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Asare P, Asante-Poku A, Osei-Wusu S, Otchere ID, Yeboah-Manu D. The Relevance of Genomic Epidemiology for Control of Tuberculosis in West Africa. Front Public Health 2021; 9:706651. [PMID: 34368069 PMCID: PMC8342769 DOI: 10.3389/fpubh.2021.706651] [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: 05/07/2021] [Accepted: 06/29/2021] [Indexed: 12/30/2022] Open
Abstract
Tuberculosis (TB), an airborne infectious disease caused by Mycobacterium tuberculosis complex (MTBC), remains a global health problem. West Africa has a unique epidemiology of TB that is characterized by medium- to high-prevalence. Moreover, the geographical restriction of M. africanum to the sub-region makes West Africa have an extra burden to deal with a two-in-one pathogen. The region is also burdened with low case detection, late reporting, poor treatment adherence leading to development of drug resistance and relapse. Sporadic studies conducted within the subregion report higher burden of drug resistant TB (DRTB) than previously thought. The need for more sensitive and robust tools for routine surveillance as well as to understand the mechanisms of DRTB and transmission dynamics for the design of effective control tools, cannot be overemphasized. The advancement in molecular biology tools including traditional fingerprinting and next generation sequencing (NGS) technologies offer reliable tools for genomic epidemiology. Genomic epidemiology provides in-depth insight of the nature of pathogens, circulating strains and their spread as well as prompt detection of the emergence of new strains. It also offers the opportunity to monitor treatment and evaluate interventions. Furthermore, genomic epidemiology can be used to understand potential emergence and spread of drug resistant strains and resistance mechanisms allowing the design of simple but rapid tools. In this review, we will describe the local epidemiology of MTBC, highlight past and current investigations toward understanding their biology and spread as well as discuss the relevance of genomic epidemiology studies to TB control in West Africa.
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Affiliation(s)
- Prince Asare
- College of Health Sciences, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Adwoa Asante-Poku
- College of Health Sciences, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Stephen Osei-Wusu
- College of Health Sciences, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Isaac Darko Otchere
- College of Health Sciences, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Dorothy Yeboah-Manu
- College of Health Sciences, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
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Muzondiwa D, Hlanze H, Reva ON. The Epistatic Landscape of Antibiotic Resistance of Different Clades of Mycobacterium tuberculosis. Antibiotics (Basel) 2021; 10:857. [PMID: 34356778 PMCID: PMC8300818 DOI: 10.3390/antibiotics10070857] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/08/2021] [Accepted: 07/13/2021] [Indexed: 11/16/2022] Open
Abstract
Drug resistance (DR) remains a global challenge in tuberculosis (TB) control. In order to develop molecular-based diagnostic methods to replace the traditional culture-based diagnostics, there is a need for a thorough understanding of the processes that govern TB drug resistance. The use of whole-genome sequencing coupled with statistical and computational methods has shown great potential in unraveling the complexity of the evolution of DR-TB. In this study, we took an innovative approach that sought to determine nonrandom associations between polymorphic sites in Mycobacterium tuberculosis (Mtb) genomes. Attributable risk statistics were applied to identify the epistatic determinants of DR in different clades of Mtb and the possible evolutionary pathways of DR development. It was found that different lineages of Mtb exploited different evolutionary trajectories towards multidrug resistance and compensatory evolution to reduce the DR-associated fitness cost. Epistasis of DR acquisition is a new area of research that will aid in the better understanding of evolutionary biological processes and allow predicting upcoming multidrug-resistant pathogens before a new outbreak strikes humanity.
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Affiliation(s)
| | | | - Oleg N. Reva
- Centre for Bioinformatics and Computational Biology, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa; (D.M.); (H.H.)
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Molecular epidemiology and drug susceptibility profiles of Mycobacterium tuberculosis complex isolates from Northern Ghana. Int J Infect Dis 2021; 109:294-303. [PMID: 34273514 DOI: 10.1016/j.ijid.2021.07.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/30/2021] [Accepted: 07/03/2021] [Indexed: 01/19/2023] Open
Abstract
OBJECTIVE We conducted a cross-sectional study in the five administrative regions of Northern Ghana to determine the diversity of Mycobacterium tuberculosis complex (MTBC) sub/lineages and their susceptibility to isoniazid (INH) and rifampicin (RIF). METHODS Sputum specimens were collected and cultured from 566 pulmonary tuberculosis patients reporting to 17 health facilities from 2015 to 2019. Mycobacterial isolates obtained from solid cultures were confirmed as members of the MTBC by PCR amplification of IS6110 and rpoß and assigned lineages and sub-lineages using spoligotyping. RESULTS Of 294 mycobacterial isolates recovered, MTBC species identified were: M. tuberculosis sensu stricto (Mtbss) 241 (82.0%), M. africanum 41 (13.9%) and M. bovis four (1.4%) with eight (2.7%) unidentified. The human-adapted lineages (L) identified (N=279) were L1 (8/279, 2.9%), L2 (15/279, 5.4%), L3 (7/279, 2.5%), L4 (208/279, 74.5%), L5 (13/279, 4.7%) and L6 (28/279, 10.0%) with three unidentified lineages. Among the 208 L4, the dominant sub-lineages in the region were the Cameroon 120/208 (57.7%) and Ghana 50/208 (24.0%). We found 4.4% (13/294) and 0.7% (2/294) of the patients infected with MTBC isolates resistant to INH only and RIF only, respectively, with 2.4% (7/294) being infected with MDR strains. Whereas L6 was associated with the elderly, we identified that the Ghana sub-lineage of L4 was associated with both INH and MDR (p<0.05), making them important TB pathogens in Northern Ghana and a growing public health concern.
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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: 7] [Impact Index Per Article: 2.3] [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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Characterization of genetic diversity and clonal complexes by whole genome sequencing of Mycobacterium tuberculosis isolates from Jalisco, Mexico. Tuberculosis (Edinb) 2021; 129:102106. [PMID: 34218194 DOI: 10.1016/j.tube.2021.102106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 06/14/2021] [Accepted: 06/20/2021] [Indexed: 11/24/2022]
Abstract
Whole genome sequencing (WGS) analysis in tuberculosis allows the prediction of drug-resistant phenotypes, identification of lineages, and to better understanding of the epidemiology and transmission chains. Nevertheless the procedure has been scarcely assessed in Mexico, in this work we analyze by WGS isolates of Mycobacterium tuberculosis circulating in Jalisco, Mexico. Lineage and phylogenetic characterization, drug resistant prediction, "in silico" spoligotyping determination, were provided by WGS in 32 M. tuberculosis clinical isolates. Lineage 4 (L4), with 28 isolates (87%) and eleven sublineages was dominant. Forty SNPs and INDELs were found in genes related to first-, and second-line drugs. Eleven isolates were sensitive, seven (22%) were predicted to be resistant to isoniazid, two resistant to rifampicin (6%) and two (6%) were multidrug-resistant tuberuclosis. Spoligotyping shows that SIT 53 (19%) and SIT 119 (16%) were dominant. Four clonal transmission complexes were found. This is the first molecular epidemiological description of TB isolates circulating in western Mexico, achieved through WGS. L4 was dominant and included a high diversity of sublineages. It was possible to track the transmission route of two clonal complexes. The WGS demonstrated to be of great utility and with further implications for clinical and epidemiological study of TB in the region.
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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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Luo T, Xu P, Zhang Y, Porter JL, Ghanem M, Liu Q, Jiang Y, Li J, Miao Q, Hu B, Howden BP, Fyfe JAM, Globan M, He W, He P, Wang Y, Liu H, Takiff HE, Zhao Y, Chen X, Pan Q, Behr MA, Stinear TP, Gao Q. Population genomics provides insights into the evolution and adaptation to humans of the waterborne pathogen Mycobacterium kansasii. Nat Commun 2021; 12:2491. [PMID: 33941780 PMCID: PMC8093194 DOI: 10.1038/s41467-021-22760-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 03/16/2021] [Indexed: 02/02/2023] Open
Abstract
Mycobacterium kansasii can cause serious pulmonary disease. It belongs to a group of closely-related species of non-tuberculous mycobacteria known as the M. kansasii complex (MKC). Here, we report a population genomics analysis of 358 MKC isolates from worldwide water and clinical sources. We find that recombination, likely mediated by distributive conjugative transfer, has contributed to speciation and on-going diversification of the MKC. Our analyses support municipal water as a main source of MKC infections. Furthermore, nearly 80% of the MKC infections are due to closely-related M. kansasii strains, forming a main cluster that apparently originated in the 1900s and subsequently expanded globally. Bioinformatic analyses indicate that several genes involved in metabolism (e.g., maintenance of the methylcitrate cycle), ESX-I secretion, metal ion homeostasis and cell surface remodelling may have contributed to M. kansasii's success and its ongoing adaptation to the human host.
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Affiliation(s)
- Tao Luo
- grid.13291.380000 0001 0807 1581Department of Pathogen Biology, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China ,grid.8547.e0000 0001 0125 2443Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Medical College and School of Basic Medical Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Peng Xu
- grid.8547.e0000 0001 0125 2443Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Medical College and School of Basic Medical Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China ,grid.417409.f0000 0001 0240 6969Key Laboratory of Characteristic Infectious Disease & Bio-safety Development of Guizhou Province Education Department, Institute of Life Sciences, Zunyi Medical University, Zunyi, China
| | - Yangyi Zhang
- Department of Tuberculosis Control, Shanghai Municipal Centre for Disease Control and Prevention, Shanghai, China
| | - Jessica L. Porter
- grid.1008.90000 0001 2179 088XDepartment of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Vic Australia ,grid.1008.90000 0001 2179 088XDoherty Applied Microbial Genomics, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Vic Australia
| | - Marwan Ghanem
- grid.14709.3b0000 0004 1936 8649Department of Microbiology and Immunology, McGill University and McGill International TB Centre, Montreal, Quebec Canada
| | - Qingyun Liu
- grid.8547.e0000 0001 0125 2443Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Medical College and School of Basic Medical Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Yuan Jiang
- Department of Tuberculosis Control, Shanghai Municipal Centre for Disease Control and Prevention, Shanghai, China
| | - Jing Li
- Department of Tuberculosis Control, Shanghai Municipal Centre for Disease Control and Prevention, Shanghai, China
| | - Qing Miao
- grid.8547.e0000 0001 0125 2443Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Bijie Hu
- grid.8547.e0000 0001 0125 2443Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Benjamin P. Howden
- grid.1008.90000 0001 2179 088XDepartment of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Vic Australia ,grid.1008.90000 0001 2179 088XDoherty Applied Microbial Genomics, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Vic Australia ,grid.1008.90000 0001 2179 088XMicrobiological Diagnostic Unit Public Health Laboratory, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000 Australia
| | - Janet A. M. Fyfe
- grid.429299.d0000 0004 0452 651XVictorian Infectious Diseases Reference Laboratory, Doherty Institute for Infection and Immunity, Melbourne Health, Melbourne, Vic Australia
| | - Maria Globan
- grid.429299.d0000 0004 0452 651XVictorian Infectious Diseases Reference Laboratory, Doherty Institute for Infection and Immunity, Melbourne Health, Melbourne, Vic Australia
| | - Wencong He
- grid.198530.60000 0000 8803 2373Chinese Center for Disease Control and Prevention and Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Ping He
- grid.198530.60000 0000 8803 2373Chinese Center for Disease Control and Prevention and Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Yiting Wang
- grid.198530.60000 0000 8803 2373Chinese Center for Disease Control and Prevention and Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Houming Liu
- grid.263817.9Department of Clinical Laboratory, The Third People’s Hospital of Shenzhen, Southern University of Science and Technology, Shenzhen, China
| | - Howard E. Takiff
- grid.428999.70000 0001 2353 6535Unité de Pathogenetique Integrée Mycobacterienne, Institut Pasteur, Paris, France ,grid.418243.80000 0001 2181 3287Laboratorio de Genética Molecular, CMBC, IVIC, Caracas, Venezuela ,Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, China
| | - Yanlin Zhao
- grid.198530.60000 0000 8803 2373Chinese Center for Disease Control and Prevention and Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Xinchun Chen
- grid.263488.30000 0001 0472 9649Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Pathogen Biology, Shenzhen University School of Medicine, Shenzhen, China
| | - Qichao Pan
- Department of Tuberculosis Control, Shanghai Municipal Centre for Disease Control and Prevention, Shanghai, China
| | - Marcel A. Behr
- grid.14709.3b0000 0004 1936 8649Department of Microbiology and Immunology, McGill University and McGill International TB Centre, Montreal, Quebec Canada
| | - Timothy P. Stinear
- grid.1008.90000 0001 2179 088XDepartment of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Vic Australia ,grid.1008.90000 0001 2179 088XDoherty Applied Microbial Genomics, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Vic Australia
| | - Qian Gao
- grid.8547.e0000 0001 0125 2443Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Medical College and School of Basic Medical Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
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Fernandez Do Porto DA, Monteserin J, Campos J, Sosa EJ, Matteo M, Serral F, Yokobori N, Benevento AF, Poklepovich T, Pardo A, Wainmayer I, Simboli N, Castello F, Paul R, Martí M, López B, Turjanski A, Ritacco V. Five-year microevolution of a multidrug-resistant Mycobacterium tuberculosis strain within a patient with inadequate compliance to treatment. BMC Infect Dis 2021; 21:394. [PMID: 33926375 PMCID: PMC8082761 DOI: 10.1186/s12879-021-06069-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 04/14/2021] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Whole-genome sequencing has shown that the Mycobacterium tuberculosis infection process can be more heterogeneous than previously thought. Compartmentalized infections, exogenous reinfections, and microevolution are manifestations of this clonal complexity. The analysis of the mechanisms causing the microevolution -the genetic variability of M. tuberculosis at short time scales- of a parental strain into clonal variants with a patient is a relevant issue that has not been yet completely addressed. To our knowledge, a whole genome sequence microevolution analysis in a single patient with inadequate adherence to treatment has not been previously reported. CASE PRESENTATION In this work, we applied whole genome sequencing analysis for a more in-depth analysis of the microevolution of a parental Mycobacterium tuberculosis strain into clonal variants within a patient with poor treatment compliance in Argentina. We analyzed the whole-genome sequence of 8 consecutive Mycobacterium tuberculosis isolates obtained from a patient within 57-months of intermittent therapy. Nineteen mutations (9 short-term, 10 fixed variants) emerged, most of them associated with drug resistance. The first isolate was already resistant to isoniazid, rifampicin, and streptomycin, thereafter the strain developed resistance to fluoroquinolones and pyrazinamide. Surprisingly, isolates remained susceptible to the pro-drug ethionamide after acquiring a frameshift mutation in ethA, a gene required for its activation. We also found a novel variant, (T-54G), in the 5' untranslated region of whiB7 (T-54G), a region allegedly related to kanamycin resistance. Notably, discrepancies between canonical and phage-based susceptibility testing to kanamycin were previously found for the isolate harboring this mutation. In our patient, microevolution was mainly driven by drug selective pressure. Rare short-term mutations fixed together with resistance-conferring mutations during therapy. CONCLUSIONS This report highlights the relevance of whole-genome sequencing analysis in the clinic for characterization of pre-XDR and MDR resistance profile, particularly in patients with incomplete and/or intermittent treatment.
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Affiliation(s)
- Darío A Fernandez Do Porto
- Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Johana Monteserin
- Instituto Nacional de Enfermedades Infecciosas-ANLIS Carlos Malbrán, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Josefina Campos
- Instituto Nacional de Enfermedades Infecciosas-ANLIS Carlos Malbrán, Buenos Aires, Argentina
| | - Ezequiel J Sosa
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, IQUIBICEN, CONICET, Buenos Aires, Argentina
| | - Mario Matteo
- Instituto de Tisioneumonología Raúl F. Vaccarezza, Hospital de Infecciosas Dr. F. J. Muñiz, Buenos Aires, Argentina
| | - Federico Serral
- Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Noemí Yokobori
- Instituto Nacional de Enfermedades Infecciosas-ANLIS Carlos Malbrán, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Andrés Fernández Benevento
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, IQUIBICEN, CONICET, Buenos Aires, Argentina
| | - Tomás Poklepovich
- Instituto Nacional de Enfermedades Infecciosas-ANLIS Carlos Malbrán, Buenos Aires, Argentina
| | - Agustín Pardo
- Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, IQUIBICEN, CONICET, Buenos Aires, Argentina
| | - Ingrid Wainmayer
- Instituto Nacional de Enfermedades Infecciosas-ANLIS Carlos Malbrán, Buenos Aires, Argentina
| | - Norberto Simboli
- Instituto Nacional de Enfermedades Infecciosas-ANLIS Carlos Malbrán, Buenos Aires, Argentina
| | - Florencia Castello
- Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Roxana Paul
- Instituto Nacional de Enfermedades Infecciosas-ANLIS Carlos Malbrán, Buenos Aires, Argentina
| | - Marcelo Martí
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, IQUIBICEN, CONICET, Buenos Aires, Argentina
| | - Beatriz López
- Instituto Nacional de Enfermedades Infecciosas-ANLIS Carlos Malbrán, Buenos Aires, Argentina
| | - Adrián Turjanski
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, IQUIBICEN, CONICET, Buenos Aires, Argentina.
| | - Viviana Ritacco
- Instituto Nacional de Enfermedades Infecciosas-ANLIS Carlos Malbrán, Buenos Aires, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
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59
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Local adaptation of Mycobacterium tuberculosis on the Tibetan Plateau. Proc Natl Acad Sci U S A 2021; 118:2017831118. [PMID: 33879609 DOI: 10.1073/pnas.2017831118] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
During its global dispersal, Mycobacterium tuberculosis (Mtb) has encountered varied geographic environments and host populations. Although local adaptation seems to be a plausible model for describing long-term host-pathogen interactions, genetic evidence for this model is lacking. Here, we analyzed 576 whole-genome sequences of Mtb strains sampled from different regions of high-altitude Tibet. Our results show that, after sequential introduction of a few ancestral strains, the Tibetan Mtb population diversified locally while maintaining strict separation from the Mtb populations on the lower altitude plain regions of China. The current population structure and estimated past population dynamics suggest that the modern Beijing sublineage strains, which expanded over most of China and other global regions, did not show an expansion advantage in Tibet. The mutations in the Tibetan strains showed a higher proportion of A > G/T > C transitions than strains from the plain regions, and genes encoding DNA repair enzymes showed evidence of positive selection. Moreover, the long-term Tibetan exclusive selection for truncating mutations in the thiol-oxidoreductase encoding sseA gene suggests that Mtb was subjected to local selective pressures associated with oxidative stress. Collectively, the population genomics of Mtb strains in the relatively isolated population of Tibet provides genetic evidence that Mtb has adapted to local environments.
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60
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Conceição EC, Salvato RS, Gomes KM, Guimarães AEDS, da Conceição ML, Souza e Guimarães RJDP, Sharma A, Furlaneto IP, Barcellos RB, Bollela VR, Anselmo LMP, Sisco MC, Niero CV, Ferrazoli L, Refrégier G, Lourenço MCDS, Gomes HM, de Brito AC, Catanho M, Duarte RS, Suffys PN, Lima KVB. Molecular epidemiology of Mycobacterium tuberculosis in Brazil before the whole genome sequencing era: a literature review. Mem Inst Oswaldo Cruz 2021; 116:e200517. [PMID: 33729319 PMCID: PMC7976556 DOI: 10.1590/0074-02760200517] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 02/11/2021] [Indexed: 11/22/2022] Open
Abstract
Molecular-typing can help in unraveling epidemiological scenarios and improvement for disease control strategies. A literature review of Mycobacterium tuberculosis transmission in Brazil through genotyping on 56 studies published from 1996-2019 was performed. The clustering rate for mycobacterial interspersed repetitive units - variable tandem repeats (MIRU-VNTR) of 1,613 isolates were: 73%, 33% and 28% based on 12, 15 and 24-loci, respectively; while for RFLP-IS6110 were: 84% among prison population in Rio de Janeiro, 69% among multidrug-resistant isolates in Rio Grande do Sul, and 56.2% in general population in São Paulo. These findings could improve tuberculosis (TB) surveillance and set up a solid basis to build a database of Mycobacterium genomes.
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Affiliation(s)
- Emilyn Costa Conceição
- Fundação Oswaldo Cruz-Fiocruz, Instituto Nacional de Infectologia
Evandro Chagas, Programa de Pós-Graduação em Pesquisa Clínica e Doenças Infecciosas,
Rio de Janeiro, RJ, Brasil
- Fundação Oswaldo Cruz-Fiocruz, Instituto Nacional de Infectologia
Evandro Chagas, Laboratório de Bacteriologia e Bioensaios em Micobactérias, Rio de
Janeiro, RJ, Brasil
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório
de Biologia Molecular Aplicada a Micobactérias, Rio de Janeiro, RJ, Brasil
| | - Richard Steiner Salvato
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação
em Biologia Celular e Molecular, Porto Alegre, RS, Brasil
- Secretaria Estadual de Saúde do Rio Grande do Sul, Centro Estadual
de Vigilância em Saúde, Centro de Desenvolvimento Científico e Tecnológico, Porto
Alegre, RS, Brasil
| | - Karen Machado Gomes
- Fundação Oswaldo Cruz-Fiocruz, Escola Nacional de Saúde Pública
Sergio Arouca, Centro de Referência Professor Hélio Fraga, Laboratório de Referência
Nacional para Tuberculose e outras Micobacterioses, Rio de Janeiro, RJ, Brasil
| | - Arthur Emil dos Santos Guimarães
- Universidade do Estado do Pará, Instituto de Ciências Biológicas e
da Saúde, Pós-Graduação Biologia Parasitária na Amazônia, Belém, PA, Brasil
- Instituto Evandro Chagas, Seção de Bacteriologia e Micologia,
Ananindeua, PA, Brasil
| | - Marília Lima da Conceição
- Universidade do Estado do Pará, Instituto de Ciências Biológicas e
da Saúde, Pós-Graduação Biologia Parasitária na Amazônia, Belém, PA, Brasil
- Instituto Evandro Chagas, Seção de Bacteriologia e Micologia,
Ananindeua, PA, Brasil
| | | | - Abhinav Sharma
- International Institute of Information Technology, Department of
Data Science, Bangalore, India
| | | | - Regina Bones Barcellos
- Secretaria Estadual de Saúde do Rio Grande do Sul, Centro Estadual
de Vigilância em Saúde, Centro de Desenvolvimento Científico e Tecnológico, Porto
Alegre, RS, Brasil
| | - Valdes Roberto Bollela
- Universidade de São Paulo, Departamento de Clínica Médica da
Faculdade de Medicina de Ribeirão Preto, Ribeirão Preto, SP, Brasil
| | - Lívia Maria Pala Anselmo
- Universidade de São Paulo, Departamento de Clínica Médica da
Faculdade de Medicina de Ribeirão Preto, Ribeirão Preto, SP, Brasil
| | - Maria Carolina Sisco
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório
de Biologia Molecular Aplicada a Micobactérias, Rio de Janeiro, RJ, Brasil
- Universidade Federal do Rio de Janeiro, Instituto de Microbiologia
Paulo de Góes, Laboratório de Micobactérias, Rio de Janeiro, RJ, Brasil
| | - Cristina Viana Niero
- Universidade Federal de São Paulo, Departamento de Microbiologia,
Imunologia e Parasitologia, São Paulo, SP, Brasil
| | - Lucilaine Ferrazoli
- Instituto Adolfo Lutz, Centro de Bacteriologia, Núcleo de
Tuberculose e Micobacterioses, São Paulo, SP, Brasil
| | - Guislaine Refrégier
- Universit e Paris-Saclay, Ecologie Systematique Evolution, Centre
National de la Recherche Scientifique, AgroParisTech, Orsay, France
| | - Maria Cristina da Silva Lourenço
- Fundação Oswaldo Cruz-Fiocruz, Instituto Nacional de Infectologia
Evandro Chagas, Laboratório de Bacteriologia e Bioensaios em Micobactérias, Rio de
Janeiro, RJ, Brasil
| | - Harrison Magdinier Gomes
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório
de Biologia Molecular Aplicada a Micobactérias, Rio de Janeiro, RJ, Brasil
| | - Artemir Coelho de Brito
- Coordenação Geral de Vigilância das Doenças de Transmissão
Respiratória de Condições Crônicas, Brasília, DF, Brasil
| | - Marcos Catanho
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório
de Genética Molecular de Microrganismos, Rio de Janeiro, RJ, Brasil
| | - Rafael Silva Duarte
- Universidade Federal do Rio de Janeiro, Instituto de Microbiologia
Paulo de Góes, Laboratório de Micobactérias, Rio de Janeiro, RJ, Brasil
| | - Philip Noel Suffys
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório
de Biologia Molecular Aplicada a Micobactérias, Rio de Janeiro, RJ, Brasil
| | - Karla Valéria Batista Lima
- Universidade do Estado do Pará, Instituto de Ciências Biológicas e
da Saúde, Pós-Graduação Biologia Parasitária na Amazônia, Belém, PA, Brasil
- Instituto Evandro Chagas, Seção de Bacteriologia e Micologia,
Ananindeua, PA, Brasil
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61
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Guyeux C, Sola C, Noûs C, Refrégier G. CRISPRbuilder-TB: "CRISPR-builder for tuberculosis". Exhaustive reconstruction of the CRISPR locus in mycobacterium tuberculosis complex using SRA. PLoS Comput Biol 2021; 17:e1008500. [PMID: 33667225 PMCID: PMC7968741 DOI: 10.1371/journal.pcbi.1008500] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 03/17/2021] [Accepted: 11/08/2020] [Indexed: 11/18/2022] Open
Abstract
Mycobacterium tuberculosis complex (MTC) CRISPR locus diversity has long been studied solely investigating the presence/absence of a known set of spacers. Unveiling the genetic mechanisms of its evolution requires a more exhaustive reconstruction in a large amount of representative strains. In this article, we point out and resolve, with a new pipeline, the problem of CRISPR reconstruction based directly on short read sequences in M. tuberculosis. We first show that the process we set up, that we coin as “CRISPRbuilder-TB” (https://github.com/cguyeux/CRISPRbuilder-TB), allows an efficient reconstruction of simulated or real CRISPRs, even when including complex evolutionary steps like the insertions of mobile elements. Compared to more generalist tools, the whole process is much more precise and robust, and requires only minimal manual investigation. Second, we show that more than 1/3 of the currently complete genomes available for this complex in the public databases contain largely erroneous CRISPR loci. Third, we highlight how both the classical experimental in vitro approach and the basic in silico spoligotyping provided by existing analytic tools miss a whole diversity of this locus in MTC, by not capturing duplications, spacer and direct repeats variants, and IS6110 insertion locations. This description is extended in a second article that describes MTC-CRISPR diversity and suggests general rules for its evolution. This work opens perspectives for an in-depth exploration of M. tuberculosis CRISPR loci diversity and of mechanisms involved in its evolution and its functionality, as well as its adaptation to other CRISPR locus-harboring bacterial species. In this article, we tackle the bioinformatical issue of the reconstruction of the Mycobacterium tuberculosis complex CRISPR locus using short read sequences without requiring genome assembly. We first show that many complete genomes, as found in public databases and often reconstructed by de novo assemblies, often contain errors on this locus as well as on other repeated sequences. We provide an in-depth description of our new method, designated as ‘CRISPRbuilder-TB’, and we show that our method provides much more exhaustive and reliable information (on DR variants, spacer diversity, global structure) than Crass and CRISPR_detector. The new and unsuspected genomic diversity we detected is described in a companion paper. Scripts are available to adapt the tool to other species.
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Affiliation(s)
- Christophe Guyeux
- FEMTO-ST Institute, UMR 6174 CNRS, DISC Computer Department, Univ. Bourgogne Franche-Comté (UBFC), Besançon, France
- * E-mail:
| | - Christophe Sola
- IAME, UMR1137 INSERM, Université Paris, Université Paris Nord
- 3 Université Paris-Saclay, Saint-Aubin, France
| | - Camille Noûs
- IAME, UMR1137 INSERM, Université Paris, Université Paris Nord
| | - Guislaine Refrégier
- 4 Ecologie Systematique Evolution, Batiment 360, Université Paris-Saclay, CNRS, AgroParisTech,Orsay 91400, France
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62
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Menardo F, Rutaihwa LK, Zwyer M, Borrell S, Comas I, Conceição EC, Coscolla M, Cox H, Joloba M, Dou HY, Feldmann J, Fenner L, Fyfe J, Gao Q, García de Viedma D, Garcia-Basteiro AL, Gygli SM, Hella J, Hiza H, Jugheli L, Kamwela L, Kato-Maeda M, Liu Q, Ley SD, Loiseau C, Mahasirimongkol S, Malla B, Palittapongarnpim P, Rakotosamimanana N, Rasolofo V, Reinhard M, Reither K, Sasamalo M, Silva Duarte R, Sola C, Suffys P, Batista Lima KV, Yeboah-Manu D, Beisel C, Brites D, Gagneux S. Local adaptation in populations of Mycobacterium tuberculosis endemic to the Indian Ocean Rim. F1000Res 2021; 10:60. [PMID: 33732436 PMCID: PMC7921886 DOI: 10.12688/f1000research.28318.2] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/22/2021] [Indexed: 12/12/2022] Open
Abstract
Background: Lineage 1 (L1) and 3 (L3) are two lineages of the Mycobacterium tuberculosis complex (MTBC) causing tuberculosis (TB) in humans. L1 and L3 are prevalent around the rim of the Indian Ocean, the region that accounts for most of the world's new TB cases. Despite their relevance for this region, L1 and L3 remain understudied. Methods: We analyzed 2,938 L1 and 2,030 L3 whole genome sequences originating from 69 countries. We reconstructed the evolutionary history of these two lineages and identified genes under positive selection. Results: We found a strongly asymmetric pattern of migration from South Asia toward neighboring regions, highlighting the historical role of South Asia in the dispersion of L1 and L3. Moreover, we found that several genes were under positive selection, including genes involved in virulence and resistance to antibiotics. For L1 we identified signatures of local adaptation at the esxH locus, a gene coding for a secreted effector that targets the human endosomal sorting complex, and is included in several vaccine candidates. Conclusions: Our study highlights the importance of genetic diversity in the MTBC, and sheds new light on two of the most important MTBC lineages affecting humans.
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Affiliation(s)
- Fabrizio Menardo
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Liliana K Rutaihwa
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Michaela Zwyer
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Sonia Borrell
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Iñaki Comas
- Institute of Biomedicine of Valencia, Valencia, Spain
| | - Emilyn Costa Conceição
- Instituto de Microbiologia, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | | | - Helen Cox
- Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Moses Joloba
- Department of Medical Microbiology, Makerere University, Kampala, Uganda
| | - Horng-Yunn Dou
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institute, Zhunan, Taiwan
| | - Julia Feldmann
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Lukas Fenner
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland.,Institute for Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Janet Fyfe
- Victorian Infectious Diseases Reference Laboratory, Melbourne, Australia
| | - Qian Gao
- Institute of Medical Microbiology, School of Basic Medical Science of Fudan University, Shanghai, China
| | - Darío García de Viedma
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.,CIBER Enfermedades Respiratorias, Madrid, Spain.,Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Alberto L Garcia-Basteiro
- Barcelona Institute for Global Health, Barcelona, Spain.,Centro de Investigação em Saúde de Manhiça, Maputo, Mozambique
| | - Sebastian M Gygli
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Jerry Hella
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland.,Ifakara Health Institute, Bagamoyo, Tanzania
| | - Hellen Hiza
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Levan Jugheli
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Lujeko Kamwela
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland.,Ifakara Health Institute, Bagamoyo, Tanzania
| | | | - Qingyun Liu
- Institute of Medical Microbiology, School of Basic Medical Science of Fudan University, Shanghai, China
| | - Serej D Ley
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland.,Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Chloe Loiseau
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Surakameth Mahasirimongkol
- Department of Microbiology, Mahidol University, Bangkok, Thailand.,National Science and Technology Development Agency, Bangkok, Thailand
| | - Bijaya Malla
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Prasit Palittapongarnpim
- Department of Microbiology, Mahidol University, Bangkok, Thailand.,National Science and Technology Development Agency, Bangkok, Thailand
| | | | | | - Miriam Reinhard
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Klaus Reither
- University of Basel, Basel, Switzerland.,Department of Medicine, Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Mohamed Sasamalo
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland.,Ifakara Health Institute, Bagamoyo, Tanzania
| | - Rafael Silva Duarte
- Instituto de Microbiologia, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Christophe Sola
- Université Paris-Saclay, Paris, France.,INSERM-Université de Paris, Paris, France
| | - Philip Suffys
- Laboratório de Biologia Molecular Aplicada a Micobactérias, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Karla Valeria Batista Lima
- Centro de Ciências Biológicas e da Saúde, Universidade do Estado do Pará, Belém, Brazil.,Instituto Evandro Chagas, Ananindeua, Brazil
| | - Dorothy Yeboah-Manu
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Christian Beisel
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Daniela Brites
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Sebastien Gagneux
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
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63
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Jiménez-Ruano AC, Madrazo-Moya CF, Cancino-Muñoz I, Mejía-Ponce PM, Licona-Cassani C, Comas I, Muñiz-Salazar R, Zenteno-Cuevas R. Whole genomic sequencing based genotyping reveals a specific X3 sublineage restricted to Mexico and related with multidrug resistance. Sci Rep 2021; 11:1870. [PMID: 33479318 PMCID: PMC7820219 DOI: 10.1038/s41598-020-80919-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 12/08/2020] [Indexed: 01/26/2023] Open
Abstract
Whole genome sequencing (WGS) has been shown to be superior to traditional procedures of genotyping in tuberculosis (TB), nevertheless, reports of its use in drug resistant TB (DR-TB) isolates circulating in Mexico, are practically unknown. Considering the above the main of this work was to identify and characterize the lineages and genomic transmission clusters present in 67 DR-TB isolates circulating in southeastern Mexico. The results show the presence of three major lineages: L1 (3%), L2 (3%) and L4 (94%), the last one included 16 sublineages. Sublineage 4.1.1.3 (X3) was predominant in 18 (27%) of the isolates, including one genomic cluster, formed by eleven multidrug resistant isolates and sharing the SIT 3278, which seems to be restricted to Mexico. By the use of WGS, it was possible to identify the high prevalence of L4 and a high number of sublineages circulating in the region, also was recognized the presence of a novel X3 sublineage, formed exclusively by multidrug resistant isolates and with restrictive circulation in Mexico for at least the past 17 years.
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Affiliation(s)
- Ana Cristina Jiménez-Ruano
- Programa de Maestría en Ciencias de la Salud, Instituto de Ciencias de la Salud, Universidad Veracruzana, Xalapa, Veracruz, México
- Instituto de Salud Pública, Universidad Veracruzana, Av. Luis Castelazo Ayala S/N, A.P. 57, Col. Industrial Animas, 91190, Xalapa, Veracruz, México
| | - Carlos Francisco Madrazo-Moya
- Programa de Maestría en Ciencias de la Salud, Instituto de Ciencias de la Salud, Universidad Veracruzana, Xalapa, Veracruz, México
- Biomedical Institute of Valencia IBV-CSIC, Valencia, Spain
| | | | - Paulina M Mejía-Ponce
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, Nuevo Leon, Mexico
| | | | - Iñaki Comas
- Biomedical Institute of Valencia IBV-CSIC, Valencia, Spain
- CIBER of Epidemiology and Public Health, Madrid, Spain
| | - 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
- Red Multidisciplinaria de Investigación en Tuberculosis, Mexico City, Mexico
| | - Roberto Zenteno-Cuevas
- Programa de Maestría en Ciencias de la Salud, Instituto de Ciencias de la Salud, Universidad Veracruzana, Xalapa, Veracruz, México.
- Instituto de Salud Pública, Universidad Veracruzana, Av. Luis Castelazo Ayala S/N, A.P. 57, Col. Industrial Animas, 91190, Xalapa, Veracruz, México.
- Red Multidisciplinaria de Investigación en Tuberculosis, Mexico City, Mexico.
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64
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Identification of a predominant genotype of Mycobacterium tuberculosis in Brazilian indigenous population. Sci Rep 2021; 11:1224. [PMID: 33441660 PMCID: PMC7806709 DOI: 10.1038/s41598-020-79621-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 12/07/2020] [Indexed: 11/30/2022] Open
Abstract
After nearly a century of vaccination and six decades of drug therapy, tuberculosis (TB) kills more people annually than any other infectious disease. Substantial challenges to disease eradication remain among vulnerable and underserved populations. The Guarani-Kaiowá people are an indigenous population in Paraguay and the Brazilian state of Mato Grosso do Sul. This community, marginalized in Brazilian society, experiences severe poverty. Like other South American indigenous populations, their TB prevalence is high, but the disease has remained largely unstudied in their communities. Herein, Mycobacterium tuberculosis isolates from local clinics were whole genome sequenced, and a population genetic framework was generated. Phylogenetics show M. tuberculosis isolates in the Guarani-Kaiowá people cluster away from selected reference strains, suggesting divergence. Most cluster in a single group, further characterized as M. tuberculosis sublineage 4.3.3. Closer analysis of SNPs showed numerous variants across the genome, including in drug resistance-associated genes, and with many unique changes fixed in each group. We report that local M. tuberculosis strains have acquired unique polymorphisms in the Guarani-Kaiowá people, and drug resistance characterization is urgently needed to inform public health to ensure proper care and avoid further evolution and spread of drug-resistant TB.
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65
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Santos-Pereira A, Magalhães C, Araújo PMM, Osório NS. Evolutionary Genetics of Mycobacterium tuberculosis and HIV-1: "The Tortoise and the Hare". Microorganisms 2021; 9:147. [PMID: 33440808 PMCID: PMC7827287 DOI: 10.3390/microorganisms9010147] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 12/24/2020] [Accepted: 01/06/2021] [Indexed: 12/16/2022] Open
Abstract
The already enormous burden caused by Mycobacterium tuberculosis and Human Immunodeficiency Virus type 1 (HIV-1) alone is aggravated by co-infection. Despite obvious differences in the rate of evolution comparing these two human pathogens, genetic diversity plays an important role in the success of both. The extreme evolutionary dynamics of HIV-1 is in the basis of a robust capacity to evade immune responses, to generate drug-resistance and to diversify the population-level reservoir of M group viral subtypes. Compared to HIV-1 and other retroviruses, M. tuberculosis generates minute levels of genetic diversity within the host. However, emerging whole-genome sequencing data show that the M. tuberculosis complex contains at least nine human-adapted phylogenetic lineages. This level of genetic diversity results in differences in M. tuberculosis interactions with the host immune system, virulence and drug resistance propensity. In co-infected individuals, HIV-1 and M. tuberculosis are likely to co-colonize host cells. However, the evolutionary impact of the interaction between the host, the slowly evolving M. tuberculosis bacteria and the HIV-1 viral "mutant cloud" is poorly understood. These evolutionary dynamics, at the cellular niche of monocytes/macrophages, are also discussed and proposed as a relevant future research topic in the context of single-cell sequencing.
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Affiliation(s)
- Ana Santos-Pereira
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; (A.S.-P.); (C.M.); (P.M.M.A.)
- ICVS/3B’s-T Government Associate Laboratory, 4710-057 Braga/Guimarães, Portugal
| | - Carlos Magalhães
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; (A.S.-P.); (C.M.); (P.M.M.A.)
- ICVS/3B’s-T Government Associate Laboratory, 4710-057 Braga/Guimarães, Portugal
| | - Pedro M. M. Araújo
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; (A.S.-P.); (C.M.); (P.M.M.A.)
- ICVS/3B’s-T Government Associate Laboratory, 4710-057 Braga/Guimarães, Portugal
| | - Nuno S. Osório
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; (A.S.-P.); (C.M.); (P.M.M.A.)
- ICVS/3B’s-T Government Associate Laboratory, 4710-057 Braga/Guimarães, Portugal
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66
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Pérez-Lago L, Monteserin J, Paul R, Maus SR, Yokobori N, Herranz M, Sicilia J, Acosta F, Fajardo S, Chiner-Oms Á, Matteo M, Simboli N, Comas I, Muñoz P, López B, Ritacco V, García de Viedma D. Recurrences of multidrug-resistant tuberculosis: Strains involved, within-host diversity, and fine-tuned allocation of reinfections. Transbound Emerg Dis 2021; 69:327-336. [PMID: 33411991 DOI: 10.1111/tbed.13982] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 12/16/2020] [Accepted: 01/03/2021] [Indexed: 11/27/2022]
Abstract
Recurrent tuberculosis occurs due to exogenous reinfection or reactivation/persistence. We analysed 90 sequential MDR Mtb isolates obtained in Argentina from 27 patients with previously diagnosed MDR-TB that recurred in 2018 (1-10 years, 2-10 isolates per patient). Three long-term predominant strains were responsible for 63% of all MDR-TB recurrences. Most of the remaining patients were infected by strains different from each other. Reactivation/persistence of the same strain caused all but one recurrence, which was due to a reinfection with a predominant strain. One of the prevalent strains showed marked stability in the recurrences, while in another strain higher SNP-based diversity was observed. Comparisons of intra- versus inter-patient SNP distances identified two possible reinfections with closely related variants circulating in the community. Our results show a complex scenario of MDR-TB infections in settings with predominant MDR Mtb strains.
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Affiliation(s)
- Laura Pérez-Lago
- Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Johana Monteserin
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina.,Instituto Nacional de Enfermedades Infecciosas ANLIS Carlos G Malbrán, Buenos Aires, Argentina
| | - Roxana Paul
- Instituto Nacional de Enfermedades Infecciosas ANLIS Carlos G Malbrán, Buenos Aires, Argentina
| | - Sandra R Maus
- Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Noemí Yokobori
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina.,Instituto Nacional de Enfermedades Infecciosas ANLIS Carlos G Malbrán, Buenos Aires, Argentina
| | - Marta Herranz
- Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.,CIBER Enfermedades Respiratorias (CIBERES), Spain
| | - Jon Sicilia
- Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Fermín Acosta
- Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Sandra Fajardo
- Centro Regional de estudios Bioquñimicos de la Tuberculosis, Rosario, Argentina
| | - Álvaro Chiner-Oms
- Centro Superior de Investigación en Salud Pública (FISABIO), Universitat de València, Valencia, Spain
| | - Mario Matteo
- Laboratorio Cetrángolo, Hospital Muñiz/Instituto de Tisioneumonología Raúl Vaccarezza, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Norberto Simboli
- Instituto Nacional de Enfermedades Infecciosas ANLIS Carlos G Malbrán, Buenos Aires, Argentina
| | - Iñaki Comas
- Instituto de Biomedicina de Valencia IBV-CSIC, Valencia, Spain.,CIBER Salud Pública (CIBERESP), Spain
| | - Patricia Muñoz
- Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.,Departamento de Medicina, Universidad Complutense, Madrid, Spain
| | - Beatriz López
- Instituto Nacional de Enfermedades Infecciosas ANLIS Carlos G Malbrán, Buenos Aires, Argentina
| | - Viviana Ritacco
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina.,Instituto Nacional de Enfermedades Infecciosas ANLIS Carlos G Malbrán, Buenos Aires, Argentina
| | - Darío García de Viedma
- Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.,CIBER Enfermedades Respiratorias (CIBERES), Spain
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67
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Hadifar S, Fateh A, Pourbarkhordar V, Siadat SD, Mostafaei S, Vaziri F. Variation in Mycobacterium tuberculosis population structure in Iran: a systemic review and meta-analysis. BMC Infect Dis 2021; 21:2. [PMID: 33397308 PMCID: PMC7784266 DOI: 10.1186/s12879-020-05639-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 11/19/2020] [Indexed: 01/30/2023] Open
Abstract
Background Acquiring comprehensive insight into the dynamics of Mycobacterium tuberculosis (Mtb) population structure is an essential step to adopt effective tuberculosis (TB) control strategies and improve therapeutic methods and vaccines. Accordingly, we performed this systematic review and meta-analysis to determine the overall prevalence of Mtb genotypes/ sublineages in Iran. Methods We carried out a comprehensive literature search using the international databases of MEDLINE and Scopus as well as Iranian databases. Articles published until April 2020 were selected based on the PRISMA flow diagram. The overall prevalence of the Mtb genotypes/sublineage in Iran was determined using the random effects or fixed effect model. The metafor R package and MedCalc software were employed for performing this meta-analysis. Results We identified 34 studies for inclusion in this study, containing 8329 clinical samples. Based on the pooled prevalence of the Mtb genotypes, NEW1 (21.94, 95% CI: 16.41–28.05%), CAS (19.21, 95% CI: 14.95–23.86%), EAI (12.95, 95% CI: 7.58–19.47%), and T (12.16, 95% CI: 9.18–15.50%) were characterized as the dominant circulating genotypes in Iran. West African (L 5/6), Cameroon, TUR and H37Rv were identified as genotypes with the lowest prevalence in Iran (< 2%). The highest pooled prevalence rates of multidrug-resistant strains were related to Beijing (2.52, 95% CI) and CAS (1.21, 95% CI). Conclusions This systematic review showed that Mtb populations are genetically diverse in Iran, and further studies are needed to gain a better insight into the national diversity of Mtb populations and their drug resistance pattern.
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Affiliation(s)
- Shima Hadifar
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Centre (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Centre (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Vahid Pourbarkhordar
- Department of Pharmacology and Toxicology, School of Pharmacy and Pharmaceutical Science, Isfahan University of Medical Science, Isfahan, Iran
| | - Seyed Davar Siadat
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Centre (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Shayan Mostafaei
- Department of Biostatistics, School of Health, Kermanshah University of Medical Sciences, Kermanshah, Iran. .,Epidemiology and Biostatistics Unit, Rheumatology Research Centre, Tehran University of Medical Sciences, Tehran, Iran.
| | - Farzam Vaziri
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran. .,Microbiology Research Centre (MRC), Pasteur Institute of Iran, Tehran, Iran.
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68
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Xu Y, Zhang S, Shen J, Wu Z, Du Z, Gao F. The phylogeographic history of tomato mosaic virus in Eurasia. Virology 2020; 554:42-47. [PMID: 33360588 DOI: 10.1016/j.virol.2020.12.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 12/14/2020] [Accepted: 12/14/2020] [Indexed: 11/19/2022]
Abstract
Tomato mosaic virus (ToMV) is a tobamovirus affecting solanaceous crops worldwide. The process of its emergence, however, is poorly understood. Here, Bayesian phylogenetic framework was employed to reconstruct the phylogeography of ToMV in Eurasia. The results showed that the ToMV in Europe, Middle East and East Asia has been evolving at a rate of 4.05 × 10-4 substitutions/site/year (95% credibility interval 2.43 × 10-4 - 5.62 × 10-4). Their most recent common ancestor (MRCA), most probably first appeared in Europe, was dated to around 1757 Common Era. The first introduction of ToMV into Middle East occurred in 1920s, with Europe as the source, while the first introduction of ToMV into East Asia occurred shortly afterwards, with Middle East as the source. From about 1950 onwards, inter-regional migrations of ToMV between Europe, Middle East and East Asia have been common. Overall, these data provide a glimpse into the phylogeographic history of ToMV in Eurasia.
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Affiliation(s)
- Yuting Xu
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shuling Zhang
- Department of Horticulture and Garden, Fujian Vocational College of Agriculture, Fuzhou, Fujian, 350119, China
| | - Jianguo Shen
- Technology Center of Fuzhou Customs District, Fuzhou, 350001, China
| | - Zujian Wu
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhenguo Du
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Fangluan Gao
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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Identification and in silico functional prediction of lineage-specific SNPs distributed in DosR-related proteins and resuscitation-promoting factor proteins of Mycobacterium tuberculosis. Heliyon 2020; 6:e05744. [PMID: 33364506 PMCID: PMC7753917 DOI: 10.1016/j.heliyon.2020.e05744] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/21/2020] [Accepted: 12/11/2020] [Indexed: 11/23/2022] Open
Abstract
One-third of the world population is infected by Mycobacterium tuberculosis, which may persist in the latent or dormant state. Bacteria can shift to dormancy when encountering harsh conditions such as low oxygen, nutrient starvation, high acidity and host immune defenses. Genes related to the dormancy survival regulator (DosR) regulon are responsible for the inhibition of aerobic respiration and replication, which is required to enter dormancy. Conversely, resuscitation-promoting factor (rpf) proteins participate in reactivation from dormancy and the development of active tuberculosis (TB). Many DosR regulon and rpf proteins are immunodominant T cell antigens that are highly expressed in latent TB infection. They could serve as TB vaccine candidates and be used for diagnostic development. We explored the genetic polymorphisms of 50 DosR-related genes and 5 rpf genes among 1,170 previously sequenced clinical M. tuberculosis genomes. Forty-three lineage- or sublineage-specific nonsynonymous single nucleotide polymorphisms (nsSNPs) were identified. Ten nsSNPs were specific to all Mtb isolates belonging to lineage 1 (L1). Two common sublineages, the Beijing family (L2.2) and EAI2 (L1.2.1), differed at as many as 26 lineage- or sublineage-specific SNPs. DosR regulon genes related to membrane proteins and the rpf family possessed mean dN/dS ratios greater than one, suggesting that they are under positive selection. Although the T cell epitope regions of DosR-related and rpf antigens were quite conserved, we found that the epitopes in L1 had higher rates of genetic polymorphisms than the other lineages. Some mutations in immunogenic epitopes of the antigens were specific to particular M. tuberculosis lineages. Therefore, the genetic diversity of the DosR regulon and rpf proteins might impact the adaptation of M. tuberculosis to the dormant state and the immunogenicity of latency antigens, which warrants further investigation.
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70
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Skhairia MA, Dekhil N, Mhenni B, Fradj SB, Mardassi H. Successful expansion of Mycobacterium tuberculosis Latin American and Mediterranean sublineage (L4.3/LAM) in Tunisia mainly driven by a single, long-established clonal complex. Int J Infect Dis 2020; 103:220-225. [PMID: 33307222 DOI: 10.1016/j.ijid.2020.11.195] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/24/2020] [Accepted: 11/26/2020] [Indexed: 11/28/2022] Open
Abstract
OBJECTIVES To explore the evolutionary history of Mycobacterium tuberculosis Latin American and Mediterranean (L4.3/LAM) sublineage in Tunisia, where it predominates. METHODS High-resolution genotyping of 252 L4.3/LAM clinical strains was undertaken, and whole-genome sequencing was performed on 31 representative isolates. RESULTS Genotyping data coupled with Bayesian analyses split the Tunisian L4.3/LAM strain collection into two divergent entities (65.07% vs 34.92%): a major subpopulation, dominated by a single clonal complex (CC), TUN4.3_CC1 (94.51%); and a minor subpopulation, dominated by TUN4.3_CC2 (42.04%). TUN4.3_CC1 is clearly thriving in Tunisia, accounting for 61.5% of the L4.3/LAM sublineage. TUN4.3_CC1 displayed higher mean allelic richness compared with TUN4.3_CC2 and predominated throughout the entire region, indicating a long-established history. The very low proportion of drug resistance among TUN4.3_CC1 isolates is indicative of their intrinsic ability to spread successfully in the host population. Genomic analyses further confirmed the clear genetic separation between the two main CCs (pairwise fixation index 0.56), and suggested the relatively ancient origin of TUN4.3_CC1. Consistent with its successful expansion, TUN4.3_CC1 showed reduced mean pairwise genetic distance between genomes. CONCLUSIONS These findings link the successful expansion of L4.3/LAM in Tunisia to a single long-established clone.
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Affiliation(s)
- Mohamed Amine Skhairia
- Unit of Typing and Genetics of Mycobacteria, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Naira Dekhil
- Unit of Typing and Genetics of Mycobacteria, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Besma Mhenni
- Unit of Typing and Genetics of Mycobacteria, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Saloua Ben Fradj
- Unit of Typing and Genetics of Mycobacteria, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Helmi Mardassi
- Unit of Typing and Genetics of Mycobacteria, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia.
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71
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Wahedi K, Biddle L, Bozorgmehr K. Cost-effectiveness of targeted screening for active pulmonary tuberculosis among asylum-seekers: A modelling study with screening data from a German federal state (2002-2015). PLoS One 2020; 15:e0241852. [PMID: 33151980 PMCID: PMC7644037 DOI: 10.1371/journal.pone.0241852] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 10/21/2020] [Indexed: 11/19/2022] Open
Abstract
Screening asylum-seekers for active pulmonary tuberculosis is common practice among many European countries with low incidence of tuberculosis. The reported yields vary substantially, partly due to the heterogeneous and dynamic nature of asylum-seeking populations. Rather than screening all new arrivals (indiscriminate screening), a few countries apply targeted screening based on incidence of tuberculosis in asylum-seekers' country of origin. However, evaluations of its cost-effectiveness have been scarce. The aim of this modelling study was to assess whether the introduction of a screening threshold based on the tuberculosis incidence in the country of origin is sensible from an economic perspective. To this end, we compare the current, indiscriminate screening policy for pulmonary tuberculosis in Germany with a hypothetical targeted screening programme using several potential screening thresholds based on WHO-reported incidence of tuberculosis in countries of origin. Screening data is taken from a large German federal state over 14 years (2002-2015). Incremental cost-effectiveness is measured as cost per case found and cost per case prevented. Our analysis shows that incremental cost-effectiveness ratios (ICERs) of screening asylum-seekers from countries with an incidence of 50 to 250/100,000 range between 15,000€ and 17,000€ per additional case found when compared to lower thresholds. The ICER for screening asylum-seekers from countries with an incidence <50/100,000 is 112,000€ per additional case found. Costs per case prevented show a similar increase in costs. The high cost per case found and per case prevented at the <50/100,000 threshold scenario suggests this threshold to be a sensible cut-off for targeted screening. Acknowledging that no screening measure can find all cases of tuberculosis, and that reactivation of latent infections makes up a large proportion of foreign-born cases, targeting asylum-seekers from countries with an incidence above 50/100,000 is likely to be a more reasonable screening measure for the prevention and control of tuberculosis than indiscriminate screening measures.
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Affiliation(s)
- Katharina Wahedi
- Department of General Practice and Health Services Research, University Hospital Heidelberg, Heidelberg, Germany
| | - Louise Biddle
- Department of General Practice and Health Services Research, University Hospital Heidelberg, Heidelberg, Germany
| | - Kayvan Bozorgmehr
- Department of General Practice and Health Services Research, University Hospital Heidelberg, Heidelberg, Germany
- Department of Population Medicine and Health Services Research, School of Public Health, Bielefeld University, Bielefeld, Germany
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Xu Y, Stockdale JE, Naidu V, Hatherell H, Stimson J, Stagg HR, Abubakar I, Colijn C. Transmission analysis of a large tuberculosis outbreak in London: a mathematical modelling study using genomic data. Microb Genom 2020; 6:mgen000450. [PMID: 33174832 PMCID: PMC7725332 DOI: 10.1099/mgen.0.000450] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 09/15/2020] [Indexed: 12/11/2022] Open
Abstract
Outbreaks of tuberculosis (TB) - such as the large isoniazid-resistant outbreak centred on London, UK, which originated in 1995 - provide excellent opportunities to model transmission of this devastating disease. Transmission chains for TB are notoriously difficult to ascertain, but mathematical modelling approaches, combined with whole-genome sequencing data, have strong potential to contribute to transmission analyses. Using such data, we aimed to reconstruct transmission histories for the outbreak using a Bayesian approach, and to use machine-learning techniques with patient-level data to identify the key covariates associated with transmission. By using our transmission reconstruction method that accounts for phylogenetic uncertainty, we are able to identify 21 transmission events with reasonable confidence, 9 of which have zero SNP distance, and a maximum distance of 3. Patient age, alcohol abuse and history of homelessness were found to be the most important predictors of being credible TB transmitters.
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Affiliation(s)
- Yuanwei Xu
- Centre for Mathematics of Precision Healthcare, Department of Mathematics, Imperial College London, London, UK
| | | | - Vijay Naidu
- Department of Mathematics, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | | | - James Stimson
- Centre for Mathematics of Precision Healthcare, Department of Mathematics, Imperial College London, London, UK
- National Infection Service, Public Health England, London, UK
| | - Helen R. Stagg
- Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Ibrahim Abubakar
- Institute for Global Health, University College London, London, UK
| | - Caroline Colijn
- Centre for Mathematics of Precision Healthcare, Department of Mathematics, Imperial College London, London, UK
- Department of Mathematics, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
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73
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Peters JS, Ismail N, Dippenaar A, Ma S, Sherman DR, Warren RM, Kana BD. Genetic Diversity in Mycobacterium tuberculosis Clinical Isolates and Resulting Outcomes of Tuberculosis Infection and Disease. Annu Rev Genet 2020; 54:511-537. [PMID: 32926793 DOI: 10.1146/annurev-genet-022820-085940] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Tuberculosis claims more human lives than any other bacterial infectious disease and represents a clear and present danger to global health as new tools for vaccination, treatment, and interruption of transmission have been slow to emerge. Additionally, tuberculosis presents with notable clinical heterogeneity, which complicates diagnosis, treatment, and the establishment of nonrelapsing cure. How this heterogeneity is driven by the diversity ofclinical isolates of the causative agent, Mycobacterium tuberculosis, has recently garnered attention. Herein, we review advances in the understanding of how naturally occurring variation in clinical isolates affects transmissibility, pathogenesis, immune modulation, and drug resistance. We also summarize how specific changes in transcriptional responses can modulate infection or disease outcome, together with strain-specific effects on gene essentiality. Further understanding of how this diversity of M. tuberculosis isolates affects disease and treatment outcomes will enable the development of more effective therapeutic options and vaccines for this dreaded disease.
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Affiliation(s)
- Julian S Peters
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg 2000, South Africa; ,
| | - Nabila Ismail
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg 7505, South Africa; ,
| | - Anzaan Dippenaar
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg 7505, South Africa; , .,Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, 2000, Belgium;
| | - Shuyi Ma
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington 98109, USA; ,
| | - David R Sherman
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington 98109, USA; ,
| | - Robin M Warren
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg 7505, South Africa; ,
| | - Bavesh D Kana
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg 2000, South Africa; ,
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74
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Cervantes J, Yokobori N, Hong BY. Genetic Identification and Drug-Resistance Characterization of Mycobacterium tuberculosis Using a Portable Sequencing Device. A Pilot Study. Antibiotics (Basel) 2020; 9:antibiotics9090548. [PMID: 32867304 PMCID: PMC7559383 DOI: 10.3390/antibiotics9090548] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/19/2020] [Accepted: 08/26/2020] [Indexed: 12/18/2022] Open
Abstract
Clinical management of tuberculosis (TB) in endemic areas is often challenged by a lack of resources including laboratories for Mycobacterium tuberculosis (Mtb) culture. Traditional phenotypic drug susceptibility testing for Mtb is costly and time consuming, while PCR-based methods are limited to selected target loci. We herein utilized a portable, USB-powered, long-read sequencing instrument (MinION), to investigate Mtb genomic DNA from clinical isolates to determine the presence of anti-TB drug-resistance conferring mutations. Data analysis platform EPI2ME and antibiotic-resistance analysis using the real time ARMA workflow, identified Mtb species as well as extensive resistance gene profiles. The approach was highly sensitive, being able to detect almost all described drug resistance conferring mutations based on previous whole genome sequencing analysis. Our findings are supportive of the practical use of this system as a suitable method for the detection of antimicrobial resistance genes, and effective in providing Mtb genomic information. Future improvements in the error rate through statistical analysis, drug resistance prediction algorithms and reference databases would make this a platform suited for the clinical setting. The small size, relatively inexpensive cost of the device, as well as its rapid and simple library preparation protocol and analysis, make it an attractive option for settings with limited laboratory infrastructure.
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Affiliation(s)
- Jorge Cervantes
- Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX 79905, USA
- Correspondence: ; Tel.: +1-915-215-4672
| | - Noemí Yokobori
- Servicio de Micobacterias, Instituto Nacional de Enfermedades Infecciosas (INEI)-ANLIS and CONICET, Buenos Aires C1282AFF, Argentina;
| | - Bo-Young Hong
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA;
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75
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Hackett EE, Sheedy FJ. An Army Marches on Its Stomach: Metabolic Intermediates as Antimicrobial Mediators in Mycobacterium tuberculosis Infection. Front Cell Infect Microbiol 2020; 10:446. [PMID: 32984072 PMCID: PMC7477320 DOI: 10.3389/fcimb.2020.00446] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 07/21/2020] [Indexed: 12/13/2022] Open
Abstract
The cells of the immune system are reliant on their metabolic state to launch effective responses to combat mycobacterial infections. The bioenergetic profile of the cell determines the molecular fuels and metabolites available to the host, as well as to the bacterial invader. How cells utilize the nutrients in their microenvironment—including glucose, lipids and amino acids—to sustain their functions and produce antimicrobial metabolites, and how mycobacteria exploit this to evade the immune system is of great interest. Changes in flux through metabolic pathways alters the intermediate metabolites present. These intermediates are beginning to be recognized as key modulators of immune signaling as well as direct antimicrobial effectors, and their impact on tuberculosis infection is becoming apparent. A better understanding of how metabolism impacts immunity to Mycobacterium tuberculosis and how it is regulated and thus can be manipulated will open the potential for novel therapeutic interventions and vaccination strategies.
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Affiliation(s)
- Emer E Hackett
- Macrophage Homeostasis, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Frederick J Sheedy
- Macrophage Homeostasis, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
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76
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Sabin S, Herbig A, Vågene ÅJ, Ahlström T, Bozovic G, Arcini C, Kühnert D, Bos KI. A seventeenth-century Mycobacterium tuberculosis genome supports a Neolithic emergence of the Mycobacterium tuberculosis complex. Genome Biol 2020; 21:201. [PMID: 32778135 PMCID: PMC7418204 DOI: 10.1186/s13059-020-02112-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 07/17/2020] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Although tuberculosis accounts for the highest mortality from a bacterial infection on a global scale, questions persist regarding its origin. One hypothesis based on modern Mycobacterium tuberculosis complex (MTBC) genomes suggests their most recent common ancestor followed human migrations out of Africa approximately 70,000 years before present. However, studies using ancient genomes as calibration points have yielded much younger dates of less than 6000 years. Here, we aim to address this discrepancy through the analysis of the highest-coverage and highest-quality ancient MTBC genome available to date, reconstructed from a calcified lung nodule of Bishop Peder Winstrup of Lund (b. 1605-d. 1679). RESULTS A metagenomic approach for taxonomic classification of whole DNA content permitted the identification of abundant DNA belonging to the human host and the MTBC, with few non-TB bacterial taxa comprising the background. Genomic enrichment enabled the reconstruction of a 141-fold coverage M. tuberculosis genome. In utilizing this high-quality, high-coverage seventeenth-century genome as a calibration point for dating the MTBC, we employed multiple Bayesian tree models, including birth-death models, which allowed us to model pathogen population dynamics and data sampling strategies more realistically than those based on the coalescent. CONCLUSIONS The results of our metagenomic analysis demonstrate the unique preservation environment calcified nodules provide for DNA. Importantly, we estimate a most recent common ancestor date for the MTBC of between 2190 and 4501 before present and for Lineage 4 of between 929 and 2084 before present using multiple models, confirming a Neolithic emergence for the MTBC.
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Affiliation(s)
- Susanna Sabin
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Alexander Herbig
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Åshild J. Vågene
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
- Present address: Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Torbjörn Ahlström
- Department of Archaeology and Ancient History, Lund University, 221 00 Lund, Sweden
| | - Gracijela Bozovic
- Department of Medical Imaging and Clinical Physiology, Skåne University Hospital Lund and Lund University, 221 00 Lund, Sweden
| | - Caroline Arcini
- Arkeologerna, National Historical Museum, 226 60 Lund, Sweden
| | - Denise Kühnert
- Transmission, Infection, Diversification & Evolution Group, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Kirsten I. Bos
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
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Nimmo C, Millard J, van Dorp L, Brien K, Moodley S, Wolf A, Grant AD, Padayatchi N, Pym AS, Balloux F, O'Donnell M. Population-level emergence of bedaquiline and clofazimine resistance-associated variants among patients with drug-resistant tuberculosis in southern Africa: a phenotypic and phylogenetic analysis. THE LANCET. MICROBE 2020; 1:e165-e174. [PMID: 32803174 PMCID: PMC7416634 DOI: 10.1016/s2666-5247(20)30031-8] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
BACKGROUND Bedaquiline and clofazimine are important drugs in the treatment of drug-resistant tuberculosis and are commonly used across southern Africa, although drug susceptibility testing is not routinely performed. In this study, we did a genotypic and phenotypic analysis of drug-resistant Mycobacterium tuberculosis isolates from cohort studies in hospitals in KwaZulu-Natal, South Africa, to identify resistance-associated variants (RAVs) and assess the extent of clofazimine and bedaquiline cross-resistance. We also used a comprehensive dataset of whole-genome sequences to investigate the phylogenetic and geographical distribution of bedaquiline and clofazimine RAVs in southern Africa. METHODS In this study, we included M tuberculosis isolates reported from the PRAXIS study of patients with drug-resistant tuberculosis treated with bedaquiline (King Dinuzulu Hospital, Durban) and three other cohort studies of drug-resistant tuberculosis in other KwaZulu-Natal hospitals, and sequential isolates from six persistently culture-positive patients with extensively drug-resistant tuberculosis at the KwaZulu-Natal provincial referral laboratory. Samples were collected between 2013 and 2019. Microbiological cultures were done as part of all parent studies. We sequenced whole genomes of included isolates and measured bedaquiline and clofazimine minimum inhibitory concentrations (MICs) for isolates identified as carrying any Rv0678 variant or previously published atpE, pepQ, and Rv1979c RAVs, which were the subject of the phenotypic study. We combined all whole-genome sequences of M tuberculosis obtained in this study with publicly available sequence data from other tuberculosis studies in southern Africa (defined as the countries of the Southern African Development Community), including isolates with Rv0678 variants identified by screening public genomic databases. We used this extended dataset to reconstruct phylogenetic relationships across lineage 2 and 4 M tuberculosis isolates. FINDINGS We sequenced the whole genome of 648 isolates from 385 patients with drug-resistant tuberculosis recruited into cohort studies in KwaZulu-Natal, and 28 isolates from six patients from the KwaZulu-Natal referral laboratory. We identified 30 isolates with Rv0678 RAVs from 16 (4%) of 391 patients. We did not identify any atpE, pepQ, or Rv1979c RAVs. MICs were measured for 21 isolates with Rv0678 RAVs. MICs were above the critical concentration for bedaquiline resistance in nine (43%) of 21 isolates, in the intermediate category in nine (43%) isolates, and within the wild-type range in three (14%) isolates. Clofazimine MICs in genetically wild-type isolates ranged from 0·12-0·5 μg/mL, and in isolates with RAVs from 0·25-4·0 μg/mL. Phylogenetic analysis of the extended dataset including M tuberculosis isolates from southern Africa resolved multiple emergences of Rv0678 variants in lineages 2 and 4, documented two likely nosocomial transmission events, and identified the spread of a possibly bedaquiline and clofazimine cross-resistant clone in eSwatini. We also identified four patients with pepQ frameshift mutations that may confer resistance. INTERPRETATION Bedaquiline and clofazimine cross-resistance in southern Africa is emerging repeatedly, with evidence of onward transmission largely due to Rv0678 mutations in M tuberculosis. Roll-out of bedaquiline and clofazimine treatment in the setting of limited drug susceptibility testing could allow further spread of resistance. Designing strong regimens would help reduce the emergence of resistance. Drug susceptibility testing is required to identify where resistance does emerge. FUNDING Wellcome Trust, National Institute of Allergy and Infectious Diseases and National Center for Advancing Translational Sciences of the National Institutes of Health.
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Affiliation(s)
- Camus Nimmo
- Division of Infection and Immunity, University College London, London, UK
- UCL Genetics Institute, University College London, London, UK
- Africa Health Research Institute, Durban, South Africa
| | - 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
| | - Lucy van Dorp
- UCL Genetics Institute, University College London, London, UK
| | - Kayleen Brien
- Africa Health Research Institute, Durban, South Africa
| | | | - Allison Wolf
- Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Alison D Grant
- Africa Health Research Institute, Durban, South Africa
- TB Centre, London School of Hygiene & Tropical Medicine, London, UK
- School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Nesri Padayatchi
- CAPRISA-MRC HIV-TB Pathogenesis and Treatment Research Unit, Centre for the Aids Programme of Research in South Africa (CAPRISA), Durban, KwaZulu-Natal, South Africa
| | | | | | - Max O'Donnell
- Department of Medicine, Columbia University Medical Center, New York, NY, USA
- Department of Epidemiology, Columbia University Medical Center, New York, NY, USA
- CAPRISA-MRC HIV-TB Pathogenesis and Treatment Research Unit, Centre for the Aids Programme of Research in South Africa (CAPRISA), Durban, KwaZulu-Natal, South Africa
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Genomic epidemiology of Mycobacterium tuberculosis in Santa Catarina, Southern Brazil. Sci Rep 2020; 10:12891. [PMID: 32732910 PMCID: PMC7393130 DOI: 10.1038/s41598-020-69755-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 06/22/2020] [Indexed: 12/18/2022] Open
Abstract
Mycobacterium tuberculosis (M.tb), the pathogen responsible for tuberculosis (TB) poses as the major cause of death among infectious diseases. The knowledge about the molecular diversity of M.tb enables the implementation of more effective surveillance and control measures and, nowadays, Whole Genome Sequencing (WGS) holds the potential to produce high-resolution epidemiological data in a high-throughput manner. Florianópolis, the state capital of Santa Catarina (SC) in south Brazil, shows a high TB incidence (46.0/100,000). Here we carried out a WGS-based evaluation of the M.tb strain diversity, drug-resistance and ongoing transmission in the capital metropolitan region. Resistance to isoniazid, rifampicin, streptomycin was identified respectively in 4.0% (n = 6), 2.0% (n = 3) and 1.3% (n = 2) of the 151 studied strains by WGS. Besides, resistance to pyrazinamide and ethambutol was detected in 0.7% (n = 1) and reistance to ethionamide and fluoroquinolone (FQ) in 1.3% (n = 2), while a single (0.7%) multidrug-resistant (MDR) strain was identified. SNP-based typing classified all isolates into M.tb Lineage 4, with high proportion of sublineages LAM (60.3%), T (16.4%) and Haarlem (7.9%). The average core-genome distance between isolates was 420.3 SNPs, with 43.7% of all isolates grouped across 22 genomic clusters thereby showing the presence of important ongoing TB transmission events. Most clusters were geographically distributed across the study setting which highlights the need for an urgent interruption of these large transmission chains. The data conveyed by this study shows the presence of important and uncontrolled TB transmission in the metropolitan area and provides precise data to support TB control measures in this region.
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Kayomo MK, Mbula VN, Aloni M, André E, Rigouts L, Boutachkourt F, de Jong BC, Nkiere NM, Dean AS. Targeted next-generation sequencing of sputum for diagnosis of drug-resistant TB: results of a national survey in Democratic Republic of the Congo. Sci Rep 2020; 10:10786. [PMID: 32612134 PMCID: PMC7329841 DOI: 10.1038/s41598-020-67479-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 06/02/2020] [Indexed: 11/23/2022] Open
Abstract
The surveillance of drug resistance among tuberculosis (TB) patients is central to preventing the spread of antimicrobial resistance. The Democratic Republic of the Congo (DR Congo) is classified by the World Health Organization (WHO) as a country with a high burden of TB and multidrug-resistant TB (MDR-TB), but there are no nationally representative data on drug resistance. In 2016-2017, a national survey of TB patients was conducted in 108 microscopy centres across all 11 provinces of the country using innovative molecular approaches. Sputum samples were collected from 1,545 new and 163 previously treated patients. These were tested by the Xpert MTB/RIF assay, followed by targeted next-generation sequencing performed directly on sputum. The prevalence of rifampicin resistance was low, at 1.8% (95% CI: 1.0-3.2) among new and 17.3% (95% CI: 11.9-24.4) among previously treated patients. Resistance to pyrazinamide, fluoroquinolones and second-line injectables was also low. The prevalence of resistance to isoniazid among rifampicin-susceptible patients was higher, at 6.6% (95% CI: 4.4-9.8) among new and 8.7% (95% : 3.2-21.2) among previously treated patients. Diagnosing and treating isoniazid-resistant patients remains a challenge, given that many will be missed by the current national diagnostic algorithm that is driven by detecting rifampicin resistance by Xpert MTB/RIF. This is the first nationwide survey incorporating targeted sequencing directly on sputum. It serves as a proof-of-concept for other settings that do yet have rapid specimen transport networks or capacity to conduct culture.
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MESH Headings
- Adolescent
- Adult
- Aged
- Child
- Child, Preschool
- Cross-Sectional Studies
- Democratic Republic of the Congo/epidemiology
- Female
- High-Throughput Nucleotide Sequencing
- Humans
- Infant
- Infant, Newborn
- Male
- Middle Aged
- Mycobacterium tuberculosis/genetics
- Prevalence
- Sputum/microbiology
- Tuberculosis, Multidrug-Resistant/diagnosis
- Tuberculosis, Multidrug-Resistant/drug therapy
- Tuberculosis, Multidrug-Resistant/epidemiology
- Tuberculosis, Multidrug-Resistant/genetics
- Tuberculosis, Pulmonary/diagnosis
- Tuberculosis, Pulmonary/drug therapy
- Tuberculosis, Pulmonary/epidemiology
- Tuberculosis, Pulmonary/genetics
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Affiliation(s)
- Michel Kaswa Kayomo
- National Tuberculosis Program et Laboratoire National de Référence des Mycobactéries (LNRM), Kinshasa, Democratic Republic of the Congo
- Faculté de Médecine, Université de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Vital Nkake Mbula
- National Tuberculosis Program et Laboratoire National de Référence des Mycobactéries (LNRM), Kinshasa, Democratic Republic of the Congo
| | - Muriel Aloni
- National Tuberculosis Program et Laboratoire National de Référence des Mycobactéries (LNRM), Kinshasa, Democratic Republic of the Congo
- Faculté de Médecine, Université de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Emmanuel André
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Leen Rigouts
- Institute of Tropical Medicine, Antwerp, Belgium
- Antwerp University, Antwerp, Belgium
| | - Fairouz Boutachkourt
- Pôle de Microbiologie Médicale, Institut de Recherche Expérimental Et Clinique, UC Louvain, Brussels, Belgium
| | | | - Nicolas M Nkiere
- World Health Organization, Kinshasa, Democratic Republic of the Congo
| | - Anna S Dean
- Global TB Programme, World Health Organization, Geneva, Switzerland.
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80
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Kone B, Somboro AM, Holl JL, Baya B, Togo AACG, Sarro YDS, Diarra B, Kodio O, Murphy RL, Bishai W, Maiga M, Doumbia S. Exploring the usefulness of molecular epidemiology of tuberculosis in Africa: a systematic review. INTERNATIONAL JOURNAL OF MOLECULAR EPIDEMIOLOGY AND GENETICS 2020; 11:1-15. [PMID: 32714498 PMCID: PMC7373718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 06/05/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Tuberculosis (TB) is caused by Mycobacterium tuberculosis complex (MTBC) and remains a serious global public health threat, especially in resource-limited settings such as the African region. Recent developments in molecular epidemiology tools have significantly improved our understanding of TB transmission patterns and revealed the high genetic diversity of TB isolates across geographical entities in Africa. This study reports the results of a systematic review of current knowledge about MTBC strain diversity and geographical distribution in African regions. METHODS Search tools (PubMed, Embase, Popline, OVID and Africa Wide Information) were employed to identify the relevant literature about prevalence, strain diversity, and geographic distribution of MTBC infection in Africa. RESULTS A total of 59 articles from 739 citations met our inclusion criteria. Most articles reported about patients with presumptive pulmonary TB (73%), fewer reports were on retreatment and treatment failure cases (12%), and presumptive drug resistance cases (3%). Spoligotyping was the most used, alone in 21 studies and in parallel with either the Mycobacterial Interspersed Repetitive Units Variable Number of Tandem Repeats or the Restriction Fragment Length Polymorphism. Various TB lineages were observed across the African continent, with the originally European lineage 4 spotted in all countries studied. CONCLUSION TB molecular epidemiology tools have substantially improved our understanding of the MTBC circulating isolates, their evolution, and diversity in this highly endemic region of Africa. We found that only TB lineage 4 is present throughout all the continent and the clusters identified provides an extended insight into the disease transmission dynamics.
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Affiliation(s)
- Bourahima Kone
- University Clinical Research Center (UCRC)-SEREFO, University of Sciences, Techniques and Technologies of Bamako (USTTB)Bamako, Mali
| | - Anou M Somboro
- University Clinical Research Center (UCRC)-SEREFO, University of Sciences, Techniques and Technologies of Bamako (USTTB)Bamako, Mali
- Medical Biochemistry, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-NatalDurban, South Africa
| | | | - Bocar Baya
- University Clinical Research Center (UCRC)-SEREFO, University of Sciences, Techniques and Technologies of Bamako (USTTB)Bamako, Mali
| | - Antieme ACG Togo
- University Clinical Research Center (UCRC)-SEREFO, University of Sciences, Techniques and Technologies of Bamako (USTTB)Bamako, Mali
| | - Yeya Dit Sadio Sarro
- University Clinical Research Center (UCRC)-SEREFO, University of Sciences, Techniques and Technologies of Bamako (USTTB)Bamako, Mali
| | - Bassirou Diarra
- University Clinical Research Center (UCRC)-SEREFO, University of Sciences, Techniques and Technologies of Bamako (USTTB)Bamako, Mali
| | - Ousmane Kodio
- University Clinical Research Center (UCRC)-SEREFO, University of Sciences, Techniques and Technologies of Bamako (USTTB)Bamako, Mali
| | - Robert L Murphy
- Institute for Global Health, Northwestern UniversityChicago, Illinois, USA
| | - William Bishai
- Center for TB Research, Johns Hopkins UniversityBaltimore, MD, USA
| | - Mamoudou Maiga
- University Clinical Research Center (UCRC)-SEREFO, University of Sciences, Techniques and Technologies of Bamako (USTTB)Bamako, Mali
- Institute for Global Health, Northwestern UniversityChicago, Illinois, USA
| | - Seydou Doumbia
- University Clinical Research Center (UCRC)-SEREFO, University of Sciences, Techniques and Technologies of Bamako (USTTB)Bamako, Mali
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Méndez MV, Abadía E, Sequera M, de Waard JH, Takiff HE. Most LAM Mycobacterium tuberculosis strains in Venezuela, but not SIT605, belong to the RD Rio subfamily. INFECTION GENETICS AND EVOLUTION 2020; 84:104380. [PMID: 32470631 DOI: 10.1016/j.meegid.2020.104380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 05/21/2020] [Accepted: 05/24/2020] [Indexed: 11/27/2022]
Abstract
Tuberculosis is a global public health problem that is resurgent in Venezuela, with 13 thousand estimated new cases in 2018. Strains of the Mycobacterium tuberculosis RDRio, subfamily belong to the Latín American Mediterranean (LAM) family and are a major cause of TB in Rio de Janeiro, Brazil. LAM strains predominate in Venezuela, where spoligotype SIT605 is common, but surprisingly not found elsewhere. We sought to assess the presence of RDRio strains in tuberculosis patients in different regions of Venezuela and determine whether SIT605 also belongs to the RDRio subfamily. Using spoligotyping and MIRU-VNTR 24 loci, we identified 86 clinical LAM and SIT605 isolates from the Venezuelan capital Caracas and several Venezuelan states. Region of difference deletion loci RD174 and RDRio, and also IS1561 were used to identify strains of the RDRio subfamily, while IS6110 at position 932,204 and the Ag85C103 polymorphism were used to validate SIT 605 as a LAM family strain. We found that 69.8% of the isolates were RDRío, including 94.3% of strains isolated in Caracas, 17.9% isolated in the state of Carabobo, the two strains analyzed from Delta Amacuro, and one each from Sucre, Apure and Aragua states. RDRio was in 100% of: SIT17 (LAM 2); SIT20 (LAM 1); SITs 93, 1694, 1696, 960, 1367 (LAM 5); and SITs 216 (LAM 9); but only 75% of SIT42 (LAM 9) strains. Thus, most of the LAM strains in Venezuela belong to the RDRío subfamily. SIT 605 strains, although LAM, are not in the RDRío subfamily.
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Affiliation(s)
- María Victoria Méndez
- Universidad de Carabobo-Escuela de Bioanálisis-Sede Aragua, Venezuela; Laboratorio de Genética Molecular, Instituto Venezolano de Investigaciones Científicas (IVIC), Caracas 1020A, Venezuela.
| | - Edgar Abadía
- Laboratorio de Genética Molecular, Instituto Venezolano de Investigaciones Científicas (IVIC), Caracas 1020A, Venezuela
| | - Mónica Sequera
- Universidad de Carabobo-Escuela de Ciencias Biomédicas-Sede Carabobo, Venezuela
| | - Jacobus H de Waard
- Instituto de Biomedicina-Universidad Central de Venezuela (UCV), Venezuela; One Health Research Group, Facultad de Ciencias de la Salud, Universidad de Las Américas, Sede Queri, Quito, Ecuador
| | - Howard Eugene Takiff
- Laboratorio de Genética Molecular, Instituto Venezolano de Investigaciones Científicas (IVIC), Caracas 1020A, Venezuela; Pathogenomique Mycobacterienne Integree, Institut Pasteur, Paris, France; Department of Tuberculosis Prevention and Control, Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, China
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82
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Berndtson AE. Increasing Globalization and the Movement of Antimicrobial Resistance between Countries. Surg Infect (Larchmt) 2020; 21:579-585. [PMID: 32434446 DOI: 10.1089/sur.2020.145] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Background: The threat of antimicrobial resistance continues to grow worldwide, exacerbated by poor antibiotic stewardship practices, limited development of new antimicrobial agents, and increasing globalization. Methods: This review covers previously published studies examining how human movement contributes to the global spread of antimicrobial resistance, including between low- and middle-income and high-income countries. Results: The emergence of resistance in one country or part of the world can become a worldwide event quickly. Human movement, including travel, medical tourism, military service, and migration, results in the globalization of resistant bacterial strains. Conclusions: Increased surveillance, whole-genome sequencing, focused infection control, and effective stewardship practices are needed to maintain the efficacy of antibiotics.
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Affiliation(s)
- Allison E Berndtson
- Division of Trauma, Surgical Critical Care, Burns, and Acute Care Surgery, University of California-San Diego, San Diego, California, USA
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83
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Epidemiology characteristics of the clonal complexes of Mycobacterium tuberculosis Lineage 4 in China. INFECTION GENETICS AND EVOLUTION 2020; 84:104363. [PMID: 32413573 DOI: 10.1016/j.meegid.2020.104363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 03/18/2020] [Accepted: 05/09/2020] [Indexed: 11/20/2022]
Abstract
Mycobacterium tuberculosis (M. tuberculosis) Lineage 4 (L4) is frequently prevailing in Western regions of China, where the tuberculosis incidence rate is high. However, the epidemiology characteristics of M. tuberculosis L4 in China remain poorly understood. Here, the 15-loci Variable number of tandem repeats (VNTR) patterns of 975 L4 isolates from a National Survey of Tuberculosis in China were used to construct a Minimum Spanning Tree (MST), which divided the 975 isolates into 5 major clonal complexes (CC; named CC1 to CC5). We found that the CCs of M. tuberculosis L4 were nationally distributed, geographically restricted, and different in epidemiology characteristics. For example, CC1 was mainly concentrated in East and Central China and significantly related to the farmer occupation and income of an individual (>4200 yuan) (p < .05); CC5 was mainly distributed in Southwest China and was associated with ethnic minorities. Notably, using whole genome sequencing (WGS) data of 141 strains that matched our samples, we found that both CC1 and CC5 were mapped to the sublineage L4.5. Nevertheless, due to the difference of geographical distribution, the epidemiology characteristics of these CCs were largely different. We found that income and occupation significantly contributed to the odds of infection by CC1 to CC5. Consequently, our findings revealed the epidemiology characteristics of the CCs of M. tuberculosis L4, and will help in the formulation of more effective intervention measures in line with regional specifications and patient characteristics in China.
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84
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Ma Y, Liu K, Yin Y, Qin J, Zhou YH, Yang J, Li S, Poon LLM, Zhang C. The Phylodynamics of Seasonal Influenza A/H1N1pdm Virus in China Between 2009 and 2019. Front Microbiol 2020; 11:735. [PMID: 32457705 PMCID: PMC7228120 DOI: 10.3389/fmicb.2020.00735] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 03/30/2020] [Indexed: 01/26/2023] Open
Abstract
Since its first introduction into China in 2009, influenza A/H1N1pdm virus has undergone a rapid expansion and replaced the classical seasonal A(H1N1) virus. To characterize the ongoing evolution and national transmission dynamics of this virus, we analyzed 335 complete genome, 1259 HA, and 1043 NA sequences of the A/H1N1pdm strains detected in China. We found that the dN/dS value and relative genetic diversity of the A/H1N1pdm virus experienced a decrease from 2009 to 2017, and then a rapid increase during 2018–2019. Importantly, elevated relative genetic diversity was observed in the A/H1N1pdm and the A/H3N2 viruses, as well as two lineages (Victoria and Yamagata) of influenza B virus during 2018–2019, suggesting the simultaneous changes of these viruses in terms of genetic diversity might be associated with the recent large outbreak of seasonal influenza epidemic in China during 2018–2019. Fifteen amino acid mutations were found to be fixed along the main trunks of both HA and NA phylogenetic trees, and some of them are located in the antigen binding site or the receptor binding site. A sequential accumulation of mutations relative to the 2009-vaccine strain was observed in the circulating A/H1N1pdm strains during 2009–2016, while a rapid accumulation of mutations relative to the 2015-vaccine strain appeared in the emerging variants in 2017 shortly after the release of the vaccine. Multiple introductions of the A/H1N1pdm lineages into China were observed during 2009–2019, and East China and South China were found to serve as two major epicenters responsible for the national migration of the virus. In summary, these data provide important insights into the understanding of the evolution, epidemiology and transmission of the A/H1N1pdm virus, and highlight the importance of strengthening influenza surveillance in East China and South China.
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Affiliation(s)
- Yingying Ma
- Chinese Academy of Sciences (CAS) Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences: University of Chinese Academy of Sciences, Shanghai, China
| | - Kai Liu
- Chinese Academy of Sciences (CAS) Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences: University of Chinese Academy of Sciences, Shanghai, China
| | - Yong Yin
- Department of Pulmonary, Shanghai Children's Medical Center Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jianru Qin
- Chinese Academy of Sciences (CAS) Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences: University of Chinese Academy of Sciences, Shanghai, China.,College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Yan-Heng Zhou
- Chinese Academy of Sciences (CAS) Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences: University of Chinese Academy of Sciences, Shanghai, China
| | - Juan Yang
- Key Laboratory of Public Health Safety, Ministry of Education, Fudan University School of Public Health, Shanghai, China
| | - Shenwei Li
- Shanghai International Travel Healthcare Center, Shanghai, China
| | - Leo L M Poon
- School of Public Health, The University of Hong Kong, Hong Kong, China
| | - Chiyu Zhang
- Chinese Academy of Sciences (CAS) Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences: University of Chinese Academy of Sciences, Shanghai, China
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Garzon-Chavez D, Garcia-Bereguiain MA, Mora-Pinargote C, Granda-Pardo JC, Leon-Benitez M, Franco-Sotomayor G, Trueba G, de Waard JH. Population structure and genetic diversity of Mycobacterium tuberculosis in Ecuador. Sci Rep 2020; 10:6237. [PMID: 32277077 PMCID: PMC7148308 DOI: 10.1038/s41598-020-62824-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 03/13/2020] [Indexed: 11/09/2022] Open
Abstract
Tuberculosis (TB) is a significant public health problem in Ecuador with an incidence of 43 per 100,000 inhabitants and an estimated multidrug-resistant-TB prevalence in all TB cases of 9%. Genotyping of Mycobacterium tuberculosis (MTBC) is important to understand regional transmission dynamics. This study aims to describe the main MTBC lineages and sublineages circulating in the country. A representative sample of 373 MTBC strains from 22 provinces of Ecuador, with data comprising geographic origin and drug susceptibility, were genotyped using 24 loci-MIRU-VNTR. For strains with an ambiguous sublineage designation, the lineage was confirmed by Regions of Difference analysis or by Whole Genome Sequencing. We show that lineage 4 is predominant in Ecuador (98.3% of the strains). Only 4 strains belong to lineages 2-sublineage Beijing and two strains to lineage 3-sublineage Delhi. Lineage 4 strains included sublineages LAM (45.7%), Haarlem (31.8%), S (13.1%), X (4.6%), Ghana (0.6%) and NEW (0.3%). The LAM sublineage showed the strongest association with antibiotic resistance. The X and S sublineages were found predominantly in the Coastal and the Andean regions respectively and the reason for the high prevalence of these strains in Ecuador should be addressed in future studies. Our database constitutes a tool for MIRU-VNTR pattern comparison of M. tuberculosis isolates for national and international epidemiologic studies and phylogenetic purposes.
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Affiliation(s)
- Daniel Garzon-Chavez
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
- Instituto Nacional de Salud Pública e Investigación Leopoldo Izquieta Pérez, Guayaquil, Ecuador
| | - Miguel Angel Garcia-Bereguiain
- One Health Research Group. Universidad de las Américas, Quito, Ecuador.
- Laboratorio para Investigaciones Biomédicas. Escuela Superior Politécnica del Litoral, Guayaquil, Ecuador.
| | - Carlos Mora-Pinargote
- Laboratorio para Investigaciones Biomédicas. Escuela Superior Politécnica del Litoral, Guayaquil, Ecuador
| | | | - Margarita Leon-Benitez
- Instituto Nacional de Salud Pública e Investigación Leopoldo Izquieta Pérez, Guayaquil, Ecuador
| | - Greta Franco-Sotomayor
- Instituto Nacional de Salud Pública e Investigación Leopoldo Izquieta Pérez, Guayaquil, Ecuador
- Facultad de Ciencias Médicas. Universidad Católica Santiago de Guayaquil, Guayaquil, Ecuador
| | - Gabriel Trueba
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador.
| | - Jacobus H de Waard
- One Health Research Group. Universidad de las Américas, Quito, Ecuador.
- Departamento de Tuberculosis, Servicio Autónomo Instituto de Biomedicina "Dr. Jacinto Convit", Universidad Central de Venezuela, Caracas, Venezuela.
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86
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Monteserin J, Pérez-Lago L, Yokobori N, Paul R, Rodríguez Maus S, Simboli N, Eldholm V, López B, García de Viedma D, Ritacco V. Trends of Two Epidemic Multidrug-Resistant Strains of Mycobacterium tuberculosis in Argentina Disclosed by Tailored Molecular Strategy. Am J Trop Med Hyg 2020; 101:1308-1311. [PMID: 31628738 DOI: 10.4269/ajtmh.19-0397] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Two Mycobacterium tuberculosis strains-M (sublineage 4.1) and Ra (sublineage 4.3)-have long prevailed in Argentina among patients with multidrug-resistant tuberculosis (MDR-TB). Recently, budget constraints have hampered the surveillance of MDR-TB transmission. Based on whole-genome sequence analysis, we used M- and Ra-specific single nucleotide polymorphisms to tailor two multiplex allele-specific polymerase chain reactions (PCRs), which we applied to 252 stored isolates (95% of all newly diagnosed MDR-TB cases countrywide, 2015-2017). Compared with the latest data available (2007-2009), the M strain has receded (80/324 to 20/252, P < 0.0001), particularly among cross-border migrants (12/58 to 0/53, P = 0.0003) and HIV-infected people (30/97 to 7/74, P = 0.0007), but it still accounts for 4/12 new cases of extensively drug-resistant TB. Differently, the Ra strain remained stable in frequency (39/324 to 33/252) and contributed marginally to the extensive drug-resistance load (1/12). Our novel strategy disclosed recent trends of the two major MDR-TB strains, providing meaningful data to allocate control interventions more efficiently.
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Affiliation(s)
- Johana Monteserin
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina.,Instituto Nacional de Enfermedades Infecciosas ANLIS, Buenos Aires, Argentina
| | - Laura Pérez-Lago
- Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Noemí Yokobori
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina.,Instituto Nacional de Enfermedades Infecciosas ANLIS, Buenos Aires, Argentina
| | - Roxana Paul
- Instituto Nacional de Enfermedades Infecciosas ANLIS, Buenos Aires, Argentina
| | - Sandra Rodríguez Maus
- Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Norberto Simboli
- Instituto Nacional de Enfermedades Infecciosas ANLIS, Buenos Aires, Argentina
| | | | - Beatriz López
- Instituto Nacional de Enfermedades Infecciosas ANLIS, Buenos Aires, Argentina
| | - Darío García de Viedma
- Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.,CIBER Enfermedades Respiratorias, CIBERES, Madrid, Spain
| | - Viviana Ritacco
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina.,Instituto Nacional de Enfermedades Infecciosas ANLIS, Buenos Aires, Argentina
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87
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Perdigão J, Gomes P, Miranda A, Maltez F, Machado D, Silva C, Phelan JE, Brum L, Campino S, Couto I, Viveiros M, Clark TG, Portugal I. Using genomics to understand the origin and dispersion of multidrug and extensively drug resistant tuberculosis in Portugal. Sci Rep 2020; 10:2600. [PMID: 32054988 PMCID: PMC7018963 DOI: 10.1038/s41598-020-59558-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 12/13/2019] [Indexed: 01/12/2023] Open
Abstract
Portugal is a low incidence country for tuberculosis (TB) disease. Now figuring among TB low incidence countries, it has since the 1990s reported multidrug resistant and extensively drug resistant (XDR) TB cases, driven predominantly by two strain-types: Lisboa3 and Q1. This study describes the largest characterization of the evolutionary trajectory of M/XDR-TB strains in Portugal, spanning a time-period of two decades. By combining whole-genome sequencing and phenotypic susceptibility data for 207 isolates, we report the geospatial patterns of drug resistant TB, particularly the dispersion of Lisboa3 and Q1 clades, which underly 64.2% and 94.0% of all MDR-TB and XDR-TB isolates, respectively. Genomic-based similarity and a phylogenetic analysis revealed multiple clusters (n = 16) reflecting ongoing and uncontrolled recent transmission of M/XDR-TB, predominantly associated with the Lisboa3 and Q1 clades. These clades are now thought to be evolving in a polycentric mode across multiple geographical districts. The inferred evolutionary history is compatible with MDR- and XDR-TB originating in Portugal in the 70's and 80's, respectively, but with subsequent multiple emergence events of MDR and XDR-TB particularly involving the Lisboa3 clade. A SNP barcode was defined for Lisboa3 and Q1 and comparison with a phylogeny of global strain-types (n = 28 385) revealed the presence of Lisboa3 and Q1 strains in Europe, South America and Africa. In summary, Portugal displays an unusual and unique epidemiological setting shaped by >40 years of uncontrolled circulation of two main phylogenetic clades, leading to a sympatric evolutionary trajectory towards XDR-TB with the potential for global reach.
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Affiliation(s)
- João Perdigão
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal.
| | - Pedro Gomes
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Anabela Miranda
- Departamento de Doenças Infeciosas, Instituto Nacional de Saúde Dr. Ricardo Jorge, Porto, Portugal
| | - Fernando Maltez
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
- Serviço de Doenças Infecciosas, Hospital de Curry Cabral, Lisboa, Portugal
| | - Diana Machado
- Unidade de Microbiologia Médica, Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Lisboa, Portugal
| | - Carla Silva
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Jody E Phelan
- London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, United Kingdom
| | | | - Susana Campino
- London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, United Kingdom
| | - Isabel Couto
- Unidade de Microbiologia Médica, Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Lisboa, Portugal
| | - Miguel Viveiros
- Unidade de Microbiologia Médica, Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Lisboa, Portugal
| | - Taane G Clark
- Unidade de Microbiologia Médica, Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Lisboa, Portugal
- London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, United Kingdom
| | - Isabel Portugal
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal.
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88
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Castro RAD, Ross A, Kamwela L, Reinhard M, Loiseau C, Feldmann J, Borrell S, Trauner A, Gagneux S. The Genetic Background Modulates the Evolution of Fluoroquinolone-Resistance in Mycobacterium tuberculosis. Mol Biol Evol 2020; 37:195-207. [PMID: 31532481 PMCID: PMC6984360 DOI: 10.1093/molbev/msz214] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Fluoroquinolones (FQ) form the backbone in experimental treatment regimens against drug-susceptible tuberculosis. However, little is known on whether the genetic variation present in natural populations of Mycobacterium tuberculosis (Mtb) affects the evolution of FQ-resistance (FQ-R). To investigate this question, we used nine genetically distinct drug-susceptible clinical isolates of Mtb and measured their frequency of resistance to the FQ ofloxacin (OFX) in vitro. We found that the Mtb genetic background led to differences in the frequency of OFX-resistance (OFX-R) that spanned two orders of magnitude and substantially modulated the observed mutational profiles for OFX-R. Further, in vitro assays showed that the genetic background also influenced the minimum inhibitory concentration and the fitness effect conferred by a given OFX-R mutation. To test the clinical relevance of our in vitro work, we surveyed the mutational profile for FQ-R in publicly available genomic sequences from clinical Mtb isolates, and found substantial Mtb lineage-dependent variability. Comparison of the clinical and the in vitro mutational profiles for FQ-R showed that 51% and 39% of the variability in the clinical frequency of FQ-R gyrA mutation events in Lineage 2 and Lineage 4 strains, respectively, can be attributed to how Mtb evolves FQ-R in vitro. As the Mtb genetic background strongly influenced the evolution of FQ-R in vitro, we conclude that the genetic background of Mtb also impacts the evolution of FQ-R in the clinic.
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Affiliation(s)
- Rhastin A D Castro
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Amanda Ross
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Lujeko Kamwela
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Miriam Reinhard
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Chloé Loiseau
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Julia Feldmann
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Sonia Borrell
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Andrej Trauner
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
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89
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Mulholland CV, Shockey AC, Aung HL, Cursons RT, O'Toole RF, Gautam SS, Brites D, Gagneux S, Roberts SA, Karalus N, Cook GM, Pepperell CS, Arcus VL. Dispersal of Mycobacterium tuberculosis Driven by Historical European Trade in the South Pacific. Front Microbiol 2019; 10:2778. [PMID: 31921003 PMCID: PMC6915100 DOI: 10.3389/fmicb.2019.02778] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 11/14/2019] [Indexed: 12/30/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) is a globally distributed bacterial pathogen whose population structure has largely been shaped by the activities of its obligate human host. Oceania was the last major global region to be reached by Europeans and is the last region for which the dispersal and evolution of Mtb remains largely unexplored. Here, we investigated the evolutionary history of the Euro-American L4.4 sublineage and its dispersal to the South Pacific. Using a phylodynamics approach and a dataset of 236 global Mtb L4.4 genomes we have traced the origins and dispersal of L4.4 strains to New Zealand. These strains are predominantly found in indigenous Māori and Pacific people and we identify a clade of European, likely French, origin that is prevalent in indigenous populations in both New Zealand and Canada. Molecular dating suggests the expansion of European trade networks in the early 19th century drove the dispersal of this clade to the South Pacific. We also identify historical and social factors within the region that have contributed to the local spread and expansion of these strains, including recent Pacific migrations to New Zealand and the rapid urbanization of Māori in the 20th century. Our results offer new insight into the expansion and dispersal of Mtb in the South Pacific and provide a striking example of the role of historical European migrations in the global dispersal of Mtb.
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Affiliation(s)
- Claire V Mulholland
- School of Science, University of Waikato, Hamilton, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand
| | - Abigail C Shockey
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Htin L Aung
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand.,Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Ray T Cursons
- School of Science, University of Waikato, Hamilton, New Zealand
| | - Ronan F O'Toole
- School of Medicine, University of Tasmania, Hobart, TAS, Australia.,School of Molecular Sciences, La Trobe University, Melbourne, VIC, Australia
| | - Sanjay S Gautam
- School of Medicine, University of Tasmania, Hobart, TAS, Australia
| | - Daniela Brites
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | | | | | - Gregory M Cook
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand.,Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Caitlin S Pepperell
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States.,Department of Medicine, Division of Infectious Diseases, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Vickery L Arcus
- School of Science, University of Waikato, Hamilton, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand
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90
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Hadifar S, Kamakoli MK, Fateh A, Siadat SD, Vaziri F. Enhancing the differentiation of specific genotypes in Mycobacterium tuberculosis population. Sci Rep 2019; 9:17946. [PMID: 31784605 PMCID: PMC6884525 DOI: 10.1038/s41598-019-54393-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 11/14/2019] [Indexed: 12/18/2022] Open
Abstract
Today, significant attention is directed towards the global lineages and sublineages of Mycobacterium tuberculosis (Mtb). NEW-1 (SIT 127) and CAS1-Delhi (SIT 26) strains are recognized as growing and circulating Mtb genotypes, especially in Asian countries. It is crucial to develop or enhance Mtb genotyping methods for a more accurate and simple differentiation of these families. We used 24-loci mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) typing for genotyping 217 Mtb isolates. To select the optimal MIRU-VNTR loci, we calculated the Hunter-Gaston discriminatory index (HGDI), allelic diversity, and accumulation of percentage differences (APDs) between the strains among different groups of genotypes (NEW-1 and non-NEW-1; CAS1-Delhi and non-CAS). Finally, the minimum spanning tree was constructed for clustering analysis. In the NEW-1 population, loci with APD > 60% were found to have a high discriminatory power. VNTR loci with APD > 50% showed high discrimination power for the CAS population. Our findings suggest that APDs, which are valuable for the selection of VNTR loci sets, may improve the discriminatory power of MIRU-VNTR typing for identification of Mtb genotypes in specific regions.
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Affiliation(s)
- Shima Hadifar
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Mansour Kargarpour Kamakoli
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Davar Siadat
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Farzam Vaziri
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran. .,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
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91
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Menardo F, Duchêne S, Brites D, Gagneux S. The molecular clock of Mycobacterium tuberculosis. PLoS Pathog 2019; 15:e1008067. [PMID: 31513651 PMCID: PMC6759198 DOI: 10.1371/journal.ppat.1008067] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 09/24/2019] [Accepted: 09/03/2019] [Indexed: 12/20/2022] Open
Abstract
The molecular clock and its phylogenetic applications to genomic data have changed how we study and understand one of the major human pathogens, Mycobacterium tuberculosis (MTB), the etiologic agent of tuberculosis. Genome sequences of MTB strains sampled at different times are increasingly used to infer when a particular outbreak begun, when a drug-resistant clone appeared and expanded, or when a strain was introduced into a specific region. Despite the growing importance of the molecular clock in tuberculosis research, there is a lack of consensus as to whether MTB displays a clocklike behavior and about its rate of evolution. Here we performed a systematic study of the molecular clock of MTB on a large genomic data set (6,285 strains), covering different epidemiological settings and most of the known global diversity. We found that sampling times below 15-20 years were often insufficient to calibrate the clock of MTB. For data sets where such calibration was possible, we obtained a clock rate between 1x10-8 and 5x10-7 nucleotide changes per-site-per-year (0.04-2.2 SNPs per-genome-per-year), with substantial differences between clades. These estimates were not strongly dependent on the time of the calibration points as they changed only marginally when we used epidemiological isolates (sampled in the last 40 years) or three ancient DNA samples (about 1,000 years old) to calibrate the tree. Additionally, the uncertainty and the discrepancies in the results of different methods were sometimes large, highlighting the importance of using different methods, and of considering carefully their assumptions and limitations.
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Affiliation(s)
- Fabrizio Menardo
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Sebastian Duchêne
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Daniela Brites
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Sebastien Gagneux
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
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92
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de-Dios T, van Dorp L, Gelabert P, Carøe C, Sandoval-Velasco M, Fregel R, Escosa R, Aranda C, Huijben S, Balloux F, Gilbert MTP, Lalueza-Fox C. Genetic affinities of an eradicated European Plasmodium falciparum strain. Microb Genom 2019; 5. [PMID: 31454309 PMCID: PMC6807384 DOI: 10.1099/mgen.0.000289] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Malaria was present in most of Europe until the second half of the 20th century, when it was eradicated through a combination of increased surveillance and mosquito control strategies, together with cross-border and political collaboration. Despite the severe burden of malaria on human populations, it remains contentious how the disease arrived and spread in Europe. Here, we report a partial Plasmodium falciparum nuclear genome derived from a set of antique medical slides stained with the blood of malaria-infected patients from Spain’s Ebro Delta, dating to the 1940s. Our analyses of the genome of this now eradicated European P. falciparum strain confirms stronger phylogeographical affinity to present-day strains in circulation in central south Asia, rather than to those in Africa. This points to a longitudinal, rather than a latitudinal, spread of malaria into Europe. In addition, this genome displays two derived alleles in the pfmrp1 gene that have been associated with drug resistance. Whilst this could represent standing variation in the ancestral P. falciparum population, these mutations may also have arisen due to the selective pressure of quinine treatment, which was an anti-malarial drug already in use by the time the sample we sequenced was mounted on a slide.
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Affiliation(s)
- Toni de-Dios
- Institute of Evolutionary Biology (CSIC-UPF), 08003 Barcelona, Spain
| | - Lucy van Dorp
- UCL Genetics Institute, University College London, Gower Street, London WC1E 6BT, UK
| | - Pere Gelabert
- Institute of Evolutionary Biology (CSIC-UPF), 08003 Barcelona, Spain
| | - Christian Carøe
- Section for Evolutionary Genomics, Department of Biology, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Marcela Sandoval-Velasco
- Section for Evolutionary Genomics, Department of Biology, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Rosa Fregel
- Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad of La Laguna, 38206 La Laguna, Spain.,Department of Genetics, Stanford University, Stanford, CA, USA
| | - Raül Escosa
- Consorci de Polítiques Ambientals de les Terres de l'Ebre (COPATE), 43580 Deltebre, Spain
| | - Carles Aranda
- Servei de Control de Mosquits, Consell Comarcal del Baix Llobregat, 08980 Sant Feliu de Llobregat, Spain
| | - Silvie Huijben
- Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - François Balloux
- UCL Genetics Institute, University College London, Gower Street, London WC1E 6BT, UK
| | - M Thomas P Gilbert
- Norwegian University of Science and Technology (NTNU) University Museum, N-7491 Trondheim, Norway.,Section for Evolutionary Genomics, Department of Biology, University of Copenhagen, 1353 Copenhagen, Denmark
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93
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Direct transmission of within-host Mycobacterium tuberculosis diversity to secondary cases can lead to variable between-host heterogeneity without de novo mutation: A genomic investigation. EBioMedicine 2019; 47:293-300. [PMID: 31420303 PMCID: PMC6796532 DOI: 10.1016/j.ebiom.2019.08.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 08/02/2019] [Accepted: 08/04/2019] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Whole genome sequencing (WGS) has enabled the development of new approaches to track Mycobacterium tuberculosis (Mtb) transmission between tuberculosis (TB) cases but its utility may be challenged by the discovery that Mtb diversifies within hosts. Nevertheless, there is limited data on the presence and degree of within-host evolution. METHODS We profiled a well-documented Mtb transmission cluster with three pulmonary TB cases to investigate within-host evolution and describe its impact on recent transmission estimates. We used deep sequencing to track minority allele frequencies (<50·0% abundance) during transmission and standard treatment. FINDINGS Pre-treatment (n = 3) and serial samples collected over 2 months of antibiotic treatment (n = 16) from all three cases were analysed. Consistent with the epidemiological data, zero fixed SNP separated all genomes. However, we identified six subclones between the three cases with an allele frequency ranging from 35·0% to 100·0% across sampling intervals. Five subclones were identified within the index case pre-treatment and shared with one secondary case, while only the dominant clone was observed in the other secondary case. By tracking the frequency of these heterogeneous alleles over the two-month therapy, we observed distinct signatures of drift and negative selection, but limited evidence for de novo mutations, even under drug pressure. INTERPRETATION We document within-host Mtb diversity in an index case, which led to transmission of minority alleles to a secondary case. Incorporating data on heterogeneous alleles may refine our understanding of Mtb transmission dynamics. However, more evidence is needed on the role of transmission bottleneck on observed heterogeneity between cases.
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94
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Chiner-Oms Á, Comas I. Large genomics datasets shed light on the evolution of the Mycobacterium tuberculosis complex. INFECTION GENETICS AND EVOLUTION 2019; 72:10-15. [DOI: 10.1016/j.meegid.2019.02.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/21/2019] [Accepted: 02/25/2019] [Indexed: 01/21/2023]
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95
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Mendis C, Thevanesam V, Kumara A, Wickramasinghe S, Madegedara D, Gamage C, Gordon SV, Suzuki Y, Ratnatunga C, Nakajima C. Insight into genetic diversity of Mycobacterium tuberculosis in Kandy, Sri Lanka reveals predominance of the Euro-American lineage. Int J Infect Dis 2019; 87:84-91. [PMID: 31299365 DOI: 10.1016/j.ijid.2019.07.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 06/24/2019] [Accepted: 07/01/2019] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVE Sri Lanka is a country where the molecular epidemiology of Mycobacterium tuberculosis (MTB) is poorly explored. Therefore, this study was performed to identify circulating lineages/sub-lineages of MTB and their transmission patterns. METHODS DNA was extracted from 89 isolates of MTB collected during 2012 and 2013 from new pulmonary tuberculosis patients in Kandy, Sri Lanka and analyzed by spoligotyping, large sequence polymorphism (LSP), mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) typing, and drug resistance-associated gene sequencing. RESULTS The predominant lineage was lineage 4 (Euro-American, 45.9%), followed by lineage 1 (Indo-Oceanic, 29.4%), lineage 2 (East-Asian, 23.5%), and lineage 3 (Central-Asian, 1.2%). Among 26 spoligotype patterns, eight were undesignated or new types and seven of these belonged to lineage 4. Undesignated lineage 4/SIT124 (n=2/8) and SIT3234 (n=8/8) clustered together based on 24-locus MIRU-VNTR typing. The dominant sub-lineage was Beijing/SIT1 (n=19), with the isoniazid resistance katG G944C mutation (Ser315Thr) detected in two of them. CONCLUSIONS The population structure of MTB in Kandy, Sri Lanka was different from that in the South Asian region. The clonal expansion of locally evolved lineage 4/SIT3234 and detection of the pre-multidrug resistant Beijing isolates from new tuberculosis patients is alarming and will require continuous monitoring.
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Affiliation(s)
- Charitha Mendis
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan; Department of Medical Laboratory Science, Faculty of Allied Health Sciences, University of Peradeniya, Sri Lanka
| | - Vasanthi Thevanesam
- Department of Microbiology, Faculty of Medicine, University of Peradeniya, Sri Lanka
| | - Athula Kumara
- Department of Microbiology, Faculty of Medicine, University of Peradeniya, Sri Lanka
| | - Susiji Wickramasinghe
- Department of Parasitology, Faculty of Medicine, University of Peradeniya, Sri Lanka
| | | | - Chandika Gamage
- Department of Microbiology, Faculty of Medicine, University of Peradeniya, Sri Lanka
| | - Stephen V Gordon
- School of Veterinary Medicine, University College Dublin, Belfield, Dublin, Ireland; Global Station for Zoonosis Control, Hokkaido University Global Institute for Collaborative Research and Education, Sapporo, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan; Global Station for Zoonosis Control, Hokkaido University Global Institute for Collaborative Research and Education, Sapporo, Japan
| | - Champa Ratnatunga
- Department of Microbiology, Faculty of Medicine, University of Peradeniya, Sri Lanka.
| | - Chie Nakajima
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan; Global Station for Zoonosis Control, Hokkaido University Global Institute for Collaborative Research and Education, Sapporo, Japan.
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96
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O'Neill MB, Shockey A, Zarley A, Aylward W, Eldholm V, Kitchen A, Pepperell CS. Lineage specific histories of Mycobacterium tuberculosis dispersal in Africa and Eurasia. Mol Ecol 2019; 28:3241-3256. [PMID: 31066139 PMCID: PMC6660993 DOI: 10.1111/mec.15120] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 04/18/2019] [Accepted: 04/23/2019] [Indexed: 12/29/2022]
Abstract
Mycobacterium tuberculosis (M.tb) is a globally distributed, obligate pathogen of humans that can be divided into seven clearly defined lineages. An emerging consensus places the origin and global dispersal of M.tb within the past 6,000 years: identifying how the ancestral clone of M.tb spread and differentiated within this timeframe is important for identifying the ecological drivers of the current pandemic. We used Bayesian phylogeographic inference to reconstruct the migratory history of M.tb in Africa and Eurasia and to investigate lineage specific patterns of spread from a geographically diverse sample of 552 M.tb genomes. Applying evolutionary rates inferred with ancient M.tb genome calibration, we estimated the timing of major events in the migratory history of the pathogen. Inferred timings contextualize M.tb dispersal within historical phenomena that altered patterns of connectivity throughout Africa and Eurasia: trans-Indian Ocean trade in spices and other goods, the Silk Road and its predecessors, the expansion of the Roman Empire, and the European Age of Exploration. We found that Eastern Africa and Southeast Asia have been critical in the dispersal of M.tb. Our results further reveal that M.tb populations have grown through range expansion, as well as in situ, and delineate the independent evolutionary trajectories of bacterial subpopulations underlying the current pandemic.
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Affiliation(s)
- Mary B. O'Neill
- Laboratory of GeneticsUniversity of Wisconsin‐MadisonMadisonWIUSA
- Department of Medical Microbiology and ImmunologyUniversity of Wisconsin‐MadisonMadisonWIUSA
- Present address:
Unit of Human Evolutionary GeneticsInstitut PasteurParisFrance
| | - Abigail Shockey
- Department of Medical Microbiology and ImmunologyUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - Alex Zarley
- Department of GeographyUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - William Aylward
- Department of Classical and Ancient Near Eastern StudiesUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - Vegard Eldholm
- Infection Control and Environmental HealthNorwegian Institute of Public HealthOsloNorway
| | - Andrew Kitchen
- Department of AnthropologyUniversity of IowaIowa CityIAUSA
| | - Caitlin S. Pepperell
- Department of Medical Microbiology and ImmunologyUniversity of Wisconsin‐MadisonMadisonWIUSA
- Department of MedicineUniversity of Wisconsin‐MadisonMadisonWIUSA
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97
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Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues. Nat Rev Microbiol 2019; 17:533-545. [DOI: 10.1038/s41579-019-0214-5] [Citation(s) in RCA: 155] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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98
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Cohen KA, Manson AL, Abeel T, Desjardins CA, Chapman SB, Hoffner S, Birren BW, Earl AM. Extensive global movement of multidrug-resistant M. tuberculosis strains revealed by whole-genome analysis. Thorax 2019; 74:882-889. [PMID: 31048508 PMCID: PMC6788793 DOI: 10.1136/thoraxjnl-2018-211616] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 01/28/2019] [Accepted: 02/25/2019] [Indexed: 11/22/2022]
Abstract
Background While the international spread of multidrug-resistant (MDR) Mycobacterium tuberculosis strains is an acknowledged public health threat, a broad and more comprehensive examination of the global spread of MDR-tuberculosis (TB) using whole-genome sequencing has not yet been performed. Methods In a global dataset of 5310 M. tuberculosis whole-genome sequences isolated from five continents, we performed a phylogenetic analysis to identify and characterise clades of MDR-TB with respect to geographic dispersion. Results Extensive international dissemination of MDR-TB was observed, with identification of 32 migrant MDR-TB clades with descendants isolated in 17 unique countries. Relatively recent movement of strains from both Beijing and non-Beijing lineages indicated successful global spread of varied genetic backgrounds. Migrant MDR-TB clade members shared relatively recent common ancestry, with a median estimate of divergence of 13–27 years. Migrant extensively drug-resistant (XDR)-TB clades were not observed, although development of XDR-TB within migratory MDR-TB clades was common. Conclusions Application of genomic techniques to investigate global MDR migration patterns revealed extensive global spread of MDR clades between countries of varying TB burden. Further expansion of genomic studies to incorporate isolates from diverse global settings into a single analysis, as well as data sharing platforms that facilitate genomic data sharing across country lines, may allow for future epidemiological analyses to monitor for international transmission of MDR-TB. In addition, efforts to perform routine whole-genome sequencing on all newly identified M. tuberculosis, like in England, will serve to better our understanding of the transmission dynamics of MDR-TB globally.
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Affiliation(s)
- Keira A Cohen
- Division of Pulmonary and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Abigail L Manson
- Broad Institute of Harvard and M.I.T, Cambridge, Massachusetts, USA
| | - Thomas Abeel
- Broad Institute of Harvard and M.I.T, Cambridge, Massachusetts, USA.,Delft Bioinformatics Lab, Technische Universiteit Delft Faculteit Technische Natuurwetenschappen, Delft, Netherlands
| | | | - Sinead B Chapman
- Broad Institute of Harvard and M.I.T, Cambridge, Massachusetts, USA
| | - Sven Hoffner
- Department of Public Health Sciences, Karolinska Institute, Stockholm, Sweden
| | - Bruce W Birren
- Broad Institute of Harvard and M.I.T, Cambridge, Massachusetts, USA
| | - Ashlee M Earl
- Broad Institute of Harvard and M.I.T, Cambridge, Massachusetts, USA
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99
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Rutaihwa LK, Menardo F, Stucki D, Gygli SM, Ley SD, Malla B, Feldmann J, Borrell S, Beisel C, Middelkoop K, Carter EJ, Diero L, Ballif M, Jugheli L, Reither K, Fenner L, Brites D, Gagneux S. Multiple Introductions of Mycobacterium tuberculosis Lineage 2–Beijing Into Africa Over Centuries. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00112] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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100
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Insights on the Mycobacterium tuberculosis population structure associated with migrants from Portuguese-speaking countries over a three-year period in Greater Lisbon, Portugal: Implications at the public health level. INFECTION GENETICS AND EVOLUTION 2019; 71:159-165. [PMID: 30928606 DOI: 10.1016/j.meegid.2019.03.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Revised: 03/22/2019] [Accepted: 03/25/2019] [Indexed: 11/22/2022]
Abstract
Tuberculosis among foreign-born patients is a key indicator of country-level epidemiological profiles and, of an increasing concern in Europe given the more intensified migratory waves of refugees. Since Portugal presents a lower immigrant-associated TB incidence rate when compared to other European countries, we sought to characterize the epidemiology and transmission dynamics among the foreign-born population coming from Portuguese-speaking countries that are associated with higher TB incidences. In the present study we analyzed 133 Mycobacterium tuberculosis isolates obtained from foreign-born individuals over a three-year period in Lisbon, Portugal, using molecular epidemiological methods such as spoligotyping and 24-loci MIRU-VNTR. Moreover, all strains were subjected to drug susceptibility testing. The genetic profiles obtained suggest that strain importation from Portuguese speaking countries plays a less important role in TB epidemiology but instead argue in favor of a high degree of penetrance of Portuguese endemic strains to the migrant population, including multidrug resistant strains, which is particularly relevant to active screening programs.
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