Simultaneous drug resistance detection and genotyping of<i>Mycobacterium tuberculosis</i>using a low-density hydrogel microarray

Zimenkov, Danila; Kulagina, Elena V.; Антонова, О. В.; Zhuravlev, Viacheslav; Gryadunov, Dmitry

doi:10.1093/jac/dkw015

Cited by 28 publications

(20 citation statements)

References 65 publications

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“…The model was used to predict hybridization kinetics of eighteen 20-mer probes targeting vancomycin resistant genes. This gene was chosen as a model because emergence of antibiotic resistance associated with pathogenic bacteria is an alarming global issue [14,15] and numerous hybridization-based biochip platforms are being developed to diagnose multi-drug resistant bacteria [16,17,18,19,20]. Effect of target concentration, temperature, recirculation flow rate and rate constants on the hybridization kinetics, with target concentration, rate constants, and temperature being the most important parameters affecting the rate of hybridization were investigated.…”

Section: Introductionmentioning

confidence: 99%

Modeling Hybridization Kinetics of Gene Probes in a DNA Biochip Using FEMLAB

et al. 2017

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Microfluidic DNA biochips capable of detecting specific DNA sequences are useful in medical diagnostics, drug discovery, food safety monitoring and agriculture. They are used as miniaturized platforms for analysis of nucleic acids-based biomarkers. Binding kinetics between immobilized single stranded DNA on the surface and its complementary strand present in the sample are of interest. To achieve optimal sensitivity with minimum sample size and rapid hybridization, ability to predict the kinetics of hybridization based on the thermodynamic characteristics of the probe is crucial. In this study, a computer aided numerical model for the design and optimization of a flow-through biochip was developed using a finite element technique packaged software tool (FEMLAB; package included in COMSOL Multiphysics) to simulate the transport of DNA through a microfluidic chamber to the reaction surface. The model accounts for fluid flow, convection and diffusion in the channel and on the reaction surface. Concentration, association rate constant, dissociation rate constant, recirculation flow rate, and temperature were key parameters affecting the rate of hybridization. The model predicted the kinetic profile and signal intensities of eighteen 20-mer probes targeting vancomycin resistance genes (VRGs). Predicted signal intensities and hybridization kinetics strongly correlated with experimental data in the biochip (R2 = 0.8131).

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Section: Introductionmentioning

confidence: 99%

Modeling Hybridization Kinetics of Gene Probes in a DNA Biochip Using FEMLAB

et al. 2017

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“…In this study, we performed the Sensititre MycoTB alongside the Bactec MGIT 960 and identified common mutations leading to drug resistance using the microarray-based method [20] with clinical isolates from the Moscow region. The selected strains had a strong bias toward drug resistance; nevertheless, a drastic difference in the MDR and XDR prevalence rates was observed in patients with a history of previous treatment.…”

Section: Discussionmentioning

confidence: 99%

“…The effectiveness of the TB-TEST assay application for the analysis of clinical material largely depended on the number of mycobacterial cells in the sample similar to any other molecular method. The TB-TEST works correctly with 96% of AFB-positive and 25% of AFB-negative clinical samples [20]. Thus, in the case of the failure of the direct genetic analysis of a clinical sample, a short-term liquid culture could be used with the Bactec MGIT automated system, and the obtained DNA from the isolate could be re-assayed using the TB-TEST.…”

Section: Discussionmentioning

confidence: 99%

“…The PCR and hybridization on the microarrays were performed as previously described [20]. The TB-TEST assay allows the detection of 28 substitutions in rpoB , 11 in katG , 5 in inhA , 5 in ahpC , 15 in gyrA , 23 in gyrB , 4 in rrs , 6 in eis and 23 in embB and established the lineages of the strains most endemic to the Russian Federation (Beijing, Haarlem, LAM and Ural).…”

Section: Methodsmentioning

confidence: 99%

“…In the present study, we used a microarray-based TB-TEST molecular assay to characterize the mutations detected in clinical MTB strains and their correlations with resistance to rifampin (RMP), isoniazide (INH), ethambutol (EMB), fluoroquinolones (FQs), and second-line injection drugs (SLID) [20]. This assay allows the detection of an extended range of genetic determinants of resistance and establishes the genotypes of the most endemic strains in the Russian Federation.…”

Section: Introductionmentioning

confidence: 99%

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A Comparison of the Sensititre MycoTB Plate, the Bactec MGIT 960, and a Microarray-Based Molecular Assay for the Detection of Drug Resistance in Clinical Mycobacterium tuberculosis Isolates in Moscow, Russia

Nosova¹,

Zimenkov

Khakhalina³

et al. 2016

PLoS ONE

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BackgroundThe goal of this study was to compare the consistency of three assays for the determination of the drug resistance of Mycobacterium tuberculosis (MTB) strains with various resistance profiles isolated from the Moscow region.MethodsA total of 144 MTB clinical isolates with a strong bias toward drug resistance were examined using Bactec MGIT 960, Sensititre MycoTB, and a microarray-based molecular assay TB-TEST to detect substitutions in the rpoB, katG, inhA, ahpC, gyrA, gyrB, rrs, eis, and embB genes that are associated with resistance to rifampin, isoniazid, fluoroquinolones, second-line injectable drugs and ethambutol.ResultsThe average correlation for the identification of resistant and susceptible isolates using the three methods was approximately 94%. An association of mutations detected with variable resistance levels was shown. We propose a change in the breakpoint minimal inhibitory concentration for kanamycin to less than 5 μg/ml in the Sensititre MycoTB system. A pairwise comparison of the minimal inhibitory concentrations (MICs) of two different drugs revealed an increased correlation in the first-line drug group and a partial correlation in the second-line drug group, reflecting the history of the preferential simultaneous use of drugs from these groups. An increased correlation with the MICs was also observed for drugs sharing common resistance mechanisms.ConclusionsThe quantitative measures of phenotypic drug resistance produced by the Sensititre MycoTB and the timely detection of mutations using the TB-TEST assay provide guidance for clinicians for the choice of the appropriate drug regimen.

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Advances in Carbon Nanotubes–Hydrogel Hybrids in Nanomedicine for Therapeutics

Vashist

Kaushik

Vashist

et al. 2018

Adv Healthcare Materials

159

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In spite of significant advancement in hydrogel technology, low mechanical strength and lack of electrical conductivity have limited their next-level biomedical applications for skeletal muscles, cardiac and neural cells. Host-guest chemistry based hybrid nanocomposites systems have gained attention as they completely overcome these pitfalls and generate bioscaffolds with tunable electrical and mechanical characteristics. In recent years, carbon nanotube (CNT)-based hybrid hydrogels have emerged as innovative candidates with diverse applications in regenerative medicines, tissue engineering, drug delivery devices, implantable devices, biosensing, and biorobotics. This article is an attempt to recapitulate the advancement in synthesis and characterization of hybrid hydrogels and provide deep insights toward their functioning and success as biomedical devices. The improved comparative performance and biocompatibility of CNT-hydrogels hybrids systems developed for targeted biomedical applications are addressed here. Recent updates toward diverse applications and limitations of CNT hybrid hydrogels is the strength of the review. This will provide a holistic approach toward understanding of CNT-based hydrogels and their applications in nanotheranostics.

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Simultaneous drug resistance detection and genotyping ofMycobacterium tuberculosisusing a low-density hydrogel microarray

Cited by 28 publications

References 65 publications

Modeling Hybridization Kinetics of Gene Probes in a DNA Biochip Using FEMLAB

Modeling Hybridization Kinetics of Gene Probes in a DNA Biochip Using FEMLAB

A Comparison of the Sensititre MycoTB Plate, the Bactec MGIT 960, and a Microarray-Based Molecular Assay for the Detection of Drug Resistance in Clinical Mycobacterium tuberculosis Isolates in Moscow, Russia

Advances in Carbon Nanotubes–Hydrogel Hybrids in Nanomedicine for Therapeutics

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