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Conceição EC, da Conceição ML, Marcon DJ, Loubser J, Andrade GL, da Silva SP, Cruz ACR, Sharma A, Suffys P, Lima KVB. Genomic Diversity of the Rarely Observed Genotype of the Mycobacterium tuberculosis Central Asian (CAS) Lineage 3 from North Brazil. Microorganisms 2023; 11:microorganisms11010132. [PMID: 36677424 PMCID: PMC9862801 DOI: 10.3390/microorganisms11010132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 12/31/2022] [Accepted: 01/03/2023] [Indexed: 01/06/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) Central Asian Strain (CAS) Lineage 3 (L3) genotype is predominantly found in East-Africa, Central-Asia, Western-Asia, and South-Asia; however, a new spoligotyping CAS/SIT2545 was found in northern regions of Brazil. We aimed to characterize and describe the genetic diversity and perform a phylogenetic assessment of this novel genotype. We performed 24-MIRU-VNTR loci and Whole-genome sequencing (WGS) of six Brazilian isolates previously spoligotyped. The libraries were prepared using a Nextera-XT kit and sequenced in a NextSeq 550 Illumina instrument. We performed lineage assignment and genomic characterization. From publicly available genomes of Mtb L3 and other lineages, we created a robust dataset to run the MTBSeq pipeline and perform a phylogenetic analysis. MIRU-VNTR and WGS confirmed CAS/SIT2545 belongs to L3. Out of 1691 genomes, 1350 (79.83%) passed in quality control (genomic coverage > 95%). Strain 431 differed in 52 single nucleotide variants (SNV), confirming it does not belong to the same transmission chain. The eight genomes from a global dataset clustered closer to Brazilian strains differed in >52 SNVs. We hypothesized L3 and L1 were introduced in Brazilian Northern in the same historical event; however, there is a need for additional studies exploring the genetic diversity of Mtb Brazilian Northern.
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Affiliation(s)
- Emilyn Costa Conceição
- Department of Science and Innovation—National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town P.O. Box 241, South Africa
- Seção de Bacteriologia e Micologia, Instituto Evandro Chagas, Ananindeua 67030-000, PA, Brazil
- Correspondence:
| | | | - Davi Josué Marcon
- Seção de Bacteriologia e Micologia, Instituto Evandro Chagas, Ananindeua 67030-000, PA, Brazil
- Centro de Genômica e Biologia de Sistemas, Universidade Federal do Pará, Belém 66075-110, PA, Brazil
| | - Johannes Loubser
- Department of Science and Innovation—National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town P.O. Box 241, South Africa
| | - Gabrielly Leite Andrade
- Seção de Bacteriologia e Micologia, Instituto Evandro Chagas, Ananindeua 67030-000, PA, Brazil
- Departamento de Medicina, Centro Universitário do Pará—CESUPA, Belém 66613-903, PA, Brazil
| | - Sandro Patroca da Silva
- Seção de Arbovírus e Febres Hemorrágicas, Instituto Evandro Chagas, Ananindeua 67030-000, PA, Brazil
| | - Ana Cecília Ribeiro Cruz
- Seção de Arbovírus e Febres Hemorrágicas, Instituto Evandro Chagas, Ananindeua 67030-000, PA, Brazil
- Programa de Pós-graduação Biologia Parasitária na Amazônia, Universidade do Estado do Pará, Belém 66087-670, PA, Brazil
| | - Abhinav Sharma
- Faculty of Engineering and Technology, Liverpool John Moores University (LJMU), Liverpool L35UX, UK
- Seqera Labs, 08005 Bacelona, Spain
| | - Philip Suffys
- Laboratório de Biologia Molecular Aplicada a Micobactéria, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil
| | - Karla Valéria Batista Lima
- Seção de Bacteriologia e Micologia, Instituto Evandro Chagas, Ananindeua 67030-000, PA, Brazil
- Programa de Pós-graduação Biologia Parasitária na Amazônia, Universidade do Estado do Pará, Belém 66087-670, PA, Brazil
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Phylogenomic Perspective on a Unique Mycobacterium bovis Clade Dominating Bovine Tuberculosis Infections among Cattle and Buffalos in Northern Brazil. Sci Rep 2020; 10:1747. [PMID: 32019968 PMCID: PMC7000724 DOI: 10.1038/s41598-020-58398-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 01/13/2020] [Indexed: 11/08/2022] Open
Abstract
Lack of routine surveillance in countries endemic for bovine tuberculosis (TB) and limited laboratory support contributes to the inability to differentiate the Mycobacterium tuberculosis Complex species, leading to an underestimated burden of the disease. Here, Whole-Genome Sequencing of Mycobacterium bovis isolated from tissues with TB-like lesions obtained from cattle and buffalos at Marajó Island, Brazil, demonstrates that recent transmission of M. bovis is ongoing at distinct sites. Moreover, the M. bovis epidemiology in this setting is herein found to be dominated by an endemic and unique clade composed of strains evolved from a common ancestor that are now genetically differentiated from other M. bovis clades. Additionally, envisioning a rapid strain differentiation and tracing across multiple settings, 28 globally validated strain-specific SNPs were identified, three of which considered as robust markers for the M. bovis Marajó strain. In conclusion, this study contributes with data regarding the identification of a novel M. bovis phylogenetic clade responsible for ongoing transmission events in both cattle and buffalo species in Brazil, provides a framework to investigate the dissemination of this highly prevalent strain and, holds the potential to inform TB control strategies that may help to prevent the spread of bovine and zoonotic TB.
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Genetic diversity of Mycobacterium tuberculosis complex isolates circulating in an area with high tuberculosis incidence: Using 24-locus MIRU-VNTR method. Tuberculosis (Edinb) 2018; 112:89-97. [PMID: 30205974 DOI: 10.1016/j.tube.2018.08.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 07/15/2018] [Accepted: 08/02/2018] [Indexed: 01/24/2023]
Abstract
We aimed to determine the genetic diversity, phylogenetic relationship and transmission dynamics of Mycobacterium tuberculosis complex (MTBC) genotypes in an area with high tuberculosis (TB) incidence. A set of 164 MTBC isolates from new TB patients of Golestan province, Iran, were subjected to genotyping using the standard 24-locus MIRU-VNTR method. Recent TB transmission was evaluated and phylogenetic relationships were analysed by minimum spanning tree and cluster-graph methods. Among the 164 isolates, 132 distinct patterns were detected. The 48 clustered isolates (29.3%) were distributed into 16 clusters ranging in size from 2 to 12 isolates. The most frequent genotype was Central Asian Strain/Delhi (CAS/Delhi) (n = 67, 40.8%), followed by NEW-1 (n = 53, 32.3%) and Beijing (n = 19, 11.6%) genotypes. Thirty five (72.9%) of NEW-1 isolates were recovered from immigrant patients and 84.2% (n = 16) of Beijing genotypes recovered from native cases. Statistically significant association was found between clustering and smoking (p = 0.047), drug addiction (p = 0.01) and prison history (p = 0.003). The estimated proportion of recent transmission was 19.5%. Presence of highly diverse MTBC isolates circulating in this province without a dominant genotype might be a consequence of importation of various genotypes in this area.
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Coll P, García de Viedma D. Molecular epidemiology of tuberculosis. Enferm Infecc Microbiol Clin 2018; 36:233-240. [PMID: 29463429 DOI: 10.1016/j.eimc.2018.01.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 01/13/2018] [Indexed: 01/05/2023]
Abstract
The application of genotyping tools allowed us to discriminate between the Mycobacterium tuberculosis isolates obtained in the laboratory. The differentiation between single strains opened the door to molecular epidemiology studies, which had helped us to progress in our knowledge of how this pathogen is transmitted in the progressively more complex socio-epidemiological scenario. The genetic stability of this microorganism led to develop specific methodologies, which are thoroughly revised in this chapter. In addition to their application in epidemiology, we review, how they can offer a response to different diagnostic and clinical challenges. Finally, we focus on describing the novel genomic revolution we are experiencing in the analysis of tuberculosis, the methodology in which it is based and the novel possibilities it offers, including new routes of integrating both the molecular and genomic languages in innovative post-genomic proposals, better suited to our real-life context.
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Affiliation(s)
- Pere Coll
- Servicio Microbiología, Hospital de Sant Pau, Barcelona, España; Departament de Genètica i Microbiologia, UniversitatAutònoma de Barcelona, , Bellaterra, España; Institut de Recerca, Hospital de Sant Pau, Barcelona, España.
| | - Darío García de Viedma
- Servicio Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, España; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, España; CIBER Enfermedades respiratorias, CIBERES, Madrid, España.
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Conceição EC, Rastogi N, Couvin D, Lopes ML, Furlaneto IP, Gomes HM, Vasconcellos SEG, Suffys PN, Schneider MPC, de Sousa MS, Sola C, de Paula Souza e Guimarães RJ, Duarte RS, Batista Lima KV. Genetic diversity of Mycobacterium tuberculosis from Pará, Brazil, reveals a higher frequency of ancestral strains than previously reported in South America. INFECTION GENETICS AND EVOLUTION 2017; 56:62-72. [DOI: 10.1016/j.meegid.2017.10.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 10/20/2017] [Accepted: 10/23/2017] [Indexed: 01/24/2023]
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