsupporting

confidence: 91%

Molecular characterisation of extensively drug-resistant Mycobacterium tuberculosis isolates in China

Zhao

Sun

Zeng

et al. 2015

International Journal of Antimicrobial Agents

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“…531 , 526 , 516 or 515 , in the RRDR region [35,36,37,38]. The most common mutation was the rpo B S531L, corroborating with previous reports [33].…”

Section: Discussionsupporting

confidence: 88%

Whole Genome Sequencing Based Characterization of Extensively Drug-Resistant Mycobacterium tuberculosis Isolates from Pakistan

et al. 2015

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Improved molecular diagnostic methods for detection drug resistance in Mycobacterium tuberculosis (MTB) strains are required. Resistance to first- and second- line anti-tuberculous drugs has been associated with single nucleotide polymorphisms (SNPs) in particular genes. However, these SNPs can vary between MTB lineages therefore local data is required to describe different strain populations. We used whole genome sequencing (WGS) to characterize 37 extensively drug-resistant (XDR) MTB isolates from Pakistan and investigated 40 genes associated with drug resistance. Rifampicin resistance was attributable to SNPs in the rpoB hot-spot region. Isoniazid resistance was most commonly associated with the katG codon 315 (92%) mutation followed by inhA S94A (8%) however, one strain did not have SNPs in katG, inhA or oxyR-ahpC. All strains were pyrazimamide resistant but only 43% had pncA SNPs. Ethambutol resistant strains predominantly had embB codon 306 (62%) mutations, but additional SNPs at embB codons 406, 378 and 328 were also present. Fluoroquinolone resistance was associated with gyrA 91–94 codons in 81% of strains; four strains had only gyrB mutations, while others did not have SNPs in either gyrA or gyrB. Streptomycin resistant strains had mutations in ribosomal RNA genes; rpsL codon 43 (42%); rrs 500 region (16%), and gidB (34%) while six strains did not have mutations in any of these genes. Amikacin/kanamycin/capreomycin resistance was associated with SNPs in rrs at nt1401 (78%) and nt1484 (3%), except in seven (19%) strains. We estimate that if only the common hot-spot region targets of current commercial assays were used, the concordance between phenotypic and genotypic testing for these XDR strains would vary between rifampicin (100%), isoniazid (92%), flouroquinolones (81%), aminoglycoside (78%) and ethambutol (62%); while pncA sequencing would provide genotypic resistance in less than half the isolates. This work highlights the importance of expanded targets for drug resistance detection in MTB isolates.

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“…In the present study, this polymorphism was found in 94.5% of isolates. The S95T polymorphism has not been implicated in FQ resistance, since it has been found in strains for which ofloxacin MIC values are less than the critical concentration (Ͻ2 g/ml) (6,33,35,42). An exception was an earlier Indian study, which found S95T in 88.2% of ofloxacin-resistant isolates, with no other mutation in the QRDR of gyrA or gyrB (24).…”

Section: Figmentioning

confidence: 90%

“…D94G is reported as the most common codon 94 substitution in most reports, as seen in studies from Pakistan, China, the Philippines, Thailand, Vietnam, Uzbekistan, Russia, Germany, France, and the United States (17,(33)(34)(35)(36)(37)(38)(39)(40)(41). All mutations at codon 94 have been associated with in vitro resistance, as seen in earlier studies (17,24,33,36,37,40,41). The codon 90 mutation A90V has also been found at a high frequency; studies from India, the Philippines, China, and Belgium have reported it as the most common mutation (23,24,35,42).…”

Section: Figmentioning

confidence: 99%

Sequence Analysis of Fluoroquinolone Resistance-Associated Genes gyrA and gyrB in Clinical Mycobacterium tuberculosis Isolates from Patients Suspected of Having Multidrug-Resistant Tuberculosis in New Delhi, India

et al. 2016

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h Fluoroquinolones (FQs) are broad-spectrum antibiotics recommended for the treatment of multidrug-resistant tuberculosis (MDR-TB) patients. FQ resistance, caused by mutations in the gyrA and gyrB genes of Mycobacterium tuberculosis, is increasingly reported worldwide; however, information on mutations occurring in strains from the Indian subcontinent is scarce. Hence, in this study, we aimed to characterize mutations in the gyrA and gyrB genes of acid-fast bacillus (AFB) smear-positive sediments or of M. tuberculosis isolates from AFB smear-negative samples from patients in India suspected of having MDR-TB. A total of 152 samples from patients suspected of having MDR-TB were included in the study. One hundred forty-six strains detected in these samples were characterized by sequencing of the gyrA and gyrB genes. The extracted DNA was subjected to successive amplifications using a nested PCR protocol, followed by sequencing. A total of 27 mutations were observed in the gyrA genes of 25 strains, while no mutations were observed in the gyrB genes. The most common mutations occurred at amino acid position 94 (13/27 [48.1%]); of these, the D94G mutation was the most prevalent. The gyrA mutations were significantly associated with patients with rifampin (RIF)-resistant TB. Heterozygosity was seen in 4/27 (14.8%) mutations, suggesting the occurrence of mixed populations with different antimicrobial susceptibilities. A high rate of FQ-resistant mutations (17.1%) was obtained among the isolates of TB patients suspected of having MDR-TB. These observations emphasize the need for accurate and rapid molecular tests for the detection of FQ-resistant mutations at the time of MDR-TB diagnosis.T reatment of multidrug-resistant tuberculosis (MDR-TB) patients, with strains resistant to rifampin (RIF) and isoniazid (INH), is further complicated by the presence of fluoroquinolone (FQ) resistance, due to prolonged, limited, and expensive treatment options (1, 2). A recent meta-analysis of the responses to treatment of 6,724 MDR-TB patients from 26 centers revealed that the frequency of treatment success was 64%, while that for patients with MDR-TB plus FQ resistance was only 48% (3). This clearly indicates the need for routine molecular screening for FQ resistance-associated molecular markers so that the treatment of such patients can be optimized without delay. Many such patients develop extensively drug resistant tuberculosis (XDR-TB), defined as MDR-TB plus resistance to any one FQ and any of the aminoglycosides/cyclic peptides (A-CP) (4). This poses an even more serious threat to TB management, since only 40% of XDR-TB patients have successful treatment outcomes (2). Previous studies have suggested that 5.4% (95% confidence interval [95% CI], 3.4 to 7.5%) of MDR-TB cases may actually be XDR-TB (2).FQs are oral antibacterial agents that have activity against Mycobacterium tuberculosis (5, 6). Hence, FQs are recommended for the treatment of MDR-TB patients and patients with intolerance to RIF (2). FQs are also being evaluated in ...

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Characterization of Mutations Conferring Extensive Drug Resistance to Mycobacterium tuberculosis Isolates in Pakistan

Cited by 43 publications

References 50 publications

Molecular characterisation of extensively drug-resistant Mycobacterium tuberculosis isolates in China

Molecular characterisation of extensively drug-resistant Mycobacterium tuberculosis isolates in China

Whole Genome Sequencing Based Characterization of Extensively Drug-Resistant Mycobacterium tuberculosis Isolates from Pakistan

Sequence Analysis of Fluoroquinolone Resistance-Associated Genes gyrA and gyrB in Clinical Mycobacterium tuberculosis Isolates from Patients Suspected of Having Multidrug-Resistant Tuberculosis in New Delhi, India

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