Strain classification of Mycobacterium tuberculosis isolates in Brazil based on genotypes obtained by spoligotyping, mycobacterial interspersed repetitive unit typing and the presence of large sequence and single nucleotide polymorphism.

Rio de Janeiro is endemic for tuberculosis (TB) and presents the second largest prevalence of the disease in Brazil. Here, we present the bacterial population structure of 218 isolates of Mycobacterium tuberculosis, derived from 186 patients that were diagnosed between January 2008 and December 2009...

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Autores principales:	Sidra E G Vasconcellos, Chyntia Carolina Acosta, Lia Lima Gomes, Emilyn Costa Conceição, Karla Valéria Lima, Marcelo Ivens de Araujo, Maria de Lourdes Leite, Flávio Tannure, Paulo Cesar de Souza Caldas, Harrison M Gomes, Adalberto Rezende Santos, Michel K Gomgnimbou, Christophe Sola, David Couvin, Nalin Rastogi, Neio Boechat, Philip Noel Suffys
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/e02453ea135745d4ab916b4a8302c025
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spelling	oai:doaj.org-article:e02453ea135745d4ab916b4a8302c0252021-11-25T05:56:40ZStrain classification of Mycobacterium tuberculosis isolates in Brazil based on genotypes obtained by spoligotyping, mycobacterial interspersed repetitive unit typing and the presence of large sequence and single nucleotide polymorphism.1932-620310.1371/journal.pone.0107747https://doaj.org/article/e02453ea135745d4ab916b4a8302c0252014-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0107747https://doaj.org/toc/1932-6203Rio de Janeiro is endemic for tuberculosis (TB) and presents the second largest prevalence of the disease in Brazil. Here, we present the bacterial population structure of 218 isolates of Mycobacterium tuberculosis, derived from 186 patients that were diagnosed between January 2008 and December 2009. Genotypes were generated by means of spoligotyping, 24 MIRU-VNTR typing and presence of fbpC103, RDRio and RD174. The results confirmed earlier data that predominant genotypes in Rio de Janeiro are those of the Euro American Lineages (99%). However, we observed differences between the classification by spoligotyping when comparing to that of 24 MIRU-VNTR typing, being respectively 43.6% vs. 62.4% of LAM, 34.9% vs. 9.6% of T and 18.3% vs. 21.5% of Haarlem. Among isolates classified as LAM by MIRU typing, 28.0% did not present the characteristic spoligotype profile with absence of spacers 21 to 24 and 32 to 36 and we designated these conveniently as "LAM-like", 79.3% of these presenting the LAM-specific SNP fbpC103. The frequency of RDRio and RD174 in the LAM strains, as defined both by spoligotyping and 24 MIRU-VNTR loci, were respectively 11% and 15.4%, demonstrating that RD174 is not always a marker for LAM/RDRio strains. We conclude that, although spoligotyping alone is a tool for classification of strains of the Euro-American lineage, when combined with MIRU-VNTRs, SNPs and RD typing, it leads to a much better understanding of the bacterial population structure and phylogenetic relationships among strains of M. tuberculosis in regions with high incidence of TB.Sidra E G VasconcellosChyntia Carolina AcostaLia Lima GomesEmilyn Costa ConceiçãoKarla Valéria LimaMarcelo Ivens de AraujoMaria de Lourdes LeiteFlávio TannurePaulo Cesar de Souza CaldasHarrison M GomesAdalberto Rezende SantosMichel K GomgnimbouChristophe SolaDavid CouvinNalin RastogiNeio BoechatPhilip Noel SuffysPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 10, p e107747 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Sidra E G Vasconcellos Chyntia Carolina Acosta Lia Lima Gomes Emilyn Costa Conceição Karla Valéria Lima Marcelo Ivens de Araujo Maria de Lourdes Leite Flávio Tannure Paulo Cesar de Souza Caldas Harrison M Gomes Adalberto Rezende Santos Michel K Gomgnimbou Christophe Sola David Couvin Nalin Rastogi Neio Boechat Philip Noel Suffys Strain classification of Mycobacterium tuberculosis isolates in Brazil based on genotypes obtained by spoligotyping, mycobacterial interspersed repetitive unit typing and the presence of large sequence and single nucleotide polymorphism.
description	Rio de Janeiro is endemic for tuberculosis (TB) and presents the second largest prevalence of the disease in Brazil. Here, we present the bacterial population structure of 218 isolates of Mycobacterium tuberculosis, derived from 186 patients that were diagnosed between January 2008 and December 2009. Genotypes were generated by means of spoligotyping, 24 MIRU-VNTR typing and presence of fbpC103, RDRio and RD174. The results confirmed earlier data that predominant genotypes in Rio de Janeiro are those of the Euro American Lineages (99%). However, we observed differences between the classification by spoligotyping when comparing to that of 24 MIRU-VNTR typing, being respectively 43.6% vs. 62.4% of LAM, 34.9% vs. 9.6% of T and 18.3% vs. 21.5% of Haarlem. Among isolates classified as LAM by MIRU typing, 28.0% did not present the characteristic spoligotype profile with absence of spacers 21 to 24 and 32 to 36 and we designated these conveniently as "LAM-like", 79.3% of these presenting the LAM-specific SNP fbpC103. The frequency of RDRio and RD174 in the LAM strains, as defined both by spoligotyping and 24 MIRU-VNTR loci, were respectively 11% and 15.4%, demonstrating that RD174 is not always a marker for LAM/RDRio strains. We conclude that, although spoligotyping alone is a tool for classification of strains of the Euro-American lineage, when combined with MIRU-VNTRs, SNPs and RD typing, it leads to a much better understanding of the bacterial population structure and phylogenetic relationships among strains of M. tuberculosis in regions with high incidence of TB.
format	article
author	Sidra E G Vasconcellos Chyntia Carolina Acosta Lia Lima Gomes Emilyn Costa Conceição Karla Valéria Lima Marcelo Ivens de Araujo Maria de Lourdes Leite Flávio Tannure Paulo Cesar de Souza Caldas Harrison M Gomes Adalberto Rezende Santos Michel K Gomgnimbou Christophe Sola David Couvin Nalin Rastogi Neio Boechat Philip Noel Suffys
author_facet	Sidra E G Vasconcellos Chyntia Carolina Acosta Lia Lima Gomes Emilyn Costa Conceição Karla Valéria Lima Marcelo Ivens de Araujo Maria de Lourdes Leite Flávio Tannure Paulo Cesar de Souza Caldas Harrison M Gomes Adalberto Rezende Santos Michel K Gomgnimbou Christophe Sola David Couvin Nalin Rastogi Neio Boechat Philip Noel Suffys
author_sort	Sidra E G Vasconcellos
title	Strain classification of Mycobacterium tuberculosis isolates in Brazil based on genotypes obtained by spoligotyping, mycobacterial interspersed repetitive unit typing and the presence of large sequence and single nucleotide polymorphism.
title_short	Strain classification of Mycobacterium tuberculosis isolates in Brazil based on genotypes obtained by spoligotyping, mycobacterial interspersed repetitive unit typing and the presence of large sequence and single nucleotide polymorphism.
title_full	Strain classification of Mycobacterium tuberculosis isolates in Brazil based on genotypes obtained by spoligotyping, mycobacterial interspersed repetitive unit typing and the presence of large sequence and single nucleotide polymorphism.
title_fullStr	Strain classification of Mycobacterium tuberculosis isolates in Brazil based on genotypes obtained by spoligotyping, mycobacterial interspersed repetitive unit typing and the presence of large sequence and single nucleotide polymorphism.
title_full_unstemmed	Strain classification of Mycobacterium tuberculosis isolates in Brazil based on genotypes obtained by spoligotyping, mycobacterial interspersed repetitive unit typing and the presence of large sequence and single nucleotide polymorphism.
title_sort	strain classification of mycobacterium tuberculosis isolates in brazil based on genotypes obtained by spoligotyping, mycobacterial interspersed repetitive unit typing and the presence of large sequence and single nucleotide polymorphism.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/e02453ea135745d4ab916b4a8302c025
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Strain classification of Mycobacterium tuberculosis isolates in Brazil based on genotypes obtained by spoligotyping, mycobacterial interspersed repetitive unit typing and the presence of large sequence and single nucleotide polymorphism.

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