Mycobacterium tuberculosis lineage 1 genetic diversity in Pará, Brazil, suggests common ancestry with east-African isolates potentially linked to historical slave trade
Autor(a) principal: | |
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Data de Publicação: | 2019 |
Outros Autores: | , , , , , , , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Digital do Instituto Evandro Chagas (Patuá) |
Texto Completo: | https://patua.iec.gov.br/handle/iec/3754 |
Resumo: | Lineage 1 (L1) is one of seven Mycobacterium tuberculosis complex (MTBC) lineages. The objective of this study was to improve the complex taxonomy of L1 using phylogenetic SNPs, and to look for the origin of the main L1 sublineage prevalent in Para, Brazil. We developed a high-throughput SNPs-typing assay based on 12-L1-specific SNPs. This assay allowed us to experimentally retrieve SNP patterns on nine of these twelve SNPs in 277 isolates previously tentatively assigned to L1 spoligotyping-based sub lineages. Three collections were used: Pará-Brazil (71); RIVM, the Netherlands (102), Madagascar (104). One-hundred more results were generated in Silico using the PolyTB database. Based on the final SNPs combination, the samples were classified into 11 clusters (C1-C11). Most isolates within a SNP-based cluster shared a mutual spoligotyping-defined lineage. However, L1/EAI1-SOM (SIT48, sp. 40) and L1/EAI6-BGD1 (SIT591, sp. 23) showed a poor correlation with SNP data and are not monophyletic. L1/EAI8-MDG and L1/EAI3-IND belonged to C5; this result suggests that they share a common ancestor. L1.1.3/SIT129, a spoligotype pattern found in SNPs-cluster C6, was found to be shared between Pará/Brazil and Malawi. SIT129 was independently found to be highly prevalent in Mozambique, which suggests a migration history from East-Africa to Brazil during the 16th–18th slave trade period to Northern Brazil. |
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Conceição, Emilyn CostaRefregier, GuislaineGomes, Harrison MagdinierOlessa-Daragon, XavierColl, FrancescRatovonirina, Noel HarijaonaRasolofo-Razanamparany, VoahangyLopes, Maria LuizaSoolingen, Dick VanRutaihwa, LilianaGagneux, SebastienBollela, Valdes RobertoSuffys, Philip NoelDuarte, Rafael SilvaLima, Karla Valéria BatistaSola, Christophe Noel2019-06-17T18:17:49Z2019-06-17T18:17:49Z2019CONCEIÇÃO, Emilyn Costa et al. Mycobacterium tuberculosis lineage 1 genetic diversity in Pará, Brazil, suggests common ancestry with east-African isolates potentially linked to historical slave trade. Infection, Genetics and Evolution, v. 73, n. 2019, p. 337-341, Sept. 2019. DOI: https://doi.org/10.1016/j.meegid.2019.06.001. 1567-7257https://patua.iec.gov.br/handle/iec/375410.1016/j.meegid.2019.06.001Lineage 1 (L1) is one of seven Mycobacterium tuberculosis complex (MTBC) lineages. The objective of this study was to improve the complex taxonomy of L1 using phylogenetic SNPs, and to look for the origin of the main L1 sublineage prevalent in Para, Brazil. We developed a high-throughput SNPs-typing assay based on 12-L1-specific SNPs. This assay allowed us to experimentally retrieve SNP patterns on nine of these twelve SNPs in 277 isolates previously tentatively assigned to L1 spoligotyping-based sub lineages. Three collections were used: Pará-Brazil (71); RIVM, the Netherlands (102), Madagascar (104). One-hundred more results were generated in Silico using the PolyTB database. Based on the final SNPs combination, the samples were classified into 11 clusters (C1-C11). Most isolates within a SNP-based cluster shared a mutual spoligotyping-defined lineage. However, L1/EAI1-SOM (SIT48, sp. 40) and L1/EAI6-BGD1 (SIT591, sp. 23) showed a poor correlation with SNP data and are not monophyletic. L1/EAI8-MDG and L1/EAI3-IND belonged to C5; this result suggests that they share a common ancestor. L1.1.3/SIT129, a spoligotype pattern found in SNPs-cluster C6, was found to be shared between Pará/Brazil and Malawi. SIT129 was independently found to be highly prevalent in Mozambique, which suggests a migration history from East-Africa to Brazil during the 16th–18th slave trade period to Northern Brazil.Université Paris-Sud. Université Paris Saclay. Institut de Biologie Intégrative de la Cellule. I2BC. UMR9198. CEA. CNRS. Gif-sur-Yvette cedex, France / Universidade Federal do Rio de Janeiro. Pós-Graduação Instituto de Microbiologia Professor Paulo de Góes. Rio de Janeiro, RJ, Brazil.Université Paris-Sud. Université Paris Saclay. Institut de Biologie Intégrative de la Cellule. I2BC. UMR9198. CEA. CNRS. Gif-sur-Yvette cedex, France.Université Paris-Sud. Université Paris Saclay. Institut de Biologie Intégrative de la Cellule. I2BC. UMR9198. CEA. CNRS. Gif-sur-Yvette cedex, France / Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Biologia Molecular Aplicada a Micobactéria. Rio de Janeiro, RJ, Brazil.Université Paris-Sud. Université Paris Saclay. Institut de Biologie Intégrative de la Cellule. I2BC. UMR9198. CEA. CNRS. Gif-sur-Yvette cedex, France.London School of Hygiene & Tropical Medicine. Faculty of Infectious and Tropical Diseases. London, UK.Université Paris-Sud. Université Paris Saclay. Institut de Biologie Intégrative de la Cellule. I2BC. UMR9198. CEA. CNRS. Gif-sur-Yvette cedex, France / Institut Pasteur de Madagascar. Unité des Mycobactéries. Antananarivo, Madagascar.Institut Pasteur de Madagascar. Unité des Mycobactéries. Antananarivo, Madagascar.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.National Institute for Public Health and the Environment. Bilthoven, the Netherlands / Radboud University Nijmegen Medical Centre. Department of Medical Microbiology. Nijmegen, the Netherlands.Swiss Tropical & Public Health Institute. Basel, Switzerland / University of Basel. Basel, Switzerland.Swiss Tropical & Public Health Institute. Basel, Switzerland / University of Basel. Basel, Switzerland.Universidade de São Paulo. Faculdade de Medicina de Ribeirão Preto. Ribeirão Preto, SP, Brazil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Biologia Molecular Aplicada a Micobactéria. Rio de Janeiro, RJ, Brazil.Universidade Federal do Rio de Janeiro. Pós-Graduação Instituto de Microbiologia Professor Paulo de Góes. Rio de Janeiro, RJ, Brazil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Université Paris-Sud. Université Paris Saclay. Institut de Biologie Intégrative de la Cellule. I2BC. UMR9198. CEA. CNRS. Gif-sur-Yvette cedex, France / Universidade de São Paulo. Faculdade de Medicina de Ribeirão Preto. 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dc.title.pt_BR.fl_str_mv |
Mycobacterium tuberculosis lineage 1 genetic diversity in Pará, Brazil, suggests common ancestry with east-African isolates potentially linked to historical slave trade |
title |
Mycobacterium tuberculosis lineage 1 genetic diversity in Pará, Brazil, suggests common ancestry with east-African isolates potentially linked to historical slave trade |
spellingShingle |
Mycobacterium tuberculosis lineage 1 genetic diversity in Pará, Brazil, suggests common ancestry with east-African isolates potentially linked to historical slave trade Conceição, Emilyn Costa Mycobacterium tuberculosis / isolamento & purificação Mycobacterium tuberculosis / patogenicidade Filogenia Evolução Molecular Polimorfismo de Nucleotídeo Único Sequenciamento Completo do Genoma / métodos Linhagem |
title_short |
Mycobacterium tuberculosis lineage 1 genetic diversity in Pará, Brazil, suggests common ancestry with east-African isolates potentially linked to historical slave trade |
title_full |
Mycobacterium tuberculosis lineage 1 genetic diversity in Pará, Brazil, suggests common ancestry with east-African isolates potentially linked to historical slave trade |
title_fullStr |
Mycobacterium tuberculosis lineage 1 genetic diversity in Pará, Brazil, suggests common ancestry with east-African isolates potentially linked to historical slave trade |
title_full_unstemmed |
Mycobacterium tuberculosis lineage 1 genetic diversity in Pará, Brazil, suggests common ancestry with east-African isolates potentially linked to historical slave trade |
title_sort |
Mycobacterium tuberculosis lineage 1 genetic diversity in Pará, Brazil, suggests common ancestry with east-African isolates potentially linked to historical slave trade |
author |
Conceição, Emilyn Costa |
author_facet |
Conceição, Emilyn Costa Refregier, Guislaine Gomes, Harrison Magdinier Olessa-Daragon, Xavier Coll, Francesc Ratovonirina, Noel Harijaona Rasolofo-Razanamparany, Voahangy Lopes, Maria Luiza Soolingen, Dick Van Rutaihwa, Liliana Gagneux, Sebastien Bollela, Valdes Roberto Suffys, Philip Noel Duarte, Rafael Silva Lima, Karla Valéria Batista Sola, Christophe Noel |
author_role |
author |
author2 |
Refregier, Guislaine Gomes, Harrison Magdinier Olessa-Daragon, Xavier Coll, Francesc Ratovonirina, Noel Harijaona Rasolofo-Razanamparany, Voahangy Lopes, Maria Luiza Soolingen, Dick Van Rutaihwa, Liliana Gagneux, Sebastien Bollela, Valdes Roberto Suffys, Philip Noel Duarte, Rafael Silva Lima, Karla Valéria Batista Sola, Christophe Noel |
author2_role |
author author author author author author author author author author author author author author author |
dc.contributor.author.fl_str_mv |
Conceição, Emilyn Costa Refregier, Guislaine Gomes, Harrison Magdinier Olessa-Daragon, Xavier Coll, Francesc Ratovonirina, Noel Harijaona Rasolofo-Razanamparany, Voahangy Lopes, Maria Luiza Soolingen, Dick Van Rutaihwa, Liliana Gagneux, Sebastien Bollela, Valdes Roberto Suffys, Philip Noel Duarte, Rafael Silva Lima, Karla Valéria Batista Sola, Christophe Noel |
dc.subject.decsPrimary.pt_BR.fl_str_mv |
Mycobacterium tuberculosis / isolamento & purificação Mycobacterium tuberculosis / patogenicidade Filogenia Evolução Molecular Polimorfismo de Nucleotídeo Único Sequenciamento Completo do Genoma / métodos Linhagem |
topic |
Mycobacterium tuberculosis / isolamento & purificação Mycobacterium tuberculosis / patogenicidade Filogenia Evolução Molecular Polimorfismo de Nucleotídeo Único Sequenciamento Completo do Genoma / métodos Linhagem |
description |
Lineage 1 (L1) is one of seven Mycobacterium tuberculosis complex (MTBC) lineages. The objective of this study was to improve the complex taxonomy of L1 using phylogenetic SNPs, and to look for the origin of the main L1 sublineage prevalent in Para, Brazil. We developed a high-throughput SNPs-typing assay based on 12-L1-specific SNPs. This assay allowed us to experimentally retrieve SNP patterns on nine of these twelve SNPs in 277 isolates previously tentatively assigned to L1 spoligotyping-based sub lineages. Three collections were used: Pará-Brazil (71); RIVM, the Netherlands (102), Madagascar (104). One-hundred more results were generated in Silico using the PolyTB database. Based on the final SNPs combination, the samples were classified into 11 clusters (C1-C11). Most isolates within a SNP-based cluster shared a mutual spoligotyping-defined lineage. However, L1/EAI1-SOM (SIT48, sp. 40) and L1/EAI6-BGD1 (SIT591, sp. 23) showed a poor correlation with SNP data and are not monophyletic. L1/EAI8-MDG and L1/EAI3-IND belonged to C5; this result suggests that they share a common ancestor. L1.1.3/SIT129, a spoligotype pattern found in SNPs-cluster C6, was found to be shared between Pará/Brazil and Malawi. SIT129 was independently found to be highly prevalent in Mozambique, which suggests a migration history from East-Africa to Brazil during the 16th–18th slave trade period to Northern Brazil. |
publishDate |
2019 |
dc.date.accessioned.fl_str_mv |
2019-06-17T18:17:49Z |
dc.date.available.fl_str_mv |
2019-06-17T18:17:49Z |
dc.date.issued.fl_str_mv |
2019 |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.citation.fl_str_mv |
CONCEIÇÃO, Emilyn Costa et al. Mycobacterium tuberculosis lineage 1 genetic diversity in Pará, Brazil, suggests common ancestry with east-African isolates potentially linked to historical slave trade. Infection, Genetics and Evolution, v. 73, n. 2019, p. 337-341, Sept. 2019. DOI: https://doi.org/10.1016/j.meegid.2019.06.001. |
dc.identifier.uri.fl_str_mv |
https://patua.iec.gov.br/handle/iec/3754 |
dc.identifier.issn.-.fl_str_mv |
1567-7257 |
dc.identifier.doi.-.fl_str_mv |
10.1016/j.meegid.2019.06.001 |
identifier_str_mv |
CONCEIÇÃO, Emilyn Costa et al. Mycobacterium tuberculosis lineage 1 genetic diversity in Pará, Brazil, suggests common ancestry with east-African isolates potentially linked to historical slave trade. Infection, Genetics and Evolution, v. 73, n. 2019, p. 337-341, Sept. 2019. DOI: https://doi.org/10.1016/j.meegid.2019.06.001. 1567-7257 10.1016/j.meegid.2019.06.001 |
url |
https://patua.iec.gov.br/handle/iec/3754 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.publisher.none.fl_str_mv |
Elsevier |
publisher.none.fl_str_mv |
Elsevier |
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