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

Institut de Biologie Intégrative de la Cellule, I2BC, UMR9198, CEA, CNRS, Univ. Paris-Sud, Univ. Paris-Saclay. Gif-sur-Yvette cedex, France / Universidade Federal do Rio de Janeiro. Instituto de Microbiologia Professor Paulo de Góes. Pós-Graduação. Rio de Janeiro, RJ, Brasil.
Institut de Biologie Intégrative de la Cellule, I2BC, UMR9198, CEA, CNRS, Univ. Paris-Sud, Univ. Paris-Saclay. Gif-sur-Yvette cedex, France.
Institut de Biologie Intégrative de la Cellule, I2BC, UMR9198, CEA, CNRS, Univ. Paris-Sud, Univ. Paris-Saclay. Gif-sur-Yvette cedex, France / Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Biologia Molecular Aplicada a Micobactéria. Rio de Janeiro, RJ, Brasil.
Institut de Biologie Intégrative de la Cellule, I2BC, UMR9198, CEA, CNRS, Univ. Paris-Sud, Univ. Paris-Saclay. Gif-sur-Yvette cedex, France.
London School of Hygiene & Tropical Medicine. Faculty of Infectious and Tropical Diseases. London, UK.
Institut de Biologie Intégrative de la Cellule, I2BC, UMR9198, CEA, CNRS, Univ. Paris-Sud, Univ. Paris-Saclay. Gif-sur-Yvette cedex, France / Institut Pasteur de Madagascar. Unité des Mycobactéries; Antananarivo, Madagascar.
Institut Pasteur de Madagascar. Unité des Mycobactéries; Antananarivo, Madagascar.
Instituto Evandro Chagas. Seção de Bacteriologia e Micologia. 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, Brasil.
Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Biologia Molecular Aplicada a Micobactéria. Rio de Janeiro, RJ, Brasil.
Universidade Federal do Rio de Janeiro. Instituto de Microbiologia Professor Paulo de Góes. Pós-Graduação. Rio de Janeiro, RJ, Brasil.
Instituto Evandro Chagas. Seção de Bacteriologia e Micologia. Ananindeua, PA, Brasil.
Institut de Biologie Intégrative de la Cellule, I2BC, UMR9198, CEA, CNRS, Univ. Paris-Sud, Univ. Paris-Saclay. Gif-sur-Yvette cedex, France / Universidade de São Paulo. Faculdade de Medicina de Ribeirão Preto. Ribeirão Preto, SP, Brasil.;

Abstract

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 sublineages. 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) and L1/EAI6-BGD1 (SIT591) 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.

Keywords in Portuguese

Complexo Mycobacterium tuberculosis
Espoligotipagem
Linhagem 1
Sequenciação do genoma inteiro
Polimorfismos de nucleotídeo único
Evolução molecular

Keywords

Mycobacterium tuberculosis complex
Spoligotyping
Lineage 1
Whole genome sequencing
Single-nucleotide polymorphisms
Molecular evolution

Publisher

Elsevier

Citation

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, p. 337-341, 2019.

DOI

10.1016/j.meegid.2019.06.001

ISSN

1567-1348

Please use this identifier to cite or link to this item: https://www.arca.fiocruz.br/handle/icict/40708

Type

Copyright

Restricted access

Embargo date

2025-01-01

Collections

Share

Statistics

Metadata

Author

Affilliation