scholarly journals Genomic Polymorphisms in Toxin-Antitoxin Systems and Identification of Novel Phylo-SNPs and Polymorphisms Associated with Drug Resistance/Susceptibility in Clinical Isolates of Mycobacterium tuberculosis from Mumbai, India

2019 ◽  
Author(s):  
Kayzad Nilgiriwala ◽  
Vidushi Chitalia ◽  
Sanchi Shah ◽  
Akshata Papewar
Keyword(s):  
Drug Resistance ◽  
Mycobacterium Tuberculosis ◽  
Central Asia ◽  
Sequence Data ◽  
Drug Susceptibility ◽  
Clinical Isolates ◽  
Whole Genome Sequence ◽  
Silent Mutation ◽  
Drug Resistance Profile ◽  
Cell Arrest

ABSTRACTToxin-antitoxin (TA) modules are one of the prominent determinants that triggers a persistent state aiding Mycobacterium tuberculosis evasion to host generated stresses. The 79 characterized and putative TA systems described in M. tuberculosis are dominated by the VapBC, MazEF, HigAB, RelBE and ParDE TA families, largely involved in persistence and cell arrest. Hence, there is a need to maintain and conserve the TA loci in the chromosome of the pathogen. It is essential to study the genomic differences of the TA systems in clinical isolates along with its association to drug susceptibility patterns and lineage. In the current study, the TA loci and their promoter sequences were analysed from the whole genome sequence data of 74 clinical isolates. Mykrobe Predictor was used for lineage identification and drug resistance predictions in the clinical isolates. Polymorphisms associated with 79.8% (63/79) TA systems were observed across 72 clinical isolates. Among the TA systems, the isolates had a varying number of polymorphisms localised primarily in the toxin genes (58.7%), antitoxin genes (40.7%) and chaperones (0.6%), due to Single Nucleotide Polymorphism (SNP) resulting in transition (67.3%), transversion or frameshift mutations. Our analysis suggests the presence of novel Phylo-SNPs by establishing high confidence association of specific lineages to polymorphisms in the TA systems. Notably, association of polymorphisms in Rv1838c-1839c (VapBC13), Rv3358-3357 (YefM/YoeB) and Rv0240-0239 (VapBC24) to Delhi/Central Asia lineage. The polymorphic loci of the 3 TA systems is localised in the antitoxin gene of the Delhi/Central Asia strains, with a resultant silent mutation. The assessment of correlation between TA polymorphisms and the drug resistance profile revealed correlation of SNPs in VapBC35 with drug resistant M. tuberculosis strains and SNPs in VapBC24, VapBC13 and YefM/YoeB to drug sensitive strains.

scholarly journals Genomic Variations in Drug Resistant Mycobacterium tuberculosis Strains Collected from Patients with Different Localization of Infection

Antibiotics ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 27
Author(s):  
Ekaterina Chernyaeva ◽  
Mikhail Rotkevich ◽  
Ksenia Krasheninnikova ◽  
Alla Lapidus ◽  
Dmitrii E. Polev ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Mycobacterium Tuberculosis ◽  
Pulmonary Tuberculosis ◽  
Central Asia ◽  
Phylogenetic Analyses ◽  
Treatment Success ◽  
Point Mutations ◽  
Whole Genome Sequence ◽  
Public Health Importance ◽  
Resistance Patterns

Mycobacterium tuberculosis is a highly studied pathogen due to public health importance. Despite this, problems like early drug resistance, diagnostics and treatment success prediction are still not fully resolved. Here, we analyze the incidence of point mutations widely used for drug resistance detection in laboratory practice and conduct comparative analysis of whole-genome sequence (WGS) for clinical M. tuberculosis strains collected from patients with pulmonary tuberculosis (PTB) and extra-pulmonary tuberculosis (XPTB) localization. A total of 72 pulmonary and 73 extrapulmonary microbiologically characterized M. tuberculosis isolates were collected from patients from 2007 to 2014 in Russia. Genomic DNA was used for WGS and obtained data allowed identifying major mutations known to be associated with drug resistance to first-line and second-line antituberculous drugs. In some cases previously described mutations were not identified. Using genome-based phylogenetic analysis we identified M. tuberculosis substrains associated with distinctions in the occurrence in PTB vs. XPTB cases. Phylogenetic analyses did reveal M. tuberculosis genetic substrains associated with TB localization. XPTB was associated with Beijing sublineages Central Asia (Beijing CAO), Central Asia Clade A (Beijing A) and 4.8 groups, while PTB localization was associated with group LAM (4.3). Further, the XPTB strain in some cases showed elevated drug resistance patterns relative to PTB isolates. HIV was significantly associated with the development of XPTB in the Beijing B0/W148 group and among unclustered Beijing isolates.

scholarly journals The whole-genome sequencing in predicting Mycobacterium tuberculosis drug susceptibility and resistance in Papua, Indonesia

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yustinus Maladan ◽  
Hana Krismawati ◽  
Tri Wahyuni ◽  
Ratna Tanjung ◽  
Kamla Awaludin ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Mycobacterium Tuberculosis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genome Mapping ◽  
Clinical Sample ◽  
Drug Susceptibility ◽  
Whole Genome ◽  
Tb Treatment ◽  
Drug Resistance Profile

Abstract Background Tuberculosis is one of the deadliest disease caused by Mycobacterium tuberculosis. Its treatment still becomes a burden for many countries including Indonesia. Drug resistance is one of the problems in TB treatment. However, a development in the molecular field through Whole-genome sequencing (WGS) can be used as a solution in detecting mutations associated with TB- drugs. This investigation intended to implement this data for supporting the scientific community in deeply understanding any TB epidemiology and evolution in Papua along with detecting any mutations in genes associated with TB-Drugs. Result A whole-genome sequencing was performed on the random samples from TB Referral Laboratory in Papua utilizing MiSeq 600 cycle Reagent Kit (V3). Furthermore, TBProfiler was used for genome analysis, RAST Server was employed for annotation, while Gview server was applied for BLAST genome mapping and a Microscope server was implemented for Regions of Genomic Plasticity (RGP). The largest genome of M. tuberculosis obtained was at the size of 4,396,040 bp with subsystems number at 309 and the number of coding sequences at 4326. One sample (TB751) contained one RGP. The drug resistance analysis revealed that several mutations associated with TB-drug resistance existed. In details, mutations of rpoB gene which were identified as S450L, D435Y, H445Y, L430P, and Q432K had caused the reduced effectiveness of rifampicin; while the mutases in katG (S315T), kasA (312S), inhA (I21V), and Rv1482c-fabG1 (C-15 T) genes had contributed to the resistance in isoniazid. In streptomycin, the resistance was triggered by the mutations in rpsL (K43R) and rrs (A514C, A514T) genes, and, in Amikacin, its resistance was led by mutations in rrs (A514C) gene. Additionally, in Ethambutol and Pyrazinamide, their reduced effectiveness was provoked by embB gene mutases (M306L, M306V, D1024N) and pncA (W119R). Conclusions The results from whole-genome sequencing of TB clinical sample in Papua, Indonesia could contribute to the surveillance of TB-drug resistance. In the drug resistance profile, there were 15 Multi Drugs Resistance (MDR) samples. However, Extensively Drug-resistant (XDR) samples have not been found, but samples were resistant to only Amikacin, a second-line drug.

scholarly journals Lack of Correlation between embB Mutation and Ethambutol MIC in Mycobacterium tuberculosis Clinical Isolates from China

2007 ◽  
Vol 51 (12) ◽  
pp. 4515-4517 ◽  
Author(s):  
Ruiru Shi ◽  
Jianyuan Zhang ◽  
Koji Otomo ◽  
Guolong Zhang ◽  
Isamu Sugawara
Keyword(s):  
Drug Resistance ◽  
Mycobacterium Tuberculosis ◽  
Susceptibility Testing ◽  
Multiple Drug Resistance ◽  
Drug Susceptibility ◽  
Drug Susceptibility Testing ◽  
Clinical Isolates ◽  
Multiple Drug

ABSTRACT Seventy-four Mycobacterium tuberculosis clinical isolates from China were subjected to drug susceptibility testing using ethambutol, isoniazid, rifampin, and ofloxacin. The results revealed that the presence of embB mutations did not correlate with ethambutol resistance but was associated with multiple-drug resistance, especially resistance to both ethambutol and rifampin.

scholarly journals Whole-genome sequence analysis and comparisons between drug-resistance mutations and minimum inhibitory concentrations of Mycobacterium tuberculosis isolates causing M/XDR-TB

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0244829
Author(s):  
Ditthawat Nonghanphithak ◽  
Orawee Kaewprasert ◽  
Pratchakan Chaiyachat ◽  
Wipa Reechaipichitkul ◽  
Angkana Chaiprasert ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Mycobacterium Tuberculosis ◽  
Drug Susceptibility ◽  
Multidrug Resistant ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Drug Resistant ◽  
Resistance Mutations ◽  
Tb 34 ◽  
Susceptibility Tests

Drug resistance (DR) remains a major challenge for tuberculosis (TB) control. Whole-genome sequencing (WGS) provides the highest genetic resolution for genotypic drug-susceptibility tests (DST). We compared DST profiles of 60 Mycobacterium tuberculosis isolates which were drug resistant according to agar proportion tests (one poly DR-TB, 34 multidrug-resistant TB and 25 extensively drug-resistant TB). We additionally performed minimum inhibitory concentration (MIC) tests using Sensititre MYCOTBI plates (MYCOTB) and a WGS-based DST. Agreement between WGS-based DST and MYCOTB was high for all drugs except ethambutol (65%) and ethionamide (62%). Isolates harboring the -15 c/t inhA promoter mutation had a significantly lower MIC for isoniazid than did isolates with the katG Ser315Thr mutation (p < 0.001). Similar patterns were seen for ethambutol (embB Gly406Asp vs. embB Met306Ile), streptomycin (gid Gly73Ala vs. rpsL Lys43Arg), moxifloxacin (gyrA Ala90Val vs. gyrA Asp94Gly) and rifabutin (rpoB Asp435Phe/Tyr/Val vs. rpoB Ser450Leu). For genotypic heteroresistance, isolates with lower proportion of mapped read tended to has lower MIC of anti-TB drugs than those with higher proportion. These results emphasize the high applicability of WGS for determination of DR-TB and the association of particular mutations with MIC levels.

scholarly journals Drug-sensitivity test and analysis of drug-resistant mutations in Mycobacterium tuberculosis isolates from Kashgar, China

2021 ◽  
Vol 19 ◽  
pp. 205873922110414
Author(s):  
Zhongchen Ma ◽  
Tianhao Sun ◽  
Xinyu Bai ◽  
Xiang Ji ◽  
Qian Zhang ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Mycobacterium Tuberculosis ◽  
Dna Sequencing ◽  
High Sensitivity ◽  
Drug Susceptibility ◽  
Resistance Rate ◽  
Clinical Isolates ◽  
Multi Drug Resistance ◽  
Drug Resistant ◽  
Resistance Rates

Introduction In recent years, drug-resistant Mycobacterium tuberculosis strains have gradually become widespread. Most drug resistance is related to specific mutations. We investigated M. tuberculosis drug resistance in the Kashgar area, China. Methods The drug-susceptibility test was conducted to clinical isolates of M. tuberculosis. Genomic-sequencing technology was used for the drug-resistant strains and the significance of DNA sequencing as a rapid aid for drug-resistance detection and the diagnosis method was evaluated. Results The resistance rates of clinical isolates to rifampicin (RFP), isoniazid (INH), streptomycin (SM), ethambutol (EMB), and ofloxacin (OFX) were, respectively, 4.4%, 12.3%, 8.8%, 2.6%, and 3.5%. The single- and multi-drug resistance rates were, respectively, 80.0% and 20.0%. The resistance genes RopB, katG, InhA, RpsL, rrs, gyrA, and embB displayed codon mutations, while InhA was mutated in its promoter region. Kappa scores, evaluating the consistency between DNA sequencing and the resistance ratio methods for the detection of isolates’ resistance to RFP, INH, SM, OFX, and EMB, were 1, 0.955, 0.721, 0.796, and 1, respectively. Conclusion The resistance rate of INH and SM is relatively high in the Kashgar area. Detection of mutations in RopB, katG, InhA, RpsL, rrs, gyrA, and embB by DNA sequencing can predict drug resistance of M. tuberculosis strains with high sensitivity and specificity, and can be used for diagnosis.

scholarly journals Whole genome sequence data of Mycobacterium tuberculosis XDR strain, isolated from patient in Kazakhstan

Data in Brief ◽  
2020 ◽  
Vol 33 ◽  
pp. 106416
Author(s):  
Asset Daniyarov ◽  
Askhat Molkenov ◽  
Saule Rakhimova ◽  
Ainur Akhmetova ◽  
Zhannur Nurkina ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Genome Sequence ◽  
Sequence Data ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Sequence Data

scholarly journals Comparison of the Performances of Two In-House Rapid Methods for Antitubercular Drug Susceptibility Testing

2008 ◽  
Vol 53 (2) ◽  
pp. 808-810 ◽  
Author(s):  
Agustina I. de la Iglesia ◽  
Emma J. Stella ◽  
Héctor R. Morbidoni
Keyword(s):  
Drug Resistance ◽  
Mycobacterium Tuberculosis ◽  
Sensitivity And Specificity ◽  
Susceptibility Testing ◽  
Drug Susceptibility ◽  
Drug Susceptibility Testing ◽  
Antitubercular Drug ◽  
Rapid Methods ◽  
Resistance Assessment

ABSTRACT Resistance to rifampin (rifampicin), isoniazid, and streptomycin of 69 Mycobacterium tuberculosis isolates was analyzed by an in-house method based on mycobacteriophage D29 and a colorimetric micromethod. Both methods showed sensitivity and specificity values ranging from 93% to 100%. These simple methods offer an option for drug resistance assessment of M. tuberculosis.

scholarly journals Diversified lineages and drug-resistance profiles of clinical isolates of Mycobacterium tuberculosis complex in Malaysia

2019 ◽  
Vol 8 (4) ◽  
pp. 320
Author(s):  
MohdSalleh Zaki ◽  
MohdNur Noorizhab Fakhruzzaman ◽  
NorzulianaZainal Abidin ◽  
ZirwatulAdilah Aziz ◽  
WaiFeng Lim ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Mycobacterium Tuberculosis ◽  
Mycobacterium Tuberculosis Complex ◽  
Clinical Isolates ◽  
Tuberculosis Complex

scholarly journals Genetic Identification and Drug-Resistance Characterization of Mycobacterium tuberculosis Using a Portable Sequencing Device. A Pilot Study

Antibiotics ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 548 ◽  
Author(s):  
Jorge Cervantes ◽  
Noemí Yokobori ◽  
Bo-Young Hong
Keyword(s):  
Drug Resistance ◽  
Mycobacterium Tuberculosis ◽  
Drug Susceptibility ◽  
Drug Susceptibility Testing ◽  
Genetic Identification ◽  
Sequencing Analysis ◽  
Antimicrobial Resistance Genes ◽  
Long Read ◽  
Drug Resistance Prediction ◽  
Almost All

Clinical management of tuberculosis (TB) in endemic areas is often challenged by a lack of resources including laboratories for Mycobacterium tuberculosis (Mtb) culture. Traditional phenotypic drug susceptibility testing for Mtb is costly and time consuming, while PCR-based methods are limited to selected target loci. We herein utilized a portable, USB-powered, long-read sequencing instrument (MinION), to investigate Mtb genomic DNA from clinical isolates to determine the presence of anti-TB drug-resistance conferring mutations. Data analysis platform EPI2ME and antibiotic-resistance analysis using the real time ARMA workflow, identified Mtb species as well as extensive resistance gene profiles. The approach was highly sensitive, being able to detect almost all described drug resistance conferring mutations based on previous whole genome sequencing analysis. Our findings are supportive of the practical use of this system as a suitable method for the detection of antimicrobial resistance genes, and effective in providing Mtb genomic information. Future improvements in the error rate through statistical analysis, drug resistance prediction algorithms and reference databases would make this a platform suited for the clinical setting. The small size, relatively inexpensive cost of the device, as well as its rapid and simple library preparation protocol and analysis, make it an attractive option for settings with limited laboratory infrastructure.

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