Global Phylogeny of
            <i>Mycobacterium tuberculosis</i>
            Based on Single Nucleotide Polymorphism (SNP) Analysis: Insights into Tuberculosis Evolution, Phylogenetic Accuracy of Other DNA Fingerprinting Systems, and Recommendations for a Minimal Standard SNP Set

Filliol, Ingrid; Motiwala, Alifiya S.; Cavatore, Magali; Qi, Weihong; Hazbón, Manzour Hernando; Bobadilla-del-Valle, Miriam; Fyfe, Janet; García-García, Lourdes; Rastogi, Nalin; Sola, Christophe; Zozio, Thierry; Guerrero, Marta Inírida; León, Clara Inés; Crabtree, Jonathan; Angiuoli, Samuel V.; Eisenach, Kathleen D.; Durmaz, Rıza; Joloba, Moses; Rendón, Adrián; Sifuentes–Osornio, José; León, Alfredo Ponce de; Cave, M. Donald; Fleischmann, Robert; Whittam, Thomas S.; Alland, David

doi:10.1128/jb.188.8.3162-3163.2006

Cited by 51 publications

(78 citation statements)

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“…21,22 Consequently, since the accuracy of current molecular diagnostic tests to identify MDRTB are based on worldwide polymorphisms frequencies, performance indicators for these diagnostic approaches in a country-by-country basis may be controversial. For example, the S315T (katG) polymorphism shows a wide variation in their incidence: although it was detected in a 100% of resistant strains in countries such as Turkey, Canada, and France, [23][24][25] in our study we found a lower frequency of 41.9%, more similar to those obtained in another study in Brazil (60%) and in places such as Russia (77%), Syria (40%) or Taiwan (51%).…”

Section: Discussionmentioning

confidence: 99%

Detection of multidrug-resistant Mycobacterium tuberculosis strains isolated in Brazil using a multimarker genetic assay for katG and rpoB genes

Oliveira

Muniz-Sobrinho

Magno

et al. 2016

The Brazilian Journal of Infectious Diseases

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Multidrug-resistant tuberculosis (MDRTB) is a serious world health problem that limits public actions to control tuberculosis, because the most used anti-tuberculosis first-line drugs fail to stop mycobacterium spread. Consequently, a quick detection through molecular diagnosis is essential to reduce morbidity and medical costs. Despite the availability of several molecular-based commercial-kits to diagnose multidrug-resistant tuberculosis, their diagnostic value might diverge worldwide since Mycobacterium tuberculosis genetic variability differs according to geographic location. Here, we studied the predictive value of four common mycobacterial mutations in strains isolated from endemic areas of Brazil. Mutations were found at the frequency of 41.9% for katG, 25.6% for inhA, and 69.8% for rpoB genes in multidrug-resistant strains. Multimarker analysis revealed that combination of only two mutations ("katG/S315T+rpoB/S531L") was a better surrogate of multidrug-resistant tuberculosis than single-marker analysis (86% sensitivity vs. 62.8%). Prediction of multidrug-resistant tuberculosis was not improved by adding a third or fourth mutation in the model. Therefore, rather than using diagnostic kits detecting several mutations, we propose a simple dual-marker panel to detect multidrug-resistant tuberculosis, with 86% sensitivity and 100% specificity. In conclusion, this approach (previous genetic study+analysis of only prevalent markers) would considerably decrease the processing costs while retaining diagnostic accuracy.

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Section: Discussionmentioning

confidence: 99%

Detection of multidrug-resistant Mycobacterium tuberculosis strains isolated in Brazil using a multimarker genetic assay for katG and rpoB genes

Oliveira

Muniz-Sobrinho

Magno

et al. 2016

The Brazilian Journal of Infectious Diseases

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“…XDR (extensively drugresistant) strains are resistant to isoniazid and rifampicin plus one of the fluoriquinolones and at least one second-line injectable drug (capreomycin, kanamycin or amikacin). Even though it is still to be established whether MTB possess plasmids [70,71] and if there is a functional conjugational apparatus in MTB [72,73], up to now all drug-resistance determinants are thought to be chromosomally encoded and to be a result of spontaneous nucleoid mutations [74] or gene inactivation by a mobile genetic element [75]. Mutations are acquired mainly by deletions, insertions or single nucleotide alterations or SNPs (single nucleotide polymorphisms).…”

Section: Mycobacteria Chemotherapy and Evolutionmentioning

confidence: 99%

DNA repair systems and the pathogenesis of Mycobacterium tuberculosis: varying activities at different stages of infection

2010

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Mycobacteria, including most of all MTB (Mycobacterium tuberculosis), cause pathogenic infections in humans and, during the infectious process, are exposed to a range of environmental insults, including the host's immune response. From the moment MTB is exhaled by infected individuals, through an active and latent phase in the body of the new host, until the time they reach the reactivation stage, MTB is exposed to many types of DNA-damaging agents. Like all cellular organisms, MTB has efficient DNA repair systems, and these are believed to play essential roles in mycobacterial pathogenesis. As different stages of infection have great variation in the conditions in which mycobacteria reside, it is possible that different repair systems are essential for progression to specific phases of infection. MTB possesses homologues of DNA repair systems that are found widely in other species of bacteria, such as nucleotide excision repair, base excision repair and repair by homologous recombination. MTB also possesses a system for non-homologous end-joining of DNA breaks, which appears to be widespread in prokaryotes, although its presence is sporadic within different species within a genus. However, MTB does not possess homologues of the typical mismatch repair system that is found in most bacteria. Recent studies have demonstrated that DNA repair genes are expressed differentially at each stage of infection. In the present review, we focus on different DNA repair systems from mycobacteria and identify questions that remain in our understanding of how these systems have an impact upon the infection processes of these important pathogens.

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“…Such studies require examination of sequence variations (single nucleotide polymorphisms: SNPs) that differentiate between subspecies and strains of the MTB complex. Such SNPs are known (Baker et al, 2004;Filliol et al, 2006), but their use in studies of ancient TB requires that information also be available about the sequences containing these SNPs in the other bacteria whose DNA might be present in the bones under study. This is because these SNPs are present not in insertion elements or other sequences specific to the MTB complex, but in regular 'housekeeping' genes possessed by all related bacteria.…”

Section: Specificity Of Polymerase Chain Reaction (Pcr) Tests For M mentioning

confidence: 99%

Deficiencies and challenges in the study of ancient tuberculosis DNA

Wilbur

Bouwman

Stone

et al. 2009

Journal of Archaeological Science

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Global Phylogeny of Mycobacterium tuberculosis Based on Single Nucleotide Polymorphism (SNP) Analysis: Insights into Tuberculosis Evolution, Phylogenetic Accuracy of Other DNA Fingerprinting Systems, and Recommendations for a Minimal Standard SNP Set

Cited by 51 publications

References 0 publications

Detection of multidrug-resistant Mycobacterium tuberculosis strains isolated in Brazil using a multimarker genetic assay for katG and rpoB genes

Detection of multidrug-resistant Mycobacterium tuberculosis strains isolated in Brazil using a multimarker genetic assay for katG and rpoB genes

DNA repair systems and the pathogenesis of Mycobacterium tuberculosis: varying activities at different stages of infection

Deficiencies and challenges in the study of ancient tuberculosis DNA

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