Single nucleotide polymorphisms in Mycobacterium tuberculosis and the need for a curated database

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.

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Geographical Differences Associated with Single-Nucleotide Polymorphisms (SNPs) in Nine Gene Targets among Resistant Clinical Isolates of Mycobacterium tuberculosis

Journal of Clinical Microbiology ◽

10.1128/jcm.00857-13 ◽

2013 ◽

Vol 52 (5) ◽

pp. 1322-1329 ◽

Cited By ~ 16

Author(s):

M. Hoshide ◽

L. Qian ◽

C. Rodrigues ◽

R. Warren ◽

T. Victor ◽

...

Keyword(s):

Mycobacterium Tuberculosis ◽

Single Nucleotide Polymorphisms ◽

Clinical Isolates ◽

Nucleotide Polymorphisms ◽

Geographical Differences ◽

Single Nucleotide

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

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.47.4.1241-1250.2003 ◽

2003 ◽

Vol 47 (4) ◽

pp. 1241-1250 ◽

Cited By ~ 202

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.

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

PLoS ONE ◽

10.1371/journal.pone.0138253 ◽

2015 ◽

Vol 10 (9) ◽

pp. e0138253 ◽

Cited By ~ 18

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

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

International Journal of Drug Delivery Technology ◽

10.25258/ijddt.10.1.21 ◽

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.

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Whole-genome sequencing and single nucleotide polymorphisms in multidrug-resistant clinical isolates of Mycobacterium tuberculosis from the Philippines

Journal of Global Antimicrobial Resistance ◽

10.1016/j.jgar.2018.08.009 ◽

2018 ◽

Vol 15 ◽

pp. 239-245 ◽

Cited By ~ 5

Author(s):

Marylette B. Roa ◽

Francis A. Tablizo ◽

El King D. Morado ◽

Lovette F. Cunanan ◽

Iris Diana C. Uy ◽

...

Keyword(s):

Mycobacterium Tuberculosis ◽

Single Nucleotide Polymorphisms ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Multidrug Resistant ◽

The Philippines ◽

Clinical Isolates ◽

Whole Genome ◽

Nucleotide Polymorphisms ◽

Single Nucleotide

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Single nucleotide polymorphisms in cell wall biosynthesis-associated genes and phylogeny of Mycobacterium tuberculosis lineages

Infection Genetics and Evolution ◽

10.1016/j.meegid.2010.03.003 ◽

2010 ◽

Vol 10 (4) ◽

pp. 459-466 ◽

Cited By ~ 8

Author(s):

Pei-Chun Chuang ◽

Yi-Ming A. Chen ◽

Huang-Yau Chen ◽

Ruwen Jou

Keyword(s):

Cell Wall ◽

Mycobacterium Tuberculosis ◽

Single Nucleotide Polymorphisms ◽

Cell Wall Biosynthesis ◽

Nucleotide Polymorphisms ◽

Single Nucleotide

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Genome-Wide Analysis of Synonymous Single Nucleotide Polymorphisms in Mycobacterium tuberculosis Complex Organisms: Resolution of Genetic Relationships Among Closely Related Microbial Strains

Genetics ◽

10.1093/genetics/162.4.1533 ◽

2002 ◽

Vol 162 (4) ◽

pp. 1533-1543

Author(s):

Michaela M Gutacker ◽

James C Smoot ◽

Cristi A Lux Migliaccio ◽

Stacy M Ricklefs ◽

Su Hua ◽

...

Keyword(s):

Mycobacterium Tuberculosis ◽

Single Nucleotide Polymorphisms ◽

Allelic Variation ◽

Genetic Relationships ◽

The United States ◽

Sensu Stricto ◽

Phylogenetic Position ◽

Nucleotide Polymorphisms ◽

Tuberculosis Complex ◽

Single Nucleotide

Abstract Several human pathogens (e.g., Bacillus anthracis, Yersinia pestis, Bordetella pertussis, Plasmodium falciparum, and Mycobacterium tuberculosis) have very restricted unselected allelic variation in structural genes, which hinders study of the genetic relationships among strains and strain-trait correlations. To address this problem in a representative pathogen, 432 M. tuberculosis complex strains from global sources were genotyped on the basis of 230 synonymous (silent) single nucleotide polymorphisms (sSNPs) identified by comparison of four genome sequences. Eight major clusters of related genotypes were identified in M. tuberculosis sensu stricto, including a single cluster representing organisms responsible for several large outbreaks in the United States and Asia. All M. tuberculosis sensu stricto isolates of previously unknown phylogenetic position could be rapidly and unambiguously assigned to one of the eight major clusters, thus providing a facile strategy for identifying organisms that are clonally related by descent. Common clones of M. tuberculosis sensu stricto and M. bovis are distinct, deeply branching genotypic complexes whose extant members did not emerge directly from one another in the recent past. sSNP genotyping rapidly delineates relationships among closely related strains of pathogenic microbes and allows construction of genetic frameworks for examining the distribution of biomedically relevant traits such as virulence, transmissibility, and host range.

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