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Shamebo T, Gumi B, Zewude A, Gashaw F, Mohammed T, Girma M, Zerihun B, Getu M, Mekasha S, Getahun M, Wondale B, Petros B, Ameni G. Molecular epidemiology and drug sensitivity of Mycobacterium tuberculosis in homeless individuals in the Addis Ababa city, Ethiopia. Sci Rep 2023; 13:21370. [PMID: 38049519 PMCID: PMC10695943 DOI: 10.1038/s41598-023-48407-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 11/26/2023] [Indexed: 12/06/2023] Open
Abstract
Although homeless segment of the society could be the hotspots for tuberculosis (TB) transmission, there is little data on TB in homeless individuals in Ethiopia. The objective of this study was to investigate the molecular epidemiology and drug sensitivity of Mycobacterium tuberculosis (M. tuberculosis) isolated from homeless individuals in Addis Ababa, Ethiopia. The study was conducted on 59 M. tuberculosis isolates, which were recovered by the clinical screening of 5600 homeless individuals and bacteriological examination of 641 individuals with symptoms of pulmonary tuberculosis (PTB). Region of difference-9 (RD9) based polymerase-chain reaction (PCR), Spoligotyping and 24-loci Mycobacterial Interspersed Repetitive Unit-Variable Number Tandem Repeat (MIRU-VNTR) typing were used for genotyping of the isolates. In addition, drug sensitivity test was performed on the isolates using BD Bactec Mycobacterial Growth Inhibition Tube (MGIT) 960. Fifty-eight of the 59 isolates were positive by spoligotyping and spoligotyping International type (SIT) 53, SIT 37, and SIT 149 were the dominant spoligotypes; each consisting of 19%, 15.5%, and10.3% of the isolates, respectively. The majority of the isolates (89.7%) were members of the Euro-American (EA) major lineage. MIRU-VNTR identified Ethiopia_3, Delhi/CAS, Ethiopia_2, TUR, X-type, Ethiopia_H37Rv-like strain, Haarlem and Latin-American Mediterranean (LAM) sub lineages. The proportion of clustering was 77.6% (45/58) in spoligotyping while it was 39.7% (23/58) in 24-loci MIRU-VNTR typing. Furthermore, the proportion of clustering was significantly lowered to 10.3% (6/58) when a combination of spoligotyping and 24-loci MIRU-VNTRplus was used. The recent transmission index (RTI) recorded by spoligotyping, 24-loci MIRU-VNTR typing, and a combination of the two genotyping methods were 58.6%, 27.6% and 5.2%, respectively. Young age and living in groups were significantly associated with strain clustering (P < 0.05). The drug sensitivity test (DST) result showed 8.9% (4/58) of the isolates were resistant to one or more first line ant-TB drugs; but multidrug resistant isolate was not detected. Clustering and RTI could suggest the transmission of TB in the homeless individuals, which could suggest a similar pattern of transmission between homeless individuals and the general population. Hence, the TB control program should consider homeless individuals during the implementation of TB control program.
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Affiliation(s)
- Tsegaye Shamebo
- Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, PO. Box 1176, Addis Ababa, Ethiopia
| | - Balako Gumi
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Po. Box 1176, Addis Ababa, Ethiopia
| | - Aboma Zewude
- Ethiopian National Tuberculosis Reference Laboratory, Ethipian Public Health Institute, PO. Box 1242 or 5654, Addis Ababa, Ethiopia
- Arba Minch University, Araba Minch, Ethiopia
| | - Fikru Gashaw
- Kotebe University of Education, Addis Ababa, Ethiopia
| | - Temesgen Mohammed
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, PO Box 15551, Al Ain, United Arab Emirates
- Arba Minch University, Araba Minch, Ethiopia
| | - Muse Girma
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Po. Box 1176, Addis Ababa, Ethiopia
| | - Betselot Zerihun
- Ethiopian National Tuberculosis Reference Laboratory, Ethipian Public Health Institute, PO. Box 1242 or 5654, Addis Ababa, Ethiopia
| | - Melak Getu
- Ethiopian National Tuberculosis Reference Laboratory, Ethipian Public Health Institute, PO. Box 1242 or 5654, Addis Ababa, Ethiopia
| | - Sindew Mekasha
- Ethiopian National Tuberculosis Reference Laboratory, Ethipian Public Health Institute, PO. Box 1242 or 5654, Addis Ababa, Ethiopia
| | - Muluwork Getahun
- Ethiopian National Tuberculosis Reference Laboratory, Ethipian Public Health Institute, PO. Box 1242 or 5654, Addis Ababa, Ethiopia
| | | | - Beyene Petros
- Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, PO. Box 1176, Addis Ababa, Ethiopia
| | - Gobena Ameni
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Po. Box 1176, Addis Ababa, Ethiopia.
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, PO Box 15551, Al Ain, United Arab Emirates.
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Phyu AN, Aung ST, Palittapongarnpim P, Htet KKK, Mahasirimongkol S, Ruangchai W, Jaemsai B, Aung HL, Maung HMW, Chaiprasert A, Pungrassami P, Chongsuvivatwong V. Genomic Sequencing Profiles of Mycobacterium tuberculosis in Mandalay Region, Myanmar. Trop Med Infect Dis 2023; 8:239. [PMID: 37104364 PMCID: PMC10141229 DOI: 10.3390/tropicalmed8040239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/05/2023] [Accepted: 04/18/2023] [Indexed: 04/28/2023] Open
Abstract
This study aimed to characterize whole-genome sequencing (WGS) information of Mycobacterium tuberculosis (Mtb) in the Mandalay region of Myanmar. It was a cross-sectional study conducted with 151 Mtb isolates obtained from the fourth nationwide anti-tuberculosis (TB) drug-resistance survey. Frequency of lineages 1, 2, 3, and 4 were 55, 65, 9, and 22, respectively. The most common sublineage was L1.1.3.1 (n = 31). Respective multi-drug resistant tuberculosis (MDR-TB) frequencies were 1, 1, 0, and 0. Four clusters of 3 (L2), 2 (L4), 2 (L1), and 2 (L2) isolates defined by a 20-single-nucleotide variant (SNV) cutoff were detected. Simpson's index for sublineages was 0.0709. Such high diversity suggests that the area probably had imported Mtb from many geographical sources. Relatively few genetic clusters and MDR-TB suggest there is a chance the future control will succeed if it is carried out properly.
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Affiliation(s)
- Aye Nyein Phyu
- National Tuberculosis Programme, Department of Public Health, Ministry of Health, Mandalay 05071, Myanmar
- Department of Epidemiology, Faculty of Medicine, Prince of Songkla University, Hat Yai 90110, Thailand
| | - Si Thu Aung
- Department of Public Health, Ministry of Health, Keng Tung 06231, Myanmar
| | - Prasit Palittapongarnpim
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Kyaw Ko Ko Htet
- Department of Epidemiology, Faculty of Medicine, Prince of Songkla University, Hat Yai 90110, Thailand
| | - Surakameth Mahasirimongkol
- Medical Life Sciences Institute, Department of Medical Sciences, Ministry of Public Health, Nonthaburi 11000, Thailand
| | - Wuthiwat Ruangchai
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Bharkbhoom Jaemsai
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Htin Lin Aung
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand
| | - Htet Myat Win Maung
- Department of Epidemiology, Faculty of Medicine, Prince of Songkla University, Hat Yai 90110, Thailand
| | - Angkana Chaiprasert
- Office of Research and Innovation, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Petchawan Pungrassami
- Department of Disease Control, Ministry of Public Health, Nonthaburi 11000, Thailand
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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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Identification of a predominant genotype of Mycobacterium tuberculosis in Brazilian indigenous population. Sci Rep 2021; 11:1224. [PMID: 33441660 PMCID: PMC7806709 DOI: 10.1038/s41598-020-79621-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 12/07/2020] [Indexed: 11/30/2022] Open
Abstract
After nearly a century of vaccination and six decades of drug therapy, tuberculosis (TB) kills more people annually than any other infectious disease. Substantial challenges to disease eradication remain among vulnerable and underserved populations. The Guarani-Kaiowá people are an indigenous population in Paraguay and the Brazilian state of Mato Grosso do Sul. This community, marginalized in Brazilian society, experiences severe poverty. Like other South American indigenous populations, their TB prevalence is high, but the disease has remained largely unstudied in their communities. Herein, Mycobacterium tuberculosis isolates from local clinics were whole genome sequenced, and a population genetic framework was generated. Phylogenetics show M. tuberculosis isolates in the Guarani-Kaiowá people cluster away from selected reference strains, suggesting divergence. Most cluster in a single group, further characterized as M. tuberculosis sublineage 4.3.3. Closer analysis of SNPs showed numerous variants across the genome, including in drug resistance-associated genes, and with many unique changes fixed in each group. We report that local M. tuberculosis strains have acquired unique polymorphisms in the Guarani-Kaiowá people, and drug resistance characterization is urgently needed to inform public health to ensure proper care and avoid further evolution and spread of drug-resistant TB.
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The contribution of stigma to the transmission and treatment of tuberculosis in a hyperendemic indigenous population in Brazil. PLoS One 2020; 15:e0243988. [PMID: 33326453 PMCID: PMC7743939 DOI: 10.1371/journal.pone.0243988] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 12/01/2020] [Indexed: 11/24/2022] Open
Abstract
Background The Guarani-Kaiowá are Brazil's second-largest indigenous group. Average annual tuberculosis (TB) incidence rates among the Guarani-Kaiowá are nearly 400/100,000 in Mato Grosso do Sul state, ten times the national average. Although stigma is considered crucial for TB control in indigenous communities, few studies have investigated TB stigma among indigenous populations. This study sought to understand the role of TB-related stigma and perceptions of TB in maintaining hyperendemic TB transmission in the Guarani-Kaiowá communities. Methods Various forms of stigma were explored through semi-structured interviews with 19 patients, 11 relatives, and 23 community members. Patients were identified from the registry of the healthcare service. Community members, selected by snowball sampling, were matched by gender and village of residence. Interviews were conducted in Guarani and Portuguese and later translated into English. Framework analysis was performed using NVivo. Results Traditional beliefs of a weakening of the body allowing the disease to enter were common, but the exact mechanism of transmission was unknown. Strong community/public stigma associated TB with uncleanliness, abuse, and irresponsibility. Anticipated stigma led to significant treatment delays for fear of exclusion and losing employment. While most patients felt supported by their families, nearly all patients related experienced/enacted stigma in the community such as gossip, avoidance, and social exclusion, leading to long-lasting internalized/self-stigma. Secondary stigmatization of relatives was widespread, and blanket latent TB infection (LTBI) treatment of patients’ households was a contributing factor in treatment delay. The healthcare service unnecessarily added to stigmatization by enforcing separate utensils and sleeping arrangements for patients. Conclusions Our findings suggest that stigma is a driver for treatment delay and continued transmission of TB in the community. The stigmatization of TB was rooted in a poor understanding of TB transmission, partly because of incorrect orientation by the healthcare service. Interventions to reduce TB-associated stigma are urgently needed.
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Walter KS, Colijn C, Cohen T, Mathema B, Liu Q, Bowers J, Engelthaler DM, Narechania A, Lemmer D, Croda J, Andrews JR. Genomic variant-identification methods may alter Mycobacterium tuberculosis transmission inferences. Microb Genom 2020; 6:mgen000418. [PMID: 32735210 PMCID: PMC7641424 DOI: 10.1099/mgen.0.000418] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/15/2020] [Indexed: 12/31/2022] Open
Abstract
Pathogen genomic data are increasingly used to characterize global and local transmission patterns of important human pathogens and to inform public health interventions. Yet, there is no current consensus on how to measure genomic variation. To test the effect of the variant-identification approach on transmission inferences for Mycobacterium tuberculosis, we conducted an experiment in which five genomic epidemiology groups applied variant-identification pipelines to the same outbreak sequence data. We compared the variants identified by each group in addition to transmission and phylogenetic inferences made with each variant set. To measure the performance of commonly used variant-identification tools, we simulated an outbreak. We compared the performance of three mapping algorithms, five variant callers and two variant filters in recovering true outbreak variants. Finally, we investigated the effect of applying increasingly stringent filters on transmission inferences and phylogenies. We found that variant-calling approaches used by different groups do not recover consistent sets of variants, which can lead to conflicting transmission inferences. Further, performance in recovering true variation varied widely across approaches. While no single variant-identification approach outperforms others in both recovering true genome-wide and outbreak-level variation, variant-identification algorithms calibrated upon real sequence data or that incorporate local reassembly outperform others in recovering true pairwise differences between isolates. The choice of variant filters contributed to extensive differences across pipelines, and applying increasingly stringent filters rapidly eroded the accuracy of transmission inferences and quality of phylogenies reconstructed from outbreak variation. Commonly used approaches to identify M. tuberculosis genomic variation have variable performance, particularly when predicting potential transmission links from pairwise genetic distances. Phylogenetic reconstruction may be improved by less stringent variant filtering. Approaches that improve variant identification in repetitive, hypervariable regions, such as long-read assemblies, may improve transmission inference.
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Affiliation(s)
- Katharine S. Walter
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Caroline Colijn
- Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada
| | - Ted Cohen
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Barun Mathema
- Department of Epidemiology, Mailman School of Public Health, Columbia University Medical Center, New York, New York, USA
| | - Qingyun Liu
- School of Basic Medical Science of Fudan University, Shanghai, PR China
| | - Jolene Bowers
- Translational Genomics Research Institute, Flagstaff, AZ, USA
| | | | | | - Darrin Lemmer
- Translational Genomics Research Institute, Flagstaff, AZ, USA
| | - Julio Croda
- School of Medicine, Federal University of Mato Grosso do Sul, Campo Grande, Brazil
- Oswaldo Cruz Foundation, Campo Grande, Brazil
| | - Jason R. Andrews
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA
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Tatara MB, Perdigão J, Viveiros M, Kritski A, Silva KED, Sacchi FPC, de Lima CC, Dos Santos PCP, Diniz JDLDCG, Almeida Silva PE, Gomes P, Gomes MMQ, Cunha EAT, Lapa E Silva JR, Portugal I, Croda J, Andrade MKDN. Genetic Diversity and Molecular Epidemiology of Mycobacterium tuberculosis in Roraima State, Brazil. Am J Trop Med Hyg 2020; 101:774-779. [PMID: 31392954 DOI: 10.4269/ajtmh.19-0324] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
National border areas are special places for the spread of Mycobacterium tuberculosis (MTB). These regions concentrate vulnerable populations and constant population movements. Understanding the dynamics of the transmission of MTB is fundamental to propose control measures and to monitor drug resistance. We conducted a population-based prospective study of tuberculosis (TB) to evaluate molecular characteristics of MTB isolates circulating in Roraima, a state on the border of Venezuela and Guyana. Eighty isolates were genotyped by IS6110-RFLP (restriction fragment length polymorphism), spoligotyping, and 24-locus mycobacterial interspersed repetitive unit-variable number of repeats tandem (MIRU-VNTR). Drug susceptibility tests were performed by using the proportion method and GeneXpert® MTB/RIF (Cepheid, Sunnyvale, CA). Isolates showing a phenotypic resistance profile were submitted to polymerase chain reaction (PCR) and sequencing. Spoligotyping showed 40 distinct patterns with a high prevalence of Latin-American and Mediterranean (LAM), Haarlem (H), and the "ill-defined" T clades. Mycobacterial interspersed repetitive unit -VNTR and IS6110-RFLP showed clustering rates of 21.3% and 30%, respectively. Drug resistance was detected in 11 (15.1%) isolates, and all were found to have primary resistance; among these, six (8.2%) isolates were streptomycin mono-resistant, four (5.4%) isoniazid mono-resistant, and one (1.3%) multidrug resistant. This is the first study on the molecular epidemiology and drug resistance profile of MTB from Roraima. Herein, we describe high diversity of genetic profiles circulating in this region that may be driven by the introduction of new strain types because of large population flow in this region. In summary, our results showed that analyses of these circulating strains can contribute to a better understanding of TB epidemiology in the northern Brazilian border and be useful to establish public health policies on TB prevention.
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Affiliation(s)
- Mariana Bento Tatara
- Laboratory of Research in Health Science, Faculty of Health Science, Federal University of Grande Dourados, Dourados, Brazil
| | - João Perdigão
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, University of Lisbon, Lisbon, Portugal
| | - Miguel Viveiros
- Institute of Hygiene and Tropical Medicine (IHMT), Global Health and Tropical Medicine (GHTM), University NOVA of Lisbon, Lisbon, Portugal
| | - Afrânio Kritski
- School of Medicine, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Kesia Esther da Silva
- Laboratory of Research in Health Science, Faculty of Health Science, Federal University of Grande Dourados, Dourados, Brazil
| | | | - Camila Camioli de Lima
- Laboratory of Research in Health Science, Faculty of Health Science, Federal University of Grande Dourados, Dourados, Brazil
| | - Paulo César Pereira Dos Santos
- Laboratory of Research in Health Science, Faculty of Health Science, Federal University of Grande Dourados, Dourados, Brazil
| | | | - Pedro Eduardo Almeida Silva
- Nucleus of Research in Medical Microbiology, Faculty of Medicine, Federal University of Rio Grande, Rio Grande, Brazil
| | - Pedro Gomes
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, University of Lisbon, Lisbon, Portugal
| | | | | | | | - Isabel Portugal
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, University of Lisbon, Lisbon, Portugal
| | - Julio Croda
- School of Medicine, Federal University of Mato Grosso do Sul, Campo Grande, Brazil.,Oswaldo Cruz Foundation, Campo Grande, Brazil
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Ross JM, Henry NJ, Dwyer-Lindgren LA, de Paula Lobo A, Marinho de Souza F, Biehl MH, Ray SE, Reiner RC, Stubbs RW, Wiens KE, Earl L, Kutz MJ, Bhattacharjee NV, Kyu HH, Naghavi M, Hay SI. Progress toward eliminating TB and HIV deaths in Brazil, 2001-2015: a spatial assessment. BMC Med 2018; 16:144. [PMID: 30185204 PMCID: PMC6125942 DOI: 10.1186/s12916-018-1131-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 07/17/2018] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Brazil has high burdens of tuberculosis (TB) and HIV, as previously estimated for the 26 states and the Federal District, as well as high levels of inequality in social and health indicators. We improved the geographic detail of burden estimation by modelling deaths due to TB and HIV and TB case fatality ratios for the more than 5400 municipalities in Brazil. METHODS This ecological study used vital registration data from the national mortality information system and TB case notifications from the national communicable disease notification system from 2001 to 2015. Mortality due to TB and HIV was modelled separately by cause and sex using a Bayesian spatially explicit mixed effects regression model. TB incidence was modelled using the same approach. Results were calibrated to the Global Burden of Disease Study 2016. Case fatality ratios were calculated for TB. RESULTS There was substantial inequality in TB and HIV mortality rates within the nation and within states. National-level TB mortality in people without HIV infection declined by nearly 50% during 2001 to 2015, but HIV mortality declined by just over 20% for males and 10% for females. TB and HIV mortality rates for municipalities in the 90th percentile nationally were more than three times rates in the 10th percentile, with nearly 70% of the worst-performing municipalities for male TB mortality and more than 75% for female mortality in 2001 also in the worst decile in 2015. The same municipality ranking metric for HIV was observed to be between 55% and 61%. Within states, the TB mortality rate ratios by sex for municipalities in the worst decile versus the best decile varied from 1.4 to 2.9, and HIV varied from 1.4 to 4.2. The World Health Organization target case fatality rate for TB of less than 10% was achieved in 9.6% of municipalities for males versus 38.4% for females in 2001 and improved to 38.4% and 56.6% of municipalities for males versus females, respectively, by 2014. CONCLUSIONS Mortality rates in municipalities within the same state exhibited nearly as much relative variation as within the nation as a whole. Monitoring the mortality burden at this level of geographic detail is critical for guiding precision public health responses.
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Affiliation(s)
- Jennifer M Ross
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA.,Institute for Health Metrics and Evaluation, University of Washington, 2301 5th Ave Suite 600, Seattle, WA, 98121, USA
| | - Nathaniel J Henry
- Institute for Health Metrics and Evaluation, University of Washington, 2301 5th Ave Suite 600, Seattle, WA, 98121, USA
| | - Laura A Dwyer-Lindgren
- Institute for Health Metrics and Evaluation, University of Washington, 2301 5th Ave Suite 600, Seattle, WA, 98121, USA
| | - Andrea de Paula Lobo
- Department of Public Health, University of Brasilia, Distrito Federal, Brazil.,Department of Health Surveillance, Ministry of Health, Brasilia, Brazil
| | | | - Molly H Biehl
- Institute for Health Metrics and Evaluation, University of Washington, 2301 5th Ave Suite 600, Seattle, WA, 98121, USA
| | - Sarah E Ray
- Institute for Health Metrics and Evaluation, University of Washington, 2301 5th Ave Suite 600, Seattle, WA, 98121, USA
| | - Robert C Reiner
- Institute for Health Metrics and Evaluation, University of Washington, 2301 5th Ave Suite 600, Seattle, WA, 98121, USA
| | - Rebecca W Stubbs
- Institute for Health Metrics and Evaluation, University of Washington, 2301 5th Ave Suite 600, Seattle, WA, 98121, USA
| | - Kirsten E Wiens
- Institute for Health Metrics and Evaluation, University of Washington, 2301 5th Ave Suite 600, Seattle, WA, 98121, USA
| | - Lucas Earl
- Institute for Health Metrics and Evaluation, University of Washington, 2301 5th Ave Suite 600, Seattle, WA, 98121, USA
| | - Michael J Kutz
- Institute for Health Metrics and Evaluation, University of Washington, 2301 5th Ave Suite 600, Seattle, WA, 98121, USA
| | - Natalia V Bhattacharjee
- Institute for Health Metrics and Evaluation, University of Washington, 2301 5th Ave Suite 600, Seattle, WA, 98121, USA
| | - Hmwe H Kyu
- Institute for Health Metrics and Evaluation, University of Washington, 2301 5th Ave Suite 600, Seattle, WA, 98121, USA
| | - Mohsen Naghavi
- Institute for Health Metrics and Evaluation, University of Washington, 2301 5th Ave Suite 600, Seattle, WA, 98121, USA
| | - Simon I Hay
- Institute for Health Metrics and Evaluation, University of Washington, 2301 5th Ave Suite 600, Seattle, WA, 98121, USA.
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