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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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2
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Nimmo C, Ortiz AT, Tan CCS, Pang J, Acman M, Millard J, Padayatchi N, Grant AD, O'Donnell M, Pym A, Brynildsrud OB, Eldholm V, Grandjean L, Didelot X, Balloux F, van Dorp L. Detection of a historic reservoir of bedaquiline/clofazimine resistance-associated variants in Mycobacterium tuberculosis. Genome Med 2024; 16:34. [PMID: 38374151 PMCID: PMC10877763 DOI: 10.1186/s13073-024-01289-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 01/19/2024] [Indexed: 02/21/2024] Open
Abstract
BACKGROUND Drug resistance in tuberculosis (TB) poses a major ongoing challenge to public health. The recent inclusion of bedaquiline into TB drug regimens has improved treatment outcomes, but this advance is threatened by the emergence of strains of Mycobacterium tuberculosis (Mtb) resistant to bedaquiline. Clinical bedaquiline resistance is most frequently conferred by off-target resistance-associated variants (RAVs) in the mmpR5 gene (Rv0678), the regulator of an efflux pump, which can also confer cross-resistance to clofazimine, another TB drug. METHODS We compiled a dataset of 3682 Mtb genomes, including 180 carrying variants in mmpR5, and its immediate background (i.e. mmpR5 promoter and adjacent mmpL5 gene), that have been associated to borderline (henceforth intermediate) or confirmed resistance to bedaquiline. We characterised the occurrence of all nonsynonymous mutations in mmpR5 in this dataset and estimated, using time-resolved phylogenetic methods, the age of their emergence. RESULTS We identified eight cases where RAVs were present in the genomes of strains collected prior to the use of bedaquiline in TB treatment regimes. Phylogenetic reconstruction points to multiple emergence events and circulation of RAVs in mmpR5, some estimated to predate the introduction of bedaquiline. However, epistatic interactions can complicate bedaquiline drug-susceptibility prediction from genetic sequence data. Indeed, in one clade, Ile67fs (a RAV when considered in isolation) was estimated to have emerged prior to the antibiotic era, together with a resistance reverting mmpL5 mutation. CONCLUSIONS The presence of a pre-existing reservoir of Mtb strains carrying bedaquiline RAVs prior to its clinical use augments the need for rapid drug susceptibility testing and individualised regimen selection to safeguard the use of bedaquiline in TB care and control.
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Affiliation(s)
- Camus Nimmo
- UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, UK.
- Division of Infection and Immunity, University College London, London, UK.
- Africa Health Research Institute, Durban, South Africa.
| | - Arturo Torres Ortiz
- UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, UK
- Department of Medicine, Imperial College, London, UK
| | - Cedric C S Tan
- UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, UK
| | - Juanita Pang
- UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, UK
- Division of Infection and Immunity, University College London, London, UK
| | - Mislav Acman
- UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, UK
| | - James Millard
- Africa Health Research Institute, Durban, South Africa
- Wellcome Trust Liverpool Glasgow Centre for Global Health Research, Liverpool, UK
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Nesri Padayatchi
- CAPRISA MRC-HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
| | - Alison D Grant
- Africa Health Research Institute, Durban, South Africa
- TB Centre, London School of Hygiene & Tropical Medicine, London, UK
| | - Max O'Donnell
- CAPRISA MRC-HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
- Department of Medicine & Epidemiology, Columbia University Irving Medical Center, New York, NY, USA
| | - Alex Pym
- Africa Health Research Institute, Durban, South Africa
| | - Ola B Brynildsrud
- Division of Infectious Diseases and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Vegard Eldholm
- Division of Infectious Diseases and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Louis Grandjean
- Division of Infection and Immunity, University College London, London, UK
- Laboratorio de Investigacion y Enfermedades Infecciosas, Universidad Peruana Cayetano Heredia, Lima, Peru
- Department of Infection, Immunity and Inflammation, Institute of Child Health, University College London, London, UK
| | - Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, Coventry, UK
| | - François Balloux
- UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, UK.
| | - Lucy van Dorp
- UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, UK.
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3
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Nimmo C, Millard J, Faulkner V, Monteserin J, Pugh H, Johnson EO. Evolution of Mycobacterium tuberculosis drug resistance in the genomic era. Front Cell Infect Microbiol 2022; 12:954074. [PMID: 36275027 PMCID: PMC9585206 DOI: 10.3389/fcimb.2022.954074] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 09/20/2022] [Indexed: 12/02/2022] Open
Abstract
Mycobacterium tuberculosis has acquired drug resistance to all drugs that have been used against it, including those only recently introduced into clinical practice. Compared to other bacteria, it has a well conserved genome due to its role as an obligate human pathogen that has adapted to a niche over five to ten thousand years. These features facilitate reconstruction and dating of M. tuberculosis phylogenies, giving key insights into how resistance has been acquired and spread globally. Resistance to each new drug has occurred within five to ten years of clinical use and has occurred even more rapidly with recently introduced drugs. In most cases, resistance-conferring mutations come with a fitness cost, but this can be overcome by compensatory mutations which restore fitness to that of wild-type bacteria. It is likely that M. tuberculosis acquires drug resistance while maintaining limited genomic variability due the generation of low frequency within-host variation, combined with ongoing purifying selection causing loss of variants without a clear fitness advantage. However, variants that do confer an advantage, such as drug resistance, can increase in prevalence amongst all bacteria within a host and become the dominant clone. These resistant strains can then be transmitted leading to primary drug resistant infection in a new host. As many countries move towards genomic methods for diagnosis of M. tuberculosis infection and drug resistance, it is important to be aware of the implications for the evolution of resistance. Currently, understanding of resistance-conferring mutations is incomplete, and some targeted genetic diagnostics create their own selective pressures. We discuss an example where a rifampicin resistance-conferring mutation which was not routinely covered by standard testing became dominant. Finally, resistance to new drugs such as bedaquiline and delamanid is caused by individually rare mutations occurring across a large mutational genomic target that have been detected over a short time, and do not provide statistical power for genotype-phenotype correlation – in contrast to longer-established drugs that form the backbone of drug-sensitive antituberculosis therapy. Therefore, we need a different approach to identify resistance-conferring mutations of new drugs before their resistance becomes widespread, abrogating their usefulness.
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Affiliation(s)
- Camus Nimmo
- Systems Chemical Biology of Infection and Resistance Laboratory, Francis Crick Institute, London, United Kingdom
- *Correspondence: Camus Nimmo,
| | - James Millard
- Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Valwynne Faulkner
- Systems Chemical Biology of Infection and Resistance Laboratory, Francis Crick Institute, London, United Kingdom
| | - Johana Monteserin
- Systems Chemical Biology of Infection and Resistance Laboratory, Francis Crick Institute, London, United Kingdom
| | - Hannah Pugh
- Systems Chemical Biology of Infection and Resistance Laboratory, Francis Crick Institute, London, United Kingdom
| | - Eachan Oliver Johnson
- Systems Chemical Biology of Infection and Resistance Laboratory, Francis Crick Institute, London, United Kingdom
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Shrestha A, Picoy J, Torres A, Moore DA, Gilman RH, Coronel J, Grandjean L. A case report of transmission and disease caused by Mycobacterium caprae and Mycobacterium bovis in Lima, Peru. BMC Infect Dis 2021; 21:1265. [PMID: 34930187 PMCID: PMC8686613 DOI: 10.1186/s12879-021-06944-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 12/03/2021] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND The Tuberculosis (TB) burden in Peru is significant with respect to both disease morbidity and mortality. Furthermore the recent diversification of farming enterprise to include a wide range of animal species has necessitated the consideration of members of the Mycobacterium Tuberculosis Complex (MTBC) with the potential for zoonotic transmission. M. bovis and M. caprae, a lesser known member of the MTBC exhibit an exceptionally wide host spectrum in animals and are capable of causing disease in humans. M. bovis has a predictable resistance profile which includes resistance to pyrazinamide. Thus, failure to identify M. bovis as the causative agent in reported TB cases leads to higher levels of treatment failure and contributes to the transmission of drug-resistant TB. CASE PRESENTATION Reported here are the clinical presentations, investigations and treatment histories of two patients identified from a population level genotyping study in Lima, Peru that were at the time of treatment thought to be M. tuberculosis patients but in retrospect were spectated using whole genome sequencing as M. caprae and M. Bovis. CONCLUSIONS The cases reported here constitute convincing evidence that M. caprae and M. bovis are causative agents of TB infection in humans in Peru and underscore the importance of species-level MTBC member identification to effectively control and treat zoonotic TB. Furthermore these cases highlight the challenges of using clinical risk factors to identify cases of zoonotic TB in humans as their clinical presentation and transmission history is often difficult to distinguish from anthroponotic TB.
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Affiliation(s)
- Amber Shrestha
- grid.420468.cDepartment of Infectious Disease, Great Ormond Street Hospital for Children, London, WC1N 3JH UK
| | - Janeth Picoy
- Department of Infectious Disease, Diresa Callao Jr, Colina #879, Bellavista, 07016 Lima, Peru
| | - Arturo Torres
- grid.7445.20000 0001 2113 8111Department of Infectious Disease, Imperial College London, South Kensington, London, SW7 2AZ UK
| | - David A. Moore
- grid.8991.90000 0004 0425 469XTB Centre, London School of Hygiene & Tropical Medicine, London, WC1E 7HT UK
| | - Robert H. Gilman
- grid.11100.310000 0001 0673 9488Laboratorio de Tuberculosis, Laboratorios de Investigación Y Desarrollo, Facultad de Ciencias Y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru ,grid.21107.350000 0001 2171 9311Department of International Health, School of Public Health, Johns Hopkins University, Baltimore, MD USA
| | - Jorge Coronel
- grid.11100.310000 0001 0673 9488Laboratorio de Investigación de Enfermedades Infecciosas, Universidad Peruana Cayetano Heredia: Lima, Lima, Peru
| | - Louis Grandjean
- Department of Infectious Disease, Great Ormond Street Hospital for Children, London, WC1N 3JH, UK. .,University College London, Gower St, Bloomsbury, London, WC1E 6BT, UK.
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Ordaz-Vázquez A, Torres-González P, Cruz-Hervert P, Ferreyra-Reyes L, Delgado-Sánchez G, García-García L, Kato-Maeda M, Ponce-De-León A, Sifuentes-Osornio J, Bobadilla-Del-Valle M. Genetic diversity and primary drug resistance transmission in Mycobacterium tuberculosis in southern Mexico. INFECTION GENETICS AND EVOLUTION 2021; 93:104994. [PMID: 34245908 DOI: 10.1016/j.meegid.2021.104994] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 06/28/2021] [Accepted: 07/04/2021] [Indexed: 11/30/2022]
Abstract
Tuberculosis is a global human health threat, especially in developing countries. The present study aimed to describe the genetic diversity of Mycobacterium tuberculosis and to measure the transmission rates of primary and acquired resistance. A total of 755 M. tuberculosis isolates from a cohort study of patients with culture-confirmed pulmonary tuberculosis in Orizaba, Veracruz, performed between 1995 and 2010 were genotyped by the 24-locus mycobacterial interspersed repetitive unit-variable number of tandem repeats (MIRU-VNTR) method. Drug susceptibility was determined. Logistic regression models were constructed to identify the variables associated with resistance and clusters. The recent transmission index (RTI), the Hunter-Gaston discrimination index (HGDI) for the MIRU-VNTR test and allelic diversity (h) were calculated. The Haarlem and LAM lineages were the most common in the population. A total of 519 isolates were grouped into 128 clusters. The overall drug resistance rate was 19%, isoniazid monoresistance (10%) was the most common, and 3.4% of the isolates were multidrug resistant. Among the 116 isolates resistant to at least one drug, the primary and acquired resistance rates were 81.9% and 18.1%, respectively. Primary resistance was associated with belonging to a cluster (aOR 4.05, 95% CI 1.5-11.2, p = 0.007). Previous treatment history (aOR 9.05, 95% CI 3.6-22.5, p < 0.001) and LAM lineage (aOR 4.25, 95% CI 1.4-12.7, p = 0.010) were associated with multidrug-resistant tuberculosis (MDR-TB). The RTI was 51.7%, and the 24-locus MIRU-VNTR HGDI was 0.98. The alleles with the greatest diversity were 4056-QUB26 (h = 0.84), 2163b-QUB11b (h = 0.79), and 424-Mtub04 (h = 0.72). Primary resistance transmission, high LAM lineage prevalence and its association with MDR-TB represent public health problems. The implementation of molecular tools is needed to improve the existing control surveillance tuberculosis program.
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Affiliation(s)
- Anabel Ordaz-Vázquez
- Departamento de Infectología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de México, Mexico
| | - Pedro Torres-González
- Departamento de Infectología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de México, Mexico
| | - Pablo Cruz-Hervert
- Departamento de Salud Pública y Epidemiología Oral, Facultad de Odontología, Universidad Nacional Autonoma de Mexico, Ciudad de México, Mexico
| | - Leticia Ferreyra-Reyes
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Mexico
| | - Guadalupe Delgado-Sánchez
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Mexico
| | - Lourdes García-García
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Mexico
| | - Midori Kato-Maeda
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Alfredo Ponce-De-León
- Departamento de Infectología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de México, Mexico
| | - José Sifuentes-Osornio
- Departamento de Medicina, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de México, Mexico
| | - Miriam Bobadilla-Del-Valle
- Departamento de Infectología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de México, Mexico.
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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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24-locus MIRU-VNTR and Spoligotyping analysis of drug-resistant Mycobacterium tuberculosis strains isolated from Northeastern Thailand. INFECTION GENETICS AND EVOLUTION 2020; 85:104449. [PMID: 32622079 DOI: 10.1016/j.meegid.2020.104449] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 06/19/2020] [Accepted: 06/25/2020] [Indexed: 01/19/2023]
Abstract
Tuberculosis, caused by Mycobacterium tuberculosis (MTB) infection, remains a global health problem with increased concerns due to drug-resistant tuberculosis. However, molecular genotyping profiles may give insight of the transmission of TB in a particular region. The present study aimed to characterize the genetic diversity of drug-resistant MTB and evaluate primer sets applied for the epidemiological study of circulating MTB in Northeastern Thailand. A total of 92 MTB isolates, resistant to rifampicin and/or isoniazid, were collected from the Office of Disease Prevention and Control between 2013 and 2016. All isolates were genotyped by 24-locus MIRU-VNTR typing combined with spoligotyping. We also analyzed the distributions of drug susceptibility pattern and demographic data among different genotypes. In comparison with different loci sets, discriminatory power based on 12, 15, 24 standard primers were investigated. Eighty-six particular profiles were found; among the patterns, two clusters were produced in 8 strains. East African Indians (EAI) were the most prevalent strains (33 isolates, 35.87%) followed by Beijing (30 isolates, 32.61%), with 23 unknown isolates strains also found. The HGDI based on combination of 24 loci analysis and spoligotyping was 0.9962. The number of tandem repeat generated was highly discriminant (HGDI>0.6) at locus 580 (0.66), 960 (0.67), 2163b (0.73), 2165 (0.62), 2461 (0.68) 3690 (0.73) and 4052 (0.79), respectively. In contrast, the diversity at locus 154 and 2059 was not revealed. The results emphasized that 24-locus MIRU-VNTR and spoligotyping could be useful for epidemiological surveillance of drug-resistant MTB in this region. At a given allelic diversity, 7 primer sets containing MIRU04, MIRU10, QUB2163b, ETRA, ETRB, Mtub39 and QUB26 may be considered for screening the VNTR patterns. In addition, this study gathered both demographics and genotypic data within the same investigation for further tuberculosis prevention and control.
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8
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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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9
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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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10
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Katale BZ, Mbugi EV, Keyyu JD, Fyumagwa RD, Rweyemamu MM, van Helden PD, Dockrell HM, Matee MI. One Health approach in the prevention and control of mycobacterial infections in Tanzania: lessons learnt and future perspectives. ONE HEALTH OUTLOOK 2019; 1:2. [PMID: 33829123 PMCID: PMC7990093 DOI: 10.1186/s42522-019-0002-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 09/24/2019] [Indexed: 06/12/2023]
Abstract
BACKGROUND One Health (OH) is an integrated approach, formed inclusive of using multiple disciplines to attain optimal health for humans, animals, and the environment. The increasing proximity between humans, livestock, and wildlife, and its role in the transmission dynamics of mycobacterial infections, necessitates an OH approach in the surveillance of zoonotic diseases. The challenge remains as humans, livestock, and wildlife share resources and interact at various interfaces. Therefore, this review explores the potential of the OH approach to understand the impact of mycobacterial infections in Tanzania in terms of lessons learnt and future perspectives. MATERIALS AND METHODS Available literature on OH and mycobacterial infections in Tanzania was searched in PubMed, Google Scholar, and Web of Science. Articles on mycobacterial infections in Tanzania, published between 1997 to 2017, were retrieved to explore the information on OH and mycobacterial infections. MAIN BODY The studies conducted in Tanzania had have reported a wide diversity of mycobacterial species in humans and animals, which necessitates an OH approach in surveillance of diseases for better control of infectious agents and to safeguard the health of humans and animals. The close proximity between humans and animals increases the chances of inter-specific transmission of infectious pathogens, including drug-resistant mycobacteria. In an era where HIV co-infection is also the case, opportunistic infection by environmental non-tuberculous mycobacteria (NTM), commonly known as mycobacteria other than tuberculosis (MOTT) may further exacerbate the impact of drug resistance. NTM from various sources have greatest potential for diverse strains among which are resistant strains due to continued evolutional changes. CONCLUSION A collaborative interdisciplinary approach among professionals could help in solving the threats posed by mycobacterial infections to public health, particularly by the spread of drug-resistant strains.
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Affiliation(s)
- Bugwesa Z. Katale
- Department of Microbiology and Immunology, School of Medicine, Muhimbili University of Health and Allied Sciences (MUHAS), Dar es Salaam, Tanzania
- Tanzania Wildlife Research Institute (TAWIRI), Arusha, Tanzania
- Southern African Centre for Infectious Diseases Surveillance (SACIDS), Sokoine University of Agriculture (SUA), Chuo Kikuu, Morogoro, Tanzania
| | - Erasto V. Mbugi
- Department of Biochemistry, School of Medicine, Muhimbili University of Health and Allied Sciences (MUHAS), Dar es Salaam, Tanzania
| | - Julius D. Keyyu
- Tanzania Wildlife Research Institute (TAWIRI), Arusha, Tanzania
| | | | - Mark M. Rweyemamu
- Southern African Centre for Infectious Diseases Surveillance (SACIDS), Sokoine University of Agriculture (SUA), Chuo Kikuu, Morogoro, Tanzania
| | - Paul D. van Helden
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/ South African Medical Research Council (MRC) Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
| | - Hazel M. Dockrell
- Department of Immunology and Infection, London School of Hygiene and Tropical Medicine (LSHTM), London, UK
| | - Mecky I. Matee
- Department of Microbiology and Immunology, School of Medicine, Muhimbili University of Health and Allied Sciences (MUHAS), Dar es Salaam, Tanzania
- Southern African Centre for Infectious Diseases Surveillance (SACIDS), Sokoine University of Agriculture (SUA), Chuo Kikuu, Morogoro, Tanzania
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11
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Madrazo-Moya CF, Cancino-Muñoz I, Cuevas-Córdoba B, González-Covarrubias V, Barbosa-Amezcua M, Soberón X, Muñiz-Salazar R, Martínez-Guarneros A, Bäcker C, Zarrabal-Meza J, Sampieri-Ramirez C, Enciso-Moreno A, Lauzardo M, Comas I, Zenteno-Cuevas R. Whole genomic sequencing as a tool for diagnosis of drug and multidrug-resistance tuberculosis in an endemic region in Mexico. PLoS One 2019; 14:e0213046. [PMID: 31166945 PMCID: PMC6550372 DOI: 10.1371/journal.pone.0213046] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 05/16/2019] [Indexed: 02/07/2023] Open
Abstract
Background Whole genome sequencing (WGS) has been proposed as a tool for diagnosing drug resistance in tuberculosis. However, reports of its effectiveness in endemic countries with important numbers of drug resistance are scarce. The goal of this study was to evaluate the effectiveness of this procedure in isolates from a tuberculosis endemic region in Mexico. Methods WGS analysis was performed in 81 tuberculosis positive clinical isolates with a known phenotypic profile of resistance against first-line drugs (isoniazid, rifampin, ethambutol, pyrazinamide and streptomycin). Mutations related to drug resistance were identified for each isolate; drug resistant genotypes were predicted and compared with the phenotypic profile. Genotypes and transmission clusters based on genetic distances were also characterized. Findings Prediction by WGS analysis of resistance against isoniazid, rifampicin, ethambutol, pyrazinamide and streptomycin showed sensitivity values of 84%, 96%, 71%, 75% and 29%, while specificity values were 100%, 94%, 90%, 90% and 98%, respectively. Prediction of multidrug resistance showed a sensitivity of 89% and specificity of 97%. Moreover, WGS analysis revealed polymorphisms related to second-line drug resistance, enabling classification of eight and two clinical isolates as pre- and extreme drug-resistant cases, respectively. Lastly, four lineages were identified in the population (L1, L2, L3 and L4). The most frequent of these was L4, which included 90% (77) of the isolates. Six transmission clusters were identified; the most frequent was TC6, which included 13 isolates with a L4.1.1 and a predominantly multidrug-resistant condition. Conclusions The results illustrate the utility of WGS for establishing the potential for prediction of resistance against first and second line drugs in isolates of tuberculosis from the region. They also demonstrate the feasibility of this procedure for use as a tool to support the epidemiological surveillance of drug- and multidrug-resistant tuberculosis.
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Affiliation(s)
- Carlos Francisco Madrazo-Moya
- Instituto de Salud Pública, Universidad Veracruzana, Veracruz, México
- Programa de Maestría en Ciencias de la Salud, Instituto de Ciencias de la Salud, Universidad Veracruzana, Veracruz, México
| | | | - Betzaida Cuevas-Córdoba
- Laboratorio de Farmacogenómica, Instituto Nacional de Medicina Genómica, Ciudad de México, México
| | | | - Martín Barbosa-Amezcua
- Laboratorio de Farmacogenómica, Instituto Nacional de Medicina Genómica, Ciudad de México, México
| | - Xavier Soberón
- Laboratorio de Farmacogenómica, Instituto Nacional de Medicina Genómica, Ciudad de México, México
| | - Raquel Muñiz-Salazar
- Laboratorio de Epidemiología y Ecología y Molecular, Escuela de Ciencias de la Salud, Universidad Autónoma de Baja California, Ensenada, Baja California, México
| | - Armando Martínez-Guarneros
- Laboratorio de Micobacterias, Instituto Nacional de Diagnóstico y Referencia Epidemiológica, Ciudad de México, México
| | - Claudia Bäcker
- Laboratorio de Micobacterias, Instituto Nacional de Diagnóstico y Referencia Epidemiológica, Ciudad de México, México
| | - José Zarrabal-Meza
- Laboratorio Estatal de Salud Pública, Secretaria de Salud, Veracruz, México
| | | | | | - Michael Lauzardo
- Division of Infectious Diseases and Global Medicine, College of Medicine, University of Florida, Gainesville, Florida, United States of America
| | - Iñaki Comas
- Biomedicine Institute of Valencia IBV-CSIC, Valencia, Spain
- CIBER of Epidemiology and Public Health, Madrid, Spain
| | - Roberto Zenteno-Cuevas
- Instituto de Salud Pública, Universidad Veracruzana, Veracruz, México
- Programa de Maestría en Ciencias de la Salud, Instituto de Ciencias de la Salud, Universidad Veracruzana, Veracruz, México
- * E-mail:
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12
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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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13
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Warren JL, Grandjean L, Moore DAJ, Lithgow A, Coronel J, Sheen P, Zelner JL, Andrews JR, Cohen T. Investigating spillover of multidrug-resistant tuberculosis from a prison: a spatial and molecular epidemiological analysis. BMC Med 2018; 16:122. [PMID: 30071850 PMCID: PMC6091024 DOI: 10.1186/s12916-018-1111-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 06/26/2018] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Congregate settings may serve as institutional amplifiers of tuberculosis (TB) and multidrug-resistant tuberculosis (MDR-TB). We analyze spatial, epidemiological, and pathogen genetic data prospectively collected from neighborhoods surrounding a prison in Lima, Peru, where inmates experience a high risk of MDR-TB, to investigate the risk of spillover into the surrounding community. METHODS Using hierarchical Bayesian statistical modeling, we address three questions regarding the MDR-TB risk: (i) Does the excess risk observed among prisoners also extend outside the prison? (ii) If so, what is the magnitude, shape, and spatial range of this spillover effect? (iii) Is there evidence of additional transmission across the region? RESULTS The region of spillover risk extends for 5.47 km outside of the prison (95% credible interval: 1.38, 9.63 km). Within this spillover region, we find that nine of the 467 non-inmate patients (35 with MDR-TB) have MDR-TB strains that are genetic matches to strains collected from current inmates with MDR-TB, compared to seven out of 1080 patients (89 with MDR-TB) outside the spillover region (p values: 0.022 and 0.008). We also identify eight spatially aggregated genetic clusters of MDR-TB, four within the spillover region, consistent with local transmission among individuals living close to the prison. CONCLUSIONS We demonstrate a clear prison spillover effect in this population, which suggests that interventions in the prison may have benefits that extend to the surrounding community.
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Affiliation(s)
- Joshua L Warren
- Department of Biostatistics, Yale University, New Haven, CT, 06510, USA.
| | - Louis Grandjean
- Paediatric Infectious Diseases, Section of Paediatrics, Department of Medicine, Imperial College, London, W2 1NY, UK.,Laboratorio de Investigacion y Desarrollo, Universidad Peruana Cayetano Heredia, San Martin de Porres, Lima, Peru
| | - David A J Moore
- Laboratorio de Investigacion y Desarrollo, Universidad Peruana Cayetano Heredia, San Martin de Porres, Lima, Peru.,TB Centre and Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, UK
| | - Anna Lithgow
- TB Centre and Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, UK
| | - Jorge Coronel
- Laboratorio de Investigacion y Desarrollo, Universidad Peruana Cayetano Heredia, San Martin de Porres, Lima, Peru
| | - Patricia Sheen
- Laboratorio de Investigacion y Desarrollo, Universidad Peruana Cayetano Heredia, San Martin de Porres, Lima, Peru
| | - Jonathan L Zelner
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jason R Andrews
- Department of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Ted Cohen
- Department of Epidemiology of Microbial Diseases, Yale University, New Haven, CT, 06510, USA
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14
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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.
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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.
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15
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Munro-Rojas D, Fernandez-Morales E, Zarrabal-Meza J, Martínez-Cazares MT, Parissi-Crivelli A, Fuentes-Domínguez J, Séraphin MN, Lauzardo M, González-y-Merchand JA, Rivera-Gutierrez S, Zenteno-Cuevas R. Genetic diversity of drug and multidrug-resistant Mycobacterium tuberculosis circulating in Veracruz, Mexico. PLoS One 2018; 13:e0193626. [PMID: 29543819 PMCID: PMC5854261 DOI: 10.1371/journal.pone.0193626] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 02/14/2018] [Indexed: 11/25/2022] Open
Abstract
Background Mexico is one of the most important contributors of drug and multidrug-resistant tuberculosis in Latin America; however, knowledge of the genetic diversity of drug-resistant tuberculosis isolates is limited. Methods In this study, the genetic structure of 112 Mycobacterium tuberculosis strains from the southeastern Mexico was determined by spoligotyping and 24-loci MIRU-VNTRs. Findings The results show eight major lineages, the most of which was T1 (24%), followed by LAM (16%) and H (15%). A total of 29 (25%) isolates were identified as orphan. The most abundant SITs were SIT53/T1 and SIT42/LAM9 with 10 isolates each and SIT50/H3 with eight isolates. Fifty-two spoligotype patterns, twenty-seven clusters and ten clonal complexes were observed, demonstrating an important genetic diversity of drug and multidrug-resistant tuberculosis isolates in circulation and transmission level of these aggravated forms of tuberculosis. Being defined as orphan or as part of an orphan cluster, was a risk factor for multidrug resistant-tuberculosis (OR 2.5, IC 1.05–5.86 and OR 3.3, IC 1–11.03, respectively). Multiple correspondence analyses showed association of some clusters and SITs with specific geographical locations. Conclusions Our study provides one of the most detailed description of the genetic structure of drug and multidrug-resistant tuberculosis strains in southeast Mexico, establishing for the first time a baseline of the genotypes observed in resistant isolates circulating, however further studies are required to better elucidate the genetic structure of tuberculosis in region and the factors that could be participating in their dispersion.
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Affiliation(s)
- Daniela Munro-Rojas
- Instituto de Salud Pública, Universidad Veracruzana, Jalapa, Veracruz, México
- Programa de Doctorado en Ciencias de la Salud, Instituto de Ciencias de la Salud, Universidad Veracruzana, Veracruz, México
| | - Esdras Fernandez-Morales
- Instituto de Salud Pública, Universidad Veracruzana, Jalapa, Veracruz, México
- Programa de Maestría en Ciencias de la Salud, Universidad Veracruzana, Veracruz, México
| | - José Zarrabal-Meza
- Laboratorio Estatal de Salud Pública, Secretaria de Salud, Veracruz, México
| | | | | | | | - Marie Nancy Séraphin
- Division of Infectious Diseases and Global Medicine, College of Medicine, University of Florida, Gainesville, Florida, United States of America
| | - Michael Lauzardo
- Division of Infectious Diseases and Global Medicine, College of Medicine, University of Florida, Gainesville, Florida, United States of America
| | | | - Sandra Rivera-Gutierrez
- Escuela Nacional de Ciencia Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
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Grandjean L, Gilman RH, Iwamoto T, Köser CU, Coronel J, Zimic M, Török ME, Ayabina D, Kendall M, Fraser C, Harris S, Parkhill J, Peacock SJ, Moore DAJ, Colijn C. Convergent evolution and topologically disruptive polymorphisms among multidrug-resistant tuberculosis in Peru. PLoS One 2017; 12:e0189838. [PMID: 29281674 PMCID: PMC5744980 DOI: 10.1371/journal.pone.0189838] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 12/01/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Multidrug-resistant tuberculosis poses a major threat to the success of tuberculosis control programs worldwide. Understanding how drug-resistant tuberculosis evolves can inform the development of new therapeutic and preventive strategies. METHODS Here, we use novel genome-wide analysis techniques to identify polymorphisms that are associated with drug resistance, adaptive evolution and the structure of the phylogenetic tree. A total of 471 samples from different patients collected between 2009 and 2013 in the Lima suburbs of Callao and Lima South were sequenced on the Illumina MiSeq platform with 150bp paired-end reads. After alignment to the reference H37Rv genome, variants were called using standardized methodology. Genome-wide analysis was undertaken using custom written scripts implemented in R software. RESULTS High quality homoplastic single nucleotide polymorphisms were observed in genes known to confer drug resistance as well as genes in the Mycobacterium tuberculosis ESX secreted protein pathway, pks12, and close to toxin/anti-toxin pairs. Correlation of homoplastic variant sites identified that many were significantly correlated, suggestive of epistasis. Variation in genes coding for ESX secreted proteins also significantly disrupted phylogenetic structure. Mutations in ESX genes in key antigenic epitope positions were also found to disrupt tree topology. CONCLUSION Variation in these genes have a biologically plausible effect on immunogenicity and virulence. This makes functional characterization warranted to determine the effects of these polymorphisms on bacterial fitness and transmission.
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Affiliation(s)
- Louis Grandjean
- University College London, Institute of Child Health, London, United Kingdom
- Academic Health Sciences Centre, Imperial College, London, United Kingdom
- Universidad Peruana Cayetano Heredia, Avenida Honorio Delgado, San Martin de Porras, Lima, Peru
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Robert H. Gilman
- Universidad Peruana Cayetano Heredia, Avenida Honorio Delgado, San Martin de Porras, Lima, Peru
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States of America
| | - Tomatada Iwamoto
- Department of Infectious Diseases, Kobe Institute of Health, Chuo-ku, Kobe, Japan
| | - Claudio U. Köser
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Jorge Coronel
- Universidad Peruana Cayetano Heredia, Avenida Honorio Delgado, San Martin de Porras, Lima, Peru
| | - Mirko Zimic
- Universidad Peruana Cayetano Heredia, Avenida Honorio Delgado, San Martin de Porras, Lima, Peru
| | - M. Estee Török
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Diepreye Ayabina
- Faculty of Natural Sciences, Department of Mathematics, Imperial College London, London, United Kingdom
| | - Michelle Kendall
- Faculty of Natural Sciences, Department of Mathematics, Imperial College London, London, United Kingdom
| | - Christophe Fraser
- Department of Infectious Diseases Epidemiology, Imperial College, London, United Kingdom
| | - Simon Harris
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Sharon J. Peacock
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
- London School of Tropical Medicine and Hygiene, London, United Kingdom
| | - David A. J. Moore
- London School of Tropical Medicine and Hygiene, London, United Kingdom
| | - Caroline Colijn
- Faculty of Natural Sciences, Department of Mathematics, Imperial College London, London, United Kingdom
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17
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Golla V, Snow K, Mandalakas AM, Schaaf HS, Du Preez K, Hesseling AC, Seddon JA. The impact of drug resistance on the risk of tuberculosis infection and disease in child household contacts: a cross sectional study. BMC Infect Dis 2017; 17:593. [PMID: 28851285 PMCID: PMC5576070 DOI: 10.1186/s12879-017-2668-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 08/03/2017] [Indexed: 11/10/2022] Open
Abstract
Background The relative fitness of organisms causing drug-susceptible (DS) and multidrug-resistant (MDR) tuberculosis (TB) is unclear. We compared the risk of TB infection and TB disease in young child household contacts of adults with confirmed DS-TB and MDR-TB. Methods In this cross-sectional analysis we included data from two community-based contact cohort investigation studies conducted in parallel in Cape Town, South Africa. Children <5 years of age with household exposure to an infectious TB case were included between August 2008 to June 2011. Children completed investigation for TB infection (tuberculin skin test) and TB disease (symptom evaluation, chest radiograph, bacteriology) in both studies using standard approaches. The impact of MDR-TB exposure on each covariate of TB infection and TB disease was assessed using univariable and multivariable logistic regression. Results Of 538 children included, 312 had DS-TB and 226 had MDR-TB exposure. 107 children with DS-TB exposure had TB infection (34.3%) vs. 101 (44.7%) of children with MDR-TB exposure (adjusted Odds Ratio [aOR]: 2.05; 95% confidence interval [CI]: 1.34–3.12). A total of 15 (6.6%) MDR-TB vs. 27 (8.7%) DS-TB child contacts had TB disease at enrolment (aOR: 0.43; 95% CI: 0.19–0.97). Conclusions Our results suggest a higher risk of TB infection in child contacts with household MDR-TB vs. DS-TB exposure, but a lower risk of TB disease. Although potentially affected by residual confounding or selection bias, our results are consistent with the hypothesis of impaired virulence in MDR-TB strains in this setting.
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Affiliation(s)
- Vera Golla
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, 8000, Cape Town, South Africa
| | - Kathryn Snow
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Anna M Mandalakas
- Global TB Program, Department of Pediatrics, Baylor College of Medicine, Houston, USA
| | - H Simon Schaaf
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, 8000, Cape Town, South Africa
| | - Karen Du Preez
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, 8000, Cape Town, South Africa
| | - Anneke C Hesseling
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, 8000, Cape Town, South Africa.
| | - James A Seddon
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, 8000, Cape Town, South Africa. .,Centre for International Child Health, Department of Paediatrics, Imperial College London, Norfolk Place, London, W2 1PG, UK.
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Lagos J, Couvin D, Arata L, Tognarelli J, Aguayo C, Leiva T, Arias F, Hormazabal JC, Rastogi N, Fernández J. Analysis of Mycobacterium tuberculosis Genotypic Lineage Distribution in Chile and Neighboring Countries. PLoS One 2016; 11:e0160434. [PMID: 27518286 PMCID: PMC4982630 DOI: 10.1371/journal.pone.0160434] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 07/19/2016] [Indexed: 10/29/2022] Open
Abstract
Tuberculosis (TB), caused by the pathogen Mycobacterium tuberculosis (MTB), remains a disease of high importance to global public health. Studies into the population structure of MTB have become vital to monitoring possible outbreaks and also to develop strategies regarding disease control. Although Chile has a low incidence of MTB, the current rates of migration have the potential to change this scenario. We collected and analyzed a total of 458 M. tuberculosis isolates (1 isolate per patient) originating from all 15 regions of Chile. The isolates were genotyped using the spoligotyping method and the data obtained were analyzed and compared with the SITVIT2 database. A total of 169 different patterns were identified, of which, 119 patterns (408 strains) corresponded to Spoligotype International Types (SITs) and 50 patterns corresponded to orphan strains. The most abundantly represented SITs/lineages were: SIT53/T1 (11.57%), SIT33/LAM3 (9.6%), SIT42/LAM9 (9.39%), SIT50/H3 (5.9%), SIT37/T3 (5%); analysis of the spoligotyping minimum spanning tree as well as spoligoforest were suggestive of a recent expansion of SIT42, SIT50 and SIT37; all of which potentially evolved from SIT53. The most abundantly represented lineages were LAM (40.6%), T (34.1%) and Haarlem (13.5%). LAM was more prevalent in the Santiago (43.6%) and Concepción (44.1%) isolates, rather than the Iquique (29.4%) strains. The proportion of X lineage was appreciably higher in Iquique and Concepción (11.7% in both) as compared to Santiago (1.6%). Global analysis of MTB lineage distribution in Chile versus neighboring countries showed that evolutionary recent lineages (LAM, T and Haarlem) accounted together for 88.2% of isolates in Chile, a pattern which mirrored MTB lineage distribution in neighboring countries (n = 7378 isolates recorded in SITVIT2 database for Peru, Brazil, Paraguay, and Argentina; and published studies), highlighting epidemiological advantage of Euro-American lineages in this region. Finally, we also observed exclusive emergence of patterns SIT4014/X1 and SIT4015 (unknown lineage signature) that have hitherto been found exclusively in Chile, indicating that conditions specific to Chile, along with the unique genetic makeup of the Chilean population, might have allowed for a possible co-evolution leading to the success of these emerging genotypes.
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Affiliation(s)
- Jaime Lagos
- Subdepartment of Molecular Genetics, Public Health Institute of Chile, Santiago, Chile
| | - David Couvin
- WHO Supranational TB Reference Laboratory, TB and Mycobacteria Unit, Institut Pasteur de la Guadeloupe, Guadeloupe, France
| | - Loredana Arata
- Subdepartment of Molecular Genetics, Public Health Institute of Chile, Santiago, Chile
| | - Javier Tognarelli
- Subdepartment of Molecular Genetics, Public Health Institute of Chile, Santiago, Chile
| | - Carolina Aguayo
- Subdepartment of Molecular Genetics, Public Health Institute of Chile, Santiago, Chile
| | - Tamara Leiva
- Mycobacteria Laboratory, Public Health Institute of Chile, Santiago, Chile
| | - Fabiola Arias
- Mycobacteria Laboratory, Public Health Institute of Chile, Santiago, Chile
| | | | - Nalin Rastogi
- WHO Supranational TB Reference Laboratory, TB and Mycobacteria Unit, Institut Pasteur de la Guadeloupe, Guadeloupe, France
- * E-mail: (JF); (NR)
| | - Jorge Fernández
- Subdepartment of Molecular Genetics, Public Health Institute of Chile, Santiago, Chile
- * E-mail: (JF); (NR)
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Wang T, Feng GD, Pang Y, Liu JY, Zhou Y, Yang YN, Dai W, Zhang L, Li Q, Gao Y, Chen P, Zhan LP, Marais BJ, Zhao YL, Zhao G. High rate of drug resistance among tuberculous meningitis cases in Shaanxi province, China. Sci Rep 2016; 6:25251. [PMID: 27143630 PMCID: PMC4855176 DOI: 10.1038/srep25251] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 04/12/2016] [Indexed: 11/18/2022] Open
Abstract
The clinical and mycobacterial features of tuberculous meningitis (TBM) cases in China are not well described; especially in western provinces with poor tuberculosis control. We prospectively enrolled patients in whom TBM was considered in Shaanxi Province, northwestern China, over a 2-year period (September 2010 to December 2012). Cerebrospinal fluid specimens were cultured for Mycobacterium tuberculosis; with phenotypic and genotypic drug susceptibility testing (DST), as well as genotyping of all positive cultures. Among 350 patients included in the study, 27 (7.7%) had culture-confirmed TBM; 84 (24.0%) had probable and 239 (68.3%) had possible TBM. DST was performed on 25/27 (92.3%) culture positive specimens; 12/25 (48.0%) had "any resistance" detected and 3 (12.0%) were multi-drug resistant (MDR). Demographic and clinical features of drug resistant and drug susceptible TBM cases were similar. Beijing was the most common genotype (20/25; 80.0%) with 9/20 (45%) of the Beijing strains exhibiting drug resistance; including all 3 MDR strains. All (4/4) isoniazid resistant strains had mutations in the katG gene; 75% (3/4) of strains with phenotypic rifampicin resistance had mutations in the rpoB gene detected by Xpert MTB/RIF®. High rates of drug resistance were found among culture-confirmed TBM cases; most were Beijing strains.
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Affiliation(s)
- Ting Wang
- Department of Neurology, Xijing Hospital, the Fourth Military Medical University, no.169 Changle West Road, Xi’an, Shaanxi, 710032, P.R.China
- Department of Neurology, Kunming Medical University affiliated Yan’an Hospital, 245 Renming East Road, Kunming, Yunnan, 650200, P.R.China
| | - Guo-Dong Feng
- Department of Neurology, Xijing Hospital, the Fourth Military Medical University, no.169 Changle West Road, Xi’an, Shaanxi, 710032, P.R.China
| | - Yu Pang
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, no.155 Changbai Road, Beijing, 102206, P.R.China
| | - Jia-Yun Liu
- Department of Inspection, Xijing Hospital, Fourth Military Medical University, no.169 Changle West Road, Xi’an, Shaanxi, 710032, P.R.China
| | - Yang Zhou
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, no.155 Changbai Road, Beijing, 102206, P.R.China
| | - Yi-Ning Yang
- Department of Neurology, Xijing Hospital, the Fourth Military Medical University, no.169 Changle West Road, Xi’an, Shaanxi, 710032, P.R.China
| | - Wen Dai
- Department of Neurology, Xijing Hospital, the Fourth Military Medical University, no.169 Changle West Road, Xi’an, Shaanxi, 710032, P.R.China
| | - Lin Zhang
- Department of Neurology, Xijing Hospital, the Fourth Military Medical University, no.169 Changle West Road, Xi’an, Shaanxi, 710032, P.R.China
| | - Qiao Li
- Department of Neurology, Xijing Hospital, the Fourth Military Medical University, no.169 Changle West Road, Xi’an, Shaanxi, 710032, P.R.China
| | - Yu Gao
- Department of Neurology, Xijing Hospital, the Fourth Military Medical University, no.169 Changle West Road, Xi’an, Shaanxi, 710032, P.R.China
| | - Ping Chen
- Department of Neurology, Xijing Hospital, the Fourth Military Medical University, no.169 Changle West Road, Xi’an, Shaanxi, 710032, P.R.China
| | - Li-Ping Zhan
- Department of Neurology, Kunming Medical University affiliated Yan’an Hospital, 245 Renming East Road, Kunming, Yunnan, 650200, P.R.China
| | - Ben J Marais
- The Children’s Hospital at Westmead and the Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Australia
| | - Yan-Lin Zhao
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, no.155 Changbai Road, Beijing, 102206, P.R.China
| | - Gang Zhao
- Department of Neurology, Xijing Hospital, the Fourth Military Medical University, no.169 Changle West Road, Xi’an, Shaanxi, 710032, P.R.China
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