Mycobacterium tuberculosis lineage 1 genetic diversity in Pará, Brazil, suggests common ancestry with east-African isolates potentially linked to historical slave trade

Detalhes bibliográficos
Autor(a) principal: Conceição, Emilyn Costa
Data de Publicação: 2019
Outros Autores: 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
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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spelling 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
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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
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