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Kumar R, Kolloli A, Singh P, Shi L, Kupz A, Subbian S. The innate memory response of macrophages to Mycobacterium tuberculosis is shaped by the nature of the antigenic stimuli. Microbiol Spectr 2024; 12:e0047324. [PMID: 38980014 PMCID: PMC11302266 DOI: 10.1128/spectrum.00473-24] [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: 02/21/2024] [Accepted: 06/07/2024] [Indexed: 07/10/2024] Open
Abstract
Innate immune cells, such as macrophages, mount an immune response upon exposure to antigens and pathogens. Emerging evidence shows that macrophages exposed to an antigen can generate a "memory-like" response (a.k.a. trained immunity), which confers a non-specific and enhanced response upon subsequent stimulation with a second antigen/microbe. This trained immunity has been implicated in the enhanced response of macrophages against several invading pathogens. However, the association between the nature of the antigen and the corresponding immune correlate of elicited trained immunity is not fully understood. Similarly, the response of macrophages trained and restimulated with homologous stimulants to subsequent infection by pathogenic Mycobacterium tuberculosis (Mtb) remains unexplored. Here, we report the immune and metabolic profiles of trained immunity in human THP-1-derived macrophages after homologous training and restimulation with BCG, LPS, purified protein Derivative (PPD), heat-killed Mtb strains HN878 (hk-HN), and CDC1551 (hk-CDC). Furthermore, the impact of training on the autophagic and antimicrobial responses of macrophages with or without subsequent infection by clinical Mtb isolates HN878 and CDC1551 was evaluated. Results show that repeated stimulation of macrophages with different antigens displays distinct pro-inflammatory, metabolic, antimicrobial, and autophagy induction profiles. These macrophages also induce a differential antimicrobial response upon infection with clinical Mtb HN878 and CDC1551 isolates. A significantly reduced intracellular bacterial load was noted in the stimulated macrophages, which was augmented by the addition of rapamycin, an autophagy inducer. These observations suggest that the nature of the antigen and the mode of stimulation shape the magnitude and breadth of macrophage innate memory response, which impacts subsequent response to Mtb infection. IMPORTANCE Trained immunity (a.k.a. innate memory response) is a novel concept that has been rapidly emerging as a mechanism underpinning the non-specific immunity of innate immune cells, such as macrophages. However, the association between the nature of the stimuli and the corresponding immune correlate of trained immunity is not fully understood. Similarly, the kinetics of immunological and metabolic characteristics of macrophages upon "training" by the same antigen as primary and secondary stimuli (homologous stimulation) are not fully characterized. Furthermore, the ability of antigens such as purified protein derivative (PPD) and heat-killed-Mtb to induce trained immunity remains unknown. Similarly, the response of macrophages primed and trained by homologous stimulants to subsequent infection by pathogenic Mtb is yet to be reported. In this study, we evaluated the hypothesis that the nature of the stimuli impacts the depth and breadth of trained immunity in macrophages, which differentially affects their response to Mtb infection.
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Affiliation(s)
- Ranjeet Kumar
- Public Health Research Institute, Rutgers-New Jersey Medical School, Newark, New Jersey, USA
| | - Afsal Kolloli
- Public Health Research Institute, Rutgers-New Jersey Medical School, Newark, New Jersey, USA
| | - Pooja Singh
- Public Health Research Institute, Rutgers-New Jersey Medical School, Newark, New Jersey, USA
| | - Lanbo Shi
- Public Health Research Institute, Rutgers-New Jersey Medical School, Newark, New Jersey, USA
| | - Andreas Kupz
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine (AITHM), James Cook University, Cairns & Townsville, Queensland, Australia
| | - Selvakumar Subbian
- Public Health Research Institute, Rutgers-New Jersey Medical School, Newark, New Jersey, USA
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2
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Faye LM, Hosu MC, Vasaikar S, Dippenaar A, Oostvogels S, Warren RM, Apalata T. Spatial Distribution of Drug-Resistant Mycobacterium tuberculosis Infections in Rural Eastern Cape Province of South Africa. Pathogens 2023; 12:pathogens12030475. [PMID: 36986397 PMCID: PMC10059723 DOI: 10.3390/pathogens12030475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 03/05/2023] [Accepted: 03/08/2023] [Indexed: 03/30/2023] Open
Abstract
Tuberculosis (TB), an infectious airborne disease caused by Mycobacterium tuberculosis (Mtb), is a serious public health threat reported as the leading cause of morbidity and mortality worldwide. South Africa is a high-TB-burden country with TB being the highest infectious disease killer. This study investigated the distribution of Mtb mutations and spoligotypes in rural Eastern Cape Province. The Mtb isolates included were 1157 from DR-TB patients and analysed by LPA followed by spoligotyping of 441 isolates. The distribution of mutations and spoligotypes was done by spatial analysis. The rpoB gene had the highest number of mutations. The distribution of rpoB and katG mutations was more prevalent in four healthcare facilities, inhA mutations were more prevalent in three healthcare facilities, and heteroresistant isolates were more prevalent in five healthcare facilities. The Mtb was genetically diverse with Beijing more prevalent and largely distributed. Spatial analysis and mapping of gene mutations and spoligotypes revealed a better picture of distribution.
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Affiliation(s)
- Lindiwe M Faye
- Department of Laboratory Medicine and Pathology, Walter Sisulu University and National Health Laboratory Services (NHLS), Private Bag X5117, Mthatha 5099, South Africa
| | - Mojisola C Hosu
- Department of Laboratory Medicine and Pathology, Walter Sisulu University and National Health Laboratory Services (NHLS), Private Bag X5117, Mthatha 5099, South Africa
| | - Sandeep Vasaikar
- Department of Laboratory Medicine and Pathology, Walter Sisulu University and National Health Laboratory Services (NHLS), Private Bag X5117, Mthatha 5099, South Africa
| | - Anzaan Dippenaar
- Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, BE-2000 Antwerp, Belgium
| | - Selien Oostvogels
- Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, BE-2000 Antwerp, Belgium
| | - Rob M Warren
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa
| | - Teke Apalata
- Department of Laboratory Medicine and Pathology, Walter Sisulu University and National Health Laboratory Services (NHLS), Private Bag X5117, Mthatha 5099, South Africa
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Guo S, Chongsuvivatwong V, Lei S. Comparison on Major Gene Mutations Related to Rifampicin and Isoniazid Resistance between Beijing and Non-Beijing Strains of Mycobacterium tuberculosis: A Systematic Review and Bayesian Meta-Analysis. Genes (Basel) 2022; 13:genes13101849. [PMID: 36292734 PMCID: PMC9601453 DOI: 10.3390/genes13101849] [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: 09/06/2022] [Revised: 10/07/2022] [Accepted: 10/08/2022] [Indexed: 11/16/2022] Open
Abstract
Objective: The Beijing strain of Mycobacterium tuberculosis (MTB) is controversially presented as the predominant genotype and is more drug resistant to rifampicin and isoniazid compared to the non-Beijing strain. We aimed to compare the major gene mutations related to rifampicin and isoniazid drug resistance between Beijing and non-Beijing genotypes, and to extract the best evidence using the evidence-based methods for improving the service of TB control programs based on genetics of MTB. Method: Literature was searched in Google Scholar, PubMed and CNKI Database. Data analysis was conducted in R software. The conventional and Bayesian random-effects models were employed for meta-analysis, combining the examinations of publication bias and sensitivity. Results: Of the 8785 strains in the pooled studies, 5225 were identified as Beijing strains and 3560 as non-Beijing strains. The maximum and minimum strain sizes were 876 and 55, respectively. The mutations prevalence of rpoB, katG, inhA and oxyR-ahpC in Beijing strains was 52.40% (2738/5225), 57.88% (2781/4805), 12.75% (454/3562) and 6.26% (108/1724), respectively, and that in non-Beijing strains was 26.12% (930/3560), 28.65% (834/2911), 10.67% (157/1472) and 7.21% (33/458), separately. The pooled posterior value of OR for the mutations of rpoB was 2.72 ((95% confidence interval (CI): 1.90, 3.94) times higher in Beijing than in non-Beijing strains. That value for katG was 3.22 (95% CI: 2.12, 4.90) times. The estimate for inhA was 1.41 (95% CI: 0.97, 2.08) times higher in the non-Beijing than in Beijing strains. That for oxyR-ahpC was 1.46 (95% CI: 0.87, 2.48) times. The principal patterns of the variants for the mutations of the four genes were rpoB S531L, katG S315T, inhA-15C > T and oxyR-ahpC intergenic region. Conclusion: The mutations in rpoB and katG genes in Beijing are significantly more common than that in non-Beijing strains of MTB. We do not have sufficient evidence to support that the prevalence of mutations of inhA and oxyR-ahpC is higher in non-Beijing than in Beijing strains, which provides a reference basis for clinical medication selection.
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Affiliation(s)
- Shengqiong Guo
- Guizhou Provincial Center for Disease Prevention and Control, Guiyang 550004, China
- Department of Epidemiology, Faculty of Medicine, Prince of Songkla University, Hat Yai 90110, Thailand
- Correspondence:
| | | | - Shiguang Lei
- Guizhou Provincial Center for Disease Prevention and Control, Guiyang 550004, China
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4
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Liu Q, Qiu B, Li G, Yang T, Tao B, Martinez L, Zhu L, Wang J, Mao X, Lu W. Tuberculosis reinfection and relapse in eastern China: A prospective study using whole-genome sequencing. Clin Microbiol Infect 2022; 28:1458-1464. [PMID: 35700940 DOI: 10.1016/j.cmi.2022.05.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 05/10/2022] [Accepted: 05/14/2022] [Indexed: 11/03/2022]
Abstract
OBJECTIVES Tuberculosis recurrence after an initial successful treatment episode can occur from either reinfection or relapse. In a population-based sample and whole genome sequencing (WGS) in eastern China, we aimed to evaluate risk factors for tuberculosis recurrence, and assess the proportion of recurrence due to either reinfection or relapse. METHODS Successfully treated pulmonary tuberculosis patients with sputum culture positive results were recruited from five cities in Jiangsu Province from 2013-2015 and followed for two years for tuberculosis recurrence. Among patients developing a second tuberculosis episode, WGS was performed to distinguish relapse or reinfection through a distance threshold of 6-single-nucleotide polymorphisms (SNP). We analyzed risk factors for recurrence and epidemiological characteristics of different types of recurrent patients. RESULTS Of 1,897 successful treated tuberculosis patients, 7.4% (141/1879) developed recurrent tuberculosis. Compared with non-recurrent tuberculosis, patients were at higher risk of recurrence in older age (Adjusted Odds Ratio [AOR], 1.02 for each additional year; 95% CI, 1.01-1.03, P=0.003), patients previously treated for tuberculosis (AOR=2.22; 95% CI, 1.52-3.26, P<0.001), or with bilateral cavities (AOR, 1.56; 95% CI, 1.05-2.32, P=0.029). Among 27.0% (38/141) recurrent tuberculosis patients with successfully sequenced pairs, relapse was substantially more common than reinfection (71.1% versus 28.9%, P=0.014). CONCLUSIONS Endogenous relapse was significantly more common than exogenous reinfection in the first two years after treatment in eastern China. Prioritization of high-risk groups for recurrence, such as the elderly, with a previous tuberculosis diagnosis, or with bilateral cavities, may provide opportunities to reduce post-tuberculosis morbidity.
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Affiliation(s)
- Qiao Liu
- Department of Chronic Communicable Disease, Center for Disease Control and Prevention of Jiangsu Province, Nanjing, Jiangsu Province, PR China
| | - Beibei Qiu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, PR China
| | - Guoli Li
- Department of Chronic Communicable Disease, Center for Disease Control and Prevention of Jiangsu Province, Nanjing, Jiangsu Province, PR China
| | - Tingting Yang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College and Shanghai Public Health Clinical Center, Fudan University, Shanghai, PR China
| | - Bilin Tao
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, PR China
| | - Leonardo Martinez
- Department of Epidemiology, School of Public Health, Boston University, Boston, Massachusetts, United States
| | - Limei Zhu
- Department of Chronic Communicable Disease, Center for Disease Control and Prevention of Jiangsu Province, Nanjing, Jiangsu Province, PR China
| | - Jianming Wang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, PR China
| | - Xuhua Mao
- Department of Clinical Laboratory, Affiliated Yixing People's Hospital, Jiangsu University, Wuxi, China.
| | - Wei Lu
- Department of Chronic Communicable Disease, Center for Disease Control and Prevention of Jiangsu Province, Nanjing, Jiangsu Province, PR China.
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5
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Qiu B, Tao B, Liu Q, Li Z, Song H, Tian D, Wu J, Wu Z, Zhan M, Lu W, Wang J. A Prospective Cohort Study on the Prevalent and Recurrent Tuberculosis Isolates Using the MIRU-VNTR Typing. Front Med (Lausanne) 2021; 8:685368. [PMID: 34595184 PMCID: PMC8476766 DOI: 10.3389/fmed.2021.685368] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 08/23/2021] [Indexed: 11/30/2022] Open
Abstract
The study aims to describe the clustering characteristics of Mycobacterium tuberculosis (M.tb) strains circulating in eastern China and determine the ratio of relapse and reinfection in recurrent patients. We recruited sputum smear-positive pulmonary tuberculosis cases from five cities of Jiangsu Province, China, during August 2013 and December 2015. Patients were followed for the treatment outcomes and recurrence based on a cohort design. M.tb strains were isolated and genotyped using the 12-locus MIRU-VNTR. The Beijing family was identified by the extended Region of Difference (RD) analysis. The Hunter-Gaston Discriminatory Index (HGDI) was used to judge the resolution ability of MIRU-VNTR. The odds ratio (OR) together with 95% confidence interval (CI) were used to estimate the strength of association. We performed a cluster analysis on 2098 M.tb isolates and classified them into 545 genotypes and five categories (I, 0.19%; II, 0.43%; III, 3.34%; IV, 77.46%; V, 18.59%). After adjusting for potential confounders, the Beijing family genotype (OR = 118.63, 95% CI: 79.61–176.79, P = 0.001) was significantly related to the dominant strain infections. Patients infected with non-dominant strains had a higher risk of the pulmonary cavity (OR = 1.39, 95% CI: 1.01–1.91, P = 0.046). Among 37 paired recurrent cases, 22 (59.46%) were determined as endogenous reactivation, and 15 (40.54%) were exogenous reinfection. The type of M.tb strains prevalent in Jiangsu Province is relatively single. Beijing family strains infection is dominant in local tuberculosis cases. Endogenous reactivation appears to be a major cause of recurrent tuberculosis in Eastern China. This finding emphasizes the importance of case follow-up and monitoring after the completion of antituberculosis treatment.
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Affiliation(s)
- Beibei Qiu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Bilin Tao
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Qiao Liu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.,Department of Chronic Communicable Disease, Center for Disease Control and Prevention of Jiangsu Province, Nanjing, China
| | - Zhongqi Li
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Huan Song
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Dan Tian
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Jizhou Wu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Zhuchao Wu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Mengyao Zhan
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Wei Lu
- Department of Chronic Communicable Disease, Center for Disease Control and Prevention of Jiangsu Province, Nanjing, China
| | - Jianming Wang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
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6
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Keikha M, Majidzadeh M. Beijing genotype of Mycobacterium tuberculosis is associated with extensively drug-resistant tuberculosis: A global analysis. New Microbes New Infect 2021; 43:100921. [PMID: 34466269 PMCID: PMC8383003 DOI: 10.1016/j.nmni.2021.100921] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/05/2021] [Accepted: 07/15/2021] [Indexed: 02/08/2023] Open
Abstract
We found that the frequency of Beijing genotype among XDR-TB strains was high. The data in this study would help guide the TB control program, and we however need further investigation to confirm the reliability of the present findings.
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Affiliation(s)
- M Keikha
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Microbiology and Virology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - M Majidzadeh
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Microbiology and Virology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
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7
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Karmakar M, Trauer JM, Ascher DB, Denholm JT. Hyper transmission of Beijing lineage Mycobacterium tuberculosis: Systematic review and meta-analysis. J Infect 2019; 79:572-581. [PMID: 31585190 DOI: 10.1016/j.jinf.2019.09.016] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 08/30/2019] [Accepted: 09/27/2019] [Indexed: 12/12/2022]
Abstract
OBJECTIVES The globally distributed "Beijing" lineage of Mycobacterium tuberculosis has been associated with outbreaks worldwide. Laboratory based studies have suggested that Beijing lineage may have increased fitness; however, it has not been established whether these differences are of epidemiological significance with regards to transmission. Therefore, we undertook a systematic review of epidemiological studies of tuberculosis clustering to compare the transmission dynamics of Beijing lineages versus the non-Beijing lineages. METHODS We systematically searched Embase and MEDLINE before 31st December 2018, for studies which provided information on the transmission dynamics of the different M. tuberculosis lineages. We included articles that conducted population-based cross-sectional or longitudinal molecular epidemiological studies reporting information about extent of transmission of different lineages. The protocol for this systematic review was prospectively registered with PROSPERO (CDR42018088579). RESULTS Of 2855 records identified by the search, 46 were included in the review, containing 42,700 patients from 27 countries. Beijing lineage was the most prevalent and highly clustered strain in 72.4% of the studies and had a higher likelihood of transmission than non-Beijing lineages (OR 1·81 [95% 1·28-2·57], I2 = 94·0%, τ2 = 0·59, p < 0·01). CONCLUSIONS Despite considerable heterogeneity across epidemiological contexts, Beijing lineage appears to be more transmissible than other lineages.
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Affiliation(s)
- Malancha Karmakar
- Victorian Tuberculosis Program, Melbourne Health, 792 Elizabeth Street, Melbourne, Victorian 3000 Australia; Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria 3010, Australia; Department of Microbiology and Immunology, at the Doherty Institute of Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia; Structural Biology and Bioinformatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - James M Trauer
- Victorian Tuberculosis Program, Melbourne Health, 792 Elizabeth Street, Melbourne, Victorian 3000 Australia; School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
| | - David B Ascher
- Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria 3010, Australia; Structural Biology and Bioinformatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia; Department of Biochemistry, University of Cambridge, CB2 1GA, UK
| | - Justin T Denholm
- Victorian Tuberculosis Program, Melbourne Health, 792 Elizabeth Street, Melbourne, Victorian 3000 Australia; Department of Microbiology and Immunology, at the Doherty Institute of Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia.
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8
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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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9
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Feyisa SG, Abdurahman AA, Jimma W, Chaka EE, Kardan-Yamchi J, Kazemian H. Resistance of Mycobacterium tuberculosis strains to Rifampicin: A systematic review and meta-analysis. Heliyon 2019; 5:e01081. [PMID: 30619960 PMCID: PMC6314001 DOI: 10.1016/j.heliyon.2018.e01081] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 11/15/2018] [Accepted: 12/18/2018] [Indexed: 12/01/2022] Open
Abstract
Introduction Antitubercular drug resistance strain is a horrifying barrier to effective TB treatment and prevention. The present study aimed to determine the prevalence and geographical distribution of rifampicin-resistance M. tuberculosis (MTB) strains. Methods We searched two electronic databases, PubMed and EMBASE, until 26 March 2017 and updated our search on 27 April 2018 and accessed all prevalence studies of MTB strain and their drug susceptibility patterns to rifampicin. The pooled prevalence estimate was determined using random effects model. Results We identified 23 studies satisfying the inclusion criteria. The proportion of rifampicin resistance strains was diverged depending on the type of strains, country and Regions. The pooled estimate of rifampicin-resistance strains of MTB for the included studies was 4% (95% CI: 3–5%). In subgroup analysis based on World Health Organization (WHO) Regions, the pooled estimate of rifampicin-resistance strains of MTB was 11% (95% CI: 9–13%) with the Western Pacific Region 24%, Europian Region 10%, South-East Asian Region 6%, African Region 3% and Region of American 1%. Beijing family was the most dominant strain resistance to rifampicin with pooled prevalence of 14% (95% CI: 10–18%). The pooled prevalence of other families, i.e. EAI, T, CAS, MANU, Haarlem, LAM and Ural, was ≤2% for each. Conclusion High burden of rifampicin resistance MTB strains was identified in the Western Pacific Region. Of these, Beijing family was predominantly resistance to rifampicin in Western Pacific Region and South-East Asian Region and also spread to European Region and Region of American.
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Affiliation(s)
- Seifu Gizaw Feyisa
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, International Campus, Tehran, Iran.,Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Department of Biology, College of Natural Sciences, Jimma University, Ethiopia
| | - Ahmed Abdulahi Abdurahman
- Department of Community Nutrition, School of Nutritional Sciences and Dietetics, Tehran University of Medical Sciences, Tehran, Iran
| | - Worku Jimma
- Department of Health Information Management, School of School of Allied Medical Sciences, Tehran University of Medical Sciences, International Campus, Tehran, Iran.,Department of Information Science, Jimma Institute of Technology, Jimma University, Ethiopia
| | - Eshetu Ejeta Chaka
- Department of Epidemiology and Biostatistics, School of Public Health, Tehran University of Medical Sciences, International Campus, Tehran, Iran.,Department of Epidemiology and Biostatistics, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.,Department of Public Health, College of Medical and Health Sciences, Ambo University, Ethiopia
| | - Jalil Kardan-Yamchi
- Department of Pathobiology, Division of Microbiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Hossein Kazemian
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran.,Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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Wiens KE, Woyczynski LP, Ledesma JR, Ross JM, Zenteno-Cuevas R, Goodridge A, Ullah I, Mathema B, Djoba Siawaya JF, Biehl MH, Ray SE, Bhattacharjee NV, Henry NJ, Reiner RC, Kyu HH, Murray CJL, Hay SI. Global variation in bacterial strains that cause tuberculosis disease: a systematic review and meta-analysis. BMC Med 2018; 16:196. [PMID: 30373589 PMCID: PMC6206891 DOI: 10.1186/s12916-018-1180-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 09/24/2018] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND The host, microbial, and environmental factors that contribute to variation in tuberculosis (TB) disease are incompletely understood. Accumulating evidence suggests that one driver of geographic variation in TB disease is the local ecology of mycobacterial genotypes or strains, and there is a need for a comprehensive and systematic synthesis of these data. The objectives of this study were to (1) map the global distribution of genotypes that cause TB disease and (2) examine whether any epidemiologically relevant clinical characteristics were associated with those genotypes. METHODS We performed a systematic review of PubMed and Scopus to create a comprehensive dataset of human TB molecular epidemiology studies that used representative sampling techniques. The methods were developed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). We extracted and synthesized data from studies that reported prevalence of bacterial genotypes and from studies that reported clinical characteristics associated with those genotypes. RESULTS The results of this study are twofold. First, we identified 206 studies for inclusion in the study, representing over 200,000 bacterial isolates collected over 27 years in 85 countries. We mapped the genotypes and found that, consistent with previously published maps, Euro-American lineage 4 and East Asian lineage 2 strains are widespread, and West African lineages 5 and 6 strains are geographically restricted. Second, 30 studies also reported transmission chains and 4 reported treatment failure associated with genotypes. We performed a meta-analysis and found substantial heterogeneity across studies. However, based on the data available, we found that lineage 2 strains may be associated with increased risk of transmission chains, while lineages 5 and 6 strains may be associated with reduced risk, compared with lineage 4 strains. CONCLUSIONS This study provides the most comprehensive systematic analysis of the evidence for diversity in bacterial strains that cause TB disease. The results show both geographic and epidemiological differences between strains, which could inform our understanding of the global burden of TB. Our findings also highlight the challenges of collecting the clinical data required to inform TB diagnosis and treatment. We urge future national TB programs and research efforts to prioritize and reinforce clinical data collection in study designs and results dissemination.
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Affiliation(s)
- Kirsten E Wiens
- Institute for Health Metrics and Evaluation, University of Washington, 2301 5th Ave, Suite 600, Seattle, WA, 98121, USA
| | - Lauren P Woyczynski
- Institute for Health Metrics and Evaluation, University of Washington, 2301 5th Ave, Suite 600, Seattle, WA, 98121, USA
| | - Jorge R Ledesma
- Institute for Health Metrics and Evaluation, University of Washington, 2301 5th Ave, Suite 600, Seattle, WA, 98121, USA
| | - Jennifer M Ross
- Institute for Health Metrics and Evaluation, University of Washington, 2301 5th Ave, Suite 600, Seattle, WA, 98121, USA
- Departments of Global Health and Medicine, University of Washington, Seattle, WA, USA
| | | | - Amador Goodridge
- Tuberculosis Biomarker Research Unit, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP), City of Knowledge, Panama, Panama
| | - Irfan Ullah
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, Khyber Pakhtunkhwa, Pakistan
- Programmatic Management of Drug-Resistant TB Unit, BSL-II TB Culture Laboratory, Mufti Mehmood Memorial Teaching Hospital, Dera Ismail Khan, Khyber Pakhtunkhwa, Pakistan
| | - Barun Mathema
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Joel Fleury Djoba Siawaya
- Unité de Recherche et de Diagnostics Spécialisés, Laboratoire National de Santé Publique, Libreville, Gabon
- Centre Hospitalier Universitaire Mère-Enfant Fondation Jeanne EBORI, Libreville, Gabon
| | - Molly H Biehl
- Institute for Health Metrics and Evaluation, University of Washington, 2301 5th Ave, Suite 600, Seattle, WA, 98121, USA
| | - Sarah E Ray
- Institute for Health Metrics and Evaluation, University of Washington, 2301 5th Ave, Suite 600, Seattle, WA, 98121, USA
| | - Natalia V Bhattacharjee
- Institute for Health Metrics and Evaluation, University of Washington, 2301 5th Ave, Suite 600, Seattle, WA, 98121, USA
| | - Nathaniel J Henry
- Institute for Health Metrics and Evaluation, University of Washington, 2301 5th Ave, Suite 600, Seattle, WA, 98121, USA
| | - Robert C Reiner
- Institute for Health Metrics and Evaluation, University of Washington, 2301 5th Ave, Suite 600, Seattle, WA, 98121, USA
| | - Hmwe H Kyu
- Institute for Health Metrics and Evaluation, University of Washington, 2301 5th Ave, Suite 600, Seattle, WA, 98121, USA
| | - Christopher J L Murray
- Institute for Health Metrics and Evaluation, University of Washington, 2301 5th Ave, Suite 600, Seattle, WA, 98121, USA
| | - Simon I Hay
- Institute for Health Metrics and Evaluation, University of Washington, 2301 5th Ave, Suite 600, Seattle, WA, 98121, USA.
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11
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Gao Y, Zhang Z, Deng J, Mansjö M, Ning Z, Li Y, Li X, Hu Y, Hoffner S, Xu B. Multi-center evaluation of GenoType MTBDRsl line probe assay for rapid detection of pre-XDR and XDR Mycobacterium tuberculosis in China. J Infect 2018; 77:328-334. [PMID: 29969597 DOI: 10.1016/j.jinf.2018.06.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 06/07/2018] [Accepted: 06/18/2018] [Indexed: 11/18/2022]
Abstract
OBJECTIVES The implementation of rapid and reliable drug susceptibilities diagnosis is fundamental for effective treatment of multidrug-resistant tuberculosis(MDR-TB). The present study aimed to assess the diagnostic performance of the 2nd-version GenoType MTBDRsl kit as well as the impact of its implementation on the turnaround time in a multi-center Chinese study. METHODS Totally 353 MDR-TB patient specimens were consecutively tested. The 2nd-version GenoType MTBDRsl assay, drug susceptibility testing with the MGIT 960 system, and sequencing were performed and compared. RESULTS MTBDRsl testing identified the major genotypes associated with fluoroquinolones resistance, predominated by gyrA MUT3B (Asp94Asn and Asp94Tyr, 26.5%) and MUT3C (Asp94Gly, 19.5%). The genotypes associated with resistance to 2nd-line injectable drugs(SLIDs) were rrsMUT1(A1401G, 64.9%) and absence of WT1(C1402T, 10.5%). The sensitivities for detection of resistance to fluoroquinolones, SLIDs, and their combination (extensively drug resistance, XDR) were 80.5%, 80.7% and 73.5% and specificities were 100.0%, 99.3% and 99.1%, respectively. Implementation of this test significantly reduced the turnaround time between sample collection and result reporting from 45 to 3 days, a reduction by 93.3% (p, 0.001). CONCLUSION With a favorable diagnostic performance and short turnaround time, the 2nd-version GenoType MTBDRsl assay proves its value for early diagnosis of resistance to 2nd-line drugs as well as of XDR-TB in China.
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Affiliation(s)
- Yazhou Gao
- Department of Epidemiology, School of Public Health, China and Key Laboratory of Public Health Safety (Fudan University), Ministry of Education, Fudan University, Shanghai 200032, China
| | - Zhengdong Zhang
- Zigong City Center for Disease Control and Prevention, Zigong City, Sichuan, China
| | - Jianping Deng
- Zigong City Center for Disease Control and Prevention, Zigong City, Sichuan, China
| | | | - Zhu Ning
- Zigong City Center for Disease Control and Prevention, Zigong City, Sichuan, China
| | - Yang Li
- Department of Epidemiology, School of Public Health, China and Key Laboratory of Public Health Safety (Fudan University), Ministry of Education, Fudan University, Shanghai 200032, China
| | - Xuliang Li
- Department of Epidemiology, School of Public Health, China and Key Laboratory of Public Health Safety (Fudan University), Ministry of Education, Fudan University, Shanghai 200032, China
| | - Yi Hu
- Department of Epidemiology, School of Public Health, China and Key Laboratory of Public Health Safety (Fudan University), Ministry of Education, Fudan University, Shanghai 200032, China.
| | - Sven Hoffner
- Department of Public Health Sciences, Karolinska Institutet, Stockholm, Sweden
| | - Biao Xu
- Department of Epidemiology, School of Public Health, China and Key Laboratory of Public Health Safety (Fudan University), Ministry of Education, Fudan University, Shanghai 200032, China; Department of Public Health Sciences, Karolinska Institutet, Stockholm, Sweden
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12
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Blanco-Guillot F, Delgado-Sánchez G, Mongua-Rodríguez N, Cruz-Hervert P, Ferreyra-Reyes L, Ferreira-Guerrero E, Yanes-Lane M, Montero-Campos R, Bobadilla-del-Valle M, Torres-González P, Ponce-de-León A, Sifuentes-Osornio J, Garcia-Garcia L. Molecular clustering of patients with diabetes and pulmonary tuberculosis: A systematic review and meta-analysis. PLoS One 2017; 12:e0184675. [PMID: 28902922 PMCID: PMC5597214 DOI: 10.1371/journal.pone.0184675] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 08/24/2017] [Indexed: 11/18/2022] Open
Abstract
Introduction Many studies have explored the relationship between diabetes mellitus (DM) and tuberculosis (TB) demonstrating increased risk of TB among patients with DM and poor prognosis of patients suffering from the association of DM/TB. Owing to a paucity of studies addressing this question, it remains unclear whether patients with DM and TB are more likely than TB patients without DM to be grouped into molecular clusters defined according to the genotype of the infecting Mycobacterium tuberculosis bacillus. That is, whether there is convincing molecular epidemiological evidence for TB transmission among DM patients. Objective: We performed a systematic review and meta-analysis to quantitatively evaluate the propensity for patients with DM and pulmonary TB (PTB) to cluster according to the genotype of the infecting M. tuberculosis bacillus. Materials and methods We conducted a systematic search in MEDLINE and LILACS from 1990 to June, 2016 with the following combinations of key words “tuberculosis AND transmission” OR “tuberculosis diabetes mellitus” OR “Mycobacterium tuberculosis molecular epidemiology” OR “RFLP-IS6110” OR “Spoligotyping” OR “MIRU-VNTR”. Studies were included if they met the following criteria: (i) studies based on populations from defined geographical areas; (ii) use of genotyping by IS6110- restriction fragment length polymorphism (RFLP) analysis and spoligotyping or mycobacterial interspersed repetitive unit-variable number of tandem repeats (MIRU-VNTR) or other amplification methods to identify molecular clustering; (iii) genotyping and analysis of 50 or more cases of PTB; (iv) study duration of 11 months or more; (v) identification of quantitative risk factors for molecular clustering including DM; (vi) > 60% coverage of the study population; and (vii) patients with PTB confirmed bacteriologically. The exclusion criteria were: (i) Extrapulmonary TB; (ii) TB caused by nontuberculous mycobacteria; (iii) patients with PTB and HIV; (iv) pediatric PTB patients; (v) TB in closed environments (e.g. prisons, elderly homes, etc.); (vi) diabetes insipidus and (vii) outbreak reports. Hartung-Knapp-Sidik-Jonkman method was used to estimate the odds ratio (OR) of the association between DM with molecular clustering of cases with TB. In order to evaluate the degree of heterogeneity a statistical Q test was done. The publication bias was examined with Begg and Egger tests. Review Manager 5.3.5 CMA v.3 and Biostat and Software package R were used. Results Selection criteria were met by six articles which included 4076 patients with PTB of which 13% had DM. Twenty seven percent of the cases were clustered. The majority of cases (48%) were reported in a study in China with 31% clustering. The highest incidence of TB occurred in two studies from China. The global OR for molecular clustering was 0.84 (IC 95% 0.40–1.72). The heterogeneity between studies was moderate (I2 = 55%, p = 0.05), although there was no publication bias (Beggs test p = 0.353 and Eggers p = 0.429). Conclusion There were very few studies meeting our selection criteria. The wide confidence interval indicates that there is not enough evidence to draw conclusions about the association. Clustering of patients with DM in TB transmission chains should be investigated in areas where both diseases are prevalent and focus on specific contexts.
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Affiliation(s)
- Francles Blanco-Guillot
- Doctorado en Ciencias en Enfermedades Infecciosas, Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
| | - Guadalupe Delgado-Sánchez
- Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
| | - Norma Mongua-Rodríguez
- Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
- Maestría en Ciencias Médicas con énfasis en Epidemiología, Facultad de Medicina, Universidad Nacional Autónoma de México, Distrito Federal, México
| | - Pablo Cruz-Hervert
- Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
| | - Leticia Ferreyra-Reyes
- Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
| | - Elizabeth Ferreira-Guerrero
- Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
| | - Mercedes Yanes-Lane
- Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
- Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, San Luis Potosí, México
| | - Rogelio Montero-Campos
- Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
| | - Miriam Bobadilla-del-Valle
- Laboratorio de Microbiología, Instituto Nacional de Ciencias Médicas y Nutrición “Salvador Zubirán”, México, Distrito Federal, México
| | - Pedro Torres-González
- Laboratorio de Microbiología, Instituto Nacional de Ciencias Médicas y Nutrición “Salvador Zubirán”, México, Distrito Federal, México
| | - Alfredo Ponce-de-León
- Laboratorio de Microbiología, Instituto Nacional de Ciencias Médicas y Nutrición “Salvador Zubirán”, México, Distrito Federal, México
| | - José Sifuentes-Osornio
- Dirección Médica, Instituto Nacional de Ciencias Médicas y Nutrición “Salvador Zubirán”, México, Distrito Federal, México
| | - Lourdes Garcia-Garcia
- Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
- * E-mail:
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Borrell S, Trauner A. Strain Diversity and the Evolution of Antibiotic Resistance. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1019:263-279. [PMID: 29116640 DOI: 10.1007/978-3-319-64371-7_14] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Drug resistance is best thought of as an ongoing biological process. Resistant bacteria must emerge, become established and ultimately transmit in order to be relevant to human health. In this context, genetic diversity can influence the rate and likelihood of resistance emerging; it can also modulate the net physiological impact of resistance and the propensity of an organism to improve any defects that arise from it. Combined, these effects can have an impact on a larger scale, with highly transmissible drug-resistant bacterial strains posing a formidable threat to global health. These considerations are pertinent to the future of tuberculosis control as well. In this chapter, we review our current understanding of the impact of genetic diversity in the broadest sense on the evolution of drug-resistant members of the Mycobacterium tuberculosis complex.
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Affiliation(s)
- Sonia Borrell
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002, Basel, Switzerland. .,University of Basel, Basel, Switzerland.
| | - Andrej Trauner
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002, Basel, Switzerland.,University of Basel, Basel, Switzerland
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14
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Schluger NW. Host-Pathogen Interactions in Tuberculosis: The Evolving Story. J Infect Dis 2016; 214:1137-8. [PMID: 27534688 DOI: 10.1093/infdis/jiw366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 08/05/2016] [Indexed: 11/12/2022] Open
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