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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ftdoajarticles:oai:doaj.org/article:ae72eb02c9f5411e8cfa6876fec2d471 2023-05-15T15:13:29+02:00 A single-step sequencing method for the identification of Mycobacterium tuberculosis complex species. Zoheira Djelouadji Didier Raoult Mamadou Daffé Michel Drancourt 2008-01-01T00:00:00Z https://doi.org/10.1371/journal.pntd.0000253 https://doaj.org/article/ae72eb02c9f5411e8cfa6876fec2d471 EN eng Public Library of Science (PLoS) http://europepmc.org/articles/PMC2453075?pdf=render https://doaj.org/toc/1935-2735 1935-2735 doi:10.1371/journal.pntd.0000253 https://doaj.org/article/ae72eb02c9f5411e8cfa6876fec2d471 PLoS Neglected Tropical Diseases, Vol 2, Iss 6, p e253 (2008) Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 article 2008 ftdoajarticles https://doi.org/10.1371/journal.pntd.0000253 2022-12-31T04:12:34Z 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. Article in Journal/Newspaper Arctic Directory of Open Access Journals: DOAJ Articles Arctic PLoS Neglected Tropical Diseases 2 6 e253 |
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Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
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ftdoajarticles |
language |
English |
topic |
Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 |
spellingShingle |
Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 Zoheira Djelouadji Didier Raoult Mamadou Daffé Michel Drancourt A single-step sequencing method for the identification of Mycobacterium tuberculosis complex species. |
topic_facet |
Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 |
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. |
format |
Article in Journal/Newspaper |
author |
Zoheira Djelouadji Didier Raoult Mamadou Daffé Michel Drancourt |
author_facet |
Zoheira Djelouadji Didier Raoult Mamadou Daffé Michel Drancourt |
author_sort |
Zoheira Djelouadji |
title |
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_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_sort |
single-step sequencing method for the identification of mycobacterium tuberculosis complex species. |
publisher |
Public Library of Science (PLoS) |
publishDate |
2008 |
url |
https://doi.org/10.1371/journal.pntd.0000253 https://doaj.org/article/ae72eb02c9f5411e8cfa6876fec2d471 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic |
genre_facet |
Arctic |
op_source |
PLoS Neglected Tropical Diseases, Vol 2, Iss 6, p e253 (2008) |
op_relation |
http://europepmc.org/articles/PMC2453075?pdf=render https://doaj.org/toc/1935-2735 1935-2735 doi:10.1371/journal.pntd.0000253 https://doaj.org/article/ae72eb02c9f5411e8cfa6876fec2d471 |
op_doi |
https://doi.org/10.1371/journal.pntd.0000253 |
container_title |
PLoS Neglected Tropical Diseases |
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2 |
container_issue |
6 |
container_start_page |
e253 |
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1766344035856809984 |