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Castro-Rodriguez B, Franco-Sotomayor G, Benitez-Medina JM, Cardenas-Franco G, Jiménez-Pizarro N, Cardenas-Franco C, Aguirre-Martinez JL, Orlando SA, Hermoso de Mendoza J, Garcia-Bereguiain MA. Prevalence, drug resistance, and genotypic diversity of the RD Rio subfamily of Mycobacterium tuberculosis in Ecuador: a retrospective analysis for years 2012-2016. Front Public Health 2024; 12:1337357. [PMID: 38689770 PMCID: PMC11060180 DOI: 10.3389/fpubh.2024.1337357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 03/15/2024] [Indexed: 05/02/2024] Open
Abstract
Introduction A major sublineage within the Mycobacterium tuberculosis (MTB) LAM family characterized by a new in-frame fusion gene Rv3346c/55c was discovered in Rio de Janeiro (Brazil) in 2007, called RDRio, associated to drug resistance. The few studies about prevalence of MTB RDRio strains in Latin America reported values ranging from 3% in Chile to 69.8% in Venezuela, although no information is available for countries like Ecuador. Methods A total of 814 MTB isolates from years 2012 to 2016 were screened by multiplex PCR for RDRio identification, followed by 24-loci MIRU-VNTR and spoligotyping. Results A total number of 17 MTB RDRio strains were identified, representing an overall prevalence of 2.09% among MTB strains in Ecuador. While 10.9% of the MTB isolates included in the study were multidrug resistance (MDR), 29.4% (5/17) of the RDRio strains were MDR. Discussion This is the first report of the prevalence of MTB RDRio in Ecuador, where a strong association with MDR was found, but also a very low prevalence compared to other countries in Latin America. It is important to improve molecular epidemiology tools as a part of MTB surveillance programs in Latin America to track the transmission of potentially dangerous MTB stains associated to MDR TB like MTB RDRio.
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Affiliation(s)
| | - Greta Franco-Sotomayor
- Instituto Nacional de Investigación en Salud Pública “Leopoldo Izquieta Pérez”, Guayaquil, Ecuador
- Universidad Católica Santiago de Guayaquil, Guayaquil, Ecuador
| | | | | | - Natalia Jiménez-Pizarro
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de Extremadura, Cáceres, Spain
| | | | | | - Solon Alberto Orlando
- Instituto Nacional de Investigación en Salud Pública “Leopoldo Izquieta Pérez”, Guayaquil, Ecuador
- Universidad Espiritu Santo, Guayaquil, Ecuador
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Santos-Lazaro D, Gavilan RG, Solari L, Vigo AN, Puyen ZM. Whole genome analysis of extensively drug resistant Mycobacterium tuberculosis strains in Peru. Sci Rep 2021; 11:9493. [PMID: 33947918 PMCID: PMC8097007 DOI: 10.1038/s41598-021-88603-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 04/14/2021] [Indexed: 02/02/2023] Open
Abstract
Peru has the highest burden of multidrug-resistant tuberculosis in the Americas region. Since 1999, the annual number of extensively drug-resistant tuberculosis (XDR-TB) Peruvian cases has been increasing, becoming a public health challenge. The objective of this study was to perform genomic characterization of Mycobacterium tuberculosis strains obtained from Peruvian patients with XDR-TB diagnosed from 2011 to 2015 in Peru. Whole genome sequencing (WGS) was performed on 68 XDR-TB strains from different regions of Peru. 58 (85.3%) strains came from the most populated districts of Lima and Callao. Concerning the lineages, 62 (91.2%) strains belonged to the Euro-American Lineage, while the remaining 6 (8.8%) strains belonged to the East-Asian Lineage. Most strains (90%) had high-confidence resistance mutations according to pre-established WHO-confident grading system. Discordant results between microbiological and molecular methodologies were caused by mutations outside the hotspot regions analysed by commercial molecular assays (rpoB I491F and inhA S94A). Cluster analysis using a cut-off ≤ 10 SNPs revealed that only 23 (34%) strains evidenced recent transmission links. This study highlights the relevance and utility of WGS as a high-resolution approach to predict drug resistance, analyse transmission of strains between groups, and determine evolutionary patterns of circulating XDR-TB strains in the country.
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Affiliation(s)
| | - Ronnie G. Gavilan
- grid.419228.40000 0004 0636 549XInstituto Nacional de Salud, Lima, Peru ,grid.441740.20000 0004 0542 2122Escuela Profesional de Medicina Humana, Universidad Privada San Juan Bautista, Lima, Peru
| | - Lely Solari
- grid.419228.40000 0004 0636 549XInstituto Nacional de Salud, Lima, Peru
| | - Aiko N. Vigo
- grid.419228.40000 0004 0636 549XInstituto Nacional de Salud, Lima, Peru
| | - Zully M. Puyen
- grid.419228.40000 0004 0636 549XInstituto Nacional de Salud, Lima, Peru ,grid.441917.e0000 0001 2196 144XEscuela de Medicina, Universidad Peruana de Ciencias Aplicadas, Lima, Peru
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Lopez K, Arriaga MB, Aliaga JG, Barreda NN, Sanabria OM, Huang CC, Zhang Z, García-de-la-Guarda R, Lecca L, Calçada Carvalho AC, Kritski AL, Calderon RI. Dysglycemia is associated with Mycobacterium tuberculosis lineages in tuberculosis patients of North Lima-Peru. PLoS One 2021; 16:e0243184. [PMID: 33507930 PMCID: PMC7843012 DOI: 10.1371/journal.pone.0243184] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 01/08/2021] [Indexed: 12/13/2022] Open
Abstract
This study was performed to investigate the role of dysglycemia on the genetic diversity of Mycobacterium tuberculosis (MTB) among pulmonary tuberculosis (TB) patients to build scientific evidence about the possible mechanisms of TB transmission. MTB isolates obtained of patients affected by pulmonary tuberculosis from health care facilities of North Lima-Peru, were analyzed using whole genome sequencing and 24-locus mycobacterial interspersed repetitive-unit -variable-number tandem repeats (MIRU-VNTR). Subsequently, clinical and epidemiological characteristics were associated with clustering, lineages and comorbid conditions. The analysis carried out 112 pulmonary TB patients from various health centers in North Lima, 17 (15%) had diabetes mellitus (DM) and 33 (29%) had pre-diabetes (PDM). Latin American-Mediterranean, Haarlem and Beijing were the most frequent MTB lineages found in those patients. Previous TB (adjusted odds ratio [aOR] = 3.65; 95%CI: 1.32-17.81), age (aOR = 1.12; 95%CI: 1.03-1.45) and Beijing lineage (aOR = 3.53; 95%CI: 1.08-13.2) were associated with TB-DM comorbidity. Alcoholism (aOR = 2.92; 95%CI: 1.10-8.28), age (aOR = 1.05; 95%CI: 1.03-1.12) and Haarlem lineage (aOR = 2.54; 95%CI: 1.04-6.51) were associated with TB-PDM comorbidity. Beijing and Haarlem lineages were independently associated with TB-DM and TB-PDM comorbidities, respectively. Although these findings may be surprising, we must be cautious to suggest that dysglycemia could be associated with a highly clustering and predisposition of MTB lineages related to a serious impact on the severity of TB disease, which requires further research.
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Affiliation(s)
- Kattya Lopez
- Socios En Salud Sucursal Peru, Lima, Peru
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima, Peru
- Division of Rheumatology, Immunity and Inflammation, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - María B. Arriaga
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Bahia, Brazil
- Faculdade de Medicina, Universidade Federal da Bahia, Salvador, Bahia, Brazil
- Instituto Brasileiro para Investigação da Tuberculose, Fundação José Silveira, Salvador, Bahia, Brazil
| | | | | | | | - Chuan-Chin Huang
- Division of Global Health Equity, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
| | - Zibiao Zhang
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | | | | | - Anna Cristina Calçada Carvalho
- Laboratório de Inovações em Terapias, Ensino e Bioprodutos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Afrânio L. Kritski
- Faculdade de Medicina, Programa Acadêmico de Tuberculose, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Roger I. Calderon
- Socios En Salud Sucursal Peru, Lima, Peru
- Faculdade de Medicina, Programa Acadêmico de Tuberculose, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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4
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Tengan FM, Figueiredo GM, Leite OH, Nunes AK, Manchiero C, Dantas BP, Magri MC, Barone AA, Bernardo WM. Prevalence of multidrug-resistant tuberculosis in Latin America and the Caribbean: a systematic review and meta-analysis. Trop Med Int Health 2020; 25:1065-1078. [PMID: 32506718 DOI: 10.1111/tmi.13453] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
OBJECTIVES To evaluate the prevalence of multidrug-resistant tuberculosis (MDR-TB) in individuals living in Latin America and the Caribbean (LAC). METHODS We searched the MEDLINE, Embase and Literatura Latino Americana e do Caribe em Ciências da Saúde (Lilacs) databases until 08 August 2019 for all studies on the subject, without time or language restrictions. Original studies reporting the prevalence of infection with Mycobacterium tuberculosis resistant to isoniazid and rifampicin simultaneously (MDR) in LAC, the prevalence of resistance in cases with no previous treatment (new cases) and the prevalence of resistance in previously treated cases were selected. Considering the expected heterogeneity between studies, all analyses were performed using the random effects model, and heterogeneity was assessed using the I2 statistic. RESULTS We included 91 studies from 16 countries. The estimated overall prevalence was 13.0% (95% CI 12.0-14.0%), and the heterogeneity between studies was substantial (I2 = 96.1%). In the subgroup analyses, it was observed that the prevalence of MDR-TB among new cases was 7.0% (95% CI 6.0-7.0%) and in previously treated cases was 26.0% (95% CI 24.0-28.0%). CONCLUSIONS This review highlights multidrug resistance to antituberculosis drugs in LAC, indicating that prevention strategies have not been effective. Government institutions should invest heavily in strategies for early diagnosis and the rapid availability of effective treatments and prioritise adequate protection for health professionals. In addition, screening programmes should be adopted to prevent secondary cases.
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Affiliation(s)
- Fátima M Tengan
- Department of Infectious and Parasitic Diseases, School of Medicine, University of São Paulo, São Paulo, Brazil.,Laboratory of Viral Medical Research in Hepatology, University of São Paulo, São Paulo, Brazil
| | - Gerusa M Figueiredo
- Department of Preventive Medicine, University of São Paulo, São Paulo, Brazil
| | - Olavo Hm Leite
- Department of Infectious and Parasitic Diseases, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Arielle Ks Nunes
- Laboratory of Viral Medical Research in Hepatology, University of São Paulo, São Paulo, Brazil
| | - Carol Manchiero
- Laboratory of Viral Medical Research in Hepatology, University of São Paulo, São Paulo, Brazil
| | - Bianca P Dantas
- Laboratory of Viral Medical Research in Hepatology, University of São Paulo, São Paulo, Brazil
| | - Mariana C Magri
- Laboratory of Viral Medical Research in Hepatology, University of São Paulo, São Paulo, Brazil
| | - Antonio A Barone
- Department of Infectious and Parasitic Diseases, School of Medicine, University of São Paulo, São Paulo, Brazil.,Laboratory of Viral Medical Research in Hepatology, University of São Paulo, São Paulo, Brazil
| | - Wanderley M Bernardo
- School of Medicine, University of São Paulo, São Paulo, Brazil.,Brazilian Medical Association, São Paulo, Brazil
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5
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Cerezo-Cortés MI, Rodríguez-Castillo JG, Hernández-Pando R, Murcia MI. Circulation of M. tuberculosis Beijing genotype in Latin America and the Caribbean. Pathog Glob Health 2020; 113:336-351. [PMID: 31903874 DOI: 10.1080/20477724.2019.1710066] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Lineage 2 (East Asian), which includes the Beijing genotype, is one of the most prevalent lineages of Mycobacterium tuberculosis (Mtb) throughout the world. The Beijing family is associated to hypervirulence and drug-resistant tuberculosis. The study of this genotype's circulation in Latin America is crucial for achieving total control of TB, the goal established by the World Health Organization, for the American sub-continent, before 2035. In this sense, the present work presents an overview of the status of the Beijing genotype for this region, with a bibliographical review, and data analysis of MIRU-VNTRs for available Beijing isolates. Certain countries present a prevalent trend of <5%, suggesting low transmissibility for the region, with the exception of Cuba (17.2%), Perú (16%) and Colombia (5%). Minimum Spanning Tree analysis, obtained from MIRU-VNTR data, shows distribution of specific clonal complex strains in each country. From this data, in most countries, we found that molecular epidemiology has not been a tool used for the control of TB, suggesting that the Beijing genotype may be underestimated in Latin America. It is recommended that countries with the highest incidence of the Beijing genotype use effective control strategies and increased care, as a requirement for public health systems.
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Affiliation(s)
- M I Cerezo-Cortés
- Grupo MICOBAC-UN, Departamento de Microbiología, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia
| | - J G Rodríguez-Castillo
- Grupo MICOBAC-UN, Departamento de Microbiología, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia
| | - R Hernández-Pando
- Experimental Pathology Section, Department of Pathology, National Institute of Medical Sciences and Nutrition, México D.F., Mexico
| | - M I Murcia
- Grupo MICOBAC-UN, Departamento de Microbiología, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia
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6
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Mora-Pinargote C, Garzon-Chavez D, Franco-Sotomayor G, Leon-Benitez M, Granda-Pardo JC, Trueba G, de Waard JH, Garcia-Bereguiain MA. Country-wide rapid screening for the Mycobacterium tuberculosis Beijing sublineage in Ecuador using a single-nucleotide polymorphism-polymerase chain reaction method. Int J Mycobacteriol 2019; 8:366-370. [PMID: 31793507 DOI: 10.4103/ijmy.ijmy_132_19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Background Strains of the Beijing sublineage of Mycobacterium tuberculosis have caused large outbreaks of tuberculosis, often involving multidrug resistance strains and this genetically highly conserved family of strains predominates in some geographic areas. For most of the countries of Latin America, no country-wide studies about the prevalence of the Beijing lineage are available. Methods In this study, we determine the prevalence of the Beijing sublineage in Ecuador, using a large nation-wide sample of 991 isolates from the years 2014-2016 and with the strains, in case-related-proportional representation, emerging from most of the provinces of the country. The isolates were genotyped with asinglenucleotidespecific polymorphism (SNP) polymerase chain reaction for the Beijing sublineage. SNPpositive strains were confirmed as belonging to this lineage with 24 mycobacterial interspersed repetitive unitvariable number of tandem repeat and DNA sequencing. Results We identified only four Beijing isolates in this collection of 991 strains and calculated a prevalence rate of 0.43%. Conclusions Our study shows a limited dissemination of the Beijing strains in the Ecuadorian population. This in contrast with the neighbor countries of Peru and Colombia were locally a prevalence of up to 16% has been reported.
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Affiliation(s)
- Carlos Mora-Pinargote
- Laboratorio Para Investigaciones Biomedicas, Facultad de Ciencias de la Vida, Escuela Superior Politecnica del Litoral, Guayaquil, Ecuador
| | | | - Greta Franco-Sotomayor
- Instituto Nacional de Salud Publica e Investigacion "Leopoldo Izquieta Perez", Guayaquil, Ecuador; Facultad de Ciencias de la Salud, Universidad Catolica Santiago de Guayaquil, Guayaquil, Venezuela
| | - Margarita Leon-Benitez
- Instituto Nacional de Salud Publica e Investigacion "Leopoldo Izquieta Perez", Guayaquil, Ecuador
| | - Juan Carlos Granda-Pardo
- Instituto Nacional de Salud Publica e Investigacion "Leopoldo Izquieta Perez", Guayaquil, Ecuador
| | - Gabriel Trueba
- Instituto de Microbiologia, Universidad San Francisco de Quito, Quito, Ecuador
| | - Jacobus Henri de Waard
- One Health Research Group, Universidad de las Americas, Quito; Laboratorio de Tuberculosis, Instituto de Biomedicina Dr. Jacinto Convit, Universidad Central de Venezuela, Caracas, Venezuela
| | - Miguel Angel Garcia-Bereguiain
- Laboratorio Para Investigaciones Biomedicas, Facultad de Ciencias de la Vida, Escuela Superior Politecnica del Litoral, Guayaquil, Ecuador; One Health Research Group, Universidad de las Americas, Quito, Venezuela
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MIRU-VNTR genotyping of Mycobacterium tuberculosis in a population of patients in Cali, Colombia, 2013-2015. BIOMEDICA 2019; 39:71-85. [PMID: 31529850 DOI: 10.7705/biomedica.v39i2.3924] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Indexed: 11/21/2022]
Abstract
Introduction: Tuberculosis continues to be one of the main public health problems in the world. Together with the HIV infection, it is one of the main causes of death due to infections worldwide. In 2016, 6.3 million new cases of the disease were reported.
Objective: To describe the genetic patterns determined by genotyping using variable-number tandem repeats of mycobacterial interspersed repetitive units (MIRU-VNTR) in the study population and compare them with other studies carried out in Cali, Colombia, and the world.
Materials and methods: We genotyped a total of 105 DNA samples extracted from sputum or culture isolates of the Mycobacterium tuberculosis complex, which were obtained from pulmonary tuberculosis diagnosed patients over the period 2013-2015, in Cali. We performed PCR amplification of 24 loci by MIRU-VNTR on the DNA extracted from the samples. The amplicons were visualized in agarose gel electrophoresis (2%) with SYBR Safe™ staining. Then, the alleles were designated by graphical analysis using the GelAnalyzer 2010 software. These results were analyzed using the UPGMA logarithm and compared with the registers from the MIRU-VNTR plus and SITVITWEB databases.
Results: We genotyped 62 of the samples completely and we obtained 58 different MIRU-VNTR profiles. By comparing with the international databases, we determined the following distributions per lineage: LAM, 54.8%; Haarlem,25.8%; S, 14.5%; Beijing, 3.2%, and Cameroon, 1.6%. The MIRU-VNTR patterns corresponded to 17 different MITs; the most frequent were MIT 190 and MIT 110, with 22.6% and 6.5%, respectively.
Conclusions: These results demonstrated previous observations about the predominance of the LAM and Haarlem lineages in the city, and the presence of the MITs found in another city of Colombia.
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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.
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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.
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Predominant Mycobacterium tuberculosis Families and High Rates of Recent Transmission among New Cases Are Not Associated with Primary Multidrug Resistance in Lima, Peru. J Clin Microbiol 2015; 53:1854-63. [PMID: 25809979 DOI: 10.1128/jcm.03585-14] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 03/20/2015] [Indexed: 11/20/2022] Open
Abstract
Sputum samples from new tuberculosis (TB) cases were collected over 2 years as part of a prospective study in the northeastern part of Lima, Peru. To measure the contribution of recent transmission to the high rates of multidrug resistance (MDR) in this area, Mycobacterium tuberculosis complex (MTBc) isolates were tested for drug susceptibility to first-line drugs and were genotyped by spoligotyping and 15-locus mycobacterial interspersed repetitive-unit (MIRU-15)-variable-number tandem repeat (VNTR) analysis. MDR was found in 6.8% of 844 isolates, of which 593 (70.3%) were identified as belonging to a known MTBc lineage, whereas 198 isolates (23.5%) could not be assigned to these lineages and 12 (1.4%) represented mixed infections. Lineage 4 accounted for 54.9% (n = 463) of the isolates, most of which belonged to the Haarlem family (n = 279). MIRU-15 analysis grouped 551/791 isolates (69.7%) in 102 clusters, with sizes ranging from 2 to 46 strains. The overall high clustering rate suggests a high level of recent transmission in this population, especially among younger patients (odds ratio [OR], 1.6; P = 0.01). Haarlem strains were more prone to cluster, compared to the other families taken together (OR, 2.0; P < 0.0001), while Beijing (OR, 0.6; P = 0.006) and LAM (OR, 0.7; P = 0.07) strains clustered less. Whereas streptomycin-resistant strains were more commonly found in clusters (OR, 1.8; P = 0.03), clustering rates did not differ between MDR and non-MDR strains (OR, 1.8; P = 0.1). Furthermore, only 16/51 MDR strains clustered with other MDR strains, suggesting that patients with primary MDR infections acquired the infections mostly from index cases outside the study population, such as retreated cases.
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Balcells ME, García P, Meza P, Peña C, Cifuentes M, Couvin D, Rastogi N. A first insight on the population structure of Mycobacterium tuberculosis complex as studied by spoligotyping and MIRU-VNTRs in Santiago, Chile. PLoS One 2015; 10:e0118007. [PMID: 25671320 PMCID: PMC4324903 DOI: 10.1371/journal.pone.0118007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 01/05/2015] [Indexed: 02/04/2023] Open
Abstract
Tuberculosis (TB) remains a significant public health problem worldwide, but the ecology of the prevalent mycobacterial strains, and their transmission, can vary depending on country and region. Chile is a country with low incidence of TB, that has a geographically isolated location in relation to the rest of South American countries due to the Andes Mountains, but recent migration from neighboring countries has changed this situation. We aimed to assess the genotypic diversity of Mycobacterium tuberculosis complex (MTBC) strains in Santiago, Chile, and compare with reports from other Latin-American countries. We analyzed MTBC isolates from pulmonary tuberculosis cases collected between years 2008 and 2013 in Central Santiago, using two genotyping methods: spoligotyping and 12-loci mycobacterial interspersed repetitive unit-variable number of tandem repeats (MIRU-VNTRs). Data obtained were analyzed and compared to the SITVIT2 database. Mean age of the patients was 47.5 years and 61% were male; 11.6% were migrants. Of 103 strains (1 isolate/patient) included, there were 56 distinct spoligotype patterns. Of these, 16 strains (15.5%) corresponded to orphan strains in the SITVIT2 database, not previously reported. Latin American and Mediterranean (LAM) (34%) and T (33%) lineages were the most prevalent strains, followed by Haarlem lineage (16.5%). Beijing family was scarcely represented with only two cases (1.9%), one of them isolated from a Peruvian migrant. The most frequent clustered spoligotypes were SIT33/LAM3 (10.7%), SIT53/T1 (8.7%), SIT50/H3 (7.8%), and SIT37/T3 (6.8%). We conclude that LAM and T genotypes are the most prevalent genotypes of MTBC in Santiago, Chile, and together correspond to almost two thirds of analyzed strains, which is similar to strain distribution reported from other countries of Latin America. Nevertheless, the high proportion of SIT37/T3, which was rarely found in other Latin American countries, may underline a specific history or demographics of Chile related to probable human migrations and evolutions.
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Affiliation(s)
- María Elvira Balcells
- Infectious Diseases Department, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Patricia García
- Microbiology Laboratory, Clinical Laboratory Department, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Paulina Meza
- Microbiology Laboratory, Clinical Laboratory Department, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Carlos Peña
- Respiratory Division and Microbiology Laboratory, Hospital San Borja Arriarán, Santiago, Chile
| | - Marcela Cifuentes
- Respiratory Division and Microbiology Laboratory, Hospital San Borja Arriarán, Santiago, Chile
| | - David Couvin
- WHO Supranational TB Reference Laboratory, Institut Pasteur de la Guadeloupe, Abymes, Guadeloupe, France
| | - Nalin Rastogi
- WHO Supranational TB Reference Laboratory, Institut Pasteur de la Guadeloupe, Abymes, Guadeloupe, France
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11
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Cáceres O, Rastogi N, Bartra C, Couvin D, Galarza M, Asencios L, Mendoza-Ticona A. Characterization of the genetic diversity of extensively-drug resistant Mycobacterium tuberculosis clinical isolates from pulmonary tuberculosis patients in Peru. PLoS One 2014; 9:e112789. [PMID: 25489950 PMCID: PMC4260790 DOI: 10.1371/journal.pone.0112789] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 10/20/2014] [Indexed: 11/18/2022] Open
Abstract
Background Peru holds the fourth highest burden of tuberculosis in the Americas. Despite an apparently well-functioning DOTS control program, the prevalence of multidrug resistant tuberculosis (MDR-TB) continues to increase. To worsen this situation, cases of extensively drug resistance tuberculosis (XDR-TB) have been detected. Little information exists about the genetic diversity of drug-susceptible vs. MDR-TB and XDR-TB. Methods Cryopreserved samples of XDR strains from 2007 to 2009 (second semester), were identified and collected. Starting from 227 frozen samples, a total of 142 XDR-TB strains of Mycobacterium tuberculosis complex (MTBC; 1 isolate per patient) were retained for this study. Each strain DNA was analyzed by spoligotyping and the 15-loci Mycobacterial Interspersed Repetitive Unit (MIRU-15). Results Among the 142 isolates analyzed, only 2 samples (1.41%) could not be matched to any lineage. The most prevalent sublineage was Haarlem (43.66%), followed by T (27.46%), LAM (16.2%), Beijing (9.15%), and X clade (1.41%). Spoligotype analysis identified clustering for 128/142 (90.1%) isolates vs. 49/142 (34.5%) with MIRUs. Of the samples, 90.85% belonged to retreated patients. The drug resistant profile demonstrated that 62.67% showed resistance to injectable drugs capreomycin (CAP) and kanamycin (KAN) vs. 15.5% to CAP alone and 21.8% to KAN alone. The SIT219/T1 and SIT50/H3 were the most prevalent patterns in our study. The spoligoforest analysis showed that SIT53/T1 was at the origin of many of the T lineage strains as well as a big proportion of Haarlem lineage strains (SIT50/H3, followed by SIT47/H1, SIT49/H3, and SIT2375/H1), as opposed to the SIT1/Beijing strains that did not appear to evolve into minor Beijing sublineages among the XDR-TB strains. Conclusion In contrast with other Latin-American countries where LAM sublineage is the most predominant, we found the Haarlem to be the most common followed by T sublineage among the XDR-TB strains.
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Affiliation(s)
- Omar Cáceres
- Biotechnology and Molecular Biology Laboratory, Instituto Nacional de Salud, Lima, Peru
- * E-mail:
| | - Nalin Rastogi
- WHO Supranational TB Reference Laboratory, TB and Mycobacteria Unit, Institut Pasteur de la Guadeloupe, Guadeloupe, France
| | - Carlos Bartra
- Mycobacterias National Reference Laboratory, Instituto Nacional de Salud, Lima, Peru
| | - David Couvin
- WHO Supranational TB Reference Laboratory, TB and Mycobacteria Unit, Institut Pasteur de la Guadeloupe, Guadeloupe, France
| | - Marco Galarza
- Biotechnology and Molecular Biology Laboratory, Instituto Nacional de Salud, Lima, Peru
| | - Luis Asencios
- Mycobacterias National Reference Laboratory, Instituto Nacional de Salud, Lima, Peru
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12
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Zenteno-Cuevas R, Mendoza-Damián F, Muñoz IC, Enciso-Moreno L, Pérez-Navarro LM, Ramírez-Hernández MD, Vázquez-Medina K, Widrobo-García L, Lauzardo M, Enciso-Moreno JA. Description of the population structure and genetic diversity of tuberculosis in Estado de México, a low prevalence setting from Mexico. APMIS 2014; 123:116-22. [DOI: 10.1111/apm.12312] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 07/25/2014] [Indexed: 11/28/2022]
Affiliation(s)
| | | | | | | | | | | | | | | | - Michael Lauzardo
- Department of Medicine; Emerging Pathogens Institute; University of Florida; Gainesville FL USA
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