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Namburete EI, Dippenaar A, Conceição EC, Feliciano C, Nascimento MMPD, Peronni KC, Silva WA, Ferro JJ, Harrison LH, Warren RM, Bollela VR. Phylogenomic assessment of drug-resistant Mycobacterium tuberculosis strains from Beira, Mozambique. Tuberculosis (Edinb) 2020; 121:101905. [PMID: 32063558 PMCID: PMC9300053 DOI: 10.1016/j.tube.2020.101905] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 12/21/2019] [Accepted: 01/26/2020] [Indexed: 11/24/2022]
Abstract
BACKGROUND Mozambique is a high-burden tuberculosis (TB) country where TB/HIV co-infection and drug resistant TB (DR-TB) incidence is increasing. Whole genome sequencing (WGS) comprehensively describes the molecular epidemiology of TB, allows prediction of DR-TB phenotypes, lineages strains identification and better understanding of transmission chains. OBJECTIVE To describe genetic diversity of DR-TB Mycobacterium tuberculosis isolated in Beira, Mozambique. METHODS Descriptive cross-sectional study with 35 M. tuberculosis isolates, resistant to at least one first-line drug on molecular drug-susceptibility tests (DST). Variant identification, DR prediction and phylogenetic analysis provided by WGS, drug-susceptibility pattern compared to line-probe assay (LPA): Genotype MTBDRTMplus and MTBDRTMsl. FINDINGS Lineage 4 (L4) was the most prevalent: 25 (71.4%) isolates; 5 (14.3%) L1 and 5 (14.3%) L2. WGS showed 33/35 (94.3%) isolates resistant to at least one drug, two pan-susceptible isolates that were previously diagnosed as DR-TB with genotype MTBDRplus. Concordance between WGS and LPA: 88.6% for isoniazid (INH), 85.7% to rifampicin (RPM), 91.4% for quinolones and 100% to second line injectable drugs. There were three possible TB transmission chains, 10 strains showing recent transmission. CONCLUSION WGS provided reliable information about the most frequent lineages related to DR-TB in Beira, Mozambique: L4.3 (LAM), L2 (Beijing) and L1 (EAI) and possible recent transmission chain.
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Affiliation(s)
- Evangelina Inacio Namburete
- Mycobacteria Research Lab at Clinics Hospital from Ribeirão Preto Medical School, University of São Paulo (FMRP-USP), Brazil; Faculty of Health Science, Catholic University of Mozambique, Beira, Mozambique.
| | - Anzaan Dippenaar
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, South Africa.
| | - Emilyn Costa Conceição
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373 - bloco i - Cidade Universitária, Rio de Janeiro, RJ, 21941-970, Brazil.
| | - Cinara Feliciano
- Mycobacteria Research Lab at Clinics Hospital from Ribeirão Preto Medical School, University of São Paulo (FMRP-USP), Brazil.
| | | | - Kamila Chagas Peronni
- Center for Medical Genomics, Clinics Hospital at Ribeirão Preto Medical School, University of São Paulo (FMRP-USP), Brazil.
| | - Wilson Araújo Silva
- Center for Medical Genomics, Clinics Hospital at Ribeirão Preto Medical School, University of São Paulo (FMRP-USP), Brazil; Department of Genetics at Ribeirão Preto Medical School, University of São Paulo (FMRP-USP), Brazil.
| | - Josefo João Ferro
- Faculty of Health Science, Catholic University of Mozambique, Beira, Mozambique.
| | - Lee H Harrison
- Infectious Diseases Epidemiology Research Unit, University of Pittsburgh, Pittsburgh, USA.
| | - Robin Mark Warren
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, South Africa.
| | - Valdes Roberto Bollela
- Mycobacteria Research Lab at Clinics Hospital from Ribeirão Preto Medical School, University of São Paulo (FMRP-USP), Brazil.
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Anselmo LMP, Conceição EC, Namburete E, Feliciano C, Spindola S, Sola C, Bollela VR. Mycobacterium tuberculosis spoligotypes and drug-resistant characterization from Beira compared to genotypes circulating in Mozambique. Rev Soc Bras Med Trop 2019; 52:e20190257. [PMID: 31778400 DOI: 10.1590/0037-8682-0257-2019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 09/24/2019] [Indexed: 11/22/2022] Open
Abstract
INTRODUCTION Mozambique is one of three countries with high prevalence of tuberculosis (TB), TB/human immunodeficiency virus coinfection, and multidrug-resistant TB. We aimed to describe Mycobacterium tuberculosis spoligotypes circulating among drug resistant (DR) strains from Beira, Mozambique comparing them with genotypes in the country. METHODS We performed spoligotyping of 79 M. tuberculosis suspected of DR-TB compared all spoligotype patterns published on the international database and PubMed. RESULTS Both in Beira and Mozambique (n=578), the main clades were Latin-American-Mediterranean, East-African-Indian, Beijing and T, with no extensively DR TB cases. CONCLUSIONS Beira and Mozambique share the same population genetic structure of M. tuberculosis.
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Affiliation(s)
- Lívia Maria Pala Anselmo
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Medicina Interna, Ribeirão Preto, SP, Brasil
| | - Emilyn Costa Conceição
- Universidade Federal do Rio de Janeiro, Instituto de Microbiologia Paulo Góes, Rio de Janeiro, RJ, Brasil
| | - Evangelina Namburete
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Medicina Interna, Ribeirão Preto, SP, Brasil.,Universidade Católica de Moçambique, Faculdade de Ciências de Saúde, Beira, Mozambique
| | - Cinara Feliciano
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Medicina Interna, Ribeirão Preto, SP, Brasil
| | - Silvana Spindola
- Universidade Federal de Minas Gerais, Faculdade de Medicina, Departamento de Medicina Interna, Belo Horizonte, MG, Brasil
| | - Christophe Sola
- Université Paris-Saclay, Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, 91198, Gif-sur-Yvette cedex, France
| | - Valdes Roberto Bollela
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Medicina Interna, Ribeirão Preto, SP, Brasil
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Floridia M, Ciccacci F, Andreotti M, Hassane A, Sidumo Z, Magid NA, Sotomane H, David M, Mutemba E, Cebola J, Mugunhe RJ, Riccardi F, Marazzi MC, Giuliano M, Palombi L, Mancinelli S. Tuberculosis Case Finding With Combined Rapid Point-of-Care Assays (Xpert MTB/RIF and Determine TB LAM) in HIV-Positive Individuals Starting Antiretroviral Therapy in Mozambique. Clin Infect Dis 2018; 65:1878-1883. [PMID: 29020319 DOI: 10.1093/cid/cix641] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 07/20/2017] [Indexed: 12/12/2022] Open
Abstract
Background Tuberculosis is a major health concern in several countries, and effective diagnostic algorithms for use in human immunodeficiency virus (HIV)-positive patients are urgently needed. Methods At prescription of antiretroviral therapy, all patients in 3 Mozambican health centers were screened for tuberculosis, with a combined approach: World Health Organization (WHO) 4-symptom screening (fever, cough, night sweats, and weight loss), a rapid test detecting mycobacterial lipoarabinomannan in urine (Determine TB LAM), and a molecular assay performed on a sputum sample (Xpert MTB/RIF; repeated if first result was negative). Patients with positive LAM or Xpert MTB/RIF results were referred for tuberculosis treatment. Results Among 972 patients with a complete diagnostic algorithm (58.5% female; median CD4 cell count, 278/μL; WHO HIV stage I, 66.8%), 98 (10.1%) tested positive with Xpert (90, 9.3%) or LAM (34, 3.5%) assays. Compared with a single-test Xpert strategy, dual Xpert tests improved case finding by 21.6%, LAM testing alone improved it by 13.5%, and dual Xpert tests plus LAM testing improved it by 32.4%. Rifampicin resistance in Xpert-positive patients was infrequent (2.5%). Among patients with positive results, 22 of 98 (22.4%) had no symptoms at WHO 4-symptom screening. Patients with tuberculosis diagnosed had significantly lower CD4 cell counts and hemoglobin levels, more advanced WHO stage, and higher HIV RNA levels. Fifteen (15.3%) did not start tuberculosis treatment, mostly owing to rapidly deteriorating clinical conditions or logistical constraints. The median interval between start of the diagnostic algorithm and start of tuberculosis treatment was 7 days. Conclusions The prevalence of tuberculosis among Mozambican HIV-positive patients starting antiretroviral therapy was 10%, with limited rifampicin resistance. Use of combined point-of-care tests increased case finding, with a short time to treatment. Interventions are needed to remove logistical barriers and prevent presentation in very advanced HIV/tuberculosis disease.
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Affiliation(s)
- Marco Floridia
- National Center for Global Health, Istituto Superiore di Sanità
| | | | - Mauro Andreotti
- National Center for Global Health, Istituto Superiore di Sanità
| | | | - Zita Sidumo
- DREAM Program, Community of S. Egidio, Maputo
| | | | | | | | - Elsa Mutemba
- DREAM Program, Community of S. Egidio, Beira, Mozambique
| | - Junia Cebola
- DREAM Program, Community of S. Egidio, Beira, Mozambique
| | | | - Fabio Riccardi
- Department of Biomedicine and Prevention, University of Rome Tor Vergata
| | | | - Marina Giuliano
- National Center for Global Health, Istituto Superiore di Sanità
| | - Leonardo Palombi
- Department of Biomedicine and Prevention, University of Rome Tor Vergata
| | - Sandro Mancinelli
- Department of Biomedicine and Prevention, University of Rome Tor Vergata
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Perdigão J, Silva C, Diniz J, Pereira C, Machado D, Ramos J, Silva H, Abilleira F, Brum C, Reis AJ, Macedo M, Scaini JL, Silva AB, Esteves L, Macedo R, Maltez F, Clemente S, Coelho E, Viegas S, Rabna P, Rodrigues A, Taveira N, Jordao L, Kritski A, Lapa E Silva JR, Mokrousov I, Couvin D, Rastogi N, Couto I, Pain A, McNerney R, Clark TG, von Groll A, Dalla-Costa ER, Rossetti ML, Silva PEA, Viveiros M, Portugal I. Clonal expansion across the seas as seen through CPLP-TB database: A joint effort in cataloguing Mycobacterium tuberculosis genetic diversity in Portuguese-speaking countries. INFECTION GENETICS AND EVOLUTION 2018; 72:44-58. [PMID: 29559379 PMCID: PMC6598853 DOI: 10.1016/j.meegid.2018.03.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 03/12/2018] [Accepted: 03/13/2018] [Indexed: 12/22/2022]
Abstract
Tuberculosis (TB) remains a major health problem within the Community of Portuguese Language Speaking Countries (CPLP). Despite the marked variation in TB incidence across its member-states and continued human migratory flux between countries, a considerable gap in the knowledge on the Mycobacterium tuberculosis population structure and strain circulation between the countries still exists. To address this, we have assembled and analysed the largest CPLP M. tuberculosis molecular and drug susceptibility dataset, comprised by a total of 1447 clinical isolates, including 423 multidrug-resistant isolates, from five CPLP countries. The data herein presented reinforces Latin American and Mediterranean (LAM) strains as the hallmark of M. tuberculosis populational structure in the CPLP coupled with country-specific differential prevalence of minor clades. Moreover, using high-resolution typing by 24-loci MIRU-VNTR, six cross-border genetic clusters were detected, thus supporting recent clonal expansion across the Lusophone space. To make this data available to the scientific community and public health authorities we developed CPLP-TB (available at http://cplp-tb.ff.ulisboa.pt), an online database coupled with web-based tools for exploratory data analysis. As a public health tool, it is expected to contribute to improved knowledge on the M. tuberculosis population structure and strain circulation within the CPLP, thus supporting the risk assessment of strain-specific trends. The Community of Portuguese Speaking Countries (CPLP) occupies a vast geographical area. Three CPLP countries are shortlisted in the WHO's list of Top 30 high-burden countries. Common Mycobacterium tuberculosis population structure denote historical strain flow. Cross-border clusters suggest recent intercontinental tuberculosis transmission. CPLP-TB: a novel strain database and framework for collaborative studies and strain tracing.
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Affiliation(s)
- João Perdigão
- iMed.ULisboa - Instituto de Investigação do Medicamento, Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal.
| | - Carla Silva
- iMed.ULisboa - Instituto de Investigação do Medicamento, Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Jaciara Diniz
- Núcleo de Pesquisa em Microbiologia Médica, Faculdade de Medicina, Universidade Federal do Rio Grande, Rio Grande, Rio Grande do Sul, Brazil
| | - Catarina Pereira
- iMed.ULisboa - Instituto de Investigação do Medicamento, Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Diana Machado
- Unidade de Microbiologia Médica, Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Lisboa, Portugal
| | - Jorge Ramos
- Unidade de Microbiologia Médica, Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Lisboa, Portugal
| | - Hugo Silva
- iMed.ULisboa - Instituto de Investigação do Medicamento, Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Fernanda Abilleira
- Núcleo de Pesquisa em Microbiologia Médica, Faculdade de Medicina, Universidade Federal do Rio Grande, Rio Grande, Rio Grande do Sul, Brazil
| | - Clarice Brum
- Núcleo de Pesquisa em Microbiologia Médica, Faculdade de Medicina, Universidade Federal do Rio Grande, Rio Grande, Rio Grande do Sul, Brazil
| | - Ana J Reis
- Núcleo de Pesquisa em Microbiologia Médica, Faculdade de Medicina, Universidade Federal do Rio Grande, Rio Grande, Rio Grande do Sul, Brazil
| | - Maíra Macedo
- Núcleo de Pesquisa em Microbiologia Médica, Faculdade de Medicina, Universidade Federal do Rio Grande, Rio Grande, Rio Grande do Sul, Brazil
| | - João L Scaini
- Núcleo de Pesquisa em Microbiologia Médica, Faculdade de Medicina, Universidade Federal do Rio Grande, Rio Grande, Rio Grande do Sul, Brazil
| | - Ana B Silva
- Núcleo de Pesquisa em Microbiologia Médica, Faculdade de Medicina, Universidade Federal do Rio Grande, Rio Grande, Rio Grande do Sul, Brazil
| | - Leonardo Esteves
- Centro de Desenvolvimento Científico e Tecnológico (CDCT), Porto Alegre, Brazil
| | - Rita Macedo
- Departamento de Doenças Infecciosas, Instituto Nacional de Saúde Dr. Ricardo Jorge, Lisboa, Portugal
| | - Fernando Maltez
- Serviço de Doenças Infecciosas, Hospital de Curry Cabral, Lisboa, Portugal
| | - Sofia Clemente
- Hospital da Divina Providência, Serviço de Doenças Infecciosas, Luanda, Angola
| | - Elizabeth Coelho
- Programa Nacional de Controlo da Tuberculose, Ministério da Saúde de Moçambique, Mozambique
| | - Sofia Viegas
- Instituto Nacional de Saúde, Ministério da Saúde de Moçambique, Mozambique
| | - Paulo Rabna
- Instituto Nacional de Saúde Pública, Projecto de Saúde de Bandim (INASA/PSB), Bissau, Guinea-Bissau
| | - Amabélia Rodrigues
- Instituto Nacional de Saúde Pública, Projecto de Saúde de Bandim (INASA/PSB), Bissau, Guinea-Bissau
| | - Nuno Taveira
- iMed.ULisboa - Instituto de Investigação do Medicamento, Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal; Centro de Investigação Interdisciplinar Egas Moniz, Instituto Superior de Ciências da Saúde Egas Moniz, Monte de Caparica, Portugal
| | - Luísa Jordao
- Departamento de Doenças Infecciosas, Instituto Nacional de Saúde Dr. Ricardo Jorge, Lisboa, Portugal
| | - Afrânio Kritski
- Academic Tuberculosis Program, School of Medicine, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - José R Lapa E Silva
- Thoracic Diseases Institute, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Igor Mokrousov
- Laboratory of Molecular Epidemiology and Evolutionary Genetics (former Laboratory of Molecular Microbiology), St. Petersburg Pasteur Institute, St. Petersburg, Russia
| | - David Couvin
- WHO Supranational TB Reference Laboratory, Tuberculosis and Mycobacteria Unit, Institut Pasteur de la Guadeloupe, Morne Jolivière Abymes, Guadeloupe, France
| | - Nalin Rastogi
- WHO Supranational TB Reference Laboratory, Tuberculosis and Mycobacteria Unit, Institut Pasteur de la Guadeloupe, Morne Jolivière Abymes, Guadeloupe, France
| | - Isabel Couto
- Unidade de Microbiologia Médica, Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Lisboa, Portugal
| | - Arnab Pain
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Ruth McNerney
- Lung Infection and Immunity Unit, UCT Lung Institute, University of Cape Town, Groote Schuur Hospital, Observatory, 7925, Cape Town, South Africa
| | - Taane G Clark
- London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
| | - Andrea von Groll
- Núcleo de Pesquisa em Microbiologia Médica, Faculdade de Medicina, Universidade Federal do Rio Grande, Rio Grande, Rio Grande do Sul, Brazil
| | - Elis R Dalla-Costa
- Centro de Desenvolvimento Científico e Tecnológico (CDCT), Porto Alegre, Brazil
| | - Maria Lúcia Rossetti
- Centro de Desenvolvimento Científico e Tecnológico (CDCT), Porto Alegre, Brazil; Universidade Luterana do Brasil (ULBRA/RS), Porto Alegre, Brazil
| | - Pedro E A Silva
- Núcleo de Pesquisa em Microbiologia Médica, Faculdade de Medicina, Universidade Federal do Rio Grande, Rio Grande, Rio Grande do Sul, Brazil
| | - Miguel Viveiros
- Unidade de Microbiologia Médica, Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Lisboa, Portugal
| | - Isabel Portugal
- iMed.ULisboa - Instituto de Investigação do Medicamento, Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal.
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