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Macedo R, Pinto M, Borges V, Nunes A, Oliveira O, Portugal I, Duarte R, Gomes JP. Evaluation of a gene-by-gene approach for prospective whole-genome sequencing-based surveillance of multidrug resistant Mycobacterium tuberculosis. Tuberculosis (Edinb) 2019; 115:81-88. [PMID: 30948181 DOI: 10.1016/j.tube.2019.02.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 01/15/2019] [Accepted: 02/22/2019] [Indexed: 11/27/2022]
Abstract
Whole-genome sequencing (WGS) offers unprecedented resolution for tracking Mycobacterium tuberculosis transmission and antibiotic-resistance spread. Still, the establishment of standardized WGS-based pipelines and the definition of epidemiological clusters based on genetic relatedness are under discussion. We aimed to implement a dynamic gene-by-gene approach, fully relying on freely available software, for prospective WGS-based tuberculosis surveillance, demonstrating its application for detecting transmission chains by retrospectively analysing all M/XDR strains isolated in 2013-2017 in Portugal. We observed a good correlation between genetic relatedness and epidemiological links, with strongly epilinked clusters displaying mean pairwise allele differences (AD) always below 0.3% (ratio of mean AD over the total number of shared loci between same-cluster strains). This data parallels the genetic distances acquired by the core-SNV analysis, while providing higher resolution and epidemiological concordance than MIRU-VNTR genotyping. The dynamic analysis of strain sub-sets (i.e., increasing the number of shared loci within each sub-set) also strengthens the confidence in detecting epilinked clusters. This gene-by-gene strategy also offers several practical benefits (e.g., reliance on freely-available software, scalability and low computational requirements) that further consolidated its suitability for a timely and robust prospective WGS-based laboratory surveillance of M/XDR-TB cases.
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Affiliation(s)
- Rita Macedo
- National Reference Laboratory for Mycobacteria, Department of Infectious Diseases, National Institute of Health, 1649-016 Lisbon, Portugal.
| | - Miguel Pinto
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, 1649-016 Lisbon, Portugal.
| | - Vítor Borges
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, 1649-016 Lisbon, Portugal.
| | - Alexandra Nunes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, 1649-016 Lisbon, Portugal.
| | - Olena Oliveira
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057 Braga, Portugal; ICVS/3B, PT Government Associate Laboratory, 4710-057, Braga/4805-017, Guimarães, Portugal; EPI Unit, Institute of Public Health, University of Porto, 4050-600 Porto, Portugal.
| | - Isabel Portugal
- iMed.ULisboa-Research Institute for Medicines, University of Lisbon, Lisbon, Portugal.
| | - Raquel Duarte
- EPI Unit, Institute of Public Health, University of Porto, 4050-600 Porto, Portugal; Clinical Epidemiology, Predictive Medicine and Public Health Department, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal; Pulmonology Department, Centro Hospitalar de Vila Nova de Gaia/Espinho EPE, 4400-129 Vila Nova de Gaia, Portugal.
| | - João Paulo Gomes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, 1649-016 Lisbon, Portugal.
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Macedo R, Duarte R. Trends of multidrug-resistant tuberculosis clustering in Portugal. ERJ Open Res 2019; 5:00151-2018. [PMID: 30792983 PMCID: PMC6378340 DOI: 10.1183/23120541.00151-2018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 01/02/2019] [Indexed: 11/05/2022] Open
Abstract
Analysis of MDR-TB rates showed consistent decreases in cases and clustering rates but did not establish valid relationships with the epidemiological information collected by the public health authorities http://ow.ly/3BnN30nxqW3.
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Affiliation(s)
- Rita Macedo
- National Reference Laboratory for Mycobacteria, Dept of Infectious Diseases, National Institute of Health, Lisbon, Portugal
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Reis AJ, David SMMD, Nunes LDS, Valim ARDM, Possuelo LG. Recent transmission of drug-resistant Mycobacterium tuberculosis in a prison population in southern Brazil. J Bras Pneumol 2017; 42:286-289. [PMID: 27832237 PMCID: PMC5063446 DOI: 10.1590/s1806-37562016000000023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 04/19/2016] [Indexed: 12/02/2022] Open
Abstract
We conducted a cross-sectional, retrospective study, characterized by classical and molecular epidemiology, involving M. tuberculosis isolates from a regional prison in southern Brazil. Between January of 2011 and August of 2014, 379 prisoners underwent sputum smear microscopy and culture; 53 (13.9%) were diagnosed with active tuberculosis. Of those, 8 (22.9%) presented with isoniazid-resistant tuberculosis. Strain genotyping was carried out by 15-locus mycobacterial interspersed repetitive unit-variable-number tandem-repeat analysis; 68.6% of the patients were distributed into five clusters, and 87.5% of the resistant cases were in the same cluster. The frequency of drug-resistant tuberculosis cases and the rate of recent transmission were high. Our data suggest the need to implement an effective tuberculosis control program within the prison system.
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Affiliation(s)
- Ana Julia Reis
- Universidade Federal do Rio Grande, Rio Grande, Rio Grande do Sul, Brasil
| | | | - Luciana de Souza Nunes
- Programa de Pós-Graduação em Promoção da Saúde, Centro de Pesquisa e Treinamento em Biotecnologia - CPTBio - Universidade de Santa Cruz do Sul, Santa Cruz do Sul, Rio Grande do Sul, Brasil
| | - Andreia Rosane de Moura Valim
- Programa de Pós-Graduação em Promoção da Saúde, Centro de Pesquisa e Treinamento em Biotecnologia - CPTBio - Universidade de Santa Cruz do Sul, Santa Cruz do Sul, Rio Grande do Sul, Brasil
| | - Lia Gonçalves Possuelo
- Programa de Pós-Graduação em Promoção da Saúde, Centro de Pesquisa e Treinamento em Biotecnologia - CPTBio - Universidade de Santa Cruz do Sul, Santa Cruz do Sul, Rio Grande do Sul, Brasil
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Viveiros M, Martins M, Couto I, Rodrigues L, Machado D, Portugal I, Amaral L. Molecular tools for rapid identification and novel effective therapy against MDRTB/XDRTB infections. Expert Rev Anti Infect Ther 2014; 8:465-80. [DOI: 10.1586/eri.10.20] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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