scholarly journals Detection of Single Nucleotide Polymorphisms (SNPs) for Genes Cause Drug-Resistant in Iraqi Mycobacterium Tuberculosis isolates by new Pyrophosphate Technique.

2020 ◽  
Vol 10 (01) ◽  
pp. 145-149
Author(s):  
Hassan Kadhim Nemir ◽  
Ismail Aziz ◽  
Alaa Kareem Mohammed
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Single Nucleotide Polymorphisms ◽  
Firefly Luciferase ◽  
Negative Control ◽  
Drug Resistant ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Taq Polymerase ◽  
Base Extension ◽  
Dna Template

In this search, a new pyrophosphate technique was proved. The technique was employed to single- nucleotide polymorphisms (SNPs), which diagnosis using a one-base extension reaction. Three Mycobacterium tuberculosis genes were chosen (Rpob, InhA, KatG) genes. Fifty-four specimens were used in this study fifty-three proved as drug-resistant specimens by The Iraqi Institute of Chest and Respiratory Diseases in Baghdad.; also one specimen was used as a negative control. The steps of this technique were by used a specific primer within each aliquot that has a short 3-OH end of the base of the target gene that was hybridized to the single-stranded DNA template. Then, the Taq polymerase enzyme and one of either α-thio-dATP, dTTP, dGTP, or dCTP were supplemented and incubated for 1 min. ATP is synthesis by convert Pyrophosphate freed by DNA polymerase using pyruvate phosphate dikinase (PPDK), and the amount of ATP estimates by the firefly luciferase reaction. This technique, which does not demand expensive equipment, can be applied to rapidly monitor a one-point mutation in the gene that causes drug-resistant in mycobacterium tuberculosis. The results showed a high variation in values of ATP formation through matching and mismatch bases added. So, this assay (which required only five minutes), enable to find the gene SNP causes resistant for the specific drug.

scholarly journals Using Mycobacterium tuberculosis Single-Nucleotide Polymorphisms To Predict Fluoroquinolone Treatment Response

2019 ◽  
Vol 63 (7) ◽  
Author(s):  
Marva Seifert ◽  
Edmund Capparelli ◽  
Donald G. Catanzaro ◽  
Timothy C. Rodwell
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Single Nucleotide Polymorphisms ◽  
Specific Resistance ◽  
Therapeutic Targets ◽  
World Health ◽  
Population Pharmacokinetic ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Content Type ◽  
Level Increase

ABSTRACT Clinical phenotypic fluoroquinolone susceptibility testing of Mycobacterium tuberculosis is currently based on M. tuberculosis growth at a single critical concentration, which provides limited information for a nuanced clinical response. We propose using specific resistance-conferring M. tuberculosis mutations in gyrA together with population pharmacokinetic and pharmacodynamic modeling as a novel tool to better inform fluoroquinolone treatment decisions. We sequenced the gyrA resistance-determining region of 138 clinical M. tuberculosis isolates collected from India, Moldova, Philippines, and South Africa and then determined each strain’s MIC against ofloxacin, moxifloxacin, levofloxacin, and gatifloxacin. Strains with specific gyrA single-nucleotide polymorphisms (SNPs) were grouped into high or low drug-specific resistance categories based on their empirically measured MICs. Published population pharmacokinetic models were then used to explore the pharmacokinetics and pharmacodynamics of each fluoroquinolone relative to the empirical MIC distribution for each resistance category to make predictions about the likelihood of patients achieving defined therapeutic targets. In patients infected with M. tuberculosis isolates containing SNPs associated with a fluoroquinolone-specific low-level increase in MIC, models suggest increased fluoroquinolone dosing improved the probability of achieving therapeutic targets for gatifloxacin and moxifloxacin but not for levofloxacin and ofloxacin. In contrast, among patients with isolates harboring SNPs associated with a high-level increase in MIC, increased dosing of levofloxacin, moxifloxacin, gatifloxacin, or ofloxacin did not meaningfully improve the probability of therapeutic target attainment. We demonstrated that quantifiable fluoroquinolone drug resistance phenotypes could be predicted from rapidly detectable gyrA SNPs and used to support dosing decisions based on the likelihood of patients reaching therapeutic targets. Our findings provide further supporting evidence for the moxifloxacin clinical breakpoint recently established by the World Health Organization.

scholarly journals Single Nucleotide Polymorphisms in Genes Associated with Isoniazid Resistance in Mycobacterium tuberculosis

2003 ◽  
Vol 47 (4) ◽  
pp. 1241-1250 ◽  
Author(s):  
Srinivas V. Ramaswamy ◽  
Robert Reich ◽  
Shu-Jun Dou ◽  
Linda Jasperse ◽  
Xi Pan ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Single Nucleotide Polymorphisms ◽  
Molecular Genetic ◽  
Mycolic Acid ◽  
Genetic Group ◽  
Clinical Isolates ◽  
Central Component ◽  
Polymorphism Analysis ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide

ABSTRACT Isoniazid (INH) is a central component of drug regimens used worldwide to treat tuberculosis. Previous studies have identified resistance-associated mutations in katG, inhA, kasA, ndh, and the oxyR-ahpC intergenic region. DNA microarray-based experiments have shown that INH induces several genes in Mycobacterium tuberculosis that encode proteins physiologically relevant to the drug's mode of action. To gain further insight into the molecular genetic basis of INH resistance, 20 genes implicated in INH resistance were sequenced for INH resistance-associated mutations. Thirty-eight INH-monoresistant clinical isolates and 86 INH-susceptible isolates of M. tuberculosis were obtained from the Texas Department of Health and the Houston Tuberculosis Initiative. Epidemiologic independence was established for all isolates by IS6110 restriction fragment length polymorphism analysis. Susceptible isolates were matched with resistant isolates by molecular genetic group and IS6110 profiles. Spoligotyping was done with isolates with five or fewer IS6110 copies. A major genetic group was established on the basis of the polymorphisms in katG codon 463 and gyrA codon 95. MICs were determined by the E-test. Semiquantitative catalase assays were performed with isolates with mutations in the katG gene. When the 20 genes were sequenced, it was found that 17 (44.7%) INH-resistant isolates had a single-locus, resistance-associated mutation in the katG, mabA, or Rv1772 gene. Seventeen (44.7%) INH-resistant isolates had resistance-associated mutations in two or more genes, and 76% of all INH-resistant isolates had a mutation in the katG gene. Mutations were also identified in the fadE24, Rv1592c, Rv1772, Rv0340, and iniBAC genes, recently shown by DNA-based microarray experiments to be upregulated in response to INH. In general, the MICs were higher for isolates with mutations in katG and the isolates had reduced catalase activities. The results show that a variety of single nucleotide polymorphisms in multiple genes are found exclusively in INH-resistant clinical isolates. These genes either are involved in mycolic acid biosynthesis or are overexpressed as a response to the buildup or cellular toxicity of INH.

Single-Base Extension and ELISA-Based Approach for Single-Nucleotide Polymorphisms Genotyping

2010 ◽  
Vol 163 (5) ◽  
pp. 573-576 ◽  
Author(s):  
Guibo Liu ◽  
Yongxia Cheng ◽  
Wei Zhao ◽  
Zaishun Jin ◽  
Hongbo Shan ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Single Base Extension ◽  
Single Nucleotide ◽  
Single Base ◽  
Base Extension

scholarly journals Mycobacterium tuberculosis Is Resistant to Isoniazid at a Slow Growth Rate by Single Nucleotide Polymorphisms in katG Codon Ser315

PLoS ONE ◽  
2015 ◽  
Vol 10 (9) ◽  
pp. e0138253 ◽  
Author(s):  
Rose E. Jeeves ◽  
Alice A. N. Marriott ◽  
Steven T. Pullan ◽  
Kim A. Hatch ◽  
Jon C. Allnutt ◽  
...  
Keyword(s):  
Growth Rate ◽  
Mycobacterium Tuberculosis ◽  
Single Nucleotide Polymorphisms ◽  
Slow Growth ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Slow Growth Rate

scholarly journals IDENTIFICATION OF SINGLE NUCLEOTIDE POLYMORPHISMS ON CATTLE BREEDS IN INDONESIA USING BOVINE 50K

2016 ◽  
Vol 16 (2) ◽  
pp. 59
Author(s):  
Puji Lestari ◽  
Habib Rijzaani ◽  
Dani Satyawan ◽  
Anneke Anggraeni ◽  
Dwinita Wikan Utami ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Beef Cattle ◽  
Dairy Cattle ◽  
Genetic Relatedness ◽  
Bovine Genome ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Snp Chip ◽  
Cattle Breeds ◽  
Base Extension

<p>Single nucleotide polymorphisms (SNPs) abundant in bovine genome influence genetic variation in biological mechanism. The study aimed to identify SNPs on Indonesian cattle breeds and analyze their genetic diversity using Bovine 50K SNP chip. Twenty eight "Ongole Grade" (OG) beef cattle and 20 "Holstein Friesian" (HF) dairy cattle were used for the Infinium II assay test. This assay included amplification of genomic DNA, fragmenta-tion, precipitation, resuspension, hybridization, processing bead chip for single-base extension, and imaging at iScan. Data and clusters were analyzed using GenomeStudio software. The Bovine 50K SNP chip containing 54,609 SNPs was observed spanning all chromosomes of bovine genome. Genotyping for the total SNPs was successfull based on Call Rate, GeneCall and GeneTrain scores. Most SNP markers had alleles that shared among the individuals or breeds, or had specific alleles at distinctive frequencies. Minor allele frequency (MAF) spreads equally with intervals of 0-0.5. The breeds of OG and HF tended to be separated in different clusters without considering their genetic history and twin or normal. This result suggests that most individuals are closely related to one another, regardless of the same breed. Some genes identified on chromosomes 3, 4, 5, 7, 13, 17 and 18 were located in the loci/regions that contained SNPs with specific alleles of either HF or OG breed. These SNPs were more powerful for differentiation of beef cattle and dairy cattle than among individuals in the same breed. These SNP variations and genetic relatedness among individuals and breeds serve basic information for cattle breeding in Indonesia.</p>

Sign in / Sign up

Export Citation Format

Share Document