Detection of second-line drug resistance in Mycobacterium tuberculosis using oligonucleotide microarrays

Zimenkov, Danila; Антонова, О. В.; Kuźmin, Alexey V.; Isaeva, Yulia D; Krylova, L. Yu.; Попов, С. А.; Заседателев, А. С.; Mikhailovich, Vladimir; Gryadunov, Dmitry

doi:10.1186/1471-2334-13-240

Cited by 42 publications

(26 citation statements)

References 27 publications

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“…Several other molecular techniques which detect resistance to the injectable drugs have been described recently. These include in-house reverse line blot hybridization assays, multiplex allele-specific PCR, mass spectrometry of PCR products using iPLEX Gold assay (MassArray System; Sequenom, Inc., San Diego, CA, USA), oligonucleotide microarray, and melting curves using dually labeled probes (19)(20)(21)(22)(23)(24). However, most of these techniques require open handling of PCR amplicons or have not been systematically validated in clinical settings.…”

mentioning

confidence: 99%

Genotypic Susceptibility Testing of Mycobacterium tuberculosis Isolates for Amikacin and Kanamycin Resistance by Use of a Rapid Sloppy Molecular Beacon-Based Assay Identifies More Cases of Low-Level Drug Resistance than Phenotypic Lowenstein-Jensen Testing

et al. 2015

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eResistance to amikacin (AMK) and kanamycin (KAN) in clinical Mycobacterium tuberculosis strains is largely determined by specific mutations in the rrs gene and eis gene promoter. We developed a rapid, multiplexed sloppy molecular beacon (SMB) assay to identify these mutations and then evaluated assay performance on 603 clinical M. tuberculosis DNA samples collected in South Korea. Assay performance was compared to gold-standard phenotypic drug susceptibility tests, including LowensteinJensen (LJ) absolute concentration, mycobacterial growth indicator tubes (MGIT), and TREK Sensititre MycoTB MIC plate (MycoTB) methods. Target amplicons were also tested for mutations by Sanger sequencing. The SMB assay correctly detected 115/116 mutant and mixed sequences and 487/487 wild-type sequences (sensitivity and specificity of 99.1 and 100%, respectively). Using the LJ method as the reference, sensitivity and specificity for AMK resistance were 92.2% and 100%, respectively, and sensitivity and specificity for KAN resistance were 87.7% and 95.6%, respectively. Mutations in the rrs gene were unequivocally associated with high-level cross-resistance to AMK and KAN in all three conventional drug susceptibility testing methods. However, eis promoter mutations were associated with KAN resistance using the MGIT or MycoTB methods but not the LJ method. No testing method associated eis promoter mutations with AMK resistance. Among the discordant samples with AMK and/or KAN resistance but wild-type sequence at the target genes, we discovered four new mutations in the whiB7 5= untranslated region (UTR) in 6/22 samples. All six samples were resistant only to KAN, suggesting the possible role of these whiB7 5= UTR mutations in KAN resistance.T uberculosis (TB) was declared a global public emergency nearly 20 years ago (1). Although the rate of new cases of TB has been decreasing worldwide, the millennium developmental goal target of a 50% disease reduction by 2015 is unlikely to be achieved (1). An increase in the incidence of multidrug-resistant (MDR) and extensively drug resistant (XDR) TB is a serious threat to these reduction goals (1). Patients with drug-resistant TB are best identified as rapidly as possible so that appropriate infection control and treatments can be quickly initiated (2).Conventional phenotypic methods can take weeks to months to fully define the drug resistance pattern of Mycobacterium tuberculosis isolates due to the very slow growth of this bacterium (3-5). Molecular tests offer the promise of more rapid drug resistance detection. A number of tests are available to detect resistance to many of the first-line anti-TB drugs (6-8). However, there are fewer rapid tests available to test for resistance to the injectable second-line drugs amikacin (AMK), kanamycin (KAN), and capreomycin (CAP). DNA sequencing studies suggest that most cases of resistance to injectable drugs can be identified by detecting mutations in positions 1401, 1402, and 1484 in the M. tuberculosis 16S rRNA (rrs) gene and between nucleotides Ϫ...

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confidence: 99%

Genotypic Susceptibility Testing of Mycobacterium tuberculosis Isolates for Amikacin and Kanamycin Resistance by Use of a Rapid Sloppy Molecular Beacon-Based Assay Identifies More Cases of Low-Level Drug Resistance than Phenotypic Lowenstein-Jensen Testing

et al. 2015

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“…Тест система "ТБ Био чип 1" позволяет выявить мутации, ответственные за устойчивость к рифампицину и изониазиду [13]. Вторая тест система направлена на определение устойчивости к фторхинолонам, аминогликозидам и капреомицину [14].…”

Section: оригинальные исследованияunclassified

Identification of drug resistance and genotyping of clinical isolates of Mycobacterium tuberculosis using the TB-TEST

Беспятых¹,

Шитиков²,

Zimenkov³

et al. 2013

Pulʹmonologiâ (Mosk.)

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“…All discrepancies between the microarray test and culture test were caused by either rare mutations not detectable by the microarray probes, or by unknown mutations. The newest generation of TB-biochips identifies mutations responsible for the emerging resistance of M. tuberculosis so the highly effective second-line fluoroquinolone antibiotics can be administered [12].…”

Section: Tuberculosismentioning

confidence: 99%

Infectious diseases detection by microarray: An overview of clinical relevant infections

Herrera-Rodríguez¹,

Elizondo-Quiroga²,

Álvarez-Maya³

2013

JBiSE

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Microarray technology is a powerful tool to investigate whole genome expression profiles to study the crosstalk between pathogens and associated hosts that cause illness. Microarrays have been used in several comparative genome hybridization studies of pathogens. In addition to detection and identification of pathogens, microarrays are ideal for characterizing genetic differences between bacteria isolates of the same species to the strain level. Furthermore, the use of microarrays has been gaining importance in the detection of viral agents. Here we explore the use of microarrays for simultaneous detection of viruses and modifications made over these techniques. Microarray technology has also been incorporated to compensate for time-consuming sequencing. The procedure of fungi identification based on sequences and studies reported the use of microarrays to identify pathogenic yeasts and molds by targeting the internal transcribed spacer regions in fungal rRNA genes. The remarkable advancement in genomics over the last decade has made it possible for microarray technology to evolve towards being the best option for clinical diagnostics because they have several advantages.

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Detection of second-line drug resistance in Mycobacterium tuberculosis using oligonucleotide microarrays

Cited by 42 publications

References 27 publications

Genotypic Susceptibility Testing of Mycobacterium tuberculosis Isolates for Amikacin and Kanamycin Resistance by Use of a Rapid Sloppy Molecular Beacon-Based Assay Identifies More Cases of Low-Level Drug Resistance than Phenotypic Lowenstein-Jensen Testing

Genotypic Susceptibility Testing of Mycobacterium tuberculosis Isolates for Amikacin and Kanamycin Resistance by Use of a Rapid Sloppy Molecular Beacon-Based Assay Identifies More Cases of Low-Level Drug Resistance than Phenotypic Lowenstein-Jensen Testing

Identification of drug resistance and genotyping of clinical isolates of Mycobacterium tuberculosis using the TB-TEST

Infectious diseases detection by microarray: An overview of clinical relevant infections

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