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Kim TW, Jang YH, Jeong MK, Seo Y, Park CH, Kang S, Lee YJ, Choi JS, Yoon SS, Kim JM. Single-nucleotide polymorphism-based epidemiological analysis of Korean Mycobacterium bovis isolates. J Vet Sci 2021; 22:e24. [PMID: 33774940 PMCID: PMC8007439 DOI: 10.4142/jvs.2021.22.e24] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 01/03/2021] [Accepted: 01/15/2021] [Indexed: 11/20/2022] Open
Abstract
Background Bovine tuberculosis (TB) is caused by Mycobacterium bovis, a well-known cause of zoonotic tuberculosis in cattle and deer, and has been investigated in many physiological and molecular studies. However, detailed genome-level studies of M. bovis have not been performed in Korea. Objectives To survey whole genome-wide single-nucleotide polymorphism (SNP) variants in Korean M. bovis field isolates and to define M. bovis groups in Korea by comparing SNP typing with spoligotyping and variable number tandem repeat typing. Methods A total of 46 M. bovis field isolates, isolated from laryngopharyngeal lymph nodes and lungs of Korean cattle, wild boar, and Korean water deer, were used to identify SNPs by performing whole-genome sequencing. SNP sites were confirmed via polymerase chain reaction using 87 primer pairs. Results We identified 34 SNP sites with different frequencies across M. bovis isolates, and performed SNP typing and epidemiological analysis, which divided the 46 field isolates into 16 subtypes. Conclusions Through SNP analysis, detailed differences in samples with identical spoligotypes could be detected. SNP analysis is, therefore, a useful epidemiological tracing tool that could enable better management of bovine TB, thus preventing further outbreaks and reducing the impact of this disease.
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Affiliation(s)
- Tae Woon Kim
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Korea
| | - Yun Ho Jang
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Korea
| | - Min Kyu Jeong
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Korea
| | - Yoonjeong Seo
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Korea
| | - Chan Ho Park
- Gangwondo Livestock & Veterinary Service, Chuncheon 24203, Korea
| | - Sinseok Kang
- Chung Cheongbukdo Livestock & Veterinary Service, Jungbu-Branch, Chungju 27336, Korea
| | - Young Ju Lee
- College of Veterinary Medicine, Kyungpook National University, Daegu 41566, Korea
| | - Jeong Soo Choi
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Korea
| | - Soon Seek Yoon
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Korea
| | - Jae Myung Kim
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Korea.
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2
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Conceição EC, Salvato RS, Gomes KM, Guimarães AEDS, da Conceição ML, Souza e Guimarães RJDP, Sharma A, Furlaneto IP, Barcellos RB, Bollela VR, Anselmo LMP, Sisco MC, Niero CV, Ferrazoli L, Refrégier G, Lourenço MCDS, Gomes HM, de Brito AC, Catanho M, Duarte RS, Suffys PN, Lima KVB. Molecular epidemiology of Mycobacterium tuberculosis in Brazil before the whole genome sequencing era: a literature review. Mem Inst Oswaldo Cruz 2021; 116:e200517. [PMID: 33729319 PMCID: PMC7976556 DOI: 10.1590/0074-02760200517] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 02/11/2021] [Indexed: 11/22/2022] Open
Abstract
Molecular-typing can help in unraveling epidemiological scenarios and improvement for disease control strategies. A literature review of Mycobacterium tuberculosis transmission in Brazil through genotyping on 56 studies published from 1996-2019 was performed. The clustering rate for mycobacterial interspersed repetitive units - variable tandem repeats (MIRU-VNTR) of 1,613 isolates were: 73%, 33% and 28% based on 12, 15 and 24-loci, respectively; while for RFLP-IS6110 were: 84% among prison population in Rio de Janeiro, 69% among multidrug-resistant isolates in Rio Grande do Sul, and 56.2% in general population in São Paulo. These findings could improve tuberculosis (TB) surveillance and set up a solid basis to build a database of Mycobacterium genomes.
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Affiliation(s)
- Emilyn Costa Conceição
- Fundação Oswaldo Cruz-Fiocruz, Instituto Nacional de Infectologia
Evandro Chagas, Programa de Pós-Graduação em Pesquisa Clínica e Doenças Infecciosas,
Rio de Janeiro, RJ, Brasil
- Fundação Oswaldo Cruz-Fiocruz, Instituto Nacional de Infectologia
Evandro Chagas, Laboratório de Bacteriologia e Bioensaios em Micobactérias, Rio de
Janeiro, RJ, Brasil
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório
de Biologia Molecular Aplicada a Micobactérias, Rio de Janeiro, RJ, Brasil
| | - Richard Steiner Salvato
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação
em Biologia Celular e Molecular, Porto Alegre, RS, Brasil
- Secretaria Estadual de Saúde do Rio Grande do Sul, Centro Estadual
de Vigilância em Saúde, Centro de Desenvolvimento Científico e Tecnológico, Porto
Alegre, RS, Brasil
| | - Karen Machado Gomes
- Fundação Oswaldo Cruz-Fiocruz, Escola Nacional de Saúde Pública
Sergio Arouca, Centro de Referência Professor Hélio Fraga, Laboratório de Referência
Nacional para Tuberculose e outras Micobacterioses, Rio de Janeiro, RJ, Brasil
| | - Arthur Emil dos Santos Guimarães
- Universidade do Estado do Pará, Instituto de Ciências Biológicas e
da Saúde, Pós-Graduação Biologia Parasitária na Amazônia, Belém, PA, Brasil
- Instituto Evandro Chagas, Seção de Bacteriologia e Micologia,
Ananindeua, PA, Brasil
| | - Marília Lima da Conceição
- Universidade do Estado do Pará, Instituto de Ciências Biológicas e
da Saúde, Pós-Graduação Biologia Parasitária na Amazônia, Belém, PA, Brasil
- Instituto Evandro Chagas, Seção de Bacteriologia e Micologia,
Ananindeua, PA, Brasil
| | | | - Abhinav Sharma
- International Institute of Information Technology, Department of
Data Science, Bangalore, India
| | | | - Regina Bones Barcellos
- Secretaria Estadual de Saúde do Rio Grande do Sul, Centro Estadual
de Vigilância em Saúde, Centro de Desenvolvimento Científico e Tecnológico, Porto
Alegre, RS, Brasil
| | - Valdes Roberto Bollela
- Universidade de São Paulo, Departamento de Clínica Médica da
Faculdade de Medicina de Ribeirão Preto, Ribeirão Preto, SP, Brasil
| | - Lívia Maria Pala Anselmo
- Universidade de São Paulo, Departamento de Clínica Médica da
Faculdade de Medicina de Ribeirão Preto, Ribeirão Preto, SP, Brasil
| | - Maria Carolina Sisco
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório
de Biologia Molecular Aplicada a Micobactérias, Rio de Janeiro, RJ, Brasil
- Universidade Federal do Rio de Janeiro, Instituto de Microbiologia
Paulo de Góes, Laboratório de Micobactérias, Rio de Janeiro, RJ, Brasil
| | - Cristina Viana Niero
- Universidade Federal de São Paulo, Departamento de Microbiologia,
Imunologia e Parasitologia, São Paulo, SP, Brasil
| | - Lucilaine Ferrazoli
- Instituto Adolfo Lutz, Centro de Bacteriologia, Núcleo de
Tuberculose e Micobacterioses, São Paulo, SP, Brasil
| | - Guislaine Refrégier
- Universit e Paris-Saclay, Ecologie Systematique Evolution, Centre
National de la Recherche Scientifique, AgroParisTech, Orsay, France
| | - Maria Cristina da Silva Lourenço
- Fundação Oswaldo Cruz-Fiocruz, Instituto Nacional de Infectologia
Evandro Chagas, Laboratório de Bacteriologia e Bioensaios em Micobactérias, Rio de
Janeiro, RJ, Brasil
| | - Harrison Magdinier Gomes
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório
de Biologia Molecular Aplicada a Micobactérias, Rio de Janeiro, RJ, Brasil
| | - Artemir Coelho de Brito
- Coordenação Geral de Vigilância das Doenças de Transmissão
Respiratória de Condições Crônicas, Brasília, DF, Brasil
| | - Marcos Catanho
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório
de Genética Molecular de Microrganismos, Rio de Janeiro, RJ, Brasil
| | - Rafael Silva Duarte
- Universidade Federal do Rio de Janeiro, Instituto de Microbiologia
Paulo de Góes, Laboratório de Micobactérias, Rio de Janeiro, RJ, Brasil
| | - Philip Noel Suffys
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório
de Biologia Molecular Aplicada a Micobactérias, Rio de Janeiro, RJ, Brasil
| | - Karla Valéria Batista Lima
- Universidade do Estado do Pará, Instituto de Ciências Biológicas e
da Saúde, Pós-Graduação Biologia Parasitária na Amazônia, Belém, PA, Brasil
- Instituto Evandro Chagas, Seção de Bacteriologia e Micologia,
Ananindeua, PA, Brasil
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3
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Pinho STR, Pereira SM, Miranda JGV, Duarte TA, Nery JS, de Oliveira MG, Freitas MYGS, De Almeida NA, Moreira FB, Gomes RBC, Kerr L, Kendall C, Gomes MGM, Bessa TCB, Andrade RFS, Barreto ML. Investigating extradomiciliary transmission of tuberculosis: An exploratory approach using social network patterns of TB cases and controls and the genotyping of Mycobacterium tuberculosis. Tuberculosis (Edinb) 2020; 125:102010. [PMID: 33166778 DOI: 10.1016/j.tube.2020.102010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 09/30/2020] [Accepted: 10/12/2020] [Indexed: 11/27/2022]
Abstract
Extradomiciliary contacts have been overlooked in the study of TB transmission due to difficulties in identifying actual contacts in large populations. Complex network analysis provides a framework to model the structure of contacts, specially extradomiciliary ones. We conducted a study of incident sputum-positive TB cases and healthy controls occurring in a moderate TB burden city. Cases and controls were interviewed to obtain data regarding the usual locations of residence, work, study, and leisure. Mycobacterium tuberculosis isolated from sputum was genotyped. The collected data were used to build networks based on a framework of putative social interactions indicating possible TB transmission. A user-friendly open source environment (GraphTube) was setup to extract information from the collected data. Networks based on the likelihood of patient-patient, patient-healthy, and healthy-healthy contacts were setup, depending on a constraint of geographical distance of places attended by the volunteers. Using a threshold for the geographical distance of 300 m, the differences between TB cases and controls are revealed. Several clusters formed by social network nodes with high genotypic similarity were characterized. The developed framework provided consistent results and can be used to support the targeted search of potentially infected individuals and to help to understand the TB transmission.
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Affiliation(s)
- Suani T R Pinho
- Instituto De Física - UFBA. R. Barão De Jeremoabo, S/n. Ondina, 40170-115, Salvador, BA, Brazil.
| | - Susan M Pereira
- Instituto De Saúde Coletiva - UFBA. R. Basílio da Gama, S/n. Canela, 40110-040, Salvador, BA, Brazil.
| | - José G V Miranda
- Instituto De Física - UFBA. R. Barão De Jeremoabo, S/n. Ondina, 40170-115, Salvador, BA, Brazil.
| | - Tonya A Duarte
- Instituto De Ciências da Saúde - UFBA. Av. Reitor Miguel Calmon, S/n. Canela, 40231-300, Salvador, BA, Brazil.
| | - Joilda S Nery
- Instituto De Saúde Coletiva - UFBA. R. Basílio da Gama, S/n. Canela, 40110-040, Salvador, BA, Brazil.
| | - Maeli G de Oliveira
- Universidade Estadual De Feira De Santana. Av. Transnordestina, S/n. Novo Horizonte, 44036-900, Feira de Santana, BA, Brazil.
| | - M Yana G S Freitas
- Universidade Estadual De Feira De Santana. Av. Transnordestina, S/n. Novo Horizonte, 44036-900, Feira de Santana, BA, Brazil.
| | - Naila A De Almeida
- Serviço Nacional De Aprendizagem Industrial - SENAI. R, Henrique Dias. Roma, 40444-000, Salvador, BA, Brazil.
| | - Fabio B Moreira
- Instituto De Física - UFBA. R. Barão De Jeremoabo, S/n. Ondina, 40170-115, Salvador, BA, Brazil.
| | - Raoni B C Gomes
- Instituto De Saúde Coletiva - UFBA. R. Basílio da Gama, S/n. Canela, 40110-040, Salvador, BA, Brazil.
| | - Ligia Kerr
- Faculdade De Medicina - UFC. R. Alexandre Baraúna, 949. Rodolfo Teófilo, 60430-160, Fortaleza, CE, Brazil.
| | - Carl Kendall
- School of Public Health and Tropical Medicine Tulane University, 1440 Canal St, New Orleans, LA, 70112, United States.
| | - M Gabriela M Gomes
- Liverpool School of Tropical Medicine, Liverpool, UK, Pembroke Pl, Liverpool L3 5QA, Reino Unido, UK.
| | - Theolis C B Bessa
- Instituto Gonçalo Moniz - IGM/FIOCRUZ. R. Waldemar Falcão, 121. Candeal, 40296-710, Salvador, BA, Brazil.
| | - Roberto F S Andrade
- Instituto De Física - UFBA. R. Barão De Jeremoabo, S/n. Ondina, 40170-115, Salvador, BA, Brazil.
| | - Mauricio L Barreto
- Centro de Integração de Dados e Conhecimentos para Saúde - CIDACS/FIOCRUZ, Parque Tecnológico Edf. Tecnocentro. Rua Mundo, 121, Salvador, BA, Brazil.
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4
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Sousa J, Cá B, Maceiras AR, Simões-Costa L, Fonseca KL, Fernandes AI, Ramos A, Carvalho T, Barros L, Magalhães C, Chiner-Oms Á, Machado H, Veiga MI, Singh A, Pereira R, Amorim A, Vieira J, Vieira CP, Bhatt A, Rodrigues F, Rodrigues PNS, Gagneux S, Castro AG, Guimarães JT, Bastos HN, Osório NS, Comas I, Saraiva M. Mycobacterium tuberculosis associated with severe tuberculosis evades cytosolic surveillance systems and modulates IL-1β production. Nat Commun 2020; 11:1949. [PMID: 32327653 PMCID: PMC7181847 DOI: 10.1038/s41467-020-15832-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 03/23/2020] [Indexed: 01/26/2023] Open
Abstract
Genetic diversity of Mycobacterium tuberculosis affects immune responses and clinical outcomes of tuberculosis (TB). However, how bacterial diversity orchestrates immune responses to direct distinct TB severities is unknown. Here we study 681 patients with pulmonary TB and show that M. tuberculosis isolates from cases with mild disease consistently induce robust cytokine responses in macrophages across multiple donors. By contrast, bacteria from patients with severe TB do not do so. Secretion of IL-1β is a good surrogate of the differences observed, and thus to classify strains as probable drivers of different TB severities. Furthermore, we demonstrate that M. tuberculosis isolates that induce low levels of IL-1β production can evade macrophage cytosolic surveillance systems, including cGAS and the inflammasome. Isolates exhibiting this evasion strategy carry candidate mutations, generating sigA recognition boxes or affecting components of the ESX-1 secretion system. Therefore, we provide evidence that M. tuberculosis strains manipulate host-pathogen interactions to drive variable TB severities.
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Grants
- The authors thank the excellent support from the i3S scientific platforms, namely Animal facility, Advanced Light Microscopy and BioSciences Screening, member of the national infrastructure PPBI - Portuguese Platform of Bioimaging (PPBI-POCI-01-0145-FEDER-022122). This work was financed by FCT - Fundação para a Ciência e a Tecnologia/ Ministério da Ciência, Tecnologia e Inovação grant POCI-01-0145-FEDER-028955 (to MS) and by the Northern Portugal Regional Operational Programme (NORTE 2020), under the Portugal 2020 Partnership Agreement, through the European Regional Development Fund (FEDER) (NORTE-01-0145-FEDER-000013, to MIV, FR, AGC and NSO). IC acknowledges the support of Ministerio de Ciencia, Innovación y Universidades (SAF2016-77346-R) and the European Research Council (638553-TB-ACCELERATE). HNB acknowledges the support of Bolsa D. Manuel de Mello and of the Portuguese Society for Pneumology; AB and MS were also recipients of an International Exchanges Grant from the Royal Society. JS is funded by a research fellow NORTE-01-0145-FEDER-000012; BC and KLF are funded by FCT PhD scholarships SFRH/BD/114403/2016 and SFRH/BD/114405/2016, respectively; MIV is funded by FCT through DL 57/2016 (CRP) and MS through Estimulo Individual ao Emprego Científico.
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Affiliation(s)
- Jeremy Sousa
- i3S-Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- IBMC-Instituto de Biologia Molecular e Celular, University of Porto, Porto, Portugal
- Doctoral Program in Molecular and Cell Biology, ICBAS-Instituto de Ciências Biomédicas Abel Salazar, University of Porto, Porto, Portugal
| | - Baltazar Cá
- i3S-Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- IBMC-Instituto de Biologia Molecular e Celular, University of Porto, Porto, Portugal
- Doctoral Program in Molecular and Cell Biology, ICBAS-Instituto de Ciências Biomédicas Abel Salazar, University of Porto, Porto, Portugal
| | - Ana Raquel Maceiras
- i3S-Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- IBMC-Instituto de Biologia Molecular e Celular, University of Porto, Porto, Portugal
| | - Luisa Simões-Costa
- i3S-Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- IBMC-Instituto de Biologia Molecular e Celular, University of Porto, Porto, Portugal
| | - Kaori L Fonseca
- i3S-Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- IBMC-Instituto de Biologia Molecular e Celular, University of Porto, Porto, Portugal
- Doctoral Program in Molecular and Cell Biology, ICBAS-Instituto de Ciências Biomédicas Abel Salazar, University of Porto, Porto, Portugal
| | - Ana Isabel Fernandes
- i3S-Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- IBMC-Instituto de Biologia Molecular e Celular, University of Porto, Porto, Portugal
| | - Angélica Ramos
- São João Hospital Center & EPIUnit-Institute of Public Health, University of Porto, Porto, Portugal
| | - Teresa Carvalho
- São João Hospital Center & EPIUnit-Institute of Public Health, University of Porto, Porto, Portugal
| | - Leandro Barros
- i3S-Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- IBMC-Instituto de Biologia Molecular e Celular, University of Porto, Porto, Portugal
| | - Carlos Magalhães
- Life and Health Sciences Research Institute, University of Minho, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | | | - Henrique Machado
- Life and Health Sciences Research Institute, University of Minho, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Maria Isabel Veiga
- Life and Health Sciences Research Institute, University of Minho, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Albel Singh
- School of Biosciences and Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Rui Pereira
- i3S-Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, University of Porto, Porto, Portugal
| | - António Amorim
- i3S-Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, University of Porto, Porto, Portugal
- Faculty of Sciences, University of Porto, Porto, Portugal
| | - Jorge Vieira
- i3S-Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- IBMC-Instituto de Biologia Molecular e Celular, University of Porto, Porto, Portugal
| | - Cristina P Vieira
- i3S-Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- IBMC-Instituto de Biologia Molecular e Celular, University of Porto, Porto, Portugal
| | - Apoorva Bhatt
- School of Biosciences and Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Fernando Rodrigues
- Life and Health Sciences Research Institute, University of Minho, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Pedro N S Rodrigues
- i3S-Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- IBMC-Instituto de Biologia Molecular e Celular, University of Porto, Porto, Portugal
- ICBAS-Instituto de Ciências Biomédicas Abel Salazar, University of Porto, Porto, Portugal
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - António Gil Castro
- Life and Health Sciences Research Institute, University of Minho, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - João Tiago Guimarães
- São João Hospital Center & EPIUnit-Institute of Public Health, University of Porto, Porto, Portugal
- Faculty of Medicine, University of Porto, Porto, Portugal
| | - Helder Novais Bastos
- i3S-Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- IBMC-Instituto de Biologia Molecular e Celular, University of Porto, Porto, Portugal
- Faculty of Medicine, University of Porto, Porto, Portugal
- São João Hospital Center, Porto, Portugal
| | - Nuno S Osório
- Life and Health Sciences Research Institute, University of Minho, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Iñaki Comas
- Biomedicine Institute of Valencia (CSIC), Valencia, Spain
- CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Margarida Saraiva
- i3S-Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal.
- IBMC-Instituto de Biologia Molecular e Celular, University of Porto, Porto, Portugal.
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5
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Sharma NK, Rathor N, Sinha R, Gupta S, Tyagi G, Garima K, Pathak R, Singh P, Jain A, Bose M, Varma-Basil M. Expression of mycolic acid in response to stress and association with differential clinical manifestations of tuberculosis. Int J Mycobacteriol 2020; 8:237-243. [PMID: 31512599 DOI: 10.4103/ijmy.ijmy_69_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Background Extrapulmonary tuberculosis (EPTB), accounting for 10%-20% of all cases of tuberculosis (TB), is known to be determined by host immunity. However, the contribution of bacterial factors to the development of EPTB has not been studied extensively. Mycolic acids are predominant lipids constituting the cell wall of Mycobacterium tuberculosis, and keto-mycolic acid is involved in the synthesis of foamy macrophages that facilitate persistence of mycobacteria. Hence, the present study was performed to gain an insight into variable expression of mycolic acids in clinical isolates of M. tuberculosis under stress. Methods Pansusceptible clinical isolates of M. tuberculosis from patients with lymph node TB (LNTB) (n = 10) and pulmonary TB (PTB) (n = 10) were subjected to sodium dodecyl sulfate (SDS) stress, and the expression of mycolic acid and its biosynthetic genes was compared. Any bias arising due to the genotype of the clinical isolates was ruled out by performing single-nucleotide polymorphism cluster grouping (SCG), wherein no significant difference was observed between the SCG of LNTB or PTB isolates. Results The expression of α-mycolic acid during the exposure to SDS was high in 7/10 (70%) LNTB and 6/10 (60%) PTB isolates. Methoxy mycolic acid showed an increased expression in 7/10 (70%) LNTB isolates and 4/10 (40%) PTB isolates. Increased expression of keto-mycolic acid on exposure with SDS was observed in 8/10 (80%) M. tuberculosis LNTB and 3/10 (30%) PTB isolates. Similarly, the mycolic acid synthesis gene, fas, was upregulated more in LNTB isolates than PTB isolates in vitro and ex vivo. SCG 3a was the most common SCG observed in 40% (8/20) of the isolates, followed by SCG 3b in 30% (6/20) of the isolates. There was no significant difference between the SCG of LNTB or PTB isolates. Conclusion The higher expression of keto-mycolic acid in LNTB as against PTB isolates may indicate better survival in LNTB isolates in the presence of stress.
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Affiliation(s)
- Naresh Kumar Sharma
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Nisha Rathor
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Rajesh Sinha
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Shraddha Gupta
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Gaurav Tyagi
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Kushal Garima
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Rakesh Pathak
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Pooja Singh
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Ashima Jain
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Mridula Bose
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Mandira Varma-Basil
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
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6
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Cancino-Muñoz I, Gil-Brusola A, Torres-Puente M, Mariner-Llicer C, Dogba J, Akinseye V, Adesokan K, Kwaghe A, Ejeh F, Cadmus S, Comas I. Development and application of affordable SNP typing approaches to genotype Mycobacterium tuberculosis complex strains in low and high burden countries. Sci Rep 2019; 9:15343. [PMID: 31653874 PMCID: PMC6814786 DOI: 10.1038/s41598-019-51326-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 09/26/2019] [Indexed: 11/21/2022] Open
Abstract
The Mycobacterium tuberculosis complex (MTBC) comprises the species that causes tuberculosis (TB) which affects 10 million people every year. A robust classification of species, lineages, and sub-lineages is important to explore associations with drug resistance, epidemiological patterns or clinical outcomes. We present a rapid and easy-to-follow methodology to classify clinical TB samples into the main MTBC clades. Approaches are based on the identification of lineage and sub-lineage diagnostic SNP using a real-time PCR high resolution melting assay and classic Sanger sequencing from low-concentrated, low quality DNA. Thus, suitable for implementation in middle and low-income countries. Once we validated our molecular procedures, we characterized a total of 491 biological samples from human and cattle hosts, representing countries with different TB burden. Overall, we managed to genotype ~95% of all samples despite coming from unpurified and low-concentrated DNA. Our approach also allowed us to detect zoonotic cases in eight human samples from Nigeria. To conclude, the molecular techniques we have developed, are accurate, discriminative and reproducible. Furthermore, it costs less than other classic typing methods, resulting in an affordable alternative method in TB laboratories.
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Affiliation(s)
- Irving Cancino-Muñoz
- Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain
- FISABIO Public Health, Genomics and Health Unit, Valencia, Spain
| | - Ana Gil-Brusola
- Hospital Universitari I Politècnic La Fe, Microbiology Department, Valencia, Spain
| | | | | | - John Dogba
- University of Ibadan, Department of Veterinary Public Health & Preventive Medicine, Ibadan, Nigeria
- University of Ibadan, Centre for Control and Prevention of Zoonosis, Ibadan, Nigeria
| | - Victor Akinseye
- University of Ibadan, Department of Veterinary Public Health & Preventive Medicine, Ibadan, Nigeria
| | - Kehinde Adesokan
- University of Ibadan, Department of Veterinary Public Health & Preventive Medicine, Ibadan, Nigeria
| | - Ayi Kwaghe
- Federal Ministry of Agriculture and Rural Development, Department of Veterinary and Pest Control Services, Garki, Nigeria
| | - Francis Ejeh
- University of Maiduguri, Department of Veterinary Microbiology, Maiduguri, Nigeria
| | - Simeon Cadmus
- University of Ibadan, Department of Veterinary Public Health & Preventive Medicine, Ibadan, Nigeria
- University of Ibadan, Centre for Control and Prevention of Zoonosis, Ibadan, Nigeria
| | - Iñaki Comas
- Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain.
- CIBER of Epidemiology and Public Health (CIBERESP), Madrid, Spain.
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Bakuła Z, Javed H, Pleń M, Jamil N, Tahir Z, Jagielski T. Genetic diversity of multidrug-resistant Mycobacterium tuberculosis isolates in Punjab, Pakistan. INFECTION GENETICS AND EVOLUTION 2019; 72:16-24. [DOI: 10.1016/j.meegid.2019.02.029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 02/13/2019] [Accepted: 02/25/2019] [Indexed: 10/27/2022]
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8
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Advances in Molecular Epidemiology of Infectious Diseases: Definitions, Approaches, and Scope of the Field. Microbiol Spectr 2019; 6. [PMID: 30387413 DOI: 10.1128/microbiolspec.ame-0001-2018] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Molecular epidemiology is a discipline that uses molecular microbiology tools to study the distribution and determinants of diseases in human populations and veterinary animals. Our understanding of epidemiology of infectious diseases has evolved with technological advancements made in molecular biology that refine our perception of the identity and dynamics of microorganisms. This review is an introduction to the Microbiology Spectrum Curated Collection: Advances in Molecular Epidemiology of Infectious Diseases that will discuss how these advancements have contributed to investigations of infectious disease outbreaks/epidemics, surveillance, transmission dynamics, risk factor identification, pathogenesis, and etiologic attribution of bacterial, viral, protozoan, and helminthic pathogens to a disease. Here we define "molecular epidemiology" and distinguish it from other disciplines that use many of the same molecular biology tools-taxonomy, phylogenetics, and molecular evolution of microorganisms. The Curated Collection will be spread throughout multiple issues of Microbiology Spectrum and will be divided into four general sections: (i) laboratory methods used to strain type microbial pathogens, (ii) methods used to analyze genotyping data, (iii) examples of molecular epidemiologic investigations of bacterial, viral, and parasitic diseases, and (iv) applications of molecular epidemiology to address new research questions in communicable and noncommunicable diseases. The major theme of this Curated Collection is to address the following question frequently asked by clinicians, clinical microbiologists, and public health professionals: what is the advantage or unique contribution of molecular epidemiology in solving infectious disease problems in the clinical and public health arenas? *This article is part of a curated collection.
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9
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Genome-wide screen for universal individual identification SNPs based on the HapMap and 1000 Genomes databases. Sci Rep 2018; 8:5553. [PMID: 29615764 PMCID: PMC5882920 DOI: 10.1038/s41598-018-23888-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 03/15/2018] [Indexed: 11/09/2022] Open
Abstract
Differences among SNP panels for individual identification in SNP-selecting and populations led to few common SNPs, compromising their universal applicability. To screen all universal SNPs, we performed a genome-wide SNP mining in multiple populations based on HapMap and 1000Genomes databases. SNPs with high minor allele frequencies (MAF) in 37 populations were selected. With MAF from ≥0.35 to ≥0.43, the number of selected SNPs decreased from 2769 to 0. A total of 117 SNPs with MAF ≥0.39 have no linkage disequilibrium with each other in every population. For 116 of the 117 SNPs, cumulative match probability (CMP) ranged from 2.01 × 10-48 to 1.93 × 10-50 and cumulative exclusion probability (CEP) ranged from 0.9999999996653 to 0.9999999999945. In 134 tested Han samples, 110 of the 117 SNPs remained within high MAF and conformed to Hardy-Weinberg equilibrium, with CMP = 4.70 × 10-47 and CEP = 0.999999999862. By analyzing the same number of autosomal SNPs as in the HID-Ion AmpliSeq Identity Panel, i.e. 90 randomized out of the 110 SNPs, our panel yielded preferable CMP and CEP. Taken together, the 110-SNPs panel is advantageous for forensic test, and this study provided plenty of highly informative SNPs for compiling final universal panels.
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10
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Rito T, Matos C, Carvalho C, Machado H, Rodrigues G, Oliveira O, Ferreira E, Gonçalves J, Maio L, Morais C, Ramos H, Guimarães JT, Santos CL, Duarte R, Correia-Neves M. A complex scenario of tuberculosis transmission is revealed through genetic and epidemiological surveys in Porto. BMC Infect Dis 2018; 18:53. [PMID: 29370774 PMCID: PMC5785791 DOI: 10.1186/s12879-018-2968-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 01/17/2018] [Indexed: 01/30/2023] Open
Abstract
Background Tuberculosis (TB) incidence is decreasing worldwide and eradication is becoming plausible. In low-incidence countries, intervention on migrant populations is considered one of the most important strategies for elimination. However, such measures are inappropriate in European areas where TB is largely endemic, such as Porto in Portugal. We aim to understand transmission chains in Porto through a genetic characterization of Mycobacterium tuberculosis strains and through a detailed epidemiological evaluation of cases. Methods We genotyped the M. tuberculosis strains using the MIRU-VNTR system. We performed an evolutionary reconstruction of the genotypes with median networks, used in this context for the first time. TB cases from a period of two years were evaluated combining genetic, epidemiological and georeferencing information. Results The data reveal a unique complex scenario in Porto where the autochthonous population acts as a genetic reservoir of M. tuberculosis diversity with discreet episodes of transmission, mostly undetected using classical epidemiology alone. Conclusions Although control policies have been successful in decreasing incidence in Porto, the discerned complexity suggests that, for elimination to be a realistic goal, strategies need to be adjusted and coupled with a continuous genetic characterization of strains and detailed epidemiological evaluation, in order to successfully identify and interrupt transmission chains.
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Affiliation(s)
- Teresa Rito
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Gualtar Campus, 4710-057, Braga, Portugal. .,ICVS/3B's, PT Government Associate Laboratory, Braga/4805-017, 4710-057, Guimarães, Portugal.
| | - Carlos Matos
- Eastern Porto Public Health Unit, (ACES Porto Oriental), 4200-510, Porto, Portugal
| | - Carlos Carvalho
- Northern Health Regional Administration, Department of Public Health, 4000-078, Porto, Portugal.,Multidisciplinary Unit for Biomedical Research (UMIB), Institute of Biomedical Sciences Abel Salazar, University of Porto, 4050-013, Porto, Portugal
| | - Henrique Machado
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Gualtar Campus, 4710-057, Braga, Portugal.,ICVS/3B's, PT Government Associate Laboratory, Braga/4805-017, 4710-057, Guimarães, Portugal
| | - Gabriela Rodrigues
- Northern Health Regional Administration, Department of Public Health, 4000-078, Porto, Portugal
| | - Olena Oliveira
- EPI Unit, Institute of Public Health, University of Porto, 4050-600, Porto, Portugal
| | - Eduarda Ferreira
- Eastern Porto Public Health Unit, (ACES Porto Oriental), 4200-510, Porto, Portugal
| | - Jorge Gonçalves
- Western Porto Public Health Unit, (ACES Porto Ocidental), 4100-503, Porto, Portugal
| | - Lurdes Maio
- Eastern Porto Public Health Unit, (ACES Porto Oriental), 4200-510, Porto, Portugal
| | - Clara Morais
- Porto TB Outpatient Centre, Centro Diagnóstico pneumológico, 4250-162, Porto, Portugal
| | - Helena Ramos
- Porto Hospital Centre, Hospital Santo António, 4099-001, Porto, Portugal
| | - João Tiago Guimarães
- EPI Unit, Institute of Public Health, University of Porto, 4050-600, Porto, Portugal.,Clinical Pathology, São João Hospital Centre, 4200-319, Porto, Portugal.,Biomedicine Department, Faculty of Medicine, University of Porto, 4200-319, Porto, Portugal
| | - Catarina L Santos
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Gualtar Campus, 4710-057, Braga, Portugal.,ICVS/3B's, PT Government Associate Laboratory, Braga/4805-017, 4710-057, Guimarães, Portugal
| | - Raquel Duarte
- EPI Unit, Institute of Public Health, University of Porto, 4050-600, Porto, Portugal.,Pulmonology Department, Centro Hospitalar de Vila Nova de Gaia/Espinho EPE, 4400-129, Vila Nova de Gaia, Portugal.,Clinical Epidemiology, Predictive Medicine and Public Health Department, Faculty of Medicine, University of Porto, 4200-319, Porto, Portugal
| | - Margarida Correia-Neves
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Gualtar Campus, 4710-057, Braga, Portugal.,ICVS/3B's, PT Government Associate Laboratory, Braga/4805-017, 4710-057, Guimarães, Portugal
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11
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Duarte TA, Nery JS, Boechat N, Pereira SM, Simonsen V, Oliveira M, Gomes MGM, Penha-Gonçalves C, Barreto ML, Barbosa T. A systematic review of East African-Indian family of Mycobacterium tuberculosis in Brazil. Braz J Infect Dis 2017; 21:317-324. [PMID: 28238627 PMCID: PMC9427636 DOI: 10.1016/j.bjid.2017.01.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 01/10/2017] [Indexed: 01/17/2023] Open
Abstract
Introduction The Mycobacterium tuberculosis East African-Indian (EAI) spoligotyping family (belonging to lineage 1, Indo-Oceanic, defined by the region of deletion RD239) is distributed worldwide, but is more prevalent in Southeast Asia, India, and East Africa. Studies in Latin America have rarely identified EAI. In this study, we describe the occurrence of the EAI family in Brazil. Methods EAI was identified in a systematic literature review of genetic diversity studies pertaining to M. tuberculosis in Brazil, as well as in a survey conducted in Salvador, Bahia, located in the northeastern region of this country. Results The EAI6-BGD1 spoligotyping family and the EAI5 Spoligotype International Type (SIT) 1983 clade were the most frequently reported, with wide distribution of this particular clade described in Brazil. The distribution of other EAI spoligotyping patterns with broader worldwide distribution was restricted to the southeastern region of the country. Conclusions EAI may be endemic at a low frequency in Brazil, with some clades indicating increased fitness with respect to this population.
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12
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Varma-Basil M, Narang A, Chakravorty S, Garima K, Gupta S, Kumar Sharma N, Giri A, Zozio T, Couvin D, Hanif M, Bhatnagar A, Menon B, Niemann S, Rastogi N, Alland D, Bose M. A snapshot of the predominant single nucleotide polymorphism cluster groups of Mycobacterium tuberculosis clinical isolates in Delhi, India. Tuberculosis (Edinb) 2016; 100:72-81. [DOI: 10.1016/j.tube.2016.07.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 07/10/2016] [Indexed: 11/25/2022]
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13
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Nogueira CL, Prim RI, Senna SG, Rovaris DB, Maurici R, Rossetti ML, Couvin D, Rastogi N, Bazzo ML. First insight into the molecular epidemiology of Mycobacterium tuberculosis in Santa Catarina, southern Brazil. Tuberculosis (Edinb) 2016; 97:57-64. [PMID: 26980497 DOI: 10.1016/j.tube.2015.12.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 12/14/2015] [Accepted: 12/20/2015] [Indexed: 12/01/2022]
Abstract
Molecular epidemiology of Mycobacterium tuberculosis is useful for understanding disease transmission dynamics, and to establish strategic measures for TB control and prevention. The aim of this study was to analyze clinical, epidemiological and molecular characteristics of MTBC clinical isolates from Santa Catarina state, southern Brazil. During one-year period, 406 clinical isolates of MTBC were collected from Central Laboratory of Public Health and typed by spoligotyping. Demographic and clinical data were collected from the Brazilian National Mandatory Disease Reporting System. The majority of cases occurred in highest population densities regions and about 50% had some condition associated with TB. Among all isolates, 5.7% were MDR, which showed association with drug addiction. LAM was the most predominant lineage with 47.5%, followed by the T superfamily with 25.9% and Haarlem with 12.3%. The MST showed two major groups: the first was formed mainly by the LAM lineage and the second was mainly formed by the T and Haarlem lineages. Others lineages were distributed in peripheral positions. This study provides the first insight into the population structure of M. tuberculosis in SC State. Spoligotyping and other genotyping analyses are important to establish strategic measures for TB control and prevention.
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Affiliation(s)
- Christiane Lourenço Nogueira
- Universidade Federal de Santa Catarina - UFSC, Campus Universitário, s/n. Florianópolis, Santa Catarina, Brazil.
| | - Rodrigo Ivan Prim
- Universidade Federal de Santa Catarina - UFSC, Campus Universitário, s/n. Florianópolis, Santa Catarina, Brazil.
| | - Simone Gonçalves Senna
- Universidade Federal de Santa Catarina - UFSC, Campus Universitário, s/n. Florianópolis, Santa Catarina, Brazil.
| | - Darcita Büerger Rovaris
- Laboratório Central Do Estado de Santa Catarina - LACEN/SC, Florianópolis, Santa Catarina, Brazil.
| | - Rosemeri Maurici
- Universidade Federal de Santa Catarina - UFSC, Campus Universitário, s/n. Florianópolis, Santa Catarina, Brazil.
| | - Maria Lúcia Rossetti
- Fundação Estadual de Produção e Pesquisa em Saúde Do Rio Grande Do Sul - FEEPS/RS, Porto Alegre, Rio Grande Do Sul, Brazil.
| | - David Couvin
- WHO Supranational TB Reference Laboratory, Institut Pasteur de la Guadeloupe, Abymes, Guadeloupe, France.
| | - Nalin Rastogi
- WHO Supranational TB Reference Laboratory, Institut Pasteur de la Guadeloupe, Abymes, Guadeloupe, France.
| | - Maria Luiza Bazzo
- Universidade Federal de Santa Catarina - UFSC, Campus Universitário, s/n. Florianópolis, Santa Catarina, Brazil.
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Reynaud Y, Millet J, Rastogi N. Genetic Structuration, Demography and Evolutionary History of Mycobacterium tuberculosis LAM9 Sublineage in the Americas as Two Distinct Subpopulations Revealed by Bayesian Analyses. PLoS One 2015; 10:e0140911. [PMID: 26517715 PMCID: PMC4627653 DOI: 10.1371/journal.pone.0140911] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 10/01/2015] [Indexed: 02/06/2023] Open
Abstract
Tuberculosis (TB) remains broadly present in the Americas despite intense global efforts for its control and elimination. Starting from a large dataset comprising spoligotyping (n = 21183 isolates) and 12-loci MIRU-VNTRs data (n = 4022 isolates) from a total of 31 countries of the Americas (data extracted from the SITVIT2 database), this study aimed to get an overview of lineages circulating in the Americas. A total of 17119 (80.8%) strains belonged to the Euro-American lineage 4, among which the most predominant genotypic family belonged to the Latin American and Mediterranean (LAM) lineage (n = 6386, 30.1% of strains). By combining classical phylogenetic analyses and Bayesian approaches, this study revealed for the first time a clear genetic structuration of LAM9 sublineage into two subpopulations named LAM9C1 and LAM9C2, with distinct genetic characteristics. LAM9C1 was predominant in Chile, Colombia and USA, while LAM9C2 was predominant in Brazil, Dominican Republic, Guadeloupe and French Guiana. Globally, LAM9C2 was characterized by higher allelic richness as compared to LAM9C1 isolates. Moreover, LAM9C2 sublineage appeared to expand close to twenty times more than LAM9C1 and showed older traces of expansion. Interestingly, a significant proportion of LAM9C2 isolates presented typical signature of ancestral LAM-RDRio MIRU-VNTR type (224226153321). Further studies based on Whole Genome Sequencing of LAM strains will provide the needed resolution to decipher the biogeographical structure and evolutionary history of this successful family.
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Affiliation(s)
- Yann Reynaud
- WHO Supranational TB Reference Laboratory, Tuberculosis and Mycobacteria Unit, Institut Pasteur de la Guadeloupe, Abymes, Guadeloupe, France
- * E-mail: (YR); (NR)
| | - Julie Millet
- WHO Supranational TB Reference Laboratory, Tuberculosis and Mycobacteria Unit, Institut Pasteur de la Guadeloupe, Abymes, Guadeloupe, France
| | - Nalin Rastogi
- WHO Supranational TB Reference Laboratory, Tuberculosis and Mycobacteria Unit, Institut Pasteur de la Guadeloupe, Abymes, Guadeloupe, France
- * E-mail: (YR); (NR)
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15
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Feasibility of mini-sequencing schemes based on nucleotide polymorphisms for microbial identification and population analyses. Appl Microbiol Biotechnol 2015; 99:2513-21. [DOI: 10.1007/s00253-015-6427-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 01/20/2015] [Accepted: 01/21/2015] [Indexed: 11/26/2022]
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16
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Vasconcellos SEG, Acosta CC, Gomes LL, Conceição EC, Lima KV, de Araujo MI, Leite MDL, Tannure F, Caldas PCDS, Gomes HM, Santos AR, Gomgnimbou MK, Sola C, Couvin D, Rastogi N, Boechat N, Suffys PN. Strain classification of Mycobacterium tuberculosis isolates in Brazil based on genotypes obtained by spoligotyping, mycobacterial interspersed repetitive unit typing and the presence of large sequence and single nucleotide polymorphism. PLoS One 2014; 9:e107747. [PMID: 25314118 PMCID: PMC4196770 DOI: 10.1371/journal.pone.0107747] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2014] [Accepted: 08/21/2014] [Indexed: 11/26/2022] Open
Abstract
Rio de Janeiro is endemic for tuberculosis (TB) and presents the second largest prevalence of the disease in Brazil. Here, we present the bacterial population structure of 218 isolates of Mycobacterium tuberculosis, derived from 186 patients that were diagnosed between January 2008 and December 2009. Genotypes were generated by means of spoligotyping, 24 MIRU-VNTR typing and presence of fbpC103, RDRio and RD174. The results confirmed earlier data that predominant genotypes in Rio de Janeiro are those of the Euro American Lineages (99%). However, we observed differences between the classification by spoligotyping when comparing to that of 24 MIRU-VNTR typing, being respectively 43.6% vs. 62.4% of LAM, 34.9% vs. 9.6% of T and 18.3% vs. 21.5% of Haarlem. Among isolates classified as LAM by MIRU typing, 28.0% did not present the characteristic spoligotype profile with absence of spacers 21 to 24 and 32 to 36 and we designated these conveniently as “LAM-like”, 79.3% of these presenting the LAM-specific SNP fbpC103. The frequency of RDRio and RD174 in the LAM strains, as defined both by spoligotyping and 24 MIRU-VNTR loci, were respectively 11% and 15.4%, demonstrating that RD174 is not always a marker for LAM/RDRio strains. We conclude that, although spoligotyping alone is a tool for classification of strains of the Euro-American lineage, when combined with MIRU-VNTRs, SNPs and RD typing, it leads to a much better understanding of the bacterial population structure and phylogenetic relationships among strains of M. tuberculosis in regions with high incidence of TB.
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Affiliation(s)
- Sidra E. G. Vasconcellos
- Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
- Multidisciplinary Research Laboratory, University Hospital Clementino Fraga Filho – HUCFF, Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Chyntia Carolina Acosta
- Laboratory of Cellular Microbiology, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lia Lima Gomes
- Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Karla Valéria Lima
- Instituto Evandro Chagas, Section of Bacteriology and Mycology, Belém, Pará, Brazil
| | - Marcelo Ivens de Araujo
- Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Maria de Lourdes Leite
- Hospital Municipal Rafael de Paula Souza, Municipal Secretary of Health, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Flávio Tannure
- Hospital Municipal Rafael de Paula Souza, Municipal Secretary of Health, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Paulo Cesar de Souza Caldas
- Centro de Referência Professor Hélio Fraga, Escola Nacional de Saúde Publica Sergio Arouca, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Harrison M. Gomes
- Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Adalberto Rezende Santos
- Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Michel K. Gomgnimbou
- CNRS–Université Paris–Sud, Institut de Génétique et Microbiologie–Infection Genetics Emerging Pathogens Evolution Team, Orsay, France
| | - Christophe Sola
- CNRS–Université Paris–Sud, Institut de Génétique et Microbiologie–Infection Genetics Emerging Pathogens Evolution Team, Orsay, France
| | - David Couvin
- Supranational TB Reference Laboratory, Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Abymes, Guadeloupe, France
| | - Nalin Rastogi
- Supranational TB Reference Laboratory, Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Abymes, Guadeloupe, France
| | - Neio Boechat
- Multidisciplinary Research Laboratory, University Hospital Clementino Fraga Filho – HUCFF, Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
- Graduate Program in Clinical Medicine, Faculty of Medicine, University Hospital Clementino Fraga Filho, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Philip Noel Suffys
- Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
- * E-mail:
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Soares P, Alves RJ, Abecasis AB, Penha-Gonçalves C, Gomes MGM, Pereira-Leal JB. inTB - a data integration platform for molecular and clinical epidemiological analysis of tuberculosis. BMC Bioinformatics 2013; 14:264. [PMID: 24001185 PMCID: PMC3847221 DOI: 10.1186/1471-2105-14-264] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 08/21/2013] [Indexed: 11/30/2022] Open
Abstract
Background Tuberculosis is currently the second highest cause of death from infectious diseases worldwide. The emergence of multi and extensive drug resistance is threatening to make tuberculosis incurable. There is growing evidence that the genetic diversity of Mycobacterium tuberculosis may have important clinical consequences. Therefore, combining genetic, clinical and socio-demographic data is critical to understand the epidemiology of this infectious disease, and how virulence and other phenotypic traits evolve over time. This requires dedicated bioinformatics platforms, capable of integrating and enabling analyses of this heterogeneous data. Results We developed inTB, a web-based system for integrated warehousing and analysis of clinical, socio-demographic and molecular data for Mycobacterium sp. isolates. As a database it can organize and display data from any of the standard genotyping methods (SNP, MIRU-VNTR, RFLP and spoligotype), as well as an extensive array of clinical and socio-demographic variables that are used in multiple countries to characterize the disease. Through the inTB interface it is possible to insert and download data, browse the database and search specific parameters. New isolates are automatically classified into strains according to an internal reference, and data uploaded or typed in is checked for internal consistency. As an analysis framework, the system provides simple, point and click analysis tools that allow multiple types of data plotting, as well as simple ways to download data for external analysis. Individual trees for each genotyping method are available, as well as a super tree combining all of them. The integrative nature of inTB grants the user the ability to generate trees for filtered subsets of data crossing molecular and clinical/socio-demografic information. inTB is built on open source software, can be easily installed locally and easily adapted to other diseases. Its design allows for use by research laboratories, hospitals or public health authorities. The full source code as well as ready to use packages is available at http://www.evocell.org/inTB. Conclusions To the best of our knowledge, this is the only system capable of integrating different types of molecular data with clinical and socio-demographic data, empowering researchers and clinicians with easy to use analysis tools that were not possible before.
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Affiliation(s)
- Patrícia Soares
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, Apartado 14, Oeiras P-2781-901, Portugal.
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