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Kho S, Seung KJ, Huerga H, Bastard M, Khan PY, Mitnick CD, Rich ML, Islam S, Zhizhilashvili D, Yeghiazaryan L, Nikolenko EN, Zarli K, Adnan S, Salahuddin N, Ahmed S, Vargas ZHR, Bekele A, Shaimerdenova A, Tamirat M, Gelin A, Vilbrun SC, Hewison C, Khan U, Franke M. Sputum culture reversion in longer treatments with bedaquiline, delamanid, and repurposed drugs for drug-resistant tuberculosis. Nat Commun 2024; 15:3927. [PMID: 38724531 PMCID: PMC11082252 DOI: 10.1038/s41467-024-48077-8] [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: 09/13/2023] [Accepted: 04/19/2024] [Indexed: 05/12/2024] Open
Abstract
Sputum culture reversion after conversion is an indicator of tuberculosis (TB) treatment failure. We analyze data from the endTB multi-country prospective observational cohort (NCT03259269) to estimate the frequency (primary endpoint) among individuals receiving a longer (18-to-20 month) regimen for multidrug- or rifampicin-resistant (MDR/RR) TB who experienced culture conversion. We also conduct Cox proportional hazard regression analyses to identify factors associated with reversion, including comorbidities, previous treatment, cavitary disease at conversion, low body mass index (BMI) at conversion, time to conversion, and number of likely-effective drugs. Of 1,286 patients, 54 (4.2%) experienced reversion, a median of 173 days (97-306) after conversion. Cavitary disease, BMI < 18.5, hepatitis C, prior treatment with second-line drugs, and longer time to initial culture conversion were positively associated with reversion. Reversion was uncommon. Those with cavitary disease, low BMI, hepatitis C, prior treatment with second-line drugs, and in whom culture conversion is delayed may benefit from close monitoring following conversion.
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Affiliation(s)
- Sooyeon Kho
- Division of Global Health Equity, Brigham and Women's Hospital, Boston, MA, USA
| | - Kwonjune J Seung
- Division of Global Health Equity, Brigham and Women's Hospital, Boston, MA, USA
- Partners in Health, 800 Boylston Street Suite 300, Boston, MA, USA
| | | | | | - Palwasha Y Khan
- Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK
- Interactive Research and Development Global, Singapore, Singapore
| | - Carole D Mitnick
- Division of Global Health Equity, Brigham and Women's Hospital, Boston, MA, USA
- Partners in Health, 800 Boylston Street Suite 300, Boston, MA, USA
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, USA
| | - Michael L Rich
- Division of Global Health Equity, Brigham and Women's Hospital, Boston, MA, USA
- Partners in Health, 800 Boylston Street Suite 300, Boston, MA, USA
| | | | | | | | | | - Khin Zarli
- Médecins sans Frontières, Yangon, Myanmar
| | - Sana Adnan
- Indus Hospital and Health Network, Karachi, Pakistan
| | | | - Saman Ahmed
- Interactive Research and Development, Karachi, Pakistan
| | | | - Amsalu Bekele
- Department of Internal Medicine, Tikur Anbessa Specialized Hospital and Addis Ababa University, College of Health Sciences, Addis Ababa, Ethiopia
| | | | | | | | - Stalz Charles Vilbrun
- Haitian Group for the Study of Kaposi's Sarcoma and Opportunistic Infections (GHESKIO), Port-au-Prince, Haiti
| | | | - Uzma Khan
- Interactive Research and Development Global, Singapore, Singapore
| | - Molly Franke
- Partners in Health, 800 Boylston Street Suite 300, Boston, MA, USA.
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, USA.
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2
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Salari N, Kanjoori AH, Hosseinian-Far A, Hasheminezhad R, Mansouri K, Mohammadi M. Global prevalence of drug-resistant tuberculosis: a systematic review and meta-analysis. Infect Dis Poverty 2023; 12:57. [PMID: 37231463 DOI: 10.1186/s40249-023-01107-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/16/2023] [Indexed: 05/27/2023] Open
Abstract
BACKGROUND Tuberculosis is a bacterial infectious disease, which affects different parts of a human body, mainly lungs and can lead to the patient's death. The aim of this study is to investigate the global prevalence of drug-resistant tuberculosis using a systematic review and meta-analysis. METHODS In this study, the PubMed, Scopus, Web of Science, Embase, ScienceDirect and Google Scholar repositories were systematically searched to find studies reporting the global prevalence of drug-resistant tuberculosis. The search did not entail a lower time limit, and articles published up until August 2022 were considered. Random effects model was used to perform the analysis. The heterogeneity of the studies was examined with the I2 test. Data analysis was conducted within the Comprehensive Meta-Analysis software. RESULTS In the review of 148 studies with a sample size of 318,430 people, the I2 index showed high heterogeneity (I2 = 99.6), and accordingly random effects method was used to analyze the results. Publication bias was also examined using the Begg and Mazumdar correlation test which indicated the existence of publication bias in the studies (P = 0.008). According to our meta-analysis, the global pooled prevalence of multi-drug resistant TB is 11.6% (95% CI: 9.1-14.5%). CONCLUSIONS The global prevalence of drug-resistant tuberculosis was found to be very high, thus health authorities should consider ways to control and manage the disease to prevent a wider spread of tuberculosis and potentially subsequent deaths.
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Affiliation(s)
- Nader Salari
- Department of Biostatistics, School of Health, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Sleep Disorders Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Amir Hossein Kanjoori
- Student Research Committee, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Amin Hosseinian-Far
- Department of Business Systems & Operations, University of Northampton, Northampton, UK
| | - Razie Hasheminezhad
- Student Research Committee, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Kamran Mansouri
- Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Masoud Mohammadi
- Cellular and Molecular Research Center, Gerash University of Medical Sciences, Gerash, Iran.
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3
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Wyllie D, Do T, Myers R, Nikolayevskyy V, Crook D, Peto T, Alexander E, Robinson E, Walker AS, Campbell C, Smith EG. M. tuberculosis microvariation is common and is associated with transmission: analysis of three years prospective universal sequencing in England. J Infect 2022; 85:31-39. [PMID: 35595102 DOI: 10.1016/j.jinf.2022.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 01/07/2022] [Accepted: 05/12/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND The prevalence, association with disease status, and public health impact of infection with mixtures of M. tuberculosis strains is unclear, in part due to limitations of existing methods for detecting mixed infections. METHODS We developed an algorithm to identify mixtures of M. tuberculosis strains using next generation sequencing data, assessing performance using simulated sequences. We identified mixed M. tuberculosis strains when there was at least one mixed nucleotide position, and where both the mixture's components were present in similar isolates from other individuals, compatible with transmission of the component strains. We determined risk factors for mixed infection among isolations of M. tuberculosis in England using logistic regression. We used survival analyses to assess the association between mixed infection and putative transmission. FINDINGS 6,560 isolations of TB were successfully sequenced in England 2016-2018. Of 3,691 (56%) specimens for which similar sequences had been isolated from at least two other individuals, 341 (9.2%) were mixed. Mixed infection was more common in lineages other than Lineage 4. Among the 1,823 individuals with pulmonary infection with Lineage 4 M. tuberculosis, mixed infection was associated with significantly increased risk of subsequent isolation of closely related organisms from a different individual (HR 1.43, 95% CI 1.05,1.94), indicative of transmission. INTERPRETATION Mixtures of transmissible strains occur in at least 5% of tuberculosis infections in England; when present in pulmonary disease, such mixtures are associated with an increased risk of tuberculosis transmission. FUNDING Public Health England; NIHR Health Protection Research Units; European Union.
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Affiliation(s)
- David Wyllie
- The National Institute for Health Research, Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, UK; PHE Field Service, Public Health England, Forvie Site, Addenbrookes' Hospital, Cambridge.
| | - Trien Do
- The National Institute for Health Research, Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, UK
| | - Richard Myers
- Infectious Disease Bioinformatics, National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Vlad Nikolayevskyy
- Public Health England National Mycobacteriology Reference Service, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Derrick Crook
- The National Institute for Health Research, Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, UK; National Institute for Health Research Biomedical Research Centre, Oxford, UK; Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Tim Peto
- The National Institute for Health Research, Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, UK; National Institute for Health Research Biomedical Research Centre, Oxford, UK; Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Eliza Alexander
- Public Health England National Mycobacteriology Reference Service, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Esther Robinson
- Public Health England National Mycobacteriology Reference Service, 61 Colindale Avenue, London NW9 5EQ, UK
| | - A Sarah Walker
- The National Institute for Health Research, Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, UK; National Institute for Health Research Biomedical Research Centre, Oxford, UK; Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Colin Campbell
- Tuberculosis Surveillance Unit, National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
| | - E Grace Smith
- Public Health England National Mycobacteriology Reference Service, 61 Colindale Avenue, London NW9 5EQ, UK
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4
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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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5
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Zhu J, Bao Z, Xie Y, Werngren J, Hu Y, Davies Forsman L, Bruchfeld J, Hoffner S. Additional drug resistance for Mycobacterium tuberculosis during turnaround time for drug-susceptibility testing in China: A multicenter observational cohort study. Int J Infect Dis 2021; 108:81-88. [PMID: 33862209 DOI: 10.1016/j.ijid.2021.04.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 04/07/2021] [Accepted: 04/08/2021] [Indexed: 10/21/2022] Open
Abstract
BACKGROUND Although phenotypic drug susceptibility testing (DST) of Mycobacterium tuberculosis (Mtb) takes up to 6-8 weeks, little is known about how drug susceptibility is affected during this period. METHODS We performed a prospective cohort study to investigate the development of drug resistance (DR) during turnaround time (TAT), including 359 pulmonary tuberculosis (PTB) patients with a baseline DST result of an Mtb isolate collected at TB diagnosis and a follow-up DST result of an Mtb isolate collected when baseline DST result was available between 2013 and 2018. Whole-genome sequencing (WGS) was used to differentiate between acquired drug resistance, exogenous reinfection, and mixed infection. RESULTS Among the studied patients, during TAT for DST, 116 (32.3%) developed DR to four first-line drugs (rifampicin, isoniazid, pyrazinamide, ethambutol). Among 116 pairs of isolates included for WGS, 21 pairs were classified as acquired drug resistance with single nucleotide polymorphisms (SNPs) differences less than 12. Four pairs with an intermediate SNPs differences displayed minor differences in related genotypes and were assessed as mixed infection. The remaining 91 pairs had high SNPs differences consistent with exogenous reinfection. CONCLUSIONS The exogenous reinfection of drug-resistant strains played a vital role in the development of DR of Mtb isolates during TAT for DST, highlighting the need for both rapid DST methods and improved infection control.
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Affiliation(s)
- Jiahui Zhu
- School of Public Health and Key Laboratory of Public Health Safety, Fudan University, Shanghai, China
| | - Ziwei Bao
- The Fifth People's Hospital of Suzhou, Infectious Disease Hospital Affiliated to Soochow University, Suzhou, China
| | - Yan Xie
- Department Tuberculosis Control, Zigong Center for Disease Control and Prevention, Zigong, China
| | - Jim Werngren
- Department of Microbiology, The Public Health Agency of Sweden, Stockholm, Sweden
| | - Yi Hu
- School of Public Health and Key Laboratory of Public Health Safety, Fudan University, Shanghai, China.
| | - Lina Davies Forsman
- Department of Infectious Disease, Karolinska University Hospital, Stockholm, Sweden; Department of Medicine, Division of Infectious Diseases, Karolinska Institutet Solna, Sweden
| | - Judith Bruchfeld
- Department of Infectious Disease, Karolinska University Hospital, Stockholm, Sweden; Department of Medicine, Division of Infectious Diseases, Karolinska Institutet Solna, Sweden
| | - Sven Hoffner
- Department of Global Public Health, Karolinska Institute, Stockholm, Sweden
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6
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Byrne AS, Goudreau A, Bissonnette N, Shamputa IC, Tahlan K. Methods for Detecting Mycobacterial Mixed Strain Infections-A Systematic Review. Front Genet 2020; 11:600692. [PMID: 33408740 PMCID: PMC7779811 DOI: 10.3389/fgene.2020.600692] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 11/19/2020] [Indexed: 12/22/2022] Open
Abstract
Mixed strain infection (MSI) refers to the concurrent infection of a susceptible host with multiple strains of a single pathogenic species. Known to occur in humans and animals, MSIs deserve special consideration when studying transmission dynamics, evolution, and treatment of mycobacterial diseases, notably tuberculosis in humans and paratuberculosis (or Johne's disease) in ruminants. Therefore, a systematic review was conducted to examine how MSIs are defined in the literature, how widespread the phenomenon is across the host species spectrum, and to document common methods used to detect such infections. Our search strategy identified 121 articles reporting MSIs in both humans and animals, the majority (78.5%) of which involved members of the Mycobacterium tuberculosis complex, while only a few (21.5%) examined non-tuberculous mycobacteria (NTM). In addition, MSIs exist across various host species, but most reports focused on humans due to the extensive amount of work done on tuberculosis. We reviewed the strain typing methods that allowed for MSI detection and found a few that were commonly employed but were associated with specific challenges. Our review notes the need for standardization, as some highly discriminatory methods are not adapted to distinguish between microevolution of one strain and concurrent infection with multiple strains. Further research is also warranted to examine the prevalence of NTM MSIs in both humans and animals. In addition, it is envisioned that the accurate identification and a better understanding of the distribution of MSIs in the future will lead to important information on the epidemiology and pathophysiology of mycobacterial diseases.
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Affiliation(s)
| | - Alex Goudreau
- Science & Health Sciences Librarian, University of New Brunswick, Saint John, NB, Canada
| | - Nathalie Bissonnette
- Sherbrooke Research and Development Center, Agriculture and Agri-Food Canada, Sherbrooke, QC, Canada
| | - Isdore Chola Shamputa
- Department of Nursing & Health Sciences, University of New Brunswick, Saint John, NB, Canada
| | - Kapil Tahlan
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada
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7
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Nikolayevskyy V, Balabanova Y, Kontsevaya I, Ignatyeva O, Skenders G, Vasiliauskiene E, Bockel DV, Drobniewski F. Biomarkers of treatment success in fully sensitive pulmonary tuberculosis patients: a multicenter longitudinal study. Biomark Med 2020; 14:1439-1452. [PMID: 33140661 DOI: 10.2217/bmm-2020-0246] [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: 11/21/2022] Open
Abstract
Aim: Novel biomarkers that are able to accurately monitor tuberculosis (TB) treatment effectiveness are needed to adjust therapy and identify a need for a regimen change. Materials & methods: In our study, conducted on a cohort comprising 100 pulmonary TB patients, we analyzed the role of plasma cytokines and Toll-like receptors expression as biomarkers of treatment response. Results: Changes in toll-interacting protein (TOLLIP) and lymphocyte antigen 96 (LY96) gene expression as well as nine cytokine levels over the first 2 months were significantly associated with successful treatment outcome. Successful treatment was associated with higher serum concentration of Toll-like receptor-2. Conclusion: Our results suggest that differential expression of specific effector molecules and dynamics of selected cytokines may help to identify those responding to TB treatment early.
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Affiliation(s)
- Vladyslav Nikolayevskyy
- Imperial College London, Du Cane Road, London W12 0NN, UK.,Public Health England, 61 Colindale Ave, London NW9 5EQ, UK
| | - Yanina Balabanova
- Imperial College London, Du Cane Road, London W12 0NN, UK.,Bayer AG, 178 Muelerstrasse, Berlin D-13353, Germany
| | - Irina Kontsevaya
- Imperial College London, Du Cane Road, London W12 0NN, UK.,Research Center Borstel, Parkallee 1-40, Borstel D-23845, Germany.,N.V. Postnikov Samara Region Clinical Tuberculosis Dispensary, 154 Novo-Sadovaya Street, Samara 443068, Russian Federation
| | - Olga Ignatyeva
- N.V. Postnikov Samara Region Clinical Tuberculosis Dispensary, 154 Novo-Sadovaya Street, Samara 443068, Russian Federation.,Medical University Reaviz, 100v Chkalova Street, Samara 443030, Russian Federation
| | - Girts Skenders
- Riga East University Hospital, Centre of Tuberculosis & Lung Diseases, 68 Lielvardes Street, Riga LV-1006, Latvia
| | - Edita Vasiliauskiene
- Department of Physiology, Biochemistry, Microbiology & Laboratory Medicine, Faculty of Medicine, Institute of Biomedical Sciences, Vilnius University, 21/27 M. K. Ciurlionio, Vilnius LT-03101, Lithuania.,Centre of Laboratory Medicine, Tuberculosis Laboratory, Vilnius University Hospital Santaros Klinikos, Santariskiu Street 2, Vilnius LT-08661, Lithuania
| | - David van Bockel
- The Kirby Institute for Infection & Immunity in Society, University of New South Wales, High Street, NSW 2052 Sydney, Australia
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8
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Application of MIRU-VNTR on smear slides: a shortcut for detection of polyclonal infections in tuberculosis patients. Mol Biol Rep 2020; 47:1681-1689. [PMID: 31939062 DOI: 10.1007/s11033-020-05257-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 01/08/2020] [Indexed: 01/20/2023]
Abstract
Mixed (polyclonal) infections are one of the main problems in tuberculosis (TB) management. The best available method for detecting polyclonal infections in TB is mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR). According to multiple studies, MIRU-VNTR method can be applied to detect TB-related polyclonal infections in sputum samples or cultures. Setup of MIRU-VNTR on smear slides can be an efficient approach, regardless of the limitations of cultures and sputum samples in many laboratories. The present study aimed at investigating the diagnostic potential of MIRU-VNTR on smear slides in detecting mixed infections. Ziehl-Neelsen-stained microscopic slides were prepared from 14 clinical specimens. For amplifying 24 MIRU-VNTR loci, PCR assay was performed on the smear slides, clinical specimens, and cultures. Based on the 24-locus MIRU-VNTR analysis, polyclonal infections were reported in 42.85% of smear slides, while the corresponding rate was estimated at 57.1% (8/14) in the clinical samples. In the corresponding cultures, the rate of mixed infection was 7.14% (1/14). Use of smear slides can be a safe option for transferring clinical specimens between environmental and reference laboratories. Considering their significant impact on TB treatment, it is essential to diagnose mixed infections in low-resource countries with a high prevalence of mixed infections. The present findings show that direct MIRU-VNTR on smear slides can be conveniently used for the detection of mixed infections.
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9
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Nikolayevskyy V, Kontsevaya I, Nikolaevskaya E, Surkova E, Samchenko S, Esipenko S. Diagnostic performance and impact of routinely implemented Xpert® MTB/RIF assay in a setting of high incidence of drug-resistant TB in Odessa Oblast, Ukraine. Clin Microbiol Infect 2019; 25:1040.e1-1040.e6. [DOI: 10.1016/j.cmi.2018.12.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 12/03/2018] [Accepted: 12/08/2018] [Indexed: 01/07/2023]
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10
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Konstantynovska O, Rekrotchuk M, Hrek I, Rohozhyn A, Rudova N, Poteiko P, Gerilovych A, Bortz E, Solodiankin O. Severe Clinical Outcomes of Tuberculosis in Kharkiv Region, Ukraine, Are Associated with Beijing Strains of Mycobacterium tuberculosis. Pathogens 2019; 8:pathogens8020075. [PMID: 31185670 PMCID: PMC6631893 DOI: 10.3390/pathogens8020075] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 06/02/2019] [Accepted: 06/06/2019] [Indexed: 11/16/2022] Open
Abstract
Genotypic variation in Beijing lineages of Mycobacterium tuberculosis (MTB), the causative agent of tuberculosis (TB), has been associated with hyper virulence and the spread of extensively and multiple drug (X/MDR) resistant MTB strains in Eastern Europe, Central Asia, and East Asia. The clinical outcomes of 215 new cases of TB among the population of the Kharkiv region of Eastern Ukraine were analyzed to uncover factors associated with severe infection. Infecting MTB strains were profiled by 5 locus exact tandem repeats (ETRs) and 15 locus mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) genotyping. Among diverse MTB genotypes discovered in Ukraine, the Beijing genotype (MIRU-VNTR 42425) was significantly associated with risk factors for severe outcomes of disease in the study population, including TB/HIV co-infection and treatment failure. Strain replacement (superinfection) was observed in 10 patients, suggesting repeated exposure to novel MTB strains in hospital or community settings. Inclusion of MTB genotyping data may identify at-risk patients and improve treatment adherence to prevent X/MDR development for effective public health response against tuberculosis in Ukraine.
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Affiliation(s)
| | - Mariia Rekrotchuk
- National Scientific Center Institute of Experimental and Clinical Veterinary Medicine (NSC IECVM), 61023 Kharkiv, Ukraine.
| | - Ivan Hrek
- Kharkiv Medical Academy of Postgraduate Education, 61176 Kharkiv, Ukraine.
| | - Anton Rohozhyn
- Kharkiv Medical Academy of Postgraduate Education, 61176 Kharkiv, Ukraine.
| | - Nataliia Rudova
- National Scientific Center Institute of Experimental and Clinical Veterinary Medicine (NSC IECVM), 61023 Kharkiv, Ukraine.
| | - Petro Poteiko
- Kharkiv Medical Academy of Postgraduate Education, 61176 Kharkiv, Ukraine.
| | - Anton Gerilovych
- National Scientific Center Institute of Experimental and Clinical Veterinary Medicine (NSC IECVM), 61023 Kharkiv, Ukraine.
| | - Eric Bortz
- Department of Biological Sciences, University of Alaska Anchorage, Anchorage, AK 99508, USA.
| | - Oleksii Solodiankin
- National Scientific Center Institute of Experimental and Clinical Veterinary Medicine (NSC IECVM), 61023 Kharkiv, Ukraine.
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11
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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: 47] [Impact Index Per Article: 9.4] [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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12
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Shin SS, Modongo C, Baik Y, Allender C, Lemmer D, Colman RE, Engelthaler DM, Warren RM, Zetola NM. Mixed Mycobacterium tuberculosis-Strain Infections Are Associated With Poor Treatment Outcomes Among Patients With Newly Diagnosed Tuberculosis, Independent of Pretreatment Heteroresistance. J Infect Dis 2018; 218:1974-1982. [PMID: 30085153 PMCID: PMC6217728 DOI: 10.1093/infdis/jiy480] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 08/02/2018] [Indexed: 11/14/2022] Open
Abstract
Background Heteroresistant Mycobacterium tuberculosis infections (defined as concomitant infection with drug-resistant and drug-susceptible strains) may explain the higher risk of poor tuberculosis treatment outcomes observed among patients with mixed-strain M. tuberculosis infections. We investigated the clinical effect of mixed-strain infections while controlling for pretreatment heteroresistance in a population-based sample of patients with tuberculosis starting first-line tuberculosis therapy in Botswana. Methods We performed 24-locus mycobacterial interspersed repetitive unit-variable number tandem-repeat analysis and targeted deep sequencing on baseline primary cultured isolates to detect mixed infections and heteroresistance, respectively. Drug-sensitive, micro-heteroresistant, macro-heteroresistant, and fixed-resistant infections were defined as infections in which the frequency of resistance was <0.1%, 0.1%-4%, 5%-94%, and ≥95%, respectively, in resistance-conferring domains of the inhA promoter, the katG gene, and the rpoB gene. Results Of the 260 patients with tuberculosis included in the study, 25 (9.6%) had mixed infections and 30 (11.5%) had poor treatment outcomes. Micro-heteroresistance, macro-heteroresistance, and fixed resistance were found among 11 (4.2%), 2 (0.8%), and 11 (4.2%), respectively, for isoniazid and 21 (8.1%), 0 (0%), and 10 (3.8%), respectively, for rifampicin. In multivariable analysis, mixed infections but not heteroresistant infections independently predicted poor treatment outcomes. Conclusions Among patients starting first-line tuberculosis therapy in Botswana, mixed infections were associated with poor tuberculosis treatment outcomes, independent of heteroresistance.
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Affiliation(s)
- Sanghyuk S Shin
- Sue and Bill Gross School of Nursing, University of California, Irvine
| | - Chawangwa Modongo
- Botswana-Upenn Partnership, Gaborone, Botswana
- Department of Infectious Disease, Gaborone, Botswana
| | - Yeonsoo Baik
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles
| | | | - Darrin Lemmer
- Translational Genomics Research Institute, Flagstaff, Arizona
| | | | | | - Robin M Warren
- NRF/DST Centre of Excellence for Biomedical Tuberculosis Research
- South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Tygerberg, South Africa
- Division of Molecular Biology and Human Genetics, Faculty of Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Nicola M Zetola
- Department of Radiation Oncology, University of Pennsylvania School of Medicine, Gaborone, Botswana
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13
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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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