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Bundhoo E, Ghoorah AW, Jaufeerally-Fakim Y. Large-scale Pan Genomic Analysis of Mycobacterium tuberculosis Reveals Key Insights Into Molecular Evolutionary Rate of Specific Processes and Functions. Evol Bioinform Online 2024; 20:11769343241239463. [PMID: 38532808 PMCID: PMC10964447 DOI: 10.1177/11769343241239463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 02/28/2024] [Indexed: 03/28/2024] Open
Abstract
Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis (TB), an infectious disease that is a major killer worldwide. Due to selection pressure caused by the use of antibacterial drugs, Mtb is characterised by mutational events that have given rise to multi drug resistant (MDR) and extensively drug resistant (XDR) phenotypes. The rate at which mutations occur is an important factor in the study of molecular evolution, and it helps understand gene evolution. Within the same species, different protein-coding genes evolve at different rates. To estimate the rates of molecular evolution of protein-coding genes, a commonly used parameter is the ratio dN/dS, where dN is the rate of non-synonymous substitutions and dS is the rate of synonymous substitutions. Here, we determined the estimated rates of molecular evolution of select biological processes and molecular functions across 264 strains of Mtb. We also investigated the molecular evolutionary rates of core genes of Mtb by computing the dN/dS values, and estimated the pan genome of the 264 strains of Mtb. Our results show that the cellular amino acid metabolic process and the kinase activity function evolve at a significantly higher rate, while the carbohydrate metabolic process evolves at a significantly lower rate for M. tuberculosis. These high rates of evolution correlate well with Mtb physiology and pathogenicity. We further propose that the core genome of M. tuberculosis likely experiences varying rates of molecular evolution which may drive an interplay between core genome and accessory genome during M. tuberculosis evolution.
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Affiliation(s)
- Eshan Bundhoo
- Department of Agricultural & Food Science, Faculty of Agriculture, University of Mauritius, Reduit, Mauritius
| | - Anisah W Ghoorah
- Department of Digital Technologies, Faculty of Information, Communication & Digital Technologies, University of Mauritius, Reduit, Mauritius
| | - Yasmina Jaufeerally-Fakim
- Department of Agricultural & Food Science, Faculty of Agriculture, University of Mauritius, Reduit, Mauritius
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2
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Rana HK, Singh AK, Kumar R, Pandey AK. Antitubercular drugs: possible role of natural products acting as antituberculosis medication in overcoming drug resistance and drug-induced hepatotoxicity. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024; 397:1251-1273. [PMID: 37665346 DOI: 10.1007/s00210-023-02679-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 08/16/2023] [Indexed: 09/05/2023]
Abstract
Mycobacterium tuberculosis (Mtb) is a pathogenic bacterium which causes tuberculosis (TB). TB control programmes are facing threats from drug resistance. Multidrug-resistant (MDR) and extensively drug-resistant (XDR) Mtb strains need longer and more expensive treatment with many medications resulting in more adverse effects and decreased chances of treatment outcomes. The World Health Organization (WHO) has emphasised the development of not just new individual anti-TB drugs, but also novel medication regimens as an alternative treatment option for the drug-resistant Mtb strains. Many plants, as well as marine creatures (sponge; Haliclona sp.) and fungi, have been continuously used to treat TB in various traditional treatment systems around the world, providing an almost limitless supply of active components. Natural products, in addition to their anti-mycobacterial action, can be used as adjuvant therapy to increase the efficacy of conventional anti-mycobacterial medications, reduce their side effects, and reverse MDR Mtb strain due to Mycobacterium's genetic flexibility and environmental adaptation. Several natural compounds such as quercetin, ursolic acid, berberine, thymoquinone, curcumin, phloretin, and propolis have shown potential anti-mycobacterial efficacy and are still being explored in preclinical and clinical investigations for confirmation of their efficacy and safety as anti-TB medication. However, more high-level randomized clinical trials are desperately required. The current review provides an overview of drug-resistant TB along with the latest anti-TB medications, drug-induced hepatotoxicity and oxidative stress. Further, the role and mechanisms of action of first and second-line anti-TB drugs and new drugs have been highlighted. Finally, the role of natural compounds as anti-TB medication and hepatoprotectants have been described and their mechanisms discussed.
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Affiliation(s)
- Harvesh Kumar Rana
- Department of Biochemistry, University of Allahabad, Prayagraj (Allahabad), 211002, India
- Department of Zoology, Feroze Gandhi College, Raebareli, 229001, India
| | - Amit Kumar Singh
- Department of Biochemistry, University of Allahabad, Prayagraj (Allahabad), 211002, India
- Department of Botany, BMK Government. Girls College, Balod, Chhattisgarh, 491226, India
| | - Ramesh Kumar
- Department of Biochemistry, University of Allahabad, Prayagraj (Allahabad), 211002, India
- Department of Biochemistry, Central University of Punjab, Bathinda, Punjab, 151401, India
| | - Abhay K Pandey
- Department of Biochemistry, University of Allahabad, Prayagraj (Allahabad), 211002, India.
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Silcocks M, Chang X, Thuong Thuong NT, Qin Y, Minh Ha DT, Khac Thai PV, Vijay S, Anh Thu DD, Ngoc Ha VT, Ngoc Nhung H, Huu Lan N, Quynh Nhu NT, Edwards D, Nath A, Pham K, Duc Bang N, Hong Chau TT, Thwaites G, Heemskerk AD, Chuen Khor C, Teo YY, Inouye M, Ong RTH, Caws M, Holt KE, Dunstan SJ. Evolution and transmission of antibiotic resistance is driven by Beijing lineage Mycobacterium tuberculosis in Vietnam. Microbiol Spectr 2023; 11:e0256223. [PMID: 37971428 PMCID: PMC10714959 DOI: 10.1128/spectrum.02562-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 10/12/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE Drug-resistant tuberculosis (TB) infection is a growing and potent concern, and combating it will be necessary to achieve the WHO's goal of a 95% reduction in TB deaths by 2035. While prior studies have explored the evolution and spread of drug resistance, we still lack a clear understanding of the fitness costs (if any) imposed by resistance-conferring mutations and the role that Mtb genetic lineage plays in determining the likelihood of resistance evolution. This study offers insight into these questions by assessing the dynamics of resistance evolution in a high-burden Southeast Asian setting with a diverse lineage composition. It demonstrates that there are clear lineage-specific differences in the dynamics of resistance acquisition and transmission and shows that different lineages evolve resistance via characteristic mutational pathways.
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Affiliation(s)
- Matthew Silcocks
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Xuling Chang
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, , Singapore
- Khoo Teck Puat–National University Children’s Medical Institute, National University Health System, Singapore
| | - Nguyen Thuy Thuong Thuong
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Youwen Qin
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Dang Thi Minh Ha
- Pham Ngoc Thach Hospital for TB and Lung Disease, District 5, Ho Chi Minh City, Vietnam
| | - Phan Vuong Khac Thai
- Pham Ngoc Thach Hospital for TB and Lung Disease, District 5, Ho Chi Minh City, Vietnam
| | - Srinivasan Vijay
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
- Theoretical Microbial Ecology, Friedrich Schiller University Jena, Jena, Germany
| | - Do Dang Anh Thu
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
| | - Vu Thi Ngoc Ha
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
| | - Hoang Ngoc Nhung
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
| | - Nguyen Huu Lan
- Pham Ngoc Thach Hospital for TB and Lung Disease, District 5, Ho Chi Minh City, Vietnam
| | - Nguyen Thi Quynh Nhu
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
| | - David Edwards
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Artika Nath
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Kym Pham
- Department of Clinical Pathology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Nguyen Duc Bang
- Pham Ngoc Thach Hospital for TB and Lung Disease, District 5, Ho Chi Minh City, Vietnam
| | - Tran Thi Hong Chau
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
- Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
| | - Guy Thwaites
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - A. Dorothee Heemskerk
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centre, Amsterdam, Netherlands
| | | | - Yik Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Michael Inouye
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Department of Public Health and Primary Care, Cambridge Baker Systems Genomics Initiative, University of Cambridge, Cambridge, United Kingdom
| | - Rick Twee-Hee Ong
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Maxine Caws
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Birat Nepal Medical Trust, Kathmandu, Nepal
| | - Kathryn E. Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Sarah J. Dunstan
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
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Wang Z, Tang Z, Heidari H, Molaeipour L, Ghanavati R, Kazemian H, Koohsar F, Kouhsari E. Global status of phenotypic pyrazinamide resistance in Mycobacterium tuberculosis clinical isolates: an updated systematic review and meta-analysis. J Chemother 2023; 35:583-595. [PMID: 37211822 DOI: 10.1080/1120009x.2023.2214473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 05/01/2023] [Accepted: 05/11/2023] [Indexed: 05/23/2023]
Abstract
Pyrazinamide (PZA) is an essential first-line tuberculosis drug for its unique mechanism of action active against multidrug-resistant-TB (MDR-TB). Thus, the aim of updated meta-analysis was to estimate the PZA weighted pooled resistance (WPR) rate in M. tuberculosis isolates based on publication date and WHO regions. We systematically searched the related reports in PubMed, Scopus, and Embase (from January 2015 to July 2022). Statistical analyses were performed using STATA software. The 115 final reports in the analysis investigated phenotypic PZA resistance data. The WPR of PZA was 57% (95% CI 48-65%) in MDR-TB cases. According to the WHO regions, the higher WPRs of PZA were reported in the Western Pacific (32%; 95% CI 18-46%), South East Asian region (37%; 95% CI 31-43%), and the Eastern Mediterranean (78%; 95% CI 54-95%) among any-TB patients, high risk of MDR-TB patients, and MDR-TB patients, respectively. A negligible increase in the rate of PZA resistance were showed in MDR-TB cases (55% to 58%). The rate of PZA resistance has been rising in recent years among MDR-TB cases, underlines the essential for both standard and novel drug regimens development.
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Affiliation(s)
- Zheming Wang
- Department of Pharmacy, Shaoxing People's Hospital, Shaoxing, China
| | - Zhihua Tang
- Department of Pharmacy, Shaoxing People's Hospital, Shaoxing, China
| | - Hamid Heidari
- Department of Microbiology, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Leila Molaeipour
- Department of Epidemiology, School of Public Health, University of Medical Sciences, Tehran, Iran
| | | | - Hossein Kazemian
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Faramarz Koohsar
- Laboratory Sciences Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Ebrahim Kouhsari
- Laboratory Sciences Research Center, Golestan University of Medical Sciences, Gorgan, Iran
- Department of Laboratory Sciences, Faculty of Paramedicine, Golestan University of Medical Sciences, Gorgan, Iran
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Auganova D, Atavliyeva S, Amirgazin A, Akisheva A, Tsepke A, Tarlykov P. Genomic Characterization of Drug-Resistant Mycobacterium tuberculosis L2/Beijing Isolates from Astana, Kazakhstan. Antibiotics (Basel) 2023; 12:1523. [PMID: 37887224 PMCID: PMC10604462 DOI: 10.3390/antibiotics12101523] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 09/25/2023] [Accepted: 10/02/2023] [Indexed: 10/28/2023] Open
Abstract
Kazakhstan ranks among the countries with the highest number of MDR-TB patients per 100,000 population worldwide. The successful transmission of local MDR strains of Mycobacterium tuberculosis (Mtb) poses a significant threat to disease control. In this study, we employed whole-genome sequencing to examine drug resistance, compensatory mutations, population structure, and transmission patterns in a sample of 24 clinical isolates of L2/Beijing Mtb collected in Astana, Kazakhstan between 2021 and 2022. The genotypic prediction of Mtb susceptibility to anti-TB agents was consistent with the phenotypic susceptibility, except for bedaquiline. An analysis of resistance-associated genes characterized most of the isolates as pre-extensively drug-resistant tuberculosis (pre-XDR-TB) (n = 15; 62.5%). The phylogenetic analysis grouped the isolates into four transmission clusters; the dominant cluster was assigned to the "aggressive" Central Asia outbreak (CAO) clade of L2/Beijing (n = 15; 62.5%). Thirteen mutations with putative compensatory effects were observed exclusively in Mtb isolates containing the rpoB S450L mutation. The putative compensatory mutations had a stabilizing effect on RpoABC protein stability and dynamics. The high prevalence of the CAO clade in the population structure of Mtb may explain the rapid spread of MDR-TB in Kazakhstan.
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Affiliation(s)
- Dana Auganova
- National Center for Biotechnology, Astana 010000, Kazakhstan (A.A.)
| | | | | | - Akmaral Akisheva
- City Center for Phthisiopulmonology of the Akimat of Astana, Astana 010000, Kazakhstan
| | - Anna Tsepke
- City Center for Phthisiopulmonology of the Akimat of Astana, Astana 010000, Kazakhstan
| | - Pavel Tarlykov
- National Center for Biotechnology, Astana 010000, Kazakhstan (A.A.)
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6
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Bui VCB, Yaniv Z, Harris M, Yang F, Kantipudi K, Hurt D, Rosenthal A, Jaeger S. Combining Radiological and Genomic TB Portals Data for Drug Resistance Analysis. IEEE ACCESS : PRACTICAL INNOVATIONS, OPEN SOLUTIONS 2023; 11:84228-84240. [PMID: 37663145 PMCID: PMC10473876 DOI: 10.1109/access.2023.3298750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Tuberculosis (TB) drug resistance is a worldwide public health problem. It decreases the likelihood of a positive outcome for the individual patient and increases the likelihood of disease spread. Therefore, early detection of TB drug resistance is crucial for improving outcomes and controlling disease transmission. While drug-sensitive tuberculosis cases are declining worldwide because of effective treatment, the threat of drug-resistant tuberculosis is growing, and the success rate of drug-resistant tuberculosis treatment is only around 60%. The TB Portals program provides a publicly accessible repository of TB case data with an emphasis on collecting drug-resistant cases. The dataset includes multi-modal information such as socioeconomic/geographic data, clinical characteristics, pathogen genomics, and radiological features. The program is an international collaboration whose participants are typically under a substantial burden of drug-resistant tuberculosis, with data collected from standard clinical care provided to the patients. Consequentially, the TB Portals dataset is heterogenous in nature, with data representing multiple treatment centers in different countries and containing cross-domain information. This study presents the challenges and methods used to address them when working with this real-world dataset. Our goal was to evaluate whether combining radiological features derived from a chest X-ray of the host and genomic features from the pathogen can potentially improve the identification of the drug susceptibility type, drug-sensitive (DS-TB) or drug-resistant (DR-TB), and the length of the first successful drug regimen. To perform these studies, significantly imbalanced data needed to be processed, which included a much larger number of DR-TB cases than DS-TB, many more cases with radiological findings than genomic ones, and the sparse high dimensional nature of the genomic information. Three evaluation studies were carried out. First, the DR-TB/DS-TB classification model achieved an average accuracy of 92.4% when using genomic features alone or when combining radiological and genomic features. Second, the regression model for the length of the first successful treatment had a relative error of 53.5% using radiological features, 25.6% using genomic features, and 22.0% using both radiological and genomic features. Finally, the relative error of the third regression model predicting the length of the first treatment using the most common drug combination varied depending on the feature type used. When using radiological features alone, the relative error was 17.8%. For genomic features alone, the relative error increased to 19.9%. The model had a relative error of 19.0% when both radiological and genomic features were combined. Although combining radiological and genomic features did not improve upon the use of genomic features when classifying DR-TB/DS-TB, the combination of the two feature types improved the relative error of the predictive model for the length of the first successful treatment. Furthermore, the regression model trained on radiological features achieved the best performance when predicting the treatment length of the most common drug combination.
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Affiliation(s)
- Vy C B Bui
- Lister Hill National Center for Biomedical Communications, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Ziv Yaniv
- Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael Harris
- Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Feng Yang
- Lister Hill National Center for Biomedical Communications, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Karthik Kantipudi
- Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Darrell Hurt
- Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alex Rosenthal
- Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Stefan Jaeger
- Lister Hill National Center for Biomedical Communications, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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7
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Shibabaw A, Gelaw B, Ghanem M, Legall N, Schooley AM, Soehnlen MK, Salvador LCM, Gebreyes W, Wang SH, Tessema B. Molecular epidemiology and transmission dynamics of multi-drug resistant tuberculosis strains using whole genome sequencing in the Amhara region, Ethiopia. BMC Genomics 2023; 24:400. [PMID: 37460951 DOI: 10.1186/s12864-023-09502-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 07/03/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND Drug resistant Mycobacterium tuberculosis prevention and care is a major challenge in Ethiopia. The World health organization has designated Ethiopia as one of the 30 high burden multi-drug resistant tuberculosis (MDR-TB) countries. There is limited information regarding genetic diversity and transmission dynamics of MDR-TB in Ethiopia. OBJECTIVE To investigate the molecular epidemiology and transmission dynamics of MDR-TB strains using whole genome sequence (WGS) in the Amhara region. METHODS Forty-five MDR-TB clinical isolates from Amhara region were collected between 2016 and 2018, and characterized using WGS and 24-loci Mycobacterium Interspersed Repetitive Units Variable Number of Tandem Repeats (MIRU-VNTR) typing. Clusters were defined based on the maximum distance of 12 single nucleotide polymorphisms (SNPs) or alleles as the upper threshold of genomic relatedness. Five or less SNPs or alleles distance or identical 24-loci VNTR typing is denoted as surrogate marker for recent transmission. RESULTS Forty-one of the 45 isolates were analyzed by WGS and 44% (18/41) of the isolates were distributed into 4 clusters. Of the 41 MDR-TB isolates, 58.5% were classified as lineage 4, 36.5% lineage 3 and 5% lineage 1. Overall, TUR genotype (54%) was the predominant in MDR-TB strains. 41% (17/41) of the isolates were clustered into four WGS groups and the remaining isolates were unique strains. The predominant cluster (Cluster 1) was composed of nine isolates belonging to lineage 4 and of these, four isolates were in the recent transmission links. CONCLUSIONS Majority of MDR-TB strain cluster and predominance of TUR lineage in the Amhara region give rise to concerns for possible ongoing transmission. Efforts to strengthen TB laboratory to advance diagnosis, intensified active case finding, and expanded contact tracing activities are needed in order to improve rapid diagnosis and initiate early treatment. This would lead to the interruption of the transmission chain and stop the spread of MDR-TB in the Amhara region.
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Affiliation(s)
- Agumas Shibabaw
- Department of Medical Laboratory Sciences, College of Medicine and Health Sciences, Wollo University, Dessie, Ethiopia.
- Global One Health Initiative (GOHi), The Ohio State University, Columbus, OH, USA.
- Department of Medical Microbiology, School of Medical Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia.
- Michigan Department of Health and Human Services, Infectious disease, Lansing, MI, USA.
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA.
| | - Baye Gelaw
- Department of Medical Microbiology, School of Medical Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Mostafa Ghanem
- Department of Veterinary Medicine, Virginia-Maryland College of Veterinary Medicine, University of Maryland, College Park, MD, USA
| | - Noah Legall
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Angie M Schooley
- Michigan Department of Health and Human Services, Infectious disease, Lansing, MI, USA
| | - Marty K Soehnlen
- Michigan Department of Health and Human Services, Infectious disease, Lansing, MI, USA
| | - Liliana C M Salvador
- School of Animal and Comparative Biomedical Sciences, College of Agriculture and life sciences, University of Arizona, Tucson, AZ, USA
| | - Wondwossen Gebreyes
- Global One Health Initiative (GOHi), The Ohio State University, Columbus, OH, USA
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
| | - Shu-Hua Wang
- Global One Health Initiative (GOHi), The Ohio State University, Columbus, OH, USA
- Department of Internal Medicine, Division of Infectious Diseases, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Belay Tessema
- Department of Medical Microbiology, School of Medical Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
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8
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Perumal R, Khan A, Naidoo K, Ngema SL, Nandlal L, Padayatchi N, Dookie N. Mycobacterium tuberculosis Intra-Host Evolution Among Drug-Resistant Tuberculosis Patients Failing Treatment. Infect Drug Resist 2023; 16:2849-2859. [PMID: 37193296 PMCID: PMC10182815 DOI: 10.2147/idr.s408976] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/29/2023] [Indexed: 05/18/2023] Open
Abstract
Background Understanding Mycobacterium tuberculosis (Mtb) intra-host evolution of drug resistance is important for successful drug-resistant tuberculosis (DR-TB) treatment and control strategies. This study aimed to characterise the acquisition of genetic mutations and low-frequency variants associated with treatment-emergent Mtb drug resistance in longitudinally profiled clinical isolates from patients who experienced DR-TB treatment failure. Patients and Methods We performed deep Whole Genome Sequencing on 23 clinical isolates obtained longitudinally across nine timepoints from five patients who experienced DR-TB treatment failure enrolled in the CAPRISA 020 InDEX study. The minimum inhibitory concentrations (MICs) were established on the BACTEC™ MGIT 960™ instrument on 15/23 longitudinal clinical isolates for eight anti-TB drugs (rifampicin, isoniazid, ethambutol, levofloxacin, moxifloxacin, linezolid, clofazimine, bedaquiline). Results In total, 22 resistance associated mutations/variants were detected. We observed four treatment-emergent mutations in two out of the five patients. Emerging resistance to the fluoroquinolones was associated with 16- and 64-fold elevated levofloxacin (2-8 mg/L) and moxifloxacin (1-2 mg/L) MICs, respectively, resulting from the D94G/N and A90V variants in the gyrA gene. We identified two novel mutations associated with elevated bedaquiline MICs (>66-fold): an emerging frameshift variant (D165) on the Rv0678 gene and R409Q variant on the Rv1979c gene present from baseline. Conclusion Genotypic and phenotypic resistance to the fluoroquinolones and bedaquiline was acquired in two out of five patients who experienced DR-TB treatment failure. Deep sequencing of multiple longitudinal clinical isolates for resistance-associated mutations coupled with phenotypic MIC testing confirmed intra-host Mtb evolution.
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Affiliation(s)
- Rubeshan Perumal
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, KwaZulu Natal, South Africa
- South African Medical Research Council (SAMRC) – CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, KwaZulu Natal, South Africa
| | - Azraa Khan
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, KwaZulu Natal, South Africa
| | - Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, KwaZulu Natal, South Africa
- South African Medical Research Council (SAMRC) – CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, KwaZulu Natal, South Africa
| | - Senamile L Ngema
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, KwaZulu Natal, South Africa
| | - Louansha Nandlal
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, KwaZulu Natal, South Africa
- South African Medical Research Council (SAMRC) – CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, KwaZulu Natal, South Africa
| | - Nesri Padayatchi
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, KwaZulu Natal, South Africa
- South African Medical Research Council (SAMRC) – CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, KwaZulu Natal, South Africa
| | - Navisha Dookie
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, KwaZulu Natal, South Africa
- South African Medical Research Council (SAMRC) – CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, KwaZulu Natal, South Africa
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9
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O'Toole RF. Antibiotic resistance acquisition versus primary transmission in the presentation of extensively drug-resistant tuberculosis. Int J Mycobacteriol 2022; 11:343-348. [PMID: 36510916 DOI: 10.4103/ijmy.ijmy_187_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Mycobacterium tuberculosis is the leading cause of mortality worldwide due to a single bacterial pathogen. Of concern is the negative impact that the COVID-19 pandemic has had on the control of tuberculosis (TB) including drug-resistant forms of the disease. Antimicrobial resistance increases the likelihood of worsened outcomes in TB patients including treatment failure and death. Multidrug-resistant (MDR) strains, resistant to first-line drugs isoniazid and rifampin, and extensively drug-resistant (XDR) strains with further resistance to second-line drugs (SLD), threaten control programs designed to lower TB incidence and end the disease as a public health challenge by 2030, in accordance with UN Sustainable Development Goals. Tackling TB requires an understanding of the pathways through which drug resistance emerges. Here, the roles of acquired resistance mutation, and primary transmission, are examined with regard to XDR-TB. It is apparent that XDR-TB can emerge from MDR-TB through a small number of additional resistance mutations that occur in patients undergoing drug treatment. Rapid detection of resistance, to first-line drugs and SLD, at the initiation of and during treatment, and prompt adjustment of regimens are required to ensure treatment success in these patients. Primary transmission is predicted to make an increasing contribution to the XDR-TB caseload in the future. Much work is required to improve the implementation of the World Health Organization-recommended infection control practices and block onward transmission of XDR-TB patients to contacts including health-care workers. Finally, limiting background resistance to fluoroquinolones in pre-XDR strains of M. tuberculosis will necessitate better antimicrobial stewardship in the broader use of this drug class.
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Affiliation(s)
- Ronan Francis O'Toole
- Department of Biomedicine and Medical Diagnostics, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland, New Zealand
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10
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Green AG, Yoon CH, Chen ML, Ektefaie Y, Fina M, Freschi L, Gröschel MI, Kohane I, Beam A, Farhat M. A convolutional neural network highlights mutations relevant to antimicrobial resistance in Mycobacterium tuberculosis. Nat Commun 2022; 13:3817. [PMID: 35780211 PMCID: PMC9250494 DOI: 10.1038/s41467-022-31236-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 06/10/2022] [Indexed: 11/30/2022] Open
Abstract
Long diagnostic wait times hinder international efforts to address antibiotic resistance in M. tuberculosis. Pathogen whole genome sequencing, coupled with statistical and machine learning models, offers a promising solution. However, generalizability and clinical adoption have been limited by a lack of interpretability, especially in deep learning methods. Here, we present two deep convolutional neural networks that predict antibiotic resistance phenotypes of M. tuberculosis isolates: a multi-drug CNN (MD-CNN), that predicts resistance to 13 antibiotics based on 18 genomic loci, with AUCs 82.6-99.5% and higher sensitivity than state-of-the-art methods; and a set of 13 single-drug CNNs (SD-CNN) with AUCs 80.1-97.1% and higher specificity than the previous state-of-the-art. Using saliency methods to evaluate the contribution of input sequence features to the SD-CNN predictions, we identify 18 sites in the genome not previously associated with resistance. The CNN models permit functional variant discovery, biologically meaningful interpretation, and clinical applicability.
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Affiliation(s)
- Anna G Green
- Department of Biomedical Informatics, Harvard Medical School, 25 Shattuck St, Boston, MA, 02115, USA
| | - Chang Ho Yoon
- Department of Biomedical Informatics, Harvard Medical School, 25 Shattuck St, Boston, MA, 02115, USA
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Oxford, OX37LF, UK
| | - Michael L Chen
- Department of Biomedical Informatics, Harvard Medical School, 25 Shattuck St, Boston, MA, 02115, USA
- Stanford University School of Medicine, 291 Campus Dr, Stanford, CA, 94305, USA
| | - Yasha Ektefaie
- Department of Biomedical Informatics, Harvard Medical School, 25 Shattuck St, Boston, MA, 02115, USA
| | - Mack Fina
- Harvard College, Cambridge, MA, 02138, USA
| | - Luca Freschi
- Department of Biomedical Informatics, Harvard Medical School, 25 Shattuck St, Boston, MA, 02115, USA
| | - Matthias I Gröschel
- Department of Biomedical Informatics, Harvard Medical School, 25 Shattuck St, Boston, MA, 02115, USA
| | - Isaac Kohane
- Department of Biomedical Informatics, Harvard Medical School, 25 Shattuck St, Boston, MA, 02115, USA
| | - Andrew Beam
- Department of Biomedical Informatics, Harvard Medical School, 25 Shattuck St, Boston, MA, 02115, USA.
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, 677 Huntington Ave, Boston, MA, 02115, USA.
| | - Maha Farhat
- Department of Biomedical Informatics, Harvard Medical School, 25 Shattuck St, Boston, MA, 02115, USA.
- Division of Pulmonary & Critical Care, Massachusetts General Hospital, 55 Fruit St, Boston, MA, 02114, USA.
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11
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Wollenberg KR, Jeffrey BM, Harris MA, Gabrielian A, Hurt DE, Rosenthal A. Patterns of genomic interrelatedness of publicly available samples in the TB portals database. Tuberculosis (Edinb) 2022; 133:102171. [PMID: 35101846 PMCID: PMC8997244 DOI: 10.1016/j.tube.2022.102171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 01/18/2022] [Accepted: 01/23/2022] [Indexed: 10/19/2022]
Abstract
The TB Portals program is an international collaboration for the collection and dissemination of tuberculosis data from patient cases focused on drug resistance. The central database is a patient-oriented resource containing both patient and pathogen clinical and genomic information. Herein we provide a summary of the pathogen genomic data available through the TB Portals and show one potential application by examining patterns of genomic pairwise distances. Distributions of pairwise distances highlight overall patterns of genome variability within and between Mycobacterium tuberculosis phylogenomic lineages. Closely related isolates (based on whole-genome pairwise distances and time between sample collection dates) from different countries were identified as potential evidence of international transmission of drug-resistant tuberculosis. These high-level views of genomic relatedness provide information that can stimulate hypotheses for further and more detailed research.
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Affiliation(s)
- Kurt R. Wollenberg
- Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, USA
| | - Brendan M. Jeffrey
- Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, USA
| | - Michael A. Harris
- Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, USA,To whom correspondence should be addressed: . Telephone: 301-761-6746
| | - Andrei Gabrielian
- Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA.
| | - Darrell E. Hurt
- Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, USA
| | - Alex Rosenthal
- Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA.
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12
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Lozano N, Lanza VF, Suárez-González J, Herranz M, Sola-Campoy PJ, Rodríguez-Grande C, Buenestado-Serrano S, Ruiz-Serrano MJ, Tudó G, Alcaide F, Muñoz P, García de Viedma D, Pérez-Lago L. Detection of Minority Variants and Mixed Infections in Mycobacterium tuberculosis by Direct Whole-Genome Sequencing on Noncultured Specimens Using a Specific-DNA Capture Strategy. mSphere 2021; 6:e0074421. [PMID: 34908457 PMCID: PMC8673255 DOI: 10.1128/msphere.00744-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 11/24/2021] [Indexed: 12/01/2022] Open
Abstract
Detection of mixed Mycobacterium tuberculosis (MTB) infections is essential, particularly when resistance mutations are present in minority bacterial populations that may affect patients' disease evolution and treatment. Whole-genome sequencing (WGS) has extended the amount of key information available for the diagnosis of MTB infection, including the identification of mixed infections. Having genomic information at diagnosis for early intervention requires carrying out WGS directly on the clinical samples. However, few studies have been successful with this approach due to the low representation of MTB DNA in sputa. In this study, we evaluated the ability of a strategy based on specific MTB DNA enrichment by using a newly designed capture platform (MycoCap) to detect minority variants and mixed infections by WGS on controlled mixtures of MTB DNAs in a simulated sputum genetic background. A pilot study was carried out with 12 samples containing 98% of a DNA pool from sputa of patients without MTB infection and 2% of MTB DNA mixtures at different proportions. Our strategy allowed us to generate sequences with a quality equivalent to those obtained from culture: 62.5× depth coverage and 95% breadth coverage (for at least 20× reads). Assessment of minority variant detection was carried out by manual analysis and allowed us to identify heterozygous positions up to a 95:5 ratio. The strategy also automatically distinguished mixed infections up to a 90:10 proportion. Our strategy efficiently captures MTB DNA in a nonspecific genetic background, allows detection of minority variants and mixed infections, and is a promising tool for performing WGS directly on clinical samples. IMPORTANCE We present a new strategy to identify mixed infections and minority variants in Mycobacterium tuberculosis by whole-genome sequencing. The objective of the strategy is the direct detection in patient sputum; in this way, minority populations of resistant strains can be identified at the time of diagnosis, facilitating identification of the most appropriate treatment for the patient from the first moment. For this, a platform for capturing M. tuberculosis-specific DNA was designed to enrich the clinical sample and obtain quality sequences.
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Affiliation(s)
- Nuria Lozano
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Val F. Lanza
- Bioinformatics Unit IRYCIS, University Hospital Ramón y Cajal, Madrid, Spain
- CIBER Enfermedades Infecciosas, Madrid, Spain
| | - Julia Suárez-González
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- Unidad de Genómica, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Marta Herranz
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias, CIBERES, Madrid, Spain
| | - Pedro J. Sola-Campoy
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Cristina Rodríguez-Grande
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Sergio Buenestado-Serrano
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - María Jesús Ruiz-Serrano
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Griselda Tudó
- Servei de Microbiologia, Hospital Clinic-CDB, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Barcelona, Spain
| | - Fernando Alcaide
- Servicio de Microbiología, Hospital Universitario de Bellvitge-IDIBELL, L’Hospitalet de Llobregat, Barcelona, Spain
- Department of Pathology and Experimental Therapy, University of Barcelona, L’Hospitalet de Llobregat, Barcelona, Spain
| | - Patricia Muñoz
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias, CIBERES, Madrid, Spain
- Departmento de Medicina, Universidad Complutense de Madrid, Madrid, Spain
| | - Darío García de Viedma
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias, CIBERES, Madrid, Spain
| | - Laura Pérez-Lago
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
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13
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Gröschel MI, Owens M, Freschi L, Vargas R, Marin MG, Phelan J, Iqbal Z, Dixit A, Farhat MR. GenTB: A user-friendly genome-based predictor for tuberculosis resistance powered by machine learning. Genome Med 2021; 13:138. [PMID: 34461978 PMCID: PMC8407037 DOI: 10.1186/s13073-021-00953-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 08/12/2021] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Multidrug-resistant Mycobacterium tuberculosis (Mtb) is a significant global public health threat. Genotypic resistance prediction from Mtb DNA sequences offers an alternative to laboratory-based drug-susceptibility testing. User-friendly and accurate resistance prediction tools are needed to enable public health and clinical practitioners to rapidly diagnose resistance and inform treatment regimens. RESULTS We present Translational Genomics platform for Tuberculosis (GenTB), a free and open web-based application to predict antibiotic resistance from next-generation sequence data. The user can choose between two potential predictors, a Random Forest (RF) classifier and a Wide and Deep Neural Network (WDNN) to predict phenotypic resistance to 13 and 10 anti-tuberculosis drugs, respectively. We benchmark GenTB's predictive performance along with leading TB resistance prediction tools (Mykrobe and TB-Profiler) using a ground truth dataset of 20,408 isolates with laboratory-based drug susceptibility data. All four tools reliably predicted resistance to first-line tuberculosis drugs but had varying performance for second-line drugs. The mean sensitivities for GenTB-RF and GenTB-WDNN across the nine shared drugs were 77.6% (95% CI 76.6-78.5%) and 75.4% (95% CI 74.5-76.4%), respectively, and marginally higher than the sensitivities of TB-Profiler at 74.4% (95% CI 73.4-75.3%) and Mykrobe at 71.9% (95% CI 70.9-72.9%). The higher sensitivities were at an expense of ≤ 1.5% lower specificity: Mykrobe 97.6% (95% CI 97.5-97.7%), TB-Profiler 96.9% (95% CI 96.7 to 97.0%), GenTB-WDNN 96.2% (95% CI 96.0 to 96.4%), and GenTB-RF 96.1% (95% CI 96.0 to 96.3%). Averaged across the four tools, genotypic resistance sensitivity was 11% and 9% lower for isoniazid and rifampicin respectively, on isolates sequenced at low depth (< 10× across 95% of the genome) emphasizing the need to quality control input sequence data before prediction. We discuss differences between tools in reporting results to the user including variants underlying the resistance calls and any novel or indeterminate variants CONCLUSIONS: GenTB is an easy-to-use online tool to rapidly and accurately predict resistance to anti-tuberculosis drugs. GenTB can be accessed online at https://gentb.hms.harvard.edu , and the source code is available at https://github.com/farhat-lab/gentb-site .
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Affiliation(s)
- Matthias I Gröschel
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Martin Owens
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Luca Freschi
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Roger Vargas
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Maximilian G Marin
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Jody Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
| | - Zamin Iqbal
- European Bioinformatics Institute, Hinxton, Cambridge, CB10 ISD, UK
| | - Avika Dixit
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, USA
| | - Maha R Farhat
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA, USA.
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14
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Castro RAD, Borrell S, Gagneux S. The within-host evolution of antimicrobial resistance in Mycobacterium tuberculosis. FEMS Microbiol Rev 2021; 45:fuaa071. [PMID: 33320947 PMCID: PMC8371278 DOI: 10.1093/femsre/fuaa071] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 12/11/2020] [Indexed: 12/12/2022] Open
Abstract
Tuberculosis (TB) has been responsible for the greatest number of human deaths due to an infectious disease in general, and due to antimicrobial resistance (AMR) in particular. The etiological agents of human TB are a closely-related group of human-adapted bacteria that belong to the Mycobacterium tuberculosis complex (MTBC). Understanding how MTBC populations evolve within-host may allow for improved TB treatment and control strategies. In this review, we highlight recent works that have shed light on how AMR evolves in MTBC populations within individual patients. We discuss the role of heteroresistance in AMR evolution, and review the bacterial, patient and environmental factors that likely modulate the magnitude of heteroresistance within-host. We further highlight recent works on the dynamics of MTBC genetic diversity within-host, and discuss how spatial substructures in patients' lungs, spatiotemporal heterogeneity in antimicrobial concentrations and phenotypic drug tolerance likely modulates the dynamics of MTBC genetic diversity in patients during treatment. We note the general characteristics that are shared between how the MTBC and other bacterial pathogens evolve in humans, and highlight the characteristics unique to the MTBC.
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Affiliation(s)
- Rhastin A D Castro
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Basel, Switzerland
- University of Basel, Petersplatz 1, 4001 Basel, Basel, Switzerland
| | - Sonia Borrell
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Basel, Switzerland
- University of Basel, Petersplatz 1, 4001 Basel, Basel, Switzerland
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Basel, Switzerland
- University of Basel, Petersplatz 1, 4001 Basel, Basel, Switzerland
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15
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Gatt YE, Margalit H. Common Adaptive Strategies Underlie Within-Host Evolution of Bacterial Pathogens. Mol Biol Evol 2021; 38:1101-1121. [PMID: 33118035 PMCID: PMC7947768 DOI: 10.1093/molbev/msaa278] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Within-host adaptation is a hallmark of chronic bacterial infections, involving substantial genomic changes. Recent large-scale genomic data from prolonged infections allow the examination of adaptive strategies employed by different pathogens and open the door to investigate whether they converge toward similar strategies. Here, we compiled extensive data of whole-genome sequences of bacterial isolates belonging to miscellaneous species sampled at sequential time points during clinical infections. Analysis of these data revealed that different species share some common adaptive strategies, achieved by mutating various genes. Although the same genes were often mutated in several strains within a species, different genes related to the same pathway, structure, or function were changed in other species utilizing the same adaptive strategy (e.g., mutating flagellar genes). Strategies exploited by various bacterial species were often predicted to be driven by the host immune system, a powerful selective pressure that is not species specific. Remarkably, we find adaptive strategies identified previously within single species to be ubiquitous. Two striking examples are shifts from siderophore-based to heme-based iron scavenging (previously shown for Pseudomonas aeruginosa) and changes in glycerol-phosphate metabolism (previously shown to decrease sensitivity to antibiotics in Mycobacterium tuberculosis). Virulence factors were often adaptively affected in different species, indicating shifts from acute to chronic virulence and virulence attenuation during infection. Our study presents a global view on common within-host adaptive strategies employed by different bacterial species and provides a rich resource for further studying these processes.
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Affiliation(s)
- Yair E Gatt
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Hanah Margalit
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
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16
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Tuberculosis Drug Susceptibility, Treatment, and Outcomes for Belarusian HIV-Positive Patients with Tuberculosis: Results from a National and International Laboratory. Tuberc Res Treat 2021; 2021:6646239. [PMID: 33868727 PMCID: PMC8035031 DOI: 10.1155/2021/6646239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 02/10/2021] [Accepted: 02/22/2021] [Indexed: 11/17/2022] Open
Abstract
Background To cure drug-resistant (DR) tuberculosis (TB), the antituberculous treatment should be guided by Mycobacterium tuberculosis drug-susceptibility testing (DST). In this study, we compared conventional DST performed in Minsk, Belarus, a TB DR high-burden country, with extensive geno- and phenotypic analyses performed at the WHO TB Supranational Reference Laboratory in Copenhagen, Denmark, for TB/HIV coinfected patients. Subsequently, DST results were related to treatment regimen and outcome. Methods Thirty TB/HIV coinfected patients from Minsk were included and descriptive statistics applied. Results Based on results from Minsk, 10 (33%) TB/HIV patients had drug-sensitive TB. Two (7%) had isoniazid monoresistant TB, 8 (27%) had multidrug-resistant (MDR) TB, 5 (17%) preextensive drug-resistant (preXDR) TB, and 5 (17%) had extensive drug-resistant (XDR) TB. For the first-line drugs rifampicin and isoniazid, there was DST agreement between Minsk and Copenhagen for 90% patients. For the second-line anti-TB drugs, discrepancies were more pronounced. For 14 (47%) patients, there were disagreements for at least one drug, and 4 (13%) patients were classified as having MDR-TB in Minsk but were classified as having preXDR-TB based on DST results in Copenhagen. Initially, all patients received standard anti-TB treatment with rifampicin, isoniazid, pyrazinamide, and ethambutol. However, this was only suitable for 40% of the patients based on DST. On average, DR-TB patients were changed to 4 (IQR 3-5) active drugs after 1.5 months (IQR 1-2). After treatment adjustment, the treatment duration was 8 months (IQR 2-11). Four (22%) patients with DR-TB received treatment for >18 months. In total, sixteen (53%) patients died during 24 months of follow-up. Conclusions We found high concordance for rifampicin and isoniazid DST between the Minsk and Copenhagen laboratories, whereas discrepancies for second-line drugs were more pronounced. For patients with DR-TB, treatment was often insufficient and relevant adjustments delayed. This example from Minsk, Belarus, underlines two crucial points in the management of DR-TB: the urgent need for implementation of rapid molecular DSTs and availability of second-line drugs in all DR-TB high-burden settings. Carefully designed individualized treatment regimens in accordance with DST patterns will likely improve patients' outcome and reduce transmission with drug-resistant Mycobacterium tuberculosis strains.
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17
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Han WM, Mahikul W, Pouplin T, Lawpoolsri S, White LJ, Pan-Ngum W. Assessing the impacts of short-course multidrug-resistant tuberculosis treatment in the Southeast Asia Region using a mathematical modeling approach. PLoS One 2021; 16:e0248846. [PMID: 33770104 PMCID: PMC7997007 DOI: 10.1371/journal.pone.0248846] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 03/07/2021] [Indexed: 12/03/2022] Open
Abstract
This study aimed to predict the impacts of shorter duration treatment regimens for multidrug-resistant tuberculosis (MDR-TB) on both MDR-TB percentage among new cases and overall MDR-TB cases in the WHO Southeast Asia Region. A deterministic compartmental model was constructed to describe both the transmission of TB and the MDR-TB situation in the Southeast Asia region. The population-level impacts of short-course treatment regimens were compared with the impacts of conventional regimens. Multi-way analysis was used to evaluate the impact by varying programmatic factors (eligibility for short-course MDR-TB treatment, treatment initiation, and drug susceptibility test (DST) coverage). The model predicted that overall TB incidence will be reduced from 246 (95% credible intervals (CrI), 221–275) per 100,000 population in 2020 to 239 (95% CrI, 215–267) per 100,000 population in 2035, with a modest reduction of 2.8% (95% CrI, 2.7%–2.9%). Despite the slight reduction in overall TB infections, the model predicted that the MDR-TB percentage among newly notified TB infections will remain steady, with 2.4% (95% CrI, 2.1–2.9) in 2020 and 2.5% (95% CrI, 2.3–3.1) in 2035, using conventional MDR-TB treatment. With the introduction of short-course regimens to treat MDR-TB, the development of resistance can be slowed by 38.6% (95% confidence intervals (CI), 35.9–41.3) reduction in MDR-TB case number, and 37.6% (95% CI, 34.9–40.3) reduction in MDR-TB percentage among new TB infections over the 30-year period compared with the baseline using the standard treatment regimen. The multi-way analysis showed eligibility for short-course treatment and treatment initiation greatly influenced the impacts of short-course treatment regimens on reductions in MDR-TB cases and percentage resistance among new infections. Policies which promote the expansion of short-course regimens and early MDR-TB treatment initiation should be considered along with other interventions to tackle antimicrobial resistance in the region.
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Affiliation(s)
- Win Min Han
- Department of Tropical Hygiene, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- HIV-NAT, Thai Red Cross AIDS Research Centre, Bangkok, Thailand
| | - Wiriya Mahikul
- Faculty of Medicine and Public Health, HRH Princess Chulabhorn College of Medical Science, Chulabhorn Royal Academy, Bangkok, Thailand
| | - Thomas Pouplin
- Pharmacology Department, Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
- Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Saranath Lawpoolsri
- Department of Tropical Hygiene, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Lisa J. White
- Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - Wirichada Pan-Ngum
- Department of Tropical Hygiene, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Mathematical and Economics Modelling (MAEMOD) Research Group, Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
- * E-mail:
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18
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Low-Level Rifampin Resistance and rpoB Mutations in Mycobacterium tuberculosis: an Analysis of Whole-Genome Sequencing and Drug Susceptibility Test Data in New York. J Clin Microbiol 2021; 59:JCM.01885-20. [PMID: 32999007 DOI: 10.1128/jcm.01885-20] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 09/05/2020] [Indexed: 01/02/2023] Open
Abstract
Rapid and reliable detection of rifampin (RIF) resistance is critical for the diagnosis and treatment of drug-resistant and multidrug-resistant (MDR) tuberculosis. Discordant RIF phenotype/genotype susceptibility results remain a challenge due to the presence of rpoB mutations that do not confer high levels of RIF resistance, as have been exhibited in strains with mutations such as Ser450Leu. These strains, termed low-level RIF resistant, exhibit elevated RIF MICs compared to fully susceptible strains but remain phenotypically susceptible by mycobacterial growth indicator tube (MGIT) testing and have been associated with poor patient outcomes. Here, we assess RIF resistance prediction by whole-genome sequencing (WGS) among a set of 1,779 prospectively tested strains by both prevalence of rpoB gene mutation and phenotype as part of routine clinical testing during a 2.5-year period. During this time, 139 strains were found to have nonsynonymous rpoB mutations, 53 of which were associated with RIF resistance, including both low-level and high-level resistance. Resistance to RIF (1.0 μg/ml in MGIT) was identified in 43 (81.1%) isolates. The remaining 10 (18.9%) strains were susceptible by MGIT but were confirmed to be low-level RIF resistant by MIC testing. Full rpoB gene sequencing overcame the limitations of critical concentration phenotyping, probe-based genotyping, and partial gene sequencing methods. Universal clinical WGS with concurrent phenotypic testing provided a more complete understanding of the prevalence and type of rpoB mutations and their association with RIF resistance in New York.
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Cheng B, Behr MA, Howden BP, Cohen T, Lee RS. Reporting practices for genomic epidemiology of tuberculosis: a systematic review of the literature using STROME-ID guidelines as a benchmark. THE LANCET. MICROBE 2021; 2:e115-e129. [PMID: 33842904 PMCID: PMC8034592 DOI: 10.1016/s2666-5247(20)30201-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND Pathogen genomics have become increasingly important in infectious disease epidemiology and public health. The Strengthening the Reporting of Molecular Epidemiology for Infectious Diseases (STROME-ID) guidelines were developed to outline a minimum set of criteria that should be reported in genomic epidemiology studies to facilitate assessment of study quality. We evaluate such reporting practices, using tuberculosis as an example. METHODS For this systematic review, we initially searched MEDLINE, Embase Classic, and Embase on May 3, 2017, using the search terms "tuberculosis" and "genom* sequencing". We updated this initial search on April 23, 2019, and also included a search of bioRxiv at this time. We included studies in English, French, or Spanish that recruited patients with microbiologically confirmed tuberculosis and used whole genome sequencing for typing of strains. Non-human studies, conference abstracts, and literature reviews were excluded. For each included study, the number and proportion of fulfilled STROME-ID criteria were recorded by two reviewers. A comparison of the mean proportion of fulfilled STROME-ID criteria before and after publication of the STROME-ID guidelines (in 2014) was done using a two-tailed t test. Quasi-Poisson regression and tobit regression were used to examine associations between study characteristics and the number and proportion of fulfilled STROME-ID criteria. This study was registered with PROSPERO, CRD42017064395. FINDINGS 976 titles and abstracts were identified by our primary search, with an additional 16 studies identified in bioRxiv. 114 full texts (published between 2009 and 2019) were eligible for inclusion. The mean proportion of STROME-ID criteria fulfilled was 50% (SD 12; range 16-75). The proportion of criteria fulfilled was similar before and after STROME-ID publication (51% [SD 11] vs 46% [14], p=0·26). The number of criteria reported (among those applicable to all studies) was not associated with impact factor, h-index, country of affiliation of senior author, or sample size of isolates. Similarly, the proportion of criteria fulfilled was not associated with these characteristics, with the exception of a sample size of isolates of 277 or more (the highest quartile). In terms of reproducibility, 100 (88%) studies reported which bioinformatic tools were used, but only 33 (33%) reported corresponding version numbers. Sequencing data were available for 86 (75%) studies. INTERPRETATION The reporting of STROME-ID criteria in genomic epidemiology studies of tuberculosis between 2009 and 2019 was low, with implications for assessment of study quality. The considerable proportion of studies without bioinformatics version numbers or sequencing data available highlights a key concern for reproducibility.
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Affiliation(s)
- Brianna Cheng
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
| | - Marcel A Behr
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
| | - Benjamin P Howden
- The Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | | | - Robyn S Lee
- Epidemiology Division, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
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20
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Chen X, He G, Lin S, Wang S, Sun F, Chen J, Zhang W. Analysis of Serial Multidrug-Resistant Tuberculosis Strains Causing Treatment Failure and Within-Host Evolution by Whole-Genome Sequencing. mSphere 2020; 5:e00884-20. [PMID: 33361124 PMCID: PMC7763549 DOI: 10.1128/msphere.00884-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/20/2020] [Indexed: 11/20/2022] Open
Abstract
The cure rate of multidrug-resistant tuberculosis (MDR-TB) is relatively low in China. The reasons for the treatment failure and within-host evolution during treatment have not been sufficiently studied. All MDR-TB patients receiving standard treatment from January 2014 to September 2016 at a designated TB Hospital in Zhejiang Province were retrospectively included and grouped according to their known treatment outcome. Clinical information was collected. Baseline strains of all patients and serial strains of treatment-failure patients were revived. Drug susceptibility tests (DSTs) of 14 drugs and single nucleotide polymorphism (SNP) analysis based on whole-genome sequencing (WGS) were performed. The genetic distance and within-host evolution were investigated based on SNPs. In total, 20 treatment failure patients and 74 patients who succeeded in treatment were included. The number of effective drugs for patients who failed treatment was no more than three. Eighteen (90.0%) treatment-failure patients were characterized by a continuous infection of the primary strain, of which 14 patients (77.8%) developed phenotypic or genotypic acquired drug resistance under ineffective treatment. Acquired resistance to amikacin and moxifloxacin (2.0 mg/ml) was detected most frequently, in 5 and 4 patients, respectively. The insufficient number of effective drugs in the combined treatment regimen was the main reason for MDR-TB treatment failure. The study emphasizes the importance of DST for second-line drugs when implementing the second-line drug regimen in MDR-TB patients. For patients with risk factors for MDR-TB, DST of second-line antituberculosis drugs should be performed at initiation of treatment. Second-line drugs should be selected based on the results of DST to avoid acquired resistance. WGS detects low-frequency resistance mutations and heterogeneous resistance with high sensitivity, which is of great significance for guiding clinical treatment and preventing acquired resistance.IMPORTANCE Few studies have focused on the reasons for the low cure rate of multidrug-resistant tuberculosis in China and within-host evolution during treatment, which is of great significance for improving clinical treatment regimens. Acquired resistance events were common during the ineffective treatment, among which resistance to amikacin and high-level moxifloxacin were the most common. The main reason for the treatment failure of MDR-TB patients was insufficient effective drugs, which may lead to higher levels of drug resistance in MDR-TB strains. Therefore, the study emphasizes the importance of DST in the development of second-line treatment regimen when there is a risk of MDR. By performing whole-genome sequencing of serial strains from patients with treatment failure, we found that WGS can detect low-frequency resistance mutations and heterogeneous resistance with high sensitivity. It is thus recommended to conduct drug susceptibility tests at the beginning of treatment and repeat the DST when the sputum bacteria remain positive.
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Affiliation(s)
- Xinchang Chen
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Guiqing He
- Department of Infectious Diseases, Wenzhou Central Hospital, Affiliated Dingli Clinical Institute of Wenzhou Medical University, Wenzhou, China
| | - Siran Lin
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Shiyong Wang
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Feng Sun
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Jiazhen Chen
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Wenhong Zhang
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Medical Molecular Virology (MOE/MOH) and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
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21
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Goig GA, Blanco S, Garcia-Basteiro AL, Comas I. Contaminant DNA in bacterial sequencing experiments is a major source of false genetic variability. BMC Biol 2020; 18:24. [PMID: 32122347 PMCID: PMC7053099 DOI: 10.1186/s12915-020-0748-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 02/11/2020] [Indexed: 12/16/2022] Open
Abstract
Background Contaminant DNA is a well-known confounding factor in molecular biology and in genomic repositories. Strikingly, analysis workflows for whole-genome sequencing (WGS) data commonly do not account for errors potentially introduced by contamination, which could lead to the wrong assessment of allele frequency both in basic and clinical research. Results We used a taxonomic filter to remove contaminant reads from more than 4000 bacterial samples from 20 different studies and performed a comprehensive evaluation of the extent and impact of contaminant DNA in WGS. We found that contamination is pervasive and can introduce large biases in variant analysis. We showed that these biases can result in hundreds of false positive and negative SNPs, even for samples with slight contamination. Studies investigating complex biological traits from sequencing data can be completely biased if contamination is neglected during the bioinformatic analysis, and we demonstrate that removing contaminant reads with a taxonomic classifier permits more accurate variant calling. We used both real and simulated data to evaluate and implement reliable, contamination-aware analysis pipelines. Conclusion As sequencing technologies consolidate as precision tools that are increasingly adopted in the research and clinical context, our results urge for the implementation of contamination-aware analysis pipelines. Taxonomic classifiers are a powerful tool to implement such pipelines.
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Affiliation(s)
- Galo A Goig
- Institute of Biomedicine of Valencia, IBV-CSIC, St. Jaume Roig 11, 46010, Valencia, Spain.
| | - Silvia Blanco
- Centro de Investigaçao em Saúde de Manhiça (CISM), Bairro Cambeve, Rua 12, Distrito da Manhiça, 1929, Maputo, Mozambique
| | - Alberto L Garcia-Basteiro
- Centro de Investigaçao em Saúde de Manhiça (CISM), Bairro Cambeve, Rua 12, Distrito da Manhiça, 1929, Maputo, Mozambique.,ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Iñaki Comas
- Institute of Biomedicine of Valencia, IBV-CSIC, St. Jaume Roig 11, 46010, Valencia, Spain.,CIBER in Epidemiology and Public Health, Madrid, Spain
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22
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Gabrielian A, Engle E, Harris M, Wollenberg K, Glogowski A, Long A, Hurt DE, Rosenthal A. Comparative analysis of genomic variability for drug-resistant strains of Mycobacterium tuberculosis: The special case of Belarus. INFECTION GENETICS AND EVOLUTION 2020; 78:104137. [DOI: 10.1016/j.meegid.2019.104137] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 12/05/2019] [Accepted: 12/06/2019] [Indexed: 01/27/2023]
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23
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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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24
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Wollenberg K, Harris M, Gabrielian A, Ciobanu N, Chesov D, Long A, Taaffe J, Hurt D, Rosenthal A, Tartakovsky M, Crudu V. A retrospective genomic analysis of drug-resistant strains of M. tuberculosis in a high-burden setting, with an emphasis on comparative diagnostics and reactivation and reinfection status. BMC Infect Dis 2020; 20:17. [PMID: 31910804 PMCID: PMC6947865 DOI: 10.1186/s12879-019-4739-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 12/27/2019] [Indexed: 12/01/2022] Open
Abstract
Background Recurrence of drug-resistant tuberculosis (DR-TB) after treatment occurs through relapse of the initial infection or reinfection by a new drug-resistant strain. Outbreaks of DR-TB in high burden regions present unique challenges in determining recurrence status for effective disease management and treatment. In the Republic of Moldova the burden of DR-TB is exceptionally high, with many cases presenting as recurrent. Methods We performed a retrospective analysis of Mycobacterium tuberculosis from Moldova to better understand the genomic basis of drug resistance and its effect on the determination of recurrence status in a high DR-burden environment. To do this we analyzed genomes from 278 isolates collected from 189 patients, including 87 patients with longitudinal samples. These pathogen genomes were sequenced using Illumina technology, and SNP panels were generated for each sample for use in phylogenetic and network analysis. Discordance between genomic resistance profiles and clinical drug-resistance test results was examined in detail to assess the possibility of mixed infection. Results There were clusters of multiple patients with 10 or fewer differences among DR-TB samples, which is evidence of person-to-person transmission of DR-TB. Analysis of longitudinally collected isolates revealed that many infections exhibited little change over time, though 35 patients demonstrated reinfection by divergent (number of differences > 10) lineages. Additionally, several same-lineage sample pairs were found to be more divergent than expected for a relapsed infection. Network analysis of the H3/4.2.1 clade found very close relationships among 61 of these samples, making differentiation of reactivation and reinfection difficult. There was discordance between genomic profile and clinical drug sensitivity test results in twelve samples, and four of these had low level (but not statistically significant) variation at DR SNPs suggesting low-level mixed infections. Conclusions Whole-genome sequencing provided a detailed view of the genealogical structure of the DR-TB epidemic in Moldova, showing that reinfection may be more prevalent than currently recognized. We also found increased evidence of mixed infection, which could be more robustly characterized with deeper levels of genomic sequencing.
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Affiliation(s)
- Kurt Wollenberg
- Office of Cyber Infrastructure & Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Michael Harris
- Office of Cyber Infrastructure & Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Andrei Gabrielian
- Office of Cyber Infrastructure & Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Nelly Ciobanu
- Microbiology and Morphology Laboratory, Institute of Phthisiopneumology, Chisnau, Moldova
| | - Dumitru Chesov
- Department of Pneumology and Allergology, Nicolae Testemitanu State University of Medicine and Pharmacy, Chisinau, Moldova.,Division of Clinical Infectious Diseases, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Alyssa Long
- Office of Cyber Infrastructure & Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jessica Taaffe
- Office of Cyber Infrastructure & Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Darrell Hurt
- Office of Cyber Infrastructure & Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Alex Rosenthal
- Office of Cyber Infrastructure & Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Michael Tartakovsky
- Office of Cyber Infrastructure & Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Valeriu Crudu
- Microbiology and Morphology Laboratory, Institute of Phthisiopneumology, Chisnau, Moldova
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25
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Green KD, Punetha A, Hou C, Garneau-Tsodikova S, Tsodikov OV. Probing the Robustness of Inhibitors of Tuberculosis Aminoglycoside Resistance Enzyme Eis by Mutagenesis. ACS Infect Dis 2019; 5:1772-1778. [PMID: 31433614 DOI: 10.1021/acsinfecdis.9b00228] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Each year, millions of people worldwide contract tuberculosis (TB), the deadliest infection. The spread of infections with drug-resistant strains of Mycobacterium tuberculosis (Mtb) that are refractory to treatment poses a major global challenge. A major cause of resistance to antitubercular drugs of last resort, aminoglycosides, is overexpression of the Eis (enhanced intracellular survival) enzyme of Mtb, which inactivates aminoglycosides by acetylating them. We showed previously that this inactivation of aminoglycosides could be overcome by our recently reported Eis inhibitors that are currently in development as potential aminoglycoside adjunctive therapeutics against drug-resistant TB. To interrogate the robustness of the Eis inhibitors, we investigated the enzymatic activity of Eis and its inhibition by Eis inhibitors from three different structural families for nine single-residue mutants of Eis, including those found in the clinic. Three engineered mutations of the substrate binding site, D26A, W36A, and F84A, abolished inhibitor binding while compromising Eis enzymatic activity 2- to 3-fold. All other Eis mutants, including clinically observed ones, were potently inhibited by at least one inhibitor. This study helps position us one step ahead of Mtb resistance to Eis inhibitors as they are being developed for TB therapy.
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Affiliation(s)
- Keith D. Green
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Ankita Punetha
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Caixia Hou
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Sylvie Garneau-Tsodikova
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Oleg V. Tsodikov
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
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26
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Cohen KA, Manson AL, Desjardins CA, Abeel T, Earl AM. Deciphering drug resistance in Mycobacterium tuberculosis using whole-genome sequencing: progress, promise, and challenges. Genome Med 2019; 11:45. [PMID: 31345251 PMCID: PMC6657377 DOI: 10.1186/s13073-019-0660-8] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Tuberculosis (TB) is a global infectious threat that is intensified by an increasing incidence of highly drug-resistant disease. Whole-genome sequencing (WGS) studies of Mycobacterium tuberculosis, the causative agent of TB, have greatly increased our understanding of this pathogen. Since the first M. tuberculosis genome was published in 1998, WGS has provided a more complete account of the genomic features that cause resistance in populations of M. tuberculosis, has helped to fill gaps in our knowledge of how both classical and new antitubercular drugs work, and has identified specific mutations that allow M. tuberculosis to escape the effects of these drugs. WGS studies have also revealed how resistance evolves both within an individual patient and within patient populations, including the important roles of de novo acquisition of resistance and clonal spread. These findings have informed decisions about which drug-resistance mutations should be included on extended diagnostic panels. From its origins as a basic science technique, WGS of M. tuberculosis is becoming part of the modern clinical microbiology laboratory, promising rapid and improved detection of drug resistance, and detailed and real-time epidemiology of TB outbreaks. We review the successes and highlight the challenges that remain in applying WGS to improve the control of drug-resistant TB through monitoring its evolution and spread, and to inform more rapid and effective diagnostic and therapeutic strategies.
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Affiliation(s)
- Keira A Cohen
- Division of Pulmonary and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MA, 21205, USA.
| | - Abigail L Manson
- Broad Institute of Harvard and Massachusetts Institute of Technology, 415 Main Street, Cambridge, MA, 02142, USA
| | - Christopher A Desjardins
- Broad Institute of Harvard and Massachusetts Institute of Technology, 415 Main Street, Cambridge, MA, 02142, USA
| | - Thomas Abeel
- Broad Institute of Harvard and Massachusetts Institute of Technology, 415 Main Street, Cambridge, MA, 02142, USA
- Delft Bioinformatics Lab, Delft University of Technology, 2628, XE, Delft, The Netherlands
| | - Ashlee M Earl
- Broad Institute of Harvard and Massachusetts Institute of Technology, 415 Main Street, Cambridge, MA, 02142, USA.
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27
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Gabrielian A, Engle E, Harris M, Wollenberg K, Juarez-Espinosa O, Glogowski A, Long A, Patti L, Hurt DE, Rosenthal A, Tartakovsky M. TB DEPOT (Data Exploration Portal): A multi-domain tuberculosis data analysis resource. PLoS One 2019; 14:e0217410. [PMID: 31120982 PMCID: PMC6532897 DOI: 10.1371/journal.pone.0217410] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 05/10/2019] [Indexed: 02/06/2023] Open
Abstract
The NIAID TB Portals Program (TBPP) established a unique and growing database repository of socioeconomic, geographic, clinical, laboratory, radiological, and genomic data from patient cases of drug-resistant tuberculosis (DR-TB). Currently, there are 2,428 total cases from nine country sites (Azerbaijan, Belarus, Moldova, Georgia, Romania, China, India, Kazakhstan, and South Africa), 1,611 (66%) of which are multidrug- or extensively-drug resistant and 1,185 (49%), 863 (36%), and 952 (39%) of which contain X-ray, computed tomography (CT) scan, and genomic data, respectively. We introduce the Data Exploration Portal (TB DEPOT, https://depot.tbportals.niaid.nih.gov) to visualize and analyze these multi-domain data. The TB DEPOT leverages the TBPP integration of clinical, socioeconomic, genomic, and imaging data into standardized formats and enables user-driven, repeatable, and reproducible analyses. It furthers the TBPP goals to provide a web-enabled analytics platform to countries with a high burden of multidrug-resistant TB (MDR-TB) but limited IT resources and inaccessible data, and enables the reusability of data, in conformity with the NIH's Findable, Accessible, Interoperable, and Reusable (FAIR) principles. TB DEPOT provides access to "analysis-ready" data and the ability to generate and test complex clinically-oriented hypotheses instantaneously with minimal statistical background and data processing skills. TB DEPOT is also promising for enhancing medical training and furnishing well annotated, hard to find, MDR-TB patient cases. TB DEPOT, as part of TBPP, further fosters collaborative research efforts to better understand drug-resistant tuberculosis and aid in the development of novel diagnostics and personalized treatment regimens.
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Affiliation(s)
- Andrei Gabrielian
- Office of Cyber Infrastructure & Computational Biology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, United States of America
| | - Eric Engle
- Office of Cyber Infrastructure & Computational Biology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, United States of America
| | - Michael Harris
- Office of Cyber Infrastructure & Computational Biology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, United States of America
| | - Kurt Wollenberg
- Office of Cyber Infrastructure & Computational Biology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, United States of America
| | - Octavio Juarez-Espinosa
- Office of Cyber Infrastructure & Computational Biology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, United States of America
| | - Alexander Glogowski
- Office of Cyber Infrastructure & Computational Biology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, United States of America
| | - Alyssa Long
- Office of Cyber Infrastructure & Computational Biology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, United States of America
| | - Lisa Patti
- Office of Cyber Infrastructure & Computational Biology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, United States of America
| | - Darrell E Hurt
- Office of Cyber Infrastructure & Computational Biology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, United States of America
| | - Alex Rosenthal
- Office of Cyber Infrastructure & Computational Biology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, United States of America
| | - Mike Tartakovsky
- Office of Cyber Infrastructure & Computational Biology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, United States of America
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28
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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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29
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Nikolayevskyy V, Niemann S, Anthony R, van Soolingen D, Tagliani E, Ködmön C, van der Werf MJ, Cirillo DM. Role and value of whole genome sequencing in studying tuberculosis transmission. Clin Microbiol Infect 2019; 25:1377-1382. [PMID: 30980928 DOI: 10.1016/j.cmi.2019.03.022] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 03/16/2019] [Accepted: 03/19/2019] [Indexed: 11/15/2022]
Abstract
BACKGROUND Tuberculosis (TB) remains a serious public health threat worldwide. Theoretically ultimate resolution of whole genome sequencing (WGS) for Mycobacterium tuberculosis complex (MTBC) strain classification makes this technology very attractive for epidemiological investigations. OBJECTIVES To summarize the evidence available in peer-reviewed publications on the role and place of WGS in detection of TB transmission. SOURCES A total of 69 peer-reviewed publications identified in Pubmed database. CONTENT Evidence from >30 publications suggests that a cut-off value of fewer than six single nucleotide polymorphisms between strains efficiently excludes cases that are not the result of recent transmission and could be used for the identification of drug-sensitive isolates involved in direct human-to-human TB transmission. Sensitivity of WGS to identify epidemiologically linked isolates is high, reaching 100% in eight studies with specificity (17%-95%) highly dependent on the settings. Drug resistance and specific phylogenetic lineages may be associated with accelerated mutation rates affecting genetic distances. WGS can be potentially used to distinguish between true relapses and re-infections but in high-incidence low-diversity settings this would require consideration of epidemiological links and minority alleles. Data from four studies looking into within-host diversity highlight a need for developing criteria for acceptance or rejection of WGS relatedness results depending on the proportion of minority alleles. IMPLICATIONS WGS will potentially allow for more targeted public health actions preventing unnecessary investigations of false clusters. Consensus on standardization of raw data quality control processing criteria, analytical pipelines and reporting language is yet to be reached.
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Affiliation(s)
- V Nikolayevskyy
- Public Health England, London, UK; Imperial College, London, UK.
| | - S Niemann
- Molecular and Experimental Mycobacteriology, National Reference Centre for Mycobacteria, Research Centre, Borstel, Germany; German Centre for Infection Research, Borstel site, Germany
| | - R Anthony
- Tuberculosis Reference Laboratory, Infectious Diseases Research, Diagnostics and Laboratory Surveillance, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - D van Soolingen
- Tuberculosis Reference Laboratory, Infectious Diseases Research, Diagnostics and Laboratory Surveillance, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - E Tagliani
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - C Ködmön
- European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - M J van der Werf
- European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - D M Cirillo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
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30
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Deciphering Within-Host Microevolution of Mycobacterium tuberculosis through Whole-Genome Sequencing: the Phenotypic Impact and Way Forward. Microbiol Mol Biol Rev 2019; 83:83/2/e00062-18. [PMID: 30918049 DOI: 10.1128/mmbr.00062-18] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The Mycobacterium tuberculosis genome is more heterogenous and less genetically stable within the host than previously thought. Currently, only limited data exist on the within-host microevolution, diversity, and genetic stability of M. tuberculosis As a direct consequence, our ability to infer M. tuberculosis transmission chains and to understand the full complexity of drug resistance profiles in individual patients is limited. Furthermore, apart from the acquisition of certain drug resistance-conferring mutations, our knowledge on the function of genetic variants that emerge within a host and their phenotypic impact remains scarce. We performed a systematic literature review of whole-genome sequencing studies of serial and parallel isolates to summarize the knowledge on genetic diversity and within-host microevolution of M. tuberculosis We identified genomic loci of within-host emerged variants found across multiple studies and determined their functional relevance. We discuss important remaining knowledge gaps and finally make suggestions on the way forward.
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31
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Chhotaray C, Tan Y, Mugweru J, Islam MM, Adnan Hameed HM, Wang S, Lu Z, Wang C, Li X, Tan S, Liu J, Zhang T. Advances in the development of molecular genetic tools for Mycobacterium tuberculosis. J Genet Genomics 2018; 45:S1673-8527(18)30114-0. [PMID: 29941353 DOI: 10.1016/j.jgg.2018.06.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Mycobacterium tuberculosis, a clinically relevant Gram-positive bacterium of great clinical relevance, is a lethal pathogen owing to its complex physiological characteristics and development of drug resistance. Several molecular genetic tools have been developed in the past few decades to study this microorganism. These tools have been instrumental in understanding how M. tuberculosis became a successful pathogen. Advanced molecular genetic tools have played a significant role in exploring the complex pathways involved in M. tuberculosis pathogenesis. Here, we review various molecular genetic tools used in the study of M. tuberculosis. Further, we discuss the applications of clustered regularly interspaced short palindromic repeat interference (CRISPRi), a novel technology recently applied in M. tuberculosis research to study target gene functions. Finally, prospective outcomes of the applications of molecular techniques in the field of M. tuberculosis genetic research are also discussed.
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Affiliation(s)
- Chiranjibi Chhotaray
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yaoju Tan
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou 510095, China
| | - Julius Mugweru
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China; Department of Biological Sciences, University of Embu, P.O Box 6 -60100, Embu, Kenya
| | - Md Mahmudul Islam
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - H M Adnan Hameed
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuai Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhili Lu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Changwei Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Xinjie Li
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou 510095, China
| | - Shouyong Tan
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou 510095, China
| | - Jianxiong Liu
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou 510095, China.
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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32
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Manson AL, Abeel T, Galagan JE, Sundaramurthi JC, Salazar A, Gehrmann T, Shanmugam SK, Palaniyandi K, Narayanan S, Swaminathan S, Earl AM. Mycobacterium tuberculosis Whole Genome Sequences From Southern India Suggest Novel Resistance Mechanisms and the Need for Region-Specific Diagnostics. Clin Infect Dis 2018; 64:1494-1501. [PMID: 28498943 PMCID: PMC5434337 DOI: 10.1093/cid/cix169] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 01/30/2017] [Indexed: 11/12/2022] Open
Abstract
Background. India is home to 25% of all tuberculosis cases and the second highest number of multidrug resistant cases worldwide. However, little is known about the genetic diversity and resistance determinants of Indian Mycobacterium tuberculosis, particularly for the primary lineages found in India, lineages 1 and 3. Methods. We whole genome sequenced 223 randomly selected M. tuberculosis strains from 196 patients within the Tiruvallur and Madurai districts of Tamil Nadu in Southern India. Using comparative genomics, we examined genetic diversity, transmission patterns, and evolution of resistance. Results. Genomic analyses revealed (11) prevalence of strains from lineages 1 and 3, (11) recent transmission of strains among patients from the same treatment centers, (11) emergence of drug resistance within patients over time, (11) resistance gained in an order typical of strains from different lineages and geographies, (11) underperformance of known resistance-conferring mutations to explain phenotypic resistance in Indian strains relative to studies focused on other geographies, and (11) the possibility that resistance arose through mutations not previously implicated in resistance, or through infections with multiple strains that confound genotype-based prediction of resistance. Conclusions. In addition to substantially expanding the genomic perspectives of lineages 1 and 3, sequencing and analysis of M. tuberculosis whole genomes from Southern India highlight challenges of infection control and rapid diagnosis of resistant tuberculosis using current technologies. Further studies are needed to fully explore the complement of diversity and resistance determinants within endemic M. tuberculosis populations.
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Affiliation(s)
| | - Thomas Abeel
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Delft Bioinformatics Lab, Delft University of Technology, The Netherlands
| | - James E Galagan
- Department of Biomedical Engineering, and.,National Emerging Infectious Diseases Laboratory, Boston University, Massachusetts
| | | | - Alex Salazar
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Delft Bioinformatics Lab, Delft University of Technology, The Netherlands
| | - Thies Gehrmann
- Delft Bioinformatics Lab, Delft University of Technology, The Netherlands
| | | | | | | | | | - Ashlee M Earl
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
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33
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Bastos HN, Osório NS, Gagneux S, Comas I, Saraiva M. The Troika Host-Pathogen-Extrinsic Factors in Tuberculosis: Modulating Inflammation and Clinical Outcomes. Front Immunol 2018; 8:1948. [PMID: 29375571 PMCID: PMC5767228 DOI: 10.3389/fimmu.2017.01948] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 12/18/2017] [Indexed: 12/30/2022] Open
Abstract
The already enormous burden caused by tuberculosis (TB) will be further aggravated by the association of this disease with modern epidemics, as human immunodeficiency virus and diabetes. Furthermore, the increasingly aging population and the wider use of suppressive immune therapies hold the potential to enhance the incidence of TB. New preventive and therapeutic strategies based on recent advances on our understanding of TB are thus needed. In particular, understanding the intricate network of events modulating inflammation in TB will help to build more effective vaccines and host-directed therapies to stop TB. This review integrates the impact of host, pathogen, and extrinsic factors on inflammation and the almost scientifically unexplored complexity emerging from the interactions between these three factors. We highlight the exciting data showing a contribution of this troika for the clinical outcome of TB and the need of incorporating it when developing novel strategies to rewire the immune response in TB.
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Affiliation(s)
- Helder Novais Bastos
- Department of Pneumology, Centro Hospitalar do São João, Porto, Portugal.,Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal.,ICVS/3B's-PT Government Associate Laboratory, Braga, Portugal
| | - Nuno S Osório
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal.,ICVS/3B's-PT Government Associate Laboratory, Braga, Portugal
| | - Sebastien Gagneux
- 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 (IBV-CSIC), Valencia, Spain.,CIBER of Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Margarida Saraiva
- i3S-Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal.,Instituto de Biologia Molecular e Celular (IBMC), University of Porto, Porto, Portugal
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34
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Population implications of the use of bedaquiline in people with extensively drug-resistant tuberculosis: are fears of resistance justified? THE LANCET. INFECTIOUS DISEASES 2017; 17:e429-e433. [DOI: 10.1016/s1473-3099(17)30299-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 04/10/2017] [Accepted: 04/11/2017] [Indexed: 11/24/2022]
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35
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Tuberculosis in Swiss captive Asian elephants: microevolution of Mycobacterium tuberculosis characterized by multilocus variable-number tandem-repeat analysis and whole-genome sequencing. Sci Rep 2017; 7:14647. [PMID: 29116204 PMCID: PMC5676744 DOI: 10.1038/s41598-017-15278-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 10/24/2017] [Indexed: 11/08/2022] Open
Abstract
Zoonotic tuberculosis is a risk for human health, especially when animals are in close contact with humans. Mycobacterium tuberculosis was cultured from several organs, including lung tissue and gastric mucosa, of three captive elephants euthanized in a Swiss zoo. The elephants presented weight loss, weakness and exercise intolerance. Molecular characterization of the M. tuberculosis isolates by spoligotyping revealed an identical profile, suggesting a single source of infection. Multilocus variable-number of tandem-repeat analysis (MLVA) elucidated two divergent populations of bacteria and mixed infection in one elephant, suggesting either different transmission chains or prolonged infection over time. A total of eight M. tuberculosis isolates were subjected to whole-genome sequence (WGS) analysis, confirming a single source of infection and indicating the route of transmission between the three animals. Our findings also show that the methods currently used for epidemiological investigations of M. tuberculosis infections should be carefully applied on isolates from elephants. Moreover the importance of multiple sampling and analysis of within-host mycobacterial clonal populations for investigations of transmission is demonstrated.
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36
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Rosenthal A, Gabrielian A, Engle E, Hurt DE, Alexandru S, Crudu V, Sergueev E, Kirichenko V, Lapitskii V, Snezhko E, Kovalev V, Astrovko A, Skrahina A, Taaffe J, Harris M, Long A, Wollenberg K, Akhundova I, Ismayilova S, Skrahin A, Mammadbayov E, Gadirova H, Abuzarov R, Seyfaddinova M, Avaliani Z, Strambu I, Zaharia D, Muntean A, Ghita E, Bogdan M, Mindru R, Spinu V, Sora A, Ene C, Vashakidze S, Shubladze N, Nanava U, Tuzikov A, Tartakovsky M. The TB Portals: an Open-Access, Web-Based Platform for Global Drug-Resistant-Tuberculosis Data Sharing and Analysis. J Clin Microbiol 2017; 55:3267-3282. [PMID: 28904183 PMCID: PMC5654911 DOI: 10.1128/jcm.01013-17] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 09/01/2017] [Indexed: 11/20/2022] Open
Abstract
The TB Portals program is an international consortium of physicians, radiologists, and microbiologists from countries with a heavy burden of drug-resistant tuberculosis working with data scientists and information technology professionals. Together, we have built the TB Portals, a repository of socioeconomic/geographic, clinical, laboratory, radiological, and genomic data from patient cases of drug-resistant tuberculosis backed by shareable, physical samples. Currently, there are 1,299 total cases from five country sites (Azerbaijan, Belarus, Moldova, Georgia, and Romania), 976 (75.1%) of which are multidrug or extensively drug resistant and 38.2%, 51.9%, and 36.3% of which contain X-ray, computed tomography (CT) scan, and genomic data, respectively. The top Mycobacterium tuberculosis lineages represented among collected samples are Beijing, T1, and H3, and single nucleotide polymorphisms (SNPs) that confer resistance to isoniazid, rifampin, ofloxacin, and moxifloxacin occur the most frequently. These data and samples have promoted drug discovery efforts and research into genomics and quantitative image analysis to improve diagnostics while also serving as a valuable resource for researchers and clinical providers. The TB Portals database and associated projects are continually growing, and we invite new partners and collaborations to our initiative. The TB Portals data and their associated analytical and statistical tools are freely available at https://tbportals.niaid.nih.gov/.
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Affiliation(s)
- Alex Rosenthal
- Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, USA
| | - Andrei Gabrielian
- Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, USA
| | - Eric Engle
- Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, USA
| | - Darrell E Hurt
- Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, USA
| | - Sofia Alexandru
- Phthysiopneumology Institute, Ministry of Health, Chisinau, Republic of Moldova
| | - Valeriu Crudu
- Phthysiopneumology Institute, Ministry of Health, Chisinau, Republic of Moldova
| | - Eugene Sergueev
- United Institute of Informatics Problems, National Academy of Sciences of Belarus, Minsk, Republic of Belarus
| | - Valery Kirichenko
- United Institute of Informatics Problems, National Academy of Sciences of Belarus, Minsk, Republic of Belarus
| | - Vladzimir Lapitskii
- United Institute of Informatics Problems, National Academy of Sciences of Belarus, Minsk, Republic of Belarus
| | - Eduard Snezhko
- United Institute of Informatics Problems, National Academy of Sciences of Belarus, Minsk, Republic of Belarus
| | - Vassili Kovalev
- United Institute of Informatics Problems, National Academy of Sciences of Belarus, Minsk, Republic of Belarus
| | - Andrei Astrovko
- Republican Scientific and Practical Centre of Pulmonology and Tuberculosis, Ministry of Health, Minsk, Republic of Belarus
| | - Alena Skrahina
- Republican Scientific and Practical Centre of Pulmonology and Tuberculosis, Ministry of Health, Minsk, Republic of Belarus
| | - Jessica Taaffe
- Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, USA
| | - Michael Harris
- Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, USA
| | - Alyssa Long
- Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, USA
| | - Kurt Wollenberg
- Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, USA
| | - Irada Akhundova
- Scientific Research Institute of Lung Diseases, Ministry of Health, Baku, Republic of Azerbaijan
| | - Sharafat Ismayilova
- Scientific Research Institute of Lung Diseases, Ministry of Health, Baku, Republic of Azerbaijan
| | | | - Elcan Mammadbayov
- Scientific Research Institute of Lung Diseases, Ministry of Health, Baku, Republic of Azerbaijan
| | - Hagigat Gadirova
- Scientific Research Institute of Lung Diseases, Ministry of Health, Baku, Republic of Azerbaijan
| | - Rafik Abuzarov
- Scientific Research Institute of Lung Diseases, Ministry of Health, Baku, Republic of Azerbaijan
| | - Mehriban Seyfaddinova
- Scientific Research Institute of Lung Diseases, Ministry of Health, Baku, Republic of Azerbaijan
| | - Zaza Avaliani
- The National Center for Tuberculosis and Lung Diseases, Tbilisi, Republic of Georgia
| | - Irina Strambu
- Marius Nasta Pneumophtisiology Institute, Ministry of Health, Bucharest, Romania
| | - Dragos Zaharia
- Marius Nasta Pneumophtisiology Institute, Ministry of Health, Bucharest, Romania
| | - Alexandru Muntean
- Marius Nasta Pneumophtisiology Institute, Ministry of Health, Bucharest, Romania
| | - Eugenia Ghita
- Marius Nasta Pneumophtisiology Institute, Ministry of Health, Bucharest, Romania
| | - Miron Bogdan
- Marius Nasta Pneumophtisiology Institute, Ministry of Health, Bucharest, Romania
| | - Roxana Mindru
- Marius Nasta Pneumophtisiology Institute, Ministry of Health, Bucharest, Romania
| | - Victor Spinu
- Marius Nasta Pneumophtisiology Institute, Ministry of Health, Bucharest, Romania
| | - Alexandra Sora
- Marius Nasta Pneumophtisiology Institute, Ministry of Health, Bucharest, Romania
| | - Catalina Ene
- Marius Nasta Pneumophtisiology Institute, Ministry of Health, Bucharest, Romania
| | - Sergo Vashakidze
- The National Center for Tuberculosis and Lung Diseases, Tbilisi, Republic of Georgia
| | - Natalia Shubladze
- The National Center for Tuberculosis and Lung Diseases, Tbilisi, Republic of Georgia
| | - Ucha Nanava
- The National Center for Tuberculosis and Lung Diseases, Tbilisi, Republic of Georgia
| | - Alexander Tuzikov
- United Institute of Informatics Problems, National Academy of Sciences of Belarus, Minsk, Republic of Belarus
| | - Michael Tartakovsky
- Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, USA
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Tarashi S, Fateh A, Mirsaeidi M, Siadat SD, Vaziri F. Mixed infections in tuberculosis: The missing part in a puzzle. Tuberculosis (Edinb) 2017; 107:168-174. [PMID: 29050766 DOI: 10.1016/j.tube.2017.09.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 09/05/2017] [Accepted: 09/13/2017] [Indexed: 11/26/2022]
Abstract
The mixed strains infection phenomenon is a major problem posing serious challenges in control of tuberculosis (TB). In patients with mixed infection, several different strains of Mycobacterium tuberculosis can be isolated simultaneously. Although different genotyping methods and various molecular approaches can be employed for detection of mixed infection in clinical samples, the MIRU-VNTR technique is more sensitive with higher discriminative power than many widely used techniques. Furthermore, the recent introduction of whole genome sequencing (WGS) promises to reveal more details about mixed infection with high resolution. WGS has been used for detection of mixed infection with high sensitivity and discriminatory, but the technology is currently limited to developed countries. Mixed infection may involve strains with different susceptibility patterns, which may alter the treatment outcome. In this report, we review the current concepts of mixed strains infection and also infection involving strains with a different susceptibility pattern in TB. We evaluate the importance of identifying mixed infection for diagnosis as well as treatment and highlight the accuracy and clinical utility of direct genotyping of clinical specimens.
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Affiliation(s)
- Samira Tarashi
- 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
| | - Mehdi Mirsaeidi
- Division of Pulmonary and Critical Care, University of Miami, Miami, FL, USA
| | - 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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38
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Protecting Pyrazinamide, a Priority for Improving Outcomes in Multidrug-Resistant Tuberculosis Treatment. Antimicrob Agents Chemother 2017; 61:61/6/e00258-17. [PMID: 28539498 DOI: 10.1128/aac.00258-17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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39
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Manson AL, Cohen KA, Abeel T, Desjardins CA, Armstrong DT, Barry CE, Brand J, Chapman SB, Cho SN, Gabrielian A, Gomez J, Jodals AM, Joloba M, Jureen P, Lee JS, Malinga L, Maiga M, Nordenberg D, Noroc E, Romancenco E, Salazar A, Ssengooba W, Velayati AA, Winglee K, Zalutskaya A, Via LE, Cassell GH, Dorman SE, Ellner J, Farnia P, Galagan JE, Rosenthal A, Crudu V, Homorodean D, Hsueh PR, Narayanan S, Pym AS, Skrahina A, Swaminathan S, Van der Walt M, Alland D, Bishai WR, Cohen T, Hoffner S, Birren BW, Earl AM. Genomic analysis of globally diverse Mycobacterium tuberculosis strains provides insights into the emergence and spread of multidrug resistance. Nat Genet 2017; 49:395-402. [PMID: 28092681 PMCID: PMC5402762 DOI: 10.1038/ng.3767] [Citation(s) in RCA: 169] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 12/14/2016] [Indexed: 11/09/2022]
Abstract
Multidrug-resistant tuberculosis (MDR-TB), caused by drug resistant strains of Mycobacterium tuberculosis, is an increasingly serious problem worldwide. In this study, we examined a dataset of 5,310 M. tuberculosis whole genome sequences from five continents. Despite great diversity with respect to geographic point of isolation, genetic background and drug resistance, patterns of drug resistance emergence were conserved globally. We have identified harbinger mutations that often precede MDR. In particular, the katG S315T mutation, conferring resistance to isoniazid, overwhelmingly arose before rifampicin resistance across all lineages, geographic regions, and time periods. Molecular diagnostics that include markers for rifampicin resistance alone will be insufficient to identify pre-MDR strains. Incorporating knowledge of pre-MDR polymorphisms, particularly katG S315, into molecular diagnostics will enable targeted treatment of patients with pre-MDR-TB to prevent further development of MDR-TB.
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Affiliation(s)
- Abigail L Manson
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Keira A Cohen
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,KwaZulu-Natal Research Institute for TB and HIV (K-RITH), Durban, South Africa.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Thomas Abeel
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Delft Bioinformatics Lab, Delft University of Technology, Delft, the Netherlands
| | | | - Derek T Armstrong
- Center for Tuberculosis Research, Johns Hopkins University, Baltimore, Maryland, USA
| | - Clifton E Barry
- National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, USA
| | - Jeannette Brand
- Medical Research Council, TB Platform, Pretoria, South Africa
| | | | - Sinéad B Chapman
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Sang-Nae Cho
- International Tuberculosis Research Center, Changwon and Department of Microbiology, Yonsei University College of Medicine, Seoul, South Korea
| | - Andrei Gabrielian
- Office of Cyber Infrastructure and Computational Biology, National Institutes of Health, Rockville, Maryland, USA
| | - James Gomez
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Andreea M Jodals
- Clinical Hospital of Pneumology Leon Daniello, Cluj Napoca, Romania
| | - Moses Joloba
- Department of Medical Microbiology, Mycobacteriology Laboratory, Makerere University, Kampala, Uganda
| | | | - Jong Seok Lee
- International Tuberculosis Research Center, Changwon and Department of Microbiology, Yonsei University College of Medicine, Seoul, South Korea
| | | | - Mamoudou Maiga
- University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | | | - Ecaterina Noroc
- Microbiology and Morphology Laboratory, Phthisiopneumology Institute, Chisinau, Moldova
| | - Elena Romancenco
- Microbiology and Morphology Laboratory, Phthisiopneumology Institute, Chisinau, Moldova
| | - Alex Salazar
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Delft Bioinformatics Lab, Delft University of Technology, Delft, the Netherlands
| | - Willy Ssengooba
- Department of Medical Microbiology, Mycobacteriology Laboratory, Makerere University, Kampala, Uganda
| | - A A Velayati
- Mycobacteriology Research Centre, National Research Institute of Tuberculosis and Lung Disease (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Kathryn Winglee
- Center for Tuberculosis Research, Johns Hopkins University, Baltimore, Maryland, USA
| | - Aksana Zalutskaya
- Republican Research and Practical Centre for Pulmonology and Tuberculosis, Minsk, Belarus
| | - Laura E Via
- National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, USA
| | - Gail H Cassell
- Department of Global Health and Social Medicine, Harvard Medical School, Division of Global Health Equity, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Susan E Dorman
- Center for Tuberculosis Research, Johns Hopkins University, Baltimore, Maryland, USA
| | - Jerrold Ellner
- Section of Infectious Diseases, Boston Medical Center, Boston, Massachusetts, USA
| | - Parissa Farnia
- Mycobacteriology Research Centre, National Research Institute of Tuberculosis and Lung Disease (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - James E Galagan
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Department of Biomedical Engineering and Microbiology, Boston University, Boston, Massachusetts, USA
| | - Alex Rosenthal
- Office of Cyber Infrastructure and Computational Biology, National Institutes of Health, Rockville, Maryland, USA
| | - Valeriu Crudu
- Microbiology and Morphology Laboratory, Phthisiopneumology Institute, Chisinau, Moldova
| | | | - Po-Ren Hsueh
- National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | | | - Alexander S Pym
- KwaZulu-Natal Research Institute for TB and HIV (K-RITH), Durban, South Africa
| | - Alena Skrahina
- Republican Research and Practical Centre for Pulmonology and Tuberculosis, Minsk, Belarus
| | | | | | - David Alland
- Rutgers-New Jersey Medical School, Newark, New Jersey, USA
| | - William R Bishai
- KwaZulu-Natal Research Institute for TB and HIV (K-RITH), Durban, South Africa.,Center for Tuberculosis Research, Johns Hopkins University, Baltimore, Maryland, USA
| | - Ted Cohen
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA.,Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | | | - Bruce W Birren
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Ashlee M Earl
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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