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

Autor: Francesc Coll, Rafael Silva Duarte, Liliana K. Rutaihwa, Maria Luiza Lopes, Valdes Roberto Bollela, Xavier Olessa-Daragon, Noël Harijaona Ratovonirina, Karla Valéria Batista Lima, Christophe Sola, Voahangy Rasolofo-Razanamparany, Philip Noel Suffys, Guislaine Refrégier, Sebastien Gagneux, Dick van Soolingen, Emilyn Costa Conceição, Harrison Magdinier Gomes
Přispěvatelé: Universidade Federal do Rio de Janeiro (UFRJ), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Infection Génétique Evolution des Pathogènes Emergents (IGEPE), Département Microbiologie (Dpt Microbio), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Fiocruz Paraná - Instituto Carlos Chagas / Carlos Chagas Institute [Curitiba, Brésil] (ICC), Fundação Oswaldo Cruz (FIOCRUZ), Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine (LSHTM), Unité des Mycobactéries [Antananarivo, Madagascar] (IPM), Institut Pasteur de Madagascar, Instituto Evandro Chagas, Swiss Tropical and Public Health Institute [Basel], Institute of Tropical Medicine [Antwerp] (ITM), Fundação Oswaldo Cruz / Oswaldo Cruz Foundation (FIOCRUZ)
Rok vydání: 2019
Předmět:
0301 basic medicine
Mycobacterium tuberculosis / patogenicidade
[SDV]Life Sciences [q-bio]
Single-nucleotide polymorphisms
Monophyly
EVOLUÇÃO MOLECULAR
Mozambique
Phylogeny
Netherlands
Spoligotyping
2. Zero hunger
Phylogenetic tree
biology
3. Good health
Polimorfismo de Nucleot?deo ?nico
Infectious Diseases
Mycobacterium tuberculosis complex
Brazil
Lineage 1
Microbiology (medical)
Genotype
030106 microbiology
Black People
Single-nucleotide polymorphism
Polymorphism
Single Nucleotide
Microbiology
Sequenciamento Completo do Genoma / m?todos
Mycobacterium tuberculosis
Mycobacterium tuberculosis / isolamento & purifica??o
Evolu??o Molecular
03 medical and health sciences
All institutes and research themes of the Radboud University Medical Center
Madagascar
Genetics
Humans
Tuberculosis
SNP
Molecular Biology
Ecology
Evolution
Behavior and Systematics
Whole genome sequencing
Genetic diversity
Genetic Variation
biology.organism_classification
lnfectious Diseases and Global Health Radboud Institute for Health Sciences [Radboudumc 4]
Filogenia
030104 developmental biology
Evolutionary biology
Molecular evolution
Linhagem
Zdroj: Repositório Institucional da USP (Biblioteca Digital da Produção Intelectual)
Universidade de São Paulo (USP)
instacron:USP
Repositório Digital do Instituto Evandro Chagas (Patuá)
Instituto Evandro Chagas (IEC)
instacron:IEC
Infection, Genetics and Evolution, 73, pp. 337-341
Infection, Genetics and Evolution: Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases
Infection, Genetics and Evolution: Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases, 2019, 73, pp.337--341. ⟨10.1016/j.meegid.2019.06.001⟩
Infection, Genetics and Evolution, 73, 337-341
ISSN: 1567-1348
Popis: Universit? Paris-Sud. Universit? Paris Saclay. Institut de Biologie Int?grative de la Cellule. I2BC. UMR9198. CEA. CNRS. Gif-sur-Yvette cedex, France / Universidade Federal do Rio de Janeiro. P?s-Gradua??o Instituto de Microbiologia Professor Paulo de G?es. Rio de Janeiro, RJ, Brazil. Universit? Paris-Sud. Universit? Paris Saclay. Institut de Biologie Int?grative de la Cellule. I2BC. UMR9198. CEA. CNRS. Gif-sur-Yvette cedex, France. Universit? Paris-Sud. Universit? Paris Saclay. Institut de Biologie Int?grative de la Cellule. I2BC. UMR9198. CEA. CNRS. Gif-sur-Yvette cedex, France / Funda??o Oswaldo Cruz. Instituto Oswaldo Cruz. Laborat?rio de Biologia Molecular Aplicada a Micobact?ria. Rio de Janeiro, RJ, Brazil. Universit? Paris-Sud. Universit? Paris Saclay. Institut de Biologie Int?grative 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. Universit? Paris-Sud. Universit? Paris Saclay. Institut de Biologie Int?grative de la Cellule. I2BC. UMR9198. CEA. CNRS. Gif-sur-Yvette cedex, France / Institut Pasteur de Madagascar. Unit? des Mycobact?ries. Antananarivo, Madagascar. Institut Pasteur de Madagascar. Unit? des Mycobact?ries. Antananarivo, Madagascar. Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. 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 S?o Paulo. Faculdade de Medicina de Ribeir?o Preto. Ribeir?o Preto, SP, Brazil. Funda??o Oswaldo Cruz. Instituto Oswaldo Cruz. Laborat?rio de Biologia Molecular Aplicada a Micobact?ria. Rio de Janeiro, RJ, Brazil. Universidade Federal do Rio de Janeiro. P?s-Gradua??o Instituto de Microbiologia Professor Paulo de G?es. Rio de Janeiro, RJ, Brazil. Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Ananindeua, PA, Brasil. Universit? Paris-Sud. Universit? Paris Saclay. Institut de Biologie Int?grative de la Cellule. I2BC. UMR9198. CEA. CNRS. Gif-sur-Yvette cedex, France / Universidade de S?o Paulo. Faculdade de Medicina de Ribeir?o Preto. Ribeir?o Preto, SP, Brazil. 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: Par?-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 Par?/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.
Databáze: OpenAIRE
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