1
|
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.
Collapse
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
| |
Collapse
|
2
|
Antibiotic resistance of Mycobacterium tuberculosis complex in Africa: A systematic review of current reports of molecular epidemiology, mechanisms and diagnostics. J Infect 2019; 79:550-571. [DOI: 10.1016/j.jinf.2019.10.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 10/13/2019] [Indexed: 12/11/2022]
|
3
|
Woodman M, Haeusler IL, Grandjean L. Tuberculosis Genetic Epidemiology: A Latin American Perspective. Genes (Basel) 2019; 10:genes10010053. [PMID: 30654542 PMCID: PMC6356704 DOI: 10.3390/genes10010053] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 01/09/2019] [Accepted: 01/11/2019] [Indexed: 11/16/2022] Open
Abstract
There are an estimated 10 million new cases of tuberculosis worldwide annually, with 282,000 new or relapsed cases each year reported from the Americas. With improvements in genome sequencing technology, it is now possible to study the genetic diversity of tuberculosis with much greater resolution. Although tuberculosis bacteria do not engage in horizontal gene transfer, the genome is far more variable than previously thought. The study of genome-wide variation in tuberculosis has improved our understanding of the evolutionary origins of tuberculosis, the arrival of tuberculosis in Latin America, the genetic determinants of drug resistance, and lineage-specific associations with important clinical phenotypes. This article reviews what is known about the arrival of tuberculosis in Latin America, the genetic diversity of tuberculosis in Latin America, and the genotypic determinants of clinical phenotypes.
Collapse
Affiliation(s)
- Marc Woodman
- Institute of Child Health, University College London, London WC1N 3JH, UK.
| | - Ilsa L Haeusler
- Institute of Child Health, University College London, London WC1N 3JH, UK.
| | - Louis Grandjean
- Institute of Child Health, University College London, London WC1N 3JH, UK.
- Department of Medicine, Imperial College London, London W2 1NY, UK.
- Great Ormond Street Hospital, Institute of Child Health, University College London, London WC1N 3JH, UK.
- Laboratorio de Investigacion y Desarollo, Universidad Peruana Cayetano Heredia, Av. Honorio Delgado 430, San Martin de Porres 15102, Lima, Peru.
| |
Collapse
|
4
|
Caleffi-Ferracioli KR, Baldin VP, Noguti ÉN, Siqueira VLD, Scodro RBL, Pavan FR, Hirata MH, Cardoso RF. Molecular characterization of Mycobacterium tuberculosis and Mycobacterium bovis isolates by Enterobacterial Repetitive Intergenic Consensus-PCR. BRAZ J PHARM SCI 2018. [DOI: 10.1590/s2175-97902018000317554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|
5
|
de Almeida AL, Scodro RBDL, de Carvalho HC, Costacurta GF, Baldin VP, Santos NCS, Ghiraldi-Lopes LD, Campanerut-Sá PAZ, Siqueira VLD, Caleffi-Ferracioli KR, Shibata FK, Sprada A, Cardoso RF. RD RioMycobacterium tuberculosis lineage in the Brazil/Paraguay/Argentina triple border. Tuberculosis (Edinb) 2018; 110:68-78. [PMID: 29779776 DOI: 10.1016/j.tube.2018.03.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 03/22/2018] [Accepted: 03/24/2018] [Indexed: 10/17/2022]
Abstract
The high tuberculosis (TB) incidence rates, the closeness of the cities and the high migration flux on the Brazil/Paraguay/Argentina border deserves an in-depth study, using Mycobacterial Interspersed Repetitive Unit (MIRU) and Spoligotyping genetic markers to explore the impact of the Mycobacterium tuberculosis RDRio lineage on disease transmission and resistance to anti-TB drugs in this setting. Although without the totality of M. tuberculosis isolates causing TB in this studied setting, a number of 97 isolates obtained from sputa samples culture of patients with confirmed TB, from 2013 to 2015, were submitted to 24 loci MIRU, Spoligotyping, detection of RDRio lineage and detection of mutation related to isoniazid and rifampicin resistance by MTBDRplus/DNA STRIP. In this sample, it was observed high clonal variability of circulating M. tuberculosis isolates causing TB in Brazilian cities bordering Paraguay and Argentina. The percentage of RDRio lineage causing TB in this setting was 15.46%, and lower than the detected in different areas of Brazil. According to 24 loci MIRU, the major MIRU International Type (MIT) related with RDRio lineage were MIT 26, MIT 738, MIT 601 with four, two and one isolates, respectively. Eight isolates with RDRio marker were classified as orphans. The mainly Spoligofamily related with RDRio lineage was LAM1 and LAM9 and no relationship between RDRio lineage and resistance in M. tuberculosis isolates circulating in this setting could be established. This work is pioneer in studying the dynamics of RDRio lineage transmission on the Brazil/Paraguay/Argentina border and deserves further studies to analyze the real contribution of the RDRio lineage in outbreaks and the risk of significant development of MDR-TB in the setting studied.
Collapse
Affiliation(s)
- Aryadne Larissa de Almeida
- Programa de Pós-Graduação em Biociências e Fisiopatologia, Universidade Estadual de Maringá, PR, Brazil.
| | - Regiane Bertin de Lima Scodro
- Departamento de Análises Clínicas e Biomedicina, Universidade Estadual de Maringá, PR, Brazil; Programa de Pós-Graduação em Ciências da Saúde, Universidade Estadual de Maringá, PR, Brazil.
| | - Hayalla Corrêa de Carvalho
- Programa de Pós-Graduação em Biociências e Fisiopatologia, Universidade Estadual de Maringá, PR, Brazil.
| | | | - Vanessa Pietrowski Baldin
- Programa de Pós-Graduação em Biociências e Fisiopatologia, Universidade Estadual de Maringá, PR, Brazil.
| | | | | | | | - Vera Lucia Dias Siqueira
- Programa de Pós-Graduação em Biociências e Fisiopatologia, Universidade Estadual de Maringá, PR, Brazil; Departamento de Análises Clínicas e Biomedicina, Universidade Estadual de Maringá, PR, Brazil.
| | | | | | | | - Rosilene Fressatti Cardoso
- Programa de Pós-Graduação em Biociências e Fisiopatologia, Universidade Estadual de Maringá, PR, Brazil; Departamento de Análises Clínicas e Biomedicina, Universidade Estadual de Maringá, PR, Brazil; Programa de Pós-Graduação em Ciências da Saúde, Universidade Estadual de Maringá, PR, Brazil.
| |
Collapse
|
6
|
Augusto CJ, Carvalho WDS, Almeida IND, Figueiredo LJDA, Dantas NGT, Suffys PN, Miranda SSD. Comparative study of RFLP-IS6110 and MIRU-VNTR from Mycobacterium tuberculosis isolated in the state of Minas Gerais, Brazil. Braz J Microbiol 2017; 49:641-646. [PMID: 29249565 PMCID: PMC6112052 DOI: 10.1016/j.bjm.2017.04.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 02/08/2017] [Accepted: 04/06/2017] [Indexed: 11/16/2022] Open
Abstract
DNA genotyping of Mycobacterium tuberculosis has been widely applied in the understanding of disease transmission in many countries. The purpose of this study was to genotype the strains of M. tuberculosis isolated in patients with new tuberculosis (TB) cases in Minas Gerais, as well as to compare the similarity, discriminatory power, and agreement of the clusters between the IS6110 Restriction Fragment Length Polymorfism (RFLP) and 12 loci Variable Number Tandem Repeat – Mycobacterial Interspersed Repetitive Units (MIRU-VNTR) techniques. It was observed that 32% (66/204) of the isolated strains in the RFLP-IS6110 and 50.9% (104/204) of the isolated strains in the MIRU-VNTR presented a similarity of equal to or above 85%. The RFLP-IS6110 and MIRU-VNTR proved to contain a high discriminatory power. The similarity index resulting from the RFLP showed no recent transmission. Good agreement was observed between the techniques when clusters were detected; however, the best epidemiological relationship was found when using the RFLP-IS6110.
Collapse
Affiliation(s)
- Cláudio José Augusto
- Fundação Ezequiel Dias, Belo Horizonte, MG, Brazil; Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | | | | | | | | | - Philip Noel Suffys
- Fundação Oswaldo Cruz Foundation (FIOCRUZ), Instituto Oswaldo Cruz, Laboratório de Biologia Molecular Aplicada a Micobactérias, Rio de Janeiro, RJ, Brazil
| | | |
Collapse
|
7
|
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: 0.6] [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.
Collapse
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
| |
Collapse
|
8
|
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.
Collapse
|
9
|
Devi KR, Bhutia R, Bhowmick S, Mukherjee K, Mahanta J, Narain K. Genetic Diversity of Mycobacterium tuberculosis Isolates from Assam, India: Dominance of Beijing Family and Discovery of Two New Clades Related to CAS1_Delhi and EAI Family Based on Spoligotyping and MIRU-VNTR Typing. PLoS One 2015; 10:e0145860. [PMID: 26701129 PMCID: PMC4689458 DOI: 10.1371/journal.pone.0145860] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 12/09/2015] [Indexed: 11/24/2022] Open
Abstract
Tuberculosis (TB) is one of the major public health concerns in Assam, a remote state located in the northeastern (NE) region of India. The present study was undertaken to explore the circulating genotypes of Mycobacterium tuberculosis complex (MTBC) in this region. A total of 189 MTBC strains were collected from smear positive pulmonary tuberculosis cases from different designated microscopy centres (DMC) from various localities of Assam. All MTBC isolates were cultured on Lowenstein-Jensen (LJ) media and subsequently genotyped using spoligotyping and 24-loci mycobacterial interspersed repetitive units-variable number of tandem repeats (MIRU-VNTR) typing. Spoligotyping of MTBC isolates revealed 89 distinct spoligo patterns. The most dominant MTBC strain belonged to Beijing lineage and was represented by 35.45% (n = 67) of total isolates, followed by MTBC strains belonging to Central Asian-Delhi (CAS/Delhi) lineage and East African Indian (EAI5) lineage. In addition, in the present study 43 unknown spoligo patterns were detected. The discriminatory power of spoligotyping was found to be 0.8637 based on Hunter Gaston Discriminatory Index (HGDI). On the other hand, 24-loci MIRU-VNTR typing revealed that out of total 189 MTBC isolates from Assam 185 (97.9%) isolates had unique MIRU-VNTR profiles and 4 isolates grouped into 2 clusters. Phylogenetic analysis of 67 Beijing isolates based on 24-loci MIRU-VNTR typing revealed that Beijing isolates from Assam represent two major groups, each comprising of several subgroups. Neighbour-Joining (NJ) phylogenetic tree analysis based on combined spoligotyping and 24-loci MIRU-VNTR data of 78 Non-Beijing isolates was carried out for strain lineage identification as implemented by MIRU-VNTRplus database. The important lineages of MTBC identified were CAS/CAS1_Delhi (41.02%, n = 78) and East-African-Indian (EAI, 33.33%). Interestingly, phylogenetic analysis of orphan (23.28%) MTBC spoligotypes revealed that majority of these orphan isolates from Assam represent two new sub-clades Assam/EAI and Assam/CAS. The prevalence of multidrug resistance (MDR) in Beijing and Non-Beijing strains was found to be 10.44% and 9.01% respectively. In conclusion, the present study has shown the predominance of Beijing isolates in Assam which is a matter of great concern because Beijing strains are considered to be ecologically more fit enabling wider dissemination of M. tuberculosis. Other interesting finding of the present study is the discovery of two new clades of MTBC isolates circulating in Assam. More elaborate longitudinal studies are required to be undertaken in this region to understand the transmission dynamics of MTBC.
Collapse
Affiliation(s)
- Kangjam Rekha Devi
- Regional Medical Research Centre, N.E. Region (Indian Council of Medical Research), Post Box #105, Dibrugarh 786 001, Assam, India
| | - Rinchenla Bhutia
- Regional Medical Research Centre, N.E. Region (Indian Council of Medical Research), Post Box #105, Dibrugarh 786 001, Assam, India
| | - Shovonlal Bhowmick
- Regional Medical Research Centre, N.E. Region (Indian Council of Medical Research), Post Box #105, Dibrugarh 786 001, Assam, India
| | - Kaustab Mukherjee
- Regional Medical Research Centre, N.E. Region (Indian Council of Medical Research), Post Box #105, Dibrugarh 786 001, Assam, India
| | - Jagadish Mahanta
- Regional Medical Research Centre, N.E. Region (Indian Council of Medical Research), Post Box #105, Dibrugarh 786 001, Assam, India
| | - Kanwar Narain
- Regional Medical Research Centre, N.E. Region (Indian Council of Medical Research), Post Box #105, Dibrugarh 786 001, Assam, India
- * E-mail:
| |
Collapse
|
10
|
Streit E, Baboolal S, Akpaka PE, Millet J, Rastogi N. Finer characterization of Mycobacterium tuberculosis using spoligotyping and 15-loci MIRU-VNTRs reveals phylogeographical specificities of isolates circulating in Guyana and Suriname. INFECTION GENETICS AND EVOLUTION 2014; 30:114-119. [PMID: 25528138 DOI: 10.1016/j.meegid.2014.12.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 12/09/2014] [Accepted: 12/10/2014] [Indexed: 11/15/2022]
Abstract
In this study we used spoligotyping and 15-loci MIRU-VNTRs for a finer characterization of Mycobacterium tuberculosis strains isolated from patients residing in Guyana (n=74) and Suriname (n=80). The mean age of the patients was 38.5years (36.5 and 40.2years for Guyana vs. Suriname), with a male-to-female sex-ratio of 2.25 for Guyana vs. 4.27 in Suriname. Spoligotyping and 15-loci MIRU-VNTRs led to a total of 41 and 65 different patterns respectively, with an overall clustering rate of 83.8% vs. 68.8%. Combined spoligotyping and VNTR analysis led to the detection of 18 clusters of 2-41 isolates, with an overall clustering of 67.5% and a recent "n-1" transmission rate of 55.8%. Importantly, Guyana was characterized by a significantly higher percentage of clustered isolates than Suriname (79.7% vs. 56.3%; p=0.0019). Three big spoligo/MIRU (SIT/MIT) clusters containing >10 isolates each were shared between the 2 countries, and concerned: T1 sublineage cluster 53/861 (n=41, 37 in Guyana vs. 4 in Suriname); EAI6-BGD1 sublineage cluster 1340/860 (n=16, 3 in Guyana vs. 13 in Suriname); and T1 sublineage cluster 131/146 (n=11, 6 in Guyana vs. 5 in Suriname); as well as 2 smaller clusters of 2 and 3 isolates respectively. However, the relative phylogeographical specificities of strains in circulation as well as a lack of drug-resistance observed among strains from Suriname suggested that trans-border transmission of drug-resistant isolates occurred less frequently than thought. Tracing and interrupting transmission channels of a specific clone (SIT53/15-MIT861) should become a priority in Guyana, not only because it is by far most abundant but also because it accounts for almost half of the drug resistant isolates (n=8/17, 47.1%) in our study, and clustered 5/12 (41.7%) MDR isolates.
Collapse
Affiliation(s)
- Elisabeth Streit
- WHO Supranational TB Reference Laboratory, Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Abymes Cedex, Guadeloupe
| | - Shirematee Baboolal
- Department of Para-Clinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Patrick E Akpaka
- Department of Para-Clinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Julie Millet
- WHO Supranational TB Reference Laboratory, Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Abymes Cedex, Guadeloupe
| | - Nalin Rastogi
- WHO Supranational TB Reference Laboratory, Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Abymes Cedex, Guadeloupe.
| |
Collapse
|
11
|
Bolado-Martínez E, Candia-Plata MDC, Zenteno-Cuevas R, Mendoza Damián F, Avilés-Acosta M, Álvarez-Hernández G. [Proposal of a five MIRU-VNTR panel to screen clinical isolates of Mycobacterium tuberculosis in Mexico]. Enferm Infecc Microbiol Clin 2014; 33:609-12. [PMID: 25500299 DOI: 10.1016/j.eimc.2014.10.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 07/30/2014] [Accepted: 10/17/2014] [Indexed: 10/24/2022]
Abstract
INTRODUCTION Tuberculosis is a public health problem across Mexico. This paper aims to select a panel, with a minimum number of repetitive elements (MIRU-VNTR) for genotypic characterization of Mycobacterium tuberculosis (M. tuberculosis) clinical isolates. METHOD In this study, a full panel of 24 MIRU-VNTR loci was used to discriminate 65 clinical isolates of M. tuberculosis from three different geographical regions of Mexico. Those loci with the highest discriminatory power were subsequently selected. RESULTS The panel, including five loci, was obtained by selecting the highest values of allelic diversity among the genotypes obtained. The dendrogram, generated by the panel MIRU-VNTR 5, showed a high discriminatory power with 65 unique genotype profiles and formed clusters according to the geographical region of origin. CONCLUSIONS The panel MIRU-VNTR 5 can be useful for characterizing clinical isolates of M. tuberculosis in Mexico.
Collapse
Affiliation(s)
- Enrique Bolado-Martínez
- Departamento de Ciencias Químico Biológicas, Universidad de Sonora, Hermosillo, Sonora, México.
| | | | | | | | | | | |
Collapse
|
12
|
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.
Collapse
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:
| |
Collapse
|
13
|
Spositto FLE, Campanerut PAZ, Ghiraldi LD, Leite CQF, Hirata MH, Hirata RDC, Siqueira VLD, Cardoso RF. Multiplex-PCR for differentiation of Mycobacterium bovis from Mycobacterium tuberculosis complex. Braz J Microbiol 2014; 45:841-3. [PMID: 25477916 PMCID: PMC4204967 DOI: 10.1590/s1517-83822014000300012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 03/14/2014] [Indexed: 11/22/2022] Open
Abstract
We evaluated a multiplex-PCR to differentiate Mycobacterium bovis from M. tuberculosis Complex (MTC) by one step amplification based on simultaneous detection of pncA 169C > G change in M. bovis and the IS6110 present in MTC species. Our findings showed the proposed multiplex-PCR is a very useful tool for complementation in differentiating M. bovis from other cultured MTC species.
Collapse
Affiliation(s)
- F L E Spositto
- Programa de Pós Graduação em Biociências e Fisiopatologia Universidade Estadual de Maringá MaringáPR Brazil Programa de Pós Graduação em Biociências e Fisiopatologia, Universidade Estadual de Maringá, Maringá, PR, Brazil
| | - P A Z Campanerut
- Departamento de Análises Clínicas e Biomedicina Universidade Estadual de Maringá PR Brazil Departamento de Análises Clínicas e Biomedicina, Universidade Estadual de Maringá, PR, Brazil
| | - L D Ghiraldi
- Departamento de Análises Clínicas e Biomedicina Universidade Estadual de Maringá PR Brazil Departamento de Análises Clínicas e Biomedicina, Universidade Estadual de Maringá, PR, Brazil
| | - C Q F Leite
- Faculdade de Ciências Farmacêuticas Universidade Estadual Paulista AraraquaraSP Brazil Faculdade de Ciências Farmacêuticas, Universidade Estadual Paulista, Araraquara, SP, Brazil
| | - M H Hirata
- Faculdade de Ciências Farmacêuticas Departamento de Análises Clínicas e Toxicológicas Universidade de São Paulo São PauloSP Brazil Faculdade de Ciências Farmacêuticas, Departamento de Análises Clínicas e Toxicológicas, Universidade de São Paulo, São Paulo, SP, Brazil
| | - R D C Hirata
- Faculdade de Ciências Farmacêuticas Departamento de Análises Clínicas e Toxicológicas Universidade de São Paulo São PauloSP Brazil Faculdade de Ciências Farmacêuticas, Departamento de Análises Clínicas e Toxicológicas, Universidade de São Paulo, São Paulo, SP, Brazil
| | - V L D Siqueira
- Departamento de Análises Clínicas e Biomedicina Universidade Estadual de Maringá PR Brazil Departamento de Análises Clínicas e Biomedicina, Universidade Estadual de Maringá, PR, Brazil
| | - R Fressatti Cardoso
- Departamento de Análises Clínicas e Biomedicina Universidade Estadual de Maringá PR Brazil Departamento de Análises Clínicas e Biomedicina, Universidade Estadual de Maringá, PR, Brazil
| |
Collapse
|
14
|
Machado LNC, Marcondes NR, Leite CQF, Santos ACB, Pavan FR, Baldin VP, Castilho AL, Siqueira VLD, Baeza LC, Berghs H, Cardoso RF. First baseline of circulating genotypic lineages of Mycobacterium tuberculosis in patients from the brazilian borders with Argentina and Paraguay. PLoS One 2014; 9:e107106. [PMID: 25202909 PMCID: PMC4159320 DOI: 10.1371/journal.pone.0107106] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 08/09/2014] [Indexed: 11/21/2022] Open
Abstract
Background At the triple border Brazil/Paraguay/Argentina there is easy mobility from one city to another for economic and tourism activities. This constant and fast population mobility is mainly to visit Iguazu Falls, in the Iguazu River, on the border of the Brazilian state of Paraná and the Argentina. As the incidence of tuberculosis is high in this setting, our study aimed to establish a first baseline of circulating genotypic lineages of Mycobacterium tuberculosis. Methodology/Principal Findings This study included 120 patients from 10 cities in southwestern Paraná, Brazil with pulmonary symptoms, from July 2009 to July 2011. Information about sex, age, clinical features and address was collected by reviewing the national tuberculosis notification database. Of these, 96 (80%) isolates were identified as M. tuberculosis and 22 (22.9%) were drug resistant (20, 20.8% INH mono-resistant and 2, 2.1% multidrug-resistant). All isolates were subjected to genotyping by Spoligotyping and MIRU-VNTR typing. The distribution of the isolates analyzed by spoligotyping revealed 30 distinct patterns. The four mainly detected clades were Latin American and Mediterranean (LAM), ill-defined T, Haarlem (H) and S. The MIRU-VNTR showed 85 distinct patterns. Spoligotyping combined to MIRU-VNTR allowed 90 distinct patterns. Conclusions/Significance Our study demonstrated that there is significant molecular diversity in circulating M. tuberculosis, with predominance of the LAM and T clades in cities of southwestern Paraná, Brazil, bordering Argentina and Paraguay.
Collapse
Affiliation(s)
- Luzia Neri C. Machado
- Postgraduate Program in Biosciences and Physiopatology, State University of Maringá, Maringá, Paraná, Brazil
| | - Nadir R. Marcondes
- Center of Medical and Pharmaceutical Sciences, State University of Western Paraná, Cascavel, Paraná, Brazil
| | - Clarice Q. Fijimura Leite
- School of Pharmaceutical Sciences, Department of Biological Sciences, Paulista State University, Araraquara, São Paulo, Brazil
| | - Adolfo C. Barreto Santos
- School of Pharmaceutical Sciences, Department of Biological Sciences, Paulista State University, Araraquara, São Paulo, Brazil
| | - Fernando Rogério Pavan
- School of Pharmaceutical Sciences, Department of Biological Sciences, Paulista State University, Araraquara, São Paulo, Brazil
| | - Vanessa Pietrowski Baldin
- Postgraduate Program in Biosciences and Physiopatology, State University of Maringá, Maringá, Paraná, Brazil
| | - Aline Lemes Castilho
- Department of Clinical Analysis and Biomedicine, State University of Maringá, Maringá, Paraná, Brazil
| | - Vera Lúcia D. Siqueira
- Department of Clinical Analysis and Biomedicine, State University of Maringá, Maringá, Paraná, Brazil
| | - Lilian Cristiane Baeza
- Department of Clinical Analysis and Biomedicine, State University of Maringá, Maringá, Paraná, Brazil
| | | | - Rosilene Fressatti Cardoso
- Department of Clinical Analysis and Biomedicine, State University of Maringá, Maringá, Paraná, Brazil
- * E-mail:
| |
Collapse
|
15
|
Differential expression of immunogenic proteins on virulent Mycobacterium tuberculosis clinical isolates. BIOMED RESEARCH INTERNATIONAL 2014; 2014:741309. [PMID: 25105140 PMCID: PMC4109345 DOI: 10.1155/2014/741309] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 05/29/2014] [Accepted: 05/31/2014] [Indexed: 11/18/2022]
Abstract
Molecular epidemiology has revealed that Mycobacterium tuberculosis (Mtb), formerly regarded as highly conserved species, displays a considerable degree of genetic variability that can influence the outcome of the disease as well as the innate and adaptive immune response. Recent studies have demonstrated that Mtb families found worldwide today differ in pathology, transmissibility, virulence, and development of immune response. By proteomic approaches seven proteins that were differentially expressed between a local clinical isolate from Latin-American-Mediterranean (LAM) and from Haarlem (H) lineages were identified. In order to analyze the immunogenic ability, recombinant Rv2241, Rv0009, Rv0407, and Rv2624c proteins were produced for testing specific antibody responses. We found that these proteins induced humoral immune responses in patients with drug-sensitive and drug-resistant tuberculosis with substantial cross-reactivity among the four proteins. Moreover, such reactivity was also correlated with anti-Mtb-cell surface IgM, but not with anti-ManLAM, anti-PPD, or anti-Mtb-surface IgG antibodies. Therefore, the present results describe new Mtb antigens with potential application as biomarkers of TB.
Collapse
|
16
|
Liu M, Jiang W, Liu Y, Zhang Y, Wei X, Wang W. Increased genetic diversity of the Mycobacterium tuberculosis W-Beijing genotype that predominates in eastern China. INFECTION GENETICS AND EVOLUTION 2014; 22:23-9. [PMID: 24412724 DOI: 10.1016/j.meegid.2013.12.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 12/28/2013] [Accepted: 12/28/2013] [Indexed: 12/30/2022]
Abstract
OBJECTIVES To determine the genetic diversity of Mycobacterium tuberculosis (M. tuberculosis) strains in a Chinese population predominately infected with strains of the W-Beijing family. METHODS A cross-sectional study was conducted in three counties of eastern China. M. tuberculosis strains were collected at TB clinics, and patients were interviewed by trained physicians at the time of TB diagnosis. RD105 and RD181 were used to identify W-Beijing and modern W-Beijing strains, respectively, while seven-locus variable numbers of tandem repeat-mycobacterial interspersed repetitive unit (VNTR-MIRU) analysis was employed to differentiate the genotypes of these strains. RESULTS Of 441 strains studied, 394 (89.3%) were identified as W-Beijing family strains; of them, 299 were modern W-Beijing strains. VNTR-MIRU identified 409 genotypes from 426 strains, including 395 unique patterns and 14 clusters. Ancestral W-Beijing strains were more likely to be clustered (OR=1.32, 95%CI: 0.58-2.97) compared to modern W-Beijing strains. The proportions of clustered strains were 14.6%, 4.2% and 0% at sites Funing (FN), Deqing (DQ) and Yinzhou (YZ), respectively. Of the seven MIRU loci, VNTR3820 was found to have the highest discriminatory power and allelic diversity. CONCLUSIONS VNTR-MIRU typing appears to be a reliable method for analyzing M. tuberculosis transmission in relatively closed populations. The low clustering proportions indicate that endogenous relapse may be a main source of TB cases in eastern China. Furthermore, our results indicate that migration has played may play an important role in the recent transmission of the W-Beijing family of M. tuberculosis.
Collapse
Affiliation(s)
- Meiling Liu
- School of Public Health & Key Laboratory of Public Health Safety (Ministry of Education), Fudan University, Shanghai, China; Hongkou District Center for Disease Control and Prevention, Shanghai, China
| | - Weili Jiang
- School of Public Health & Key Laboratory of Public Health Safety (Ministry of Education), Fudan University, Shanghai, China
| | - Yuan Liu
- School of Public Health & Key Laboratory of Public Health Safety (Ministry of Education), Fudan University, Shanghai, China
| | - Yue Zhang
- School of Public Health & Key Laboratory of Public Health Safety (Ministry of Education), Fudan University, Shanghai, China
| | - Xiaolin Wei
- School of Public Health and Primary Care, Chinese University of Hong Kong, China
| | - Weibing Wang
- School of Public Health & Key Laboratory of Public Health Safety (Ministry of Education), Fudan University, Shanghai, China.
| |
Collapse
|
17
|
Santos ACB, Gaspareto RM, Viana BHJ, Mendes NH, Pandolfi JRC, Cardoso RF, Sato DN, David SCDM, Saad MHF, Rastogi N, Leite CQF. Mycobacterium tuberculosis population structure shift in a 5-year molecular epidemiology surveillance follow-up study in a low endemic agro-industrial setting in São Paulo, Brazil. Int J Mycobacteriol 2013; 2:156-65. [PMID: 26785984 DOI: 10.1016/j.ijmyco.2013.06.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 06/30/2013] [Indexed: 10/26/2022] Open
Abstract
Starting with 257 outpatients attending the specialized health service for tuberculosis (TB) between 2002 and 2006 in Araraquara, an agro-industrial area with low tuberculosis (TB) incidence in São Paulo state, Brazil, positive mycobacterial cultures were obtained in 130 cases, of which 121 were confirmed as Mycobacterium tuberculosis complex. This report assesses the genetic diversity observed on 69.42% (n=84) of the clinical isolates, for which both spoligotyping and 12-loci MIRU typing data were fully interpretable. In order to monitor changes in the population dynamics of circulating M. tuberculosis strains over time, spoligotypes were compared from this study (n=84) with an earlier study from 1998 to 2001 (n=70 strains); and these two datasets from low-incidence Araraquara area were also compared with a 2-year cohort in the nearby higher-incidence São Paulo city area from 2006 to 2008 (n=93). The results obtained showed that with 58.3% (49/84) of the strains, the Latin-American-Mediterranean (LAM) was the predominant lineage in the present follow-up study; major patterns being SIT42/LAM9 11.9% (10/84), and SIT20/LAM1 10.7% (9/84). As compared with the 1998-2001 period when 40% (28/70) of the isolates belonged to the ill-defined T family, it was replaced by LAM strains between 2002 and 2006 with a visible shift to a population structure characteristic of the metropolitan São Paulo city. Further typing of the follow-up isolates from 2002 to 2006 using 12 loci MIRUs in conjunction with conventional epidemiology did not link this population structure shift to an increase in ongoing transmission or drug-resistance. Instead, it is most probably linked to movements of the important migrant community of Araraquara to higher TB incidence metropolitan areas such as São Paulo city. This is of particular concern owing to the increment in the global burden of LAM strains and the recent association of certain LAM sublineages with multidrug- and extensively drug-resistant TB. These observations suggest the need for further molecular monitoring of the TB population structure and the evaluation of transmission trends amongst migrant workers and other risk groups, such as persons in homeless shelters, in correctional facilities, drug users, and those with HIV infection, etc.
Collapse
Affiliation(s)
- Adolfo Carlos Barreto Santos
- Department of Biological Sciences, School of Pharmaceutical Sciences, São Paulo State University - UNESP, Araraquara, SP, Brazil
| | | | | | - Natália Helena Mendes
- Department of Biological Sciences, School of Pharmaceutical Sciences, São Paulo State University - UNESP, Araraquara, SP, Brazil
| | - José Rodrigo Cláudio Pandolfi
- Department of Biological Sciences, School of Pharmaceutical Sciences, São Paulo State University - UNESP, Araraquara, SP, Brazil
| | | | - Daisy Nakamura Sato
- Department of Biological Sciences, School of Pharmaceutical Sciences, São Paulo State University - UNESP, Araraquara, SP, Brazil
| | | | | | - Nalin Rastogi
- WHO Supranational TB Reference Laboratory, TB & Mycobacteria Unit, Institut Pasteur de la Guadeloupe, F97183 Abymes, Guadeloupe, France.
| | - Clarice Queico Fujimura Leite
- Department of Biological Sciences, School of Pharmaceutical Sciences, São Paulo State University - UNESP, Araraquara, SP, Brazil
| |
Collapse
|
18
|
Comparison of three molecular typing methods to assess genetic diversity for Mycobacterium tuberculosis. J Microbiol Methods 2013; 93:42-8. [DOI: 10.1016/j.mimet.2013.01.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2012] [Revised: 01/29/2013] [Accepted: 01/31/2013] [Indexed: 11/21/2022]
|
19
|
Martins MC, Giampaglia CMS, Oliveira RS, Simonsen V, Latrilha FO, Moniz LL, Couvin D, Rastogi N, Ferrazoli L. Population structure and circulating genotypes of drug-sensitive and drug-resistant Mycobacterium tuberculosis clinical isolates in São Paulo state, Brazil. INFECTION GENETICS AND EVOLUTION 2012. [PMID: 23201043 DOI: 10.1016/j.meegid.2012.10.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
São Paulo is the most populous Brazilian state and reports the largest number of tuberculosis cases in the country annually (over 18,500). This study included 193 isolates obtained during the 2nd Nationwide Survey on Mycobacterium tuberculosis Drug Resistance that was conducted in São Paulo state and 547 isolates from a laboratory based study of drug resistance that were analyzed by the Mycobacteria Reference Laboratory at the Institute Adolfo Lutz. Both studies were conducted from 2006 to 2008 and sought to determine the genetic diversity and pattern of drug resistance of M. tuberculosis isolates (MTC) circulating in São Paulo. The patterns obtained from the spoligotyping analysis demonstrated that 51/740 (6.9%) of the isolates corresponded to orphan patterns and that 689 (93.1%) of the isolates distributed into 144 shared types, including 119 that matched a preexisting shared type in the SITVIT2 database and 25 that were new isolates. A total of 77/144 patterns corresponded to unique isolates, while the remaining 67 corresponded to clustered patterns (n=612 isolates clustered into groups of 2-84 isolates each). The evolutionarily ancient PGG1 lineages (Beijing, CAS1-DEL, EAI3-IND, and PINI2) were rarely detected in São Paulo and comprised only 13/740, or 1.76%, of the total isolates; all of the remaining 727/740, or 98.24%, of the MTC isolates from São Paulo state were from the recent PGG2/3 evolutionary isolates belonging to the LAM, T, S, X, and Haarlem lineages, i.e., the Euro-American group. This study provides the first overview of circulating genotypes of M. tuberculosis in São Paulo state and demonstrates that the clustered shared types containing seven or more M. tuberculosis isolates that are spread in São Paulo state included both resistant and susceptible isolates.
Collapse
Affiliation(s)
- Maria Conceição Martins
- Núcleo de Tuberculose e Micobacterioses, Centro de Bacteriologia, Instituto Adolfo Lutz, São Paulo, Brazil.
| | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Zamani S, Aflaki M, Fooladi AAI, Darban-Sarokhalil D, Bameri Z, Khazaee S, Nasiri MJ, Feizabadi MM. MIRU-VNTR analysis of the Mycobacterium tuberculosis isolates from three provinces of Iran. ACTA ACUST UNITED AC 2012; 45:124-30. [PMID: 22954102 DOI: 10.3109/00365548.2012.717233] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND Iran borders 2 high-burden tuberculosis (TB) countries to the east, and has the highest rates of TB in one of its eastern provinces. Limited information is available on the genetic diversity and transmission dynamics of Mycobacterium tuberculosis (MTB) in Iran. To examine the genetic diversity and transmission dynamics of MTB strains we genotyped a collection of isolates from different parts of Iran. METHODS Standard 15-locus variable number tandem repeat (VNTR) typing was applied to genotype 121 MTB clinical isolates collected from 3 provinces of Iran, including Tehran (the capital of Iran), Sistan-Baluchestan (southeast province of Iran, with the highest rate of TB), and Kermanshah (western part of Iran with high TB/human immunodeficiency virus cases). Antibiotic susceptibility for all isolates was determined using the proportion method. RESULTS Sixty-six distinct mycobacterial interspersed repetitive unit (MIRU)-VNTR patterns were detected among 121 isolates. Seventy-five strains grouped into 20 clusters, and 46 isolates were unique. The genetic diversity of strains from Sistan-Baluchestan was higher than that in the other provinces. All isolates from Tehran or Kermanshah that grouped into clusters shared identical patterns with Sistan-Baluchestan. The Hunter-Gaston discriminatory index (HGDI) was 0.972, indicating a high power of discrimination for MIRU-VNTR typing. The MIRU 16 and ETRA loci were designated as highly discriminative. The rates of monoresistance and multidrug resistance were 9.9% and 2.4%, respectively. CONCLUSIONS MIRU-VNTR typing revealed high genetic diversity and suggests the possibility of transmission from Sistan-Baluchestan to other provinces of Iran. This method has potential for genetic analysis and for studying the transmission routes of TB.
Collapse
Affiliation(s)
- Samin Zamani
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | | | | | | | | | | | | | | |
Collapse
|
21
|
Mendes NH, Melo FAF, Santos ACB, Pandolfi JRC, Almeida EA, Cardoso RF, Berghs H, David S, Johansen FK, Espanha LG, Leite SRA, Leite CQF. Characterization of the genetic diversity of Mycobacterium tuberculosis in São Paulo city, Brazil. BMC Res Notes 2011; 4:269. [PMID: 21801364 PMCID: PMC3160979 DOI: 10.1186/1756-0500-4-269] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Accepted: 07/29/2011] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Tuberculosis is a major health problem in São Paulo, Brazil, which is the most populous and one of the most cosmopolitan cities in South America. To characterize the genetic diversity of Mycobacterium tuberculosis in the population of this city, the genotyping techniques of spoligotyping and MIRU were applied to 93 isolates collected in two consecutive years from 93 different tuberculosis patients residing in São Paulo city and attending the Clemente Ferreira Institute (the reference clinic for the treatment of tuberculosis). FINDINGS Spoligotyping generated 53 different spoligotype patterns. Fifty-one isolates (54.8%) were grouped into 13 spoligotyping clusters. Seventy- two strains (77.4%) showed spoligotypes described in the international databases (SpolDB4, SITVIT), and 21 (22.6%) showed unidentified patterns. The most frequent spoligotype families were Latin American Mediterranean (LAM) (26 isolates), followed by the T family (24 isolates) and Haarlem (H) (11 isolates), which together accounted for 65.4% of all the isolates. These three families represent the major genotypes found in Africa, Central America, South America and Europe. Six Spoligo-International-types (designated SITs by the database) comprised 51.8% (37/72) of all the identified spoligotypes (SIT53, SIT50, SIT42, SIT60, SIT17 and SIT1). Other SITs found in this study indicated the great genetic diversity of M. tuberculosis, reflecting the remarkable ethnic diversity of São Paulo city inhabitants. The MIRU technique was more discriminatory and did not identify any genetic clusters with 100% similarity among the 93 isolates. The allelic analysis showed that MIRU loci 26, 40, 23 and 10 were the most discriminatory. When MIRU and spoligotyping techniques were combined, all isolates grouped in the 13 spoligotyping clusters were separated. CONCLUSIONS Our data indicated the genomic stability of over 50% of spoligotypes identified in São Paulo and the great genetic diversity of M. tuberculosis isolates in the remaining SITs, reflecting the large ethnic mix of the São Paulo city inhabitants. The results also indicated that in this city, M. tuberculosis isolates acquired drug resistance independently of genotype and that resistance was more dependent on the selective pressure of treatment failure and the environmental circumstances of patients.
Collapse
Affiliation(s)
- Natália H Mendes
- Laboratory of Micobacteriology, Faculty of Pharmacy, São Paulo State University at Araraquara, UNESP. Araraquara-Jaú Road Km 01, Araraquara, SP, 14801-902, Brazil
| | - Fernando AF Melo
- Clemente Ferreira Institute. 717 Consolação St, São Paulo, SP, 01301-000, Brazil
| | - Adolfo CB Santos
- Laboratory of Micobacteriology, Faculty of Pharmacy, São Paulo State University at Araraquara, UNESP. Araraquara-Jaú Road Km 01, Araraquara, SP, 14801-902, Brazil
| | - José RC Pandolfi
- Laboratory of Micobacteriology, Faculty of Pharmacy, São Paulo State University at Araraquara, UNESP. Araraquara-Jaú Road Km 01, Araraquara, SP, 14801-902, Brazil
| | - Elisabete A Almeida
- Clemente Ferreira Institute. 717 Consolação St, São Paulo, SP, 01301-000, Brazil
| | - Rosilene F Cardoso
- State University of Maringá. 5790 Colombo Ave, Maringá, PR, 87020-900, Brazil
| | - Henri Berghs
- Fairport Ltda. 293 Jacarandá St, São Paulo, SP, 04926-160, Brazil
| | - Suzana David
- National Institute of Heath Dr. Ricardo Jorge. Padre Cruz Ave, Lisbon, 1649-016, Portugal
| | - Faber K Johansen
- Laboratory of Micobacteriology, Faculty of Pharmacy, São Paulo State University at Araraquara, UNESP. Araraquara-Jaú Road Km 01, Araraquara, SP, 14801-902, Brazil
| | - Lívia G Espanha
- Laboratory of Micobacteriology, Faculty of Pharmacy, São Paulo State University at Araraquara, UNESP. Araraquara-Jaú Road Km 01, Araraquara, SP, 14801-902, Brazil
| | - Sergio RA Leite
- Institute of Chemistry, São Paulo State University at Araraquara, UNESP, 55 Prof. Francisco Degni St, Araraquara, SP, 14800-060, Brazil
| | - Clarice QF Leite
- Laboratory of Micobacteriology, Faculty of Pharmacy, São Paulo State University at Araraquara, UNESP. Araraquara-Jaú Road Km 01, Araraquara, SP, 14801-902, Brazil
| |
Collapse
|