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A Single-Step Sequencing Method for the Identification of Mycobacterium tuberculosis Complex Species

BACKGROUND: The Mycobacterium tuberculosis complex (MTC) comprises closely related species responsible for strictly human and zoonotic tuberculosis. Accurate species determination is useful for the identification of outbreaks and epidemiological links. Mycobacterium africanum and Mycobacterium canet...

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Autores principales: Djelouadji, Zoheira, Raoult, Didier, Daffé, Mamadou, Drancourt, Michel
Formato: Texto
Lenguaje:English
Publicado: Public Library of Science 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2453075/
https://www.ncbi.nlm.nih.gov/pubmed/18618024
http://dx.doi.org/10.1371/journal.pntd.0000253
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author Djelouadji, Zoheira
Raoult, Didier
Daffé, Mamadou
Drancourt, Michel
author_facet Djelouadji, Zoheira
Raoult, Didier
Daffé, Mamadou
Drancourt, Michel
author_sort Djelouadji, Zoheira
collection PubMed
description BACKGROUND: The Mycobacterium tuberculosis complex (MTC) comprises closely related species responsible for strictly human and zoonotic tuberculosis. Accurate species determination is useful for the identification of outbreaks and epidemiological links. Mycobacterium africanum and Mycobacterium canettii are typically restricted to Africa and M. bovis is a re-emerging pathogen. Identification of these species is difficult and expensive. METHODOLOGY/PRINCIPAL FINDINGS: The Exact Tandem Repeat D (ETR-D; alias Mycobacterial Interspersed Repetitive Unit 4) was sequenced in MTC species type strains and 110 clinical isolates, in parallel to reference polyphasic identification based on phenotype profiling and sequencing of pncA, oxyR, hsp65, gyrB genes and the major polymorphism tandem repeat. Inclusion of M. tuberculosis isolates in the expanding, antibiotic-resistant Beijing clone was determined by Rv0927c gene sequencing. The ETR-D (780-bp) sequence unambiguously identified MTC species type strain except M. pinnipedii and M. microti thanks to six single nucleotide polymorphisms, variable numbers (1–7 copies) of the tandem repeat and two deletions/insertions. The ETR-D sequencing agreed with phenotypic identification in 107/110 clinical isolates and with reference polyphasic molecular identification in all isolates, comprising 98 M. tuberculosis, 5 M. bovis BCG type, 5 M. canettii, and 2 M. africanum. For M. tuberculosis isolates, the ETR-D sequence was not significantly associated with the Beijing clone. CONCLUSIONS/SIGNIFICANCE: ETR-D sequencing allowed accurate, single-step identification of the MTC at the species level. It circumvented the current expensive, time-consuming polyphasic approach. It could be used to depict epidemiology of zoonotic and human tuberculosis, especially in African countries where several MTC species are emerging.
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spelling pubmed-24530752008-07-11 A Single-Step Sequencing Method for the Identification of Mycobacterium tuberculosis Complex Species Djelouadji, Zoheira Raoult, Didier Daffé, Mamadou Drancourt, Michel PLoS Negl Trop Dis Research Article BACKGROUND: The Mycobacterium tuberculosis complex (MTC) comprises closely related species responsible for strictly human and zoonotic tuberculosis. Accurate species determination is useful for the identification of outbreaks and epidemiological links. Mycobacterium africanum and Mycobacterium canettii are typically restricted to Africa and M. bovis is a re-emerging pathogen. Identification of these species is difficult and expensive. METHODOLOGY/PRINCIPAL FINDINGS: The Exact Tandem Repeat D (ETR-D; alias Mycobacterial Interspersed Repetitive Unit 4) was sequenced in MTC species type strains and 110 clinical isolates, in parallel to reference polyphasic identification based on phenotype profiling and sequencing of pncA, oxyR, hsp65, gyrB genes and the major polymorphism tandem repeat. Inclusion of M. tuberculosis isolates in the expanding, antibiotic-resistant Beijing clone was determined by Rv0927c gene sequencing. The ETR-D (780-bp) sequence unambiguously identified MTC species type strain except M. pinnipedii and M. microti thanks to six single nucleotide polymorphisms, variable numbers (1–7 copies) of the tandem repeat and two deletions/insertions. The ETR-D sequencing agreed with phenotypic identification in 107/110 clinical isolates and with reference polyphasic molecular identification in all isolates, comprising 98 M. tuberculosis, 5 M. bovis BCG type, 5 M. canettii, and 2 M. africanum. For M. tuberculosis isolates, the ETR-D sequence was not significantly associated with the Beijing clone. CONCLUSIONS/SIGNIFICANCE: ETR-D sequencing allowed accurate, single-step identification of the MTC at the species level. It circumvented the current expensive, time-consuming polyphasic approach. It could be used to depict epidemiology of zoonotic and human tuberculosis, especially in African countries where several MTC species are emerging. Public Library of Science 2008-06-18 /pmc/articles/PMC2453075/ /pubmed/18618024 http://dx.doi.org/10.1371/journal.pntd.0000253 Text en Djelouadji et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Djelouadji, Zoheira
Raoult, Didier
Daffé, Mamadou
Drancourt, Michel
A Single-Step Sequencing Method for the Identification of Mycobacterium tuberculosis Complex Species
title A Single-Step Sequencing Method for the Identification of Mycobacterium tuberculosis Complex Species
title_full A Single-Step Sequencing Method for the Identification of Mycobacterium tuberculosis Complex Species
title_fullStr A Single-Step Sequencing Method for the Identification of Mycobacterium tuberculosis Complex Species
title_full_unstemmed A Single-Step Sequencing Method for the Identification of Mycobacterium tuberculosis Complex Species
title_short A Single-Step Sequencing Method for the Identification of Mycobacterium tuberculosis Complex Species
title_sort single-step sequencing method for the identification of mycobacterium tuberculosis complex species
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2453075/
https://www.ncbi.nlm.nih.gov/pubmed/18618024
http://dx.doi.org/10.1371/journal.pntd.0000253
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