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Mane SS, Shrotriya P. Current Epidemiology of Pediatric Tuberculosis. Indian J Pediatr 2024; 91:711-716. [PMID: 37919487 DOI: 10.1007/s12098-023-04910-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 10/16/2023] [Indexed: 11/04/2023]
Abstract
Tuberculosis (TB) is a communicable disease that is a major cause of ill health and one of the leading causes of death worldwide. Children act as reservoirs of infection out of which future cases develop. Without the successful detection and treatment of TB infection and disease in children, elimination strategies for TB will be ineffective. India has a severe problem with TB in children, which accounts for around 31% of the global pediatric TB load. However, over the past 10 y, children have consistently made up 6-7% of all patients treated yearly under the National Tuberculosis Elimination Programme (NTEP). There is an estimated detection gap of 56% in India, which is the reason for many missed cases of TB in children. Only 3% of children less than 14 y with MDR/RR-TB, are reported from India, which again is an underestimation of the actual incident cases. Population density, housing and living conditions, environmental conditions, cultural practices, age of the child, exposure to tobacco and other environmental pollutants, the virulence of the mycobacterial strain and their genetics, host genetics, BCG vaccination, malnutrition, immunodeficiency are some of the risk factors for TB exposure, infection and disease in children. Understanding the natural history as well as the epidemiology of childhood TB is important to assess which children are the most vulnerable. It would also guide us in understanding the burden of pediatric TB on a regional, national, or global level, thus facilitating the appropriate targeting of health resources and also guiding policy-making decisions.
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Affiliation(s)
- Sushant Satish Mane
- State Pediatric Center of Excellence for TB, Department of Pediatrics, Grant Govt. Medical College, Sir JJ Group of Hospitals, Mumbai, India.
| | - Pragya Shrotriya
- State Pediatric Center of Excellence for TB, Department of Pediatrics, Grant Govt. Medical College, Sir JJ Group of Hospitals, Mumbai, India
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He H, Xu J, Peng Q, Li Y, Huang Y, Zhang YL, Li X. The application value of cerebrospinal fluid immunoglobulin in tuberculous meningitis. Microbiol Spectr 2024; 12:e0015724. [PMID: 38666897 PMCID: PMC11237685 DOI: 10.1128/spectrum.00157-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 03/17/2024] [Indexed: 06/06/2024] Open
Abstract
This article aims to study the value of cerebrospinal fluid (CSF) immunoglobulin in differential diagnosis, prediction, and prognosis of tuberculous meningitis (TBM). The clinical data of 65 patients with TBM in our hospital were collected, and 65 patients with cryptococcal meningitis (CM) were enrolled in 1:1 matching. Relevant data were collected for comparison. CSFs IgG [331.51 (164.85, 645.00) vs 129.00 (55.05, 251.00) ng/mL], IgM [22.38 (8.52, 40.18) vs 6.08 (2.19, 23.30) ng/mL], and IgA [64.11 (21.44, 115.48) vs 16.55 (4.76, 30.36) ng/mL] in the TBM group were higher than those in the CM group (P < 0.001). In the TBM group, after 24 weeks of treatment, the CSFs IgG, IgM, and IgA were significantly decreased, and the difference was statistically significant (P < 0.05). The predictive results of CSF immunoglobulin for TBM showed that IgG, IgM, and IgA all had some predictive value for TBM, and the combined predictive value of the three was the highest, with an area under the curve of 0.831 (95% CI: 0.774-0.881). Logistic regression analysis of CSF immunoglobulins and TBM prognosis showed that IgG [odds ratio (OR) = 4.796, 95% confidence interval (CI): 2.575-8.864], IgM (OR = 3.456, 95% CI: 2.757-5.754), and IgA (OR = 4.371, 95% CI: 2.731-5.856) were TBM risk factors for poor prognosis in patients. The levels of IgG, IgM, and IgA in CSF were positively correlated with the severity of cranial magnetic resonance imaging (MRI) in TBM patients (R2 = 0.542, F = 65.392, P < 0.05). CSFs IgG, IgM, and IgA can be used as a routine monitoring index for TBM patients, which has a certain reference value in differential diagnosis and efficacy evaluation. IMPORTANCE In clinical practice, physicians can determine the physical conditions of patients based on the levels of cerebrospinal fluids (CSFs) IgG, IgM, and IgA. Higher levels of CSFs IgG, IgM, and IgA suggest more possibility of tuberculous meningitis and worse prognosis and magnetic resonance imaging manifestations.
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Affiliation(s)
- Hua He
- Department of Infectious Disease, The Third People's Hospital of Kunming/Yunnan Clinical Medical Center for Infectious Diseases, Kunming, Yunnan, China
| | - Jun Xu
- Department of Infectious Disease, The Third People's Hospital of Kunming/Yunnan Clinical Medical Center for Infectious Diseases, Kunming, Yunnan, China
| | - Qin Peng
- Department of Infectious Disease, The Third People's Hospital of Kunming/Yunnan Clinical Medical Center for Infectious Diseases, Kunming, Yunnan, China
| | - Yang Li
- Department of Infectious Disease, The Third People's Hospital of Kunming/Yunnan Clinical Medical Center for Infectious Diseases, Kunming, Yunnan, China
| | - Ying Huang
- Department of Infectious Disease, The Third People's Hospital of Kunming/Yunnan Clinical Medical Center for Infectious Diseases, Kunming, Yunnan, China
| | - Yan-Ling Zhang
- Department of Infectious Disease, The Third People's Hospital of Kunming/Yunnan Clinical Medical Center for Infectious Diseases, Kunming, Yunnan, China
| | - Xiang Li
- Department of Radiology, The Third People's Hospital of Kunming/ Yunnan Clinical Medical Center for Infectious Diseases, Kunming, Yunnan, China
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Burusie A, Enquesilassie F, Salazar-Austin N, Addissie A. Determinants of tuberculosis disease development in children in central Ethiopia: A matched case-control study. PLoS One 2024; 19:e0300731. [PMID: 38722971 PMCID: PMC11081268 DOI: 10.1371/journal.pone.0300731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 03/04/2024] [Indexed: 05/13/2024] Open
Abstract
BACKGROUND The risk factors for tuberculosis (TB) disease development in children remained understudied, particularly in low-income countries like Ethiopia. The objective of this study was to identify determinants of TB disease development in general and in relation to BCG vaccination in children in central Ethiopia. METHODS We employed a 1:1 age-matched case-control design to compare the characteristics of children who developed TB (cases) with those who did not (controls). Data were collected in healthcare facilities in Addis Ababa city, Adama, and Bishoftu towns between September 25, 2021, and June 24, 2022. Two hundred and fifty-six cases were drawn at random from a list of childhood TB patients entered into SPSS software, and 256 controls were selected sequentially at triage from the same healthcare facilities where the cases were treated. A bivariate conditional logistic regression analysis was performed first to select candidate variables with p-values less than or equal to 0.20 for the multivariable model. Finally, variables with a p-value less than 0.05 for a matched adjusted odds ratio (mORadj) were reported as independent determinants of TB disease development. RESULTS The mean age of the cases was nine years, while that of the controls was 10 years. Males comprised 126 cases (49.2%) and 119 controls (46.5%), with the remainder being females. Ninety-nine (38.7%) of the cases were not BCG-vaccinated, compared to 58 (22.7%) of the controls. Household TB contact was experienced by 43 (16.8%) of the cases and 10 (3.9%) of the controls. Twenty-two (8.6%) of the cases and six (2.3%) of the controls were exposed to a cigarette smoker in their household. Twenty-two (8.6%) of the cases and three (1.2%) of the controls were positive for HIV. Children who were not vaccinated with BCG at birth or within two weeks of birth had more than twice the odds (mORadj = 2.11, 95% CI = 1.28-3.48) of developing TB compared to those who were. Children who ever lived with a TB-sick family member (mORadj = 4.28, 95% CI = 1.95-9.39), smoking family members (mORadj = 3.15, 95% CI = 1.07-9.27), and HIV-infected children (mORadj = 8.71, 95% CI = 1.96-38.66) also had higher odds of developing TB disease than their counterparts. CONCLUSIONS Being BCG-unvaccinated, having household TB contact, having a smoker in the household, and being HIV-infected were found to be independent determinants of TB disease development among children.
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Affiliation(s)
- Abay Burusie
- Department of Public Health, College of Health Sciences, Arsi University, Asella, Ethiopia
- School of Public Health, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Fikre Enquesilassie
- School of Public Health, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Nicole Salazar-Austin
- Division of Pediatric Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Adamu Addissie
- School of Public Health, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
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Gordhan BG, Padarath K, Sewcharran A, McIvor A, VanNieuwenhze MS, Waja Z, Martinson N, Kana BD. Clinical Strains of Mycobacterium tuberculosis Representing Different Genotype Families Exhibit Distinct Propensities to Adopt the Differentially Culturable State. Pathogens 2024; 13:318. [PMID: 38668273 PMCID: PMC11054447 DOI: 10.3390/pathogens13040318] [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: 01/31/2024] [Revised: 03/20/2024] [Accepted: 03/27/2024] [Indexed: 04/29/2024] Open
Abstract
Growing evidence points to the presence of differentially culturable tubercle bacteria (DCTB) in clinical specimens from individuals with active tuberculosis (TB) disease. These bacteria are unable to grow on solid media but can resuscitate in liquid media. Given the epidemiological success of certain clinical genotype families of Mycobacterium tuberculosis, we hypothesize that different strains may have distinct mechanisms of adaptation and tolerance. We used an in vitro carbon starvation model to determine the propensity of strains from lineages 2 and 4 that included the Beijing and LAM families respectively, to generate DCTB. Beijing strains were associated with a greater propensity to produce DCTB compared to LAM strains. Furthermore, LAM strains required culture filtrate (CF) for resuscitation whilst starved Beijing strains were not dependent on CF. Moreover, Beijing strains showed improved resuscitation with cognate CF, suggesting the presence of unique growth stimulatory molecules in this family. Analysis of starved Beijing and LAM strains showed longer cells, which with resuscitation were restored to a shorter length. Cell wall staining with fluorescent D-amino acids identified strain-specific incorporation patterns, indicating that cell surface remodeling during resuscitation was distinct between clinical strains. Collectively, our data demonstrate that M. tuberculosis clinical strains from different genotype lineages have differential propensities to generate DCTB, which may have implications for TB treatment success.
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Affiliation(s)
- Bhavna Gowan Gordhan
- Department of Science and Innovation and the National Research Foundation Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2017, South Africa; (B.G.G.); (K.P.); (A.S.); (A.M.)
- National Health Laboratory Service, Johannesburg 2000, South Africa
| | - Kiyasha Padarath
- Department of Science and Innovation and the National Research Foundation Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2017, South Africa; (B.G.G.); (K.P.); (A.S.); (A.M.)
- National Health Laboratory Service, Johannesburg 2000, South Africa
| | - Astika Sewcharran
- Department of Science and Innovation and the National Research Foundation Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2017, South Africa; (B.G.G.); (K.P.); (A.S.); (A.M.)
- National Health Laboratory Service, Johannesburg 2000, South Africa
| | - Amanda McIvor
- Department of Science and Innovation and the National Research Foundation Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2017, South Africa; (B.G.G.); (K.P.); (A.S.); (A.M.)
- National Health Laboratory Service, Johannesburg 2000, South Africa
| | | | - Ziyaad Waja
- Perinatal HIV Research Unit (PHRU), University of the Witwatersrand, Johannesburg 2017, South Africa; (Z.W.); (N.M.)
| | - Neil Martinson
- Perinatal HIV Research Unit (PHRU), University of the Witwatersrand, Johannesburg 2017, South Africa; (Z.W.); (N.M.)
- Center for TB Research, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Bavesh Davandra Kana
- Department of Science and Innovation and the National Research Foundation Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2017, South Africa; (B.G.G.); (K.P.); (A.S.); (A.M.)
- National Health Laboratory Service, Johannesburg 2000, South Africa
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Schami A, Islam MN, Belisle JT, Torrelles JB. Drug-resistant strains of Mycobacterium tuberculosis: cell envelope profiles and interactions with the host. Front Cell Infect Microbiol 2023; 13:1274175. [PMID: 38029252 PMCID: PMC10664572 DOI: 10.3389/fcimb.2023.1274175] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 10/02/2023] [Indexed: 12/01/2023] Open
Abstract
In the past few decades, drug-resistant (DR) strains of Mycobacterium tuberculosis (M.tb), the causative agent of tuberculosis (TB), have become increasingly prevalent and pose a threat to worldwide public health. These strains range from multi (MDR) to extensively (XDR) drug-resistant, making them very difficult to treat. Further, the current and future impact of the Coronavirus Disease 2019 (COVID-19) pandemic on the development of DR-TB is still unknown. Although exhaustive studies have been conducted depicting the uniqueness of the M.tb cell envelope, little is known about how its composition changes in relation to drug resistance acquisition. This knowledge is critical to understanding the capacity of DR-M.tb strains to resist anti-TB drugs, and to inform us on the future design of anti-TB drugs to combat these difficult-to-treat strains. In this review, we discuss the complexities of the M.tb cell envelope along with recent studies investigating how M.tb structurally and biochemically changes in relation to drug resistance. Further, we will describe what is currently known about the influence of M.tb drug resistance on infection outcomes, focusing on its impact on fitness, persister-bacteria, and subclinical TB.
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Affiliation(s)
- Alyssa Schami
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX, United States
- Integrated Biomedical Sciences Program, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - M. Nurul Islam
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States
| | - John T. Belisle
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States
| | - Jordi B. Torrelles
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX, United States
- International Center for the Advancement of Research & Education, International Center for the Advancement of Research & Education, Texas Biomedical Research Institute, San Antonio, TX, United States
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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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Renardy ME, Gillen C, Yang Z, Mukasa L, Bates J, Butler R, Kirschner DE. Disease phenotypic and geospatial features vary across genetic lineages for Tuberculosis within Arkansas, 2010-2020. PLOS GLOBAL PUBLIC HEALTH 2023; 3:e0001580. [PMID: 36963087 PMCID: PMC10022325 DOI: 10.1371/journal.pgph.0001580] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 01/16/2023] [Indexed: 02/25/2023]
Abstract
Tuberculosis (TB) elimination in the United States remains elusive, and community-specific, localized intervention strategies may be necessary to meet elimination goals. A better understanding of the genotypic diversity of Mtb, the population subgroups affected by different TB strains, and differences in disease presentation associated with these strains can aid in identifying risk groups and designing tailored interventions. We analyze TB incidence and genotype data from all Arkansas counties over an 11-year time span from 2010 through 2020. We use statistical methods and geographic information systems (GIS) to identify demographic and disease phenotypic characteristics that are associated with different Mtb genetic lineages in the study area. We found the following variables to be significantly associated with genetic lineage (p<0.05): patient county, patient birth country, patient ethnicity, race, IGRA result, disease site, chest X-ray result, whether or not a case was identified as part of a cluster, patient age, occupation risk, and date arrived in the US. Different Mtb lineages affect different subpopulations in Arkansas. Lineage 4 (EuroAmerican) and Lineage 2 (East Asian) are most prevalent, although the spatial distributions differ substantially, and lineage 2 (East Asian) is more frequently associated with case clusters. The Marshallese remain a particularly high-risk group for TB in Arkansas.
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Affiliation(s)
- Marissa E Renardy
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Craig Gillen
- Department of Biology, AdventHealth University, Orlando, FL, United States of America
| | - Zhenhua Yang
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Leonard Mukasa
- Arkansas Department of Health, Little Rock, AR, United States of America
- Epidemiology Department in the, Boozman College of Public Health at the University of Arkansas Center for Health Sciences, Little Rock, AR, United States of America
| | - Joseph Bates
- Arkansas Department of Health, Little Rock, AR, United States of America
- Epidemiology Department in the, Boozman College of Public Health at the University of Arkansas Center for Health Sciences, Little Rock, AR, United States of America
| | - Russ Butler
- Department of Biology, AdventHealth University, Orlando, FL, United States of America
| | - Denise E Kirschner
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
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Multiplexed Strain Phenotyping Defines Consequences of Genetic Diversity in Mycobacterium tuberculosis for Infection and Vaccination Outcomes. mSystems 2022; 7:e0011022. [PMID: 35430871 PMCID: PMC9239107 DOI: 10.1128/msystems.00110-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
There is growing evidence that genetic diversity in Mycobacterium tuberculosis, the causative agent of tuberculosis, contributes to the outcomes of infection and public health interventions, such as vaccination. Epidemiological studies suggest that among the phylogeographic lineages of M. tuberculosis, strains belonging to a sublineage of Lineage 2 (mL2) are associated with concerning clinical features, including hypervirulence, treatment failure, and vaccine escape. The global expansion and increasing prevalence of this sublineage has been attributed to the selective advantage conferred by these characteristics, yet confounding host and environmental factors make it difficult to identify the bacterial determinants driving these associations in human studies. Here, we developed a molecular barcoding strategy to facilitate high-throughput, experimental phenotyping of M. tuberculosis clinical isolates. This approach allowed us to characterize growth dynamics for a panel of genetically diverse M. tuberculosis strains during infection and after vaccination in the mouse model. We found that mL2 strains exhibit distinct growth dynamics in vivo and are resistant to the immune protection conferred by Bacillus Calmette-Guerin (BCG) vaccination. The latter finding corroborates epidemiological observations and demonstrates that mycobacterial features contribute to vaccine efficacy. To investigate the genetic and biological basis of mL2 strains’ distinctive phenotypes, we performed variant analysis, transcriptional studies, and genome-wide transposon sequencing. We identified functional genetic changes across multiple stress and host response pathways in a representative mL2 strain that are associated with variants in regulatory genes. These adaptive changes may underlie the distinct clinical characteristics and epidemiological success of this lineage. IMPORTANCE Tuberculosis, caused by the bacterium Mycobacterium tuberculosis, is a remarkably heterogeneous disease, a feature that complicates clinical care and public health interventions. The contributions of pathogen genetic diversity to this heterogeneity are uncertain, in part due to the challenges of experimentally manipulating M. tuberculosis, a slow-growing, biosafety level 3 organism. To overcome these challenges, we applied a molecular barcoding strategy to a panel of M. tuberculosis clinical isolates. This novel application of barcoding permitted the high-throughput characterization of M. tuberculosis strain growth dynamics and vaccine resistance in the mouse model of infection. Integrating these results with genomic analyses, we uncover bacterial pathways that contribute to infection outcomes, suggesting targets for improved therapeutics and vaccines.
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Mokrousov I, Pasechnik O, Vyazovaya A, Yarusova I, Gerasimova A, Blokh A, Zhuravlev V. Impact of pathobiological diversity of Mycobacterium tuberculosis on clinical features and lethal outcome of tuberculosis. BMC Microbiol 2022; 22:50. [PMID: 35135478 PMCID: PMC8822639 DOI: 10.1186/s12866-022-02461-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 01/31/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mycobacterium tuberculosis population in Russia is dominated by the notorious Beijing genotype whose major variants are characterized by contrasting resistance and virulence properties. Here we studied how these strain features could impact the progression of pulmonary tuberculosis (TB) concerning clinical manifestation and lethal outcome. RESULTS The study sample included 548 M. tuberculosis isolates from 548 patients with newly diagnosed pulmonary TB in Omsk, West Siberia, Russia. Strains were subjected to drug susceptibility testing and genotyping to detect lineages, sublineages, and subtypes (within Beijing genotype). The Beijing genotype was detected in 370 (67.5%) of the studied strains. The strongest association with multidrug resistance (MDR) was found for epidemic cluster Beijing B0/W148 (modern sublineage) and two recently discovered MDR clusters 1071-32 and 14717-15 of the ancient Beijing sublineage. The group of patients infected with hypervirulent and highly lethal (in a mouse model) Beijing 14717-15 showed the highest rate of lethal outcome (58.3%) compared to Beijing B0/W148 (31.4%; P = 0.06), Beijing Central Asian/Russian (29.7%, P = 0.037), and non-Beijing (15.2%, P = 0.001). The 14717-15 cluster mostly included isolates from patients with infiltrative but not with fibrous-cavernous and disseminated TB. In contrast, a group infected with low virulent 1071-32-cluster had the highest rate of fibrous-cavernous TB, possibly reflecting the capacity of these strains for prolonged survival and chronicity of the TB process. CONCLUSIONS The group of patients infected with hypervirulent and highly lethal in murine model 14717-15 cluster had the highest proportion of the lethal outcome (58.3%) compared to the groups infected with Beijing B0/W148 (31.4%) and non-Beijing (15.2%) isolates. This study carried out in the TB high-burden area highlights that not only drug resistance but also strain virulence should be considered in the implementation of personalized TB treatment.
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Affiliation(s)
- Igor Mokrousov
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, 14 Mira street, St. Petersburg, 197101, Russia.
| | - Oksana Pasechnik
- Department of Public Health, Omsk State Medical University, Omsk, Russia
| | - Anna Vyazovaya
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, 14 Mira street, St. Petersburg, 197101, Russia
| | - Irina Yarusova
- Bacteriology Laboratory, Clinical Tuberculosis Dispensary, Omsk, Russia
| | - Alena Gerasimova
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, 14 Mira street, St. Petersburg, 197101, Russia
| | - Aleksey Blokh
- Department of Epidemiology, Omsk State Medical University, Omsk, Russia
| | - Viacheslav Zhuravlev
- St. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia
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Genetic Diversity and Transmission of Multidrug Resistant Mycobacterium tuberculosis strains in Lusaka, Zambia. Int J Infect Dis 2021; 114:142-150. [PMID: 34718155 DOI: 10.1016/j.ijid.2021.10.044] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 10/15/2021] [Accepted: 10/19/2021] [Indexed: 11/20/2022] Open
Abstract
OBJECTIVE Zambia is among the 30 high tuberculosis burden countries in the world. Despite increasing reports of multidrug resistant tuberculosis (MDR-TB) in routine surveillance, information on the transmission of MDR Mycobacterium tuberculosis strains is largely unknown. This study elucidated genetic diversity and transmission of MDR M. tuberculosis strains in Lusaka, Zambia. METHODS Eighty-five MDR M. tuberculosis samples collected from the year 2013 to 2017 at the University Teaching Hospital were used. Drug-resistance associated gene sequencing, spoligotyping, 24-loci mycobacterial interspersed repetitive units-variable number of tandem repeats, and multiplex PCR for RD-Rio sub-lineage identification were applied. RESULTS Clades identified were LAM (48%), CAS (29%), T (14%), X (6%) and Harlem (2%). Strains belonging to SITs 21/CAS1-Kili and 20/LAM1 formed the largest clonal complexes. Combined spoligotyping and 24 loci-MIRU-VNTR revealed 47 genotypic patterns with clustering rate of 63%. Ninety five percent of LAM strains belonged to RD-Rio sub-lineage. CONCLUSION The high clustering rate suggested that a large proportion of MDR-TB was due to recent transmission rather than independent acquisition of MDR. This spread was attributed to clonal expansion of SIT21/CAS1-Kili and SIT20/LAM1 strains. Therefore, TB control programs recommending genotyping coupled with conventional epidemiological methods can guide measures for stopping the spread of MDR-TB.
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Negrete-Paz AM, Vázquez-Marrufo G, Vázquez-Garcidueñas MS. Whole-genome comparative analysis at the lineage/sublineage level discloses relationships between Mycobacterium tuberculosis genotype and clinical phenotype. PeerJ 2021; 9:e12128. [PMID: 34589306 PMCID: PMC8434806 DOI: 10.7717/peerj.12128] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 08/17/2021] [Indexed: 11/20/2022] Open
Abstract
Background Human tuberculosis (TB) caused by members of the Mycobacterium tuberculosis complex (MTBC) is the main cause of death among infectious diseases worldwide. Pulmonary TB (PTB) is the most common clinical phenotype of the disease, but some patients develop an extrapulmonary (EPTB) phenotype in which any organ or tissue can be affected. MTBC species include nine phylogenetic lineages, with some appearing globally and others being geographically restricted. EPTB can or not have pulmonary involvement, challenging its diagnosis when lungs are not implicated, thus causing an inadequate treatment. Finding evidence of a specific M. tuberculosis genetic background associated with EPTB is epidemiologically relevant due to the virulent and multidrug-resistant strains isolated from such cases. Until now, the studies conducted to establish associations between M. tuberculosis lineages and PTB/EPTB phenotypes have shown inconsistent results, which are attributed to the strain predominance from specific M. tuberculosis lineages/sublineages in the samples analyzed and the use of low-resolution phylogenetic tools that have impaired sublineage discrimination abilities. The present work elucidates the relationships between the MTBC strain lineages/sublineages and the clinical phenotypes of the disease as well as the antibiotic resistance of the strains. Methods To avoid biases, we retrieved the raw genomic reads (RGRs) of all (n = 245) the M. tuberculosis strains worldwide causing EPTB available in databases and an equally representative sample of the RGRs (n = 245) of PTB strains. A multiple alignment was constructed, and a robust maximum likelihood phylogeny based on single-nucleotide polymorphisms was generated, allowing effective strain lineage/sublineage assignment. Results A significant Odds Ratio (OR range: 1.8–8.1) association was found between EPTB and the 1.1.1, 1.2.1, 4.1.2.1 and ancestral Beijing sublineages. Additionally, a significant association between PTB with 4.3.1, 4.3.3, and 4.5 and Asian African 2 and Europe/Russia B0/W148 modern Beijing sublineages was found. We also observed a significant association of Lineage 3 strains with multidrug resistance (OR 3.8; 95% CI [1.1–13.6]), as well as between modern Beijing sublineages and antibiotic resistance (OR 4.3; 3.8–8.6). In this work, it was found that intralineage diversity can drive differences in the immune response that triggers the PTB/EPTB phenotype.
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Affiliation(s)
- Andrea Monserrat Negrete-Paz
- Centro Multidisciplinario de Estudios en Biotecnología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Michoacana de San Nicolás de Hidalgo, Tarímbaro, Michoacán, Mexico
| | - Gerardo Vázquez-Marrufo
- Centro Multidisciplinario de Estudios en Biotecnología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Michoacana de San Nicolás de Hidalgo, Tarímbaro, Michoacán, Mexico
| | - Ma Soledad Vázquez-Garcidueñas
- División de Estudios de Posgrado, Facultad de Ciencias Médicas y Biológicas "Dr. Ignacio Chávez", Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, Mexico
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12
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Nguyen NTB, Le Ngoc H, Nguyen NV, Dinh LV, Nguyen HV, Nguyen HT, Denning DW. Chronic Pulmonary Aspergillosis Situation among Post Tuberculosis Patients in Vietnam: An Observational Study. J Fungi (Basel) 2021; 7:532. [PMID: 34209322 PMCID: PMC8307285 DOI: 10.3390/jof7070532] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 06/25/2021] [Accepted: 06/28/2021] [Indexed: 12/28/2022] Open
Abstract
This study provides a brief view of chronic pulmonary aspergillosis (CPA) in the post-tuberculosis treatment community in Vietnam, a high burden tuberculosis (TB) country. In three months in late 2019, 70 post-TB patients managed at Vietnam National Lung Hospital were enrolled. Of these, 38 (54.3%) had CPA. The male/female ratio was 3/1 (28 males and ten females). CPA patients had a mean age of 59 ± 2.3 years (95%CI 54.4-63.6). The mean Body mass index (BMI) was 19.0 ± 0.5 (18.0-20.0) and 16 of 38 (42.1%) patients had concurrent diseases, the most common of which were chronic obstructive pulmonary disease (COPD) and diabetes. Twenty-six patients (68.4%) developed hemoptysis, 21 (55.3%) breathlessness, and weight loss was seen in 30 (78.9%). Anaemia was seen in 15 (39.5%) and 27 of 38 (71.1%) patients had an elevated C-reactive protein (CRP). The most common radiological findings were multiple cavities (52.6%) and pleural thickening (42.7%), followed by aspergilloma (29.0%) and non-specific infiltrates. There were five of 38 patients (13.2%) with a cavity containing a fungal ball on the chest X-ray, but when the high resolution computed tomography (HRCT) was examined, the number of patients with fungal balls rose to 11 (28.9%). Overall, 34 of 38 (89.5%) cases had an elevated Aspergillus IgG with an optical density ≥ 1, and in 2 cases, it was 0.9-1.0 (5%), borderline positive. In nine patients (23.7%) Aspergillus fumigatus was cultured from sputum. CPA is an under-recognised problem in Vietnam and other high burden TB countries, requiring a different diagnostic approach and treatment and careful management. HRCT and Aspergillus IgG serum test are recommended as initial diagnostic tools for CPA diagnosis.
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Affiliation(s)
- Ngoc Thi Bich Nguyen
- Vietnam National Lung Hospital, Hanoi 10000, Vietnam; (N.V.N.); (L.V.D.); (H.V.N.); (H.T.N.)
| | - Huy Le Ngoc
- Vietnam National Lung Hospital, Hanoi 10000, Vietnam; (N.V.N.); (L.V.D.); (H.V.N.); (H.T.N.)
| | - Nhung Viet Nguyen
- Vietnam National Lung Hospital, Hanoi 10000, Vietnam; (N.V.N.); (L.V.D.); (H.V.N.); (H.T.N.)
| | - Luong Van Dinh
- Vietnam National Lung Hospital, Hanoi 10000, Vietnam; (N.V.N.); (L.V.D.); (H.V.N.); (H.T.N.)
| | - Hung Van Nguyen
- Vietnam National Lung Hospital, Hanoi 10000, Vietnam; (N.V.N.); (L.V.D.); (H.V.N.); (H.T.N.)
| | - Huyen Thi Nguyen
- Vietnam National Lung Hospital, Hanoi 10000, Vietnam; (N.V.N.); (L.V.D.); (H.V.N.); (H.T.N.)
| | - David W. Denning
- Manchester Academic Health Science Centre, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M23 9LT, UK
- Global Action Fund for Fungal Infections, 1208 Geneva, Switzerland
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13
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Asare-Baah M, Séraphin MN, Salmon LAT, Lauzardo M. Effect of mixed strain infections on clinical and epidemiological features of tuberculosis in Florida. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2021; 87:104659. [PMID: 33276149 PMCID: PMC7855629 DOI: 10.1016/j.meegid.2020.104659] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 11/18/2020] [Accepted: 11/29/2020] [Indexed: 10/22/2022]
Abstract
Mixed infections with genetically distinct Mycobacterium tuberculosis (MTB) strains within a single host have been documented in different settings; however, this phenomenon is rarely considered in the management and care of new and relapse tuberculosis (T.B.) cases. This study aims to establish the epidemiological and clinical features of mixed infections among culture-confirmed T.B. patients enrolled in tuberculosis care at the Florida Department of Health (FDOH) and measure its association with T.B. mortality. We analyzed de-identified surveillance data of T.B. cases enrolled in T.B. care from April 2008 to January 2018. Mixed MTB infection was determined by the presence of more than one Copy Number Variant (CNV) in at least one locus, based on the genotype profile pattern of at least one isolate using 24-locus Mycobacterial Interspersed Repetitive Unit-Variable Number Tandem Repeat (MIRU-VNTR). The prevalence of mixed MTB infections among the 4944 culture-confirmed TB cases included in this analysis was 2.6% (129). Increased odds of mixed infections were observed among middle-aged patients, 45-64 years (AOR = 2.38; 95% CI: 0.99, 5.69; p = 0.0513), older adults 65 years and above (AOR = 3.95; 95% CI: 1.63, 9.58; p = 0.0023) and patients with diabetes (OR = 1.77; 95% CI: 1.12, 2.80; p = 0.0150). There was no significant association between mixed infections and death. Our study provides insight into the epidemiological and clinical characteristics of patients with mixed MTB infections, which is essential in the management of T.B. patients.
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Affiliation(s)
- Michael Asare-Baah
- Department of Epidemiology, University of Florida, College of Public Health and Health Professions, College of Medicine, 2004 Mowry Road, P.O. Box 100231, Gainesville, FL 32610, United States; Emerging Pathogens Institute, University of Florida, 2055 Mowry Road, P.O. Box 100009, Gainesville, FL 32610, United States.
| | - Marie Nancy Séraphin
- Emerging Pathogens Institute, University of Florida, 2055 Mowry Road, P.O. Box 100009, Gainesville, FL 32610, United States; Division of Infectious Diseases and Global Medicine, University of Florida, College of Medicine, 2055 Mowry Road, P.O. Box 103600, Gainesville, FL 32610, United States
| | - LaTweika A T Salmon
- Florida Department of Health, Bureau of Tuberculosis Control, 4052 Bald Cypress Way, Bin A-20, Tallahassee, FL 32399, United States
| | - Michael Lauzardo
- Emerging Pathogens Institute, University of Florida, 2055 Mowry Road, P.O. Box 100009, Gainesville, FL 32610, United States; Division of Infectious Diseases and Global Medicine, University of Florida, College of Medicine, 2055 Mowry Road, P.O. Box 103600, Gainesville, FL 32610, United States
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14
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Krishnakumariamma K, Ellappan K, Muthuraj M, Tamilarasu K, Kumar SV, Joseph NM. Molecular diagnosis, genetic diversity and drug sensitivity patterns of Mycobacterium tuberculosis strains isolated from tuberculous meningitis patients at a tertiary care hospital in South India. PLoS One 2020; 15:e0240257. [PMID: 33017455 PMCID: PMC7535050 DOI: 10.1371/journal.pone.0240257] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 09/23/2020] [Indexed: 12/13/2022] Open
Abstract
Tuberculous meningitis (TBM) is the most severe form of Mycobacterium tuberculosis (Mtb) infection in humans and is a public health concern worldwide. We evaluated the performance of GeneXpert MTB/RIF (GeneXpert) for the diagnosis of TBM. In addition, genetic diversity and drug susceptibility profiling of Mtb strains isolated from TBM patients were also investigated. A total of 293 TBM suspected cerebrospinal fluid (CSF) samples were collected and subjected to GeneXpert and Mycobacterial Growth Indicator Tube (MGIT 960) culture, respectively. Sensitivity and specificity of GeneXpert was 72.7% and 98.5%, respectively by using MGIT 960 as a gold standard (GeneXpert (n = 20, 6.8%) vs MGIT 960 (n = 22, 7.5%)). All Mtb positive cultures were subjected to 24-locus Mycobacterial Interspersed Repetitive Unit Variable Number Tandem Repeat (MIRU-VNTR) typing, Line probe assay (LPA) and MGIT 960- Drug Susceptibility Testing (DST). The rpoB gene was amplified and sequenced for selected isolates. Among our TBM patients, East African Indian (EAI) lineage (n = 16, 72.7%) was most predominant followed by Beijing (n = 3, 13.6%), S-family (n = 2, 9.1%) and Delhi/CAS (n = 1, 4.5%). Three Mtb strains were found to be Isoniazid (INH) resistant by MGIT 960; however LPA revealed that two strains were INH resistant and one strain was multi drug resistant (MDR) (Resistant to Isoniazid and Rifampicin (RIF)). We identified rifampicin resistant isolate with the mutation D516F in rifampicin resistance-determining region (RRDR) and observed discordant results between LPA, GeneXpert and MGIT 960. In addition, GeneXpert showing false RIF resistance was identified (no mutation in RRDR). We conclude that GeneXpert is useful for the diagnostic confirmation of TBM; however a GeneXpert negative sample should be subjected to MGIT 960 culture or LPA to rule out TBM. EAI lineage was the most predominant among TBM patients in South India and associated with drug resistance. The discordance between GeneXpert, MGIT 960 and LPA with respect to rifampicin resistance has to be ruled out to avoid TB treatment failure or relapse.
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Affiliation(s)
- Krishnapriya Krishnakumariamma
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Pondicherry, India
| | - Kalaiarasan Ellappan
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Pondicherry, India
| | - Muthaiah Muthuraj
- Intermediate Reference Laboratory, Government Hospital for Chest Diseases, Pondicherry, India
| | - Kadhiravan Tamilarasu
- Department of Medicine, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Pondicherry, India
| | - Saka Vinod Kumar
- Department of Pulmonary Medicine, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Pondicherry, India
| | - Noyal Mariya Joseph
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Pondicherry, India
- * E-mail:
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15
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Peters JS, Ismail N, Dippenaar A, Ma S, Sherman DR, Warren RM, Kana BD. Genetic Diversity in Mycobacterium tuberculosis Clinical Isolates and Resulting Outcomes of Tuberculosis Infection and Disease. Annu Rev Genet 2020; 54:511-537. [PMID: 32926793 DOI: 10.1146/annurev-genet-022820-085940] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Tuberculosis claims more human lives than any other bacterial infectious disease and represents a clear and present danger to global health as new tools for vaccination, treatment, and interruption of transmission have been slow to emerge. Additionally, tuberculosis presents with notable clinical heterogeneity, which complicates diagnosis, treatment, and the establishment of nonrelapsing cure. How this heterogeneity is driven by the diversity ofclinical isolates of the causative agent, Mycobacterium tuberculosis, has recently garnered attention. Herein, we review advances in the understanding of how naturally occurring variation in clinical isolates affects transmissibility, pathogenesis, immune modulation, and drug resistance. We also summarize how specific changes in transcriptional responses can modulate infection or disease outcome, together with strain-specific effects on gene essentiality. Further understanding of how this diversity of M. tuberculosis isolates affects disease and treatment outcomes will enable the development of more effective therapeutic options and vaccines for this dreaded disease.
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Affiliation(s)
- Julian S Peters
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg 2000, South Africa; ,
| | - Nabila Ismail
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg 7505, South Africa; ,
| | - Anzaan Dippenaar
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg 7505, South Africa; , .,Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, 2000, Belgium;
| | - Shuyi Ma
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington 98109, USA; ,
| | - David R Sherman
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington 98109, USA; ,
| | - Robin M Warren
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg 7505, South Africa; ,
| | - Bavesh D Kana
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg 2000, South Africa; ,
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16
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Pokam BDT, Yeboah-Manu D, Lawson L, Guemdjom PW, Okonu R, Madukaji L, Yhiler NY, Asuquo AE. Molecular Analysis of Mycobacterium tuberculosis Isolated in the North Central Zone of Nigeria. J Epidemiol Glob Health 2020; 9:259-265. [PMID: 31854167 PMCID: PMC7310797 DOI: 10.2991/jegh.k.191015.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 10/05/2019] [Indexed: 11/10/2022] Open
Abstract
Tuberculosis (TB) incidence in Nigeria is high, with a significant burden of TB/Human Immunodeficiency Virus (HIV). Genotyping and drug susceptibility of Mycobacterium tuberculosis Complex (MTBC) are important in order to improve the control of the disease. This study sought to determine drug susceptibility and genetic diversity of MTBC in the country. The sputum samples of 202 patients [133 (65.8%) males/69 (34.2%) females] were collected in the North Central zone of Nigeria and cultured using Lowenstein–Jensen medium. Immunochromatography for the primary identification and Drug Susceptibility Testing (DST) by proportion method, as well as IS6110 typing, regions of difference 1, 4, 9, 12, 702, and 711, and spoligotyping were carried out on the isolates. Following the DST on 202 isolates, 51 (25.2%) showed resistance to at least one drug. Multidrug resistance was observed in 29/202 (14.4%) cases. HIV positivity [37/202 (18.3%) patients] was associated with rifampicin 9/37 (24.3%) resistance (p = 0.012) as well as gender (p = 0.009). Of the 202 isolates, 150 (74.3%) were identified as the Cameroon sublineage, followed by the UgandaI, Haarlem, and West Africa 1 with 18 (8.9%), 10 (5%), and 6 (3%), respectively. The LAM10_CAM was the most prevalent genetic family [128/202 (63.4%)], with the shared international type 61 [111 (55%) isolates] the largest cluster. Gender (p = 0.038) and age (p = 0.015) had significant associations with the LAM10_CAM family but neither with HIV (p = 0.479) nor drug resistance. Rifampicin resistance in TB/HIV coinfected patient is a major concern in the study area. The Mycobacterium africanum lineage showed a marked decrease, and the need to educate females most at risk of TB/HIV coinfection is advocated.
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Affiliation(s)
- Benjamin David Thumamo Pokam
- Department of Medical Laboratory Science, Faculty of Health Sciences, University of Buea, Buea, Cameroon.,Bacteriology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Dorothy Yeboah-Manu
- Bacteriology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | | | - Prisca Wabo Guemdjom
- Department of Public Health, Faculty of Health Sciences, University of Buea, Buea, Cameroon
| | - Ruth Okonu
- Bacteriology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | | | - Nchawa Yangkam Yhiler
- Department of Medical Laboratory Science, Faculty of Health Sciences, University of Buea, Buea, Cameroon.,Department of Allied Health, Biaka University Institute, Buea, Cameroon
| | - Anne Ebri Asuquo
- Department of Medical Laboratory Science, Faculty of Allied Medical Sciences, College of Medicine, University of Calabar, Calabar, Nigeria
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17
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Mousavi S, Amini S, Mirsaeidi M, Dabiri H, Hamzehloo G, Goudarzi H, Nasiri M. Genotyping and drug susceptibility testing of Mycobacterium tuberculosis in Iran: a multi-centre study. New Microbes New Infect 2020; 37:100729. [PMID: 32774869 PMCID: PMC7404542 DOI: 10.1016/j.nmni.2020.100729] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 02/24/2020] [Accepted: 07/09/2020] [Indexed: 01/20/2023] Open
Abstract
Tuberculosis (TB) is a deadly infection and caused 1.4 million deaths in 2018. Assessing the geographic distribution of major lineages of Mycobacterium tuberculosis can contribute greatly to TB control. Mycobacterial interspersed repetitive unit variable number tandem repeat (MIRU-VNTR) typing is commonly used to differentiate various lineages of M. tuberculosis. A total of 2747 clinical specimens were collected consecutively from October 2018 through June 2019. Clinical isolates were identified as M. tuberculosis using standard biochemical tests. The standard 15-locus MIRU-VNTR typing was used for the genotyping of clinical isolates. Drug susceptibility testing was performed using the conventional proportion method. From the collected specimens, 100 were culture positive for M. tuberculosis. Using MIRU-VNTR, 99 different patterns were detected among the 100 isolates. They were distributed in one cluster comprising two strains and 98 unique patterns. Most of our isolates were similar to New-1 and Delhi/CAS strains. Of the M. tuberculosis isolates, 83 (83.0%) were pan-susceptible and 17 (17.0%) were resistant to at least one drug. Our study showed that MIRU-VNTR is a useful method for studying the genetic diversity of M. tuberculosis isolates in different regional settings and will help the health authorities to construct a preventive programme for TB.
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Affiliation(s)
- S.M.J. Mousavi
- Department of Microbiology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - S. Amini
- Regional Tuberculosis Reference Laboratory, Tehran University of Medical Science, Tehran, Iran
| | - M. Mirsaeidi
- Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - H. Dabiri
- Department of Microbiology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - G. Hamzehloo
- Regional Tuberculosis Reference Laboratory, Tehran University of Medical Science, Tehran, Iran
| | - H. Goudarzi
- Department of Microbiology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - M.J. Nasiri
- Department of Microbiology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Sibandze DB, Magazi BT, Malinga LA, Maningi NE, Shey BA, Pasipanodya JG, Mbelle NN. Machine learning reveals that Mycobacterium tuberculosis genotypes and anatomic disease site impacts drug resistance and disease transmission among patients with proven extra-pulmonary tuberculosis. BMC Infect Dis 2020; 20:556. [PMID: 32736602 PMCID: PMC7393820 DOI: 10.1186/s12879-020-05256-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 07/14/2020] [Indexed: 11/10/2022] Open
Abstract
Background There is a general dearth of information on extrapulmonary tuberculosis (EPTB). Here, we investigated Mycobacterium tuberculosis (Mtb) drug resistance and transmission patterns in EPTB patients treated in the Tshwane metropolitan area, in South Africa. Methods Consecutive Mtb culture-positive non-pulmonary samples from unique EPTB patients underwent mycobacterial genotyping and were assigned to phylogenetic lineages and transmission clusters based on spoligotypes. MTBDRplus assay was used to search mutations for isoniazid and rifampin resistance. Machine learning algorithms were used to identify clinically meaningful patterns in data. We computed odds ratio (OR), attributable risk (AR) and corresponding 95% confidence intervals (CI). Results Of the 70 isolates examined, the largest cluster comprised 25 (36%) Mtb strains that belonged to the East Asian lineage. East Asian lineage was significantly more likely to occur within chains of transmission when compared to the Euro-American and East-African Indian lineages: OR = 10.11 (95% CI: 1.56–116). Lymphadenitis, meningitis and cutaneous TB, were significantly more likely to be associated with drug resistance: OR = 12.69 (95% CI: 1.82–141.60) and AR = 0.25 (95% CI: 0.06–0.43) when compared with other EPTB sites, which suggests that poor rifampin penetration might be a contributing factor. Conclusions The majority of Mtb strains circulating in the Tshwane metropolis belongs to East Asian, Euro-American and East-African Indian lineages. Each of these are likely to be clustered, suggesting on-going EPTB transmission. Since 25% of the drug resistance was attributable to sanctuary EPTB sites notorious for poor rifampin penetration, we hypothesize that poor anti-tuberculosis drug dosing might have a role in the development of resistance.
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Affiliation(s)
- Doctor B Sibandze
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Arcadia, Pretoria, 0007, South Africa.,National Tuberculosis Control Program, Ministry of Health, Manzini, Kingdom of Eswatini
| | - Beki T Magazi
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Arcadia, Pretoria, 0007, South Africa.,Tshwane Division, National Health Laboratory Services, Pretoria, South Africa
| | - Lesibana A Malinga
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Arcadia, Pretoria, 0007, South Africa.,Tuberculosis Platform, South African Medical Research Council, Pretoria, South Africa
| | - Nontuthuko E Maningi
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Arcadia, Pretoria, 0007, South Africa
| | - Bong-Akee Shey
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Arcadia, Pretoria, 0007, South Africa
| | - Jotam G Pasipanodya
- Center For Infectious Diseases Research and Experimental Therapeutics, Texas Tech University Health Sciences Center, 5920 Forest Park Road, Dallas, TX, 75235, USA. .,Praedicare Laboratories, 14830 Venture Drive, Dallas, TX, 75234, USA.
| | - Nontombi N Mbelle
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Arcadia, Pretoria, 0007, South Africa.,Tshwane Division, National Health Laboratory Services, Pretoria, South Africa
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19
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TbD1 deletion as a driver of the evolutionary success of modern epidemic Mycobacterium tuberculosis lineages. Nat Commun 2020; 11:684. [PMID: 32019932 PMCID: PMC7000671 DOI: 10.1038/s41467-020-14508-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 01/09/2020] [Indexed: 11/29/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) strains are classified into different phylogenetic lineages (L), three of which (L2/L3/L4) emerged from a common progenitor after the loss of the MmpS6/MmpL6-encoding Mtb-specific deletion 1 region (TbD1). These TbD1-deleted “modern” lineages are responsible for globally-spread tuberculosis epidemics, whereas TbD1-intact “ancestral” lineages tend to be restricted to specific geographical areas, such as South India and South East Asia (L1) or East Africa (L7). By constructing and characterizing a panel of recombinant TbD1-knock-in and knock-out strains and comparison with clinical isolates, here we show that deletion of TbD1 confers to Mtb a significant increase in resistance to oxidative stress and hypoxia, which correlates with enhanced virulence in selected cellular, guinea pig and C3HeB/FeJ mouse infection models, the latter two mirroring in part the development of hypoxic granulomas in human disease progression. Our results suggest that loss of TbD1 at the origin of the L2/L3/L4 Mtb lineages was a key driver for their global epidemic spread and outstanding evolutionary success. Mycobacterium tuberculosis (Mtb) modern strains emerged from a common progenitor after the loss of Mtb-specific deletion 1 region (TbD1). Here, the authors show that deletion of TbD1 correlates with enhanced Mtb virulence in animal models, mirroring the development of hypoxic granulomas in human disease progression.
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Poonawala H, Kumar N, Peacock SJ. A review of published spoligotype data indicates the diversity of Mycobacterium tuberculosis from India is under-represented in global databases. INFECTION GENETICS AND EVOLUTION 2019; 78:104072. [PMID: 31618692 DOI: 10.1016/j.meegid.2019.104072] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 10/07/2019] [Accepted: 10/11/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND Mycobacterium tuberculosis (MTBC) lineages differ in clinical presentation, virulence, transmission, drug resistance and immunological responses. Despite having the largest burden of tuberculosis (TB) in the world, strains from India are underrepresented in international databases. We reviewed published spoligotype data to determine the distribution and diversity of MTBC lineages in India. METHODS A Pubmed/MEDLINE search identified 34 M. tuberculosis spoligotyping studies from India. Spoligotype patterns were extracted and the Spoligotype International Type (SIT) number, sub-lineage and lineage determined. Minimum Spanning Trees were used to determine relationships between patterns. RESULTS We identified 1528 spoligotype patterns distributed across 8300 isolates; 6733 isolates belonged to 472 SITs, with 53% of all isolates belonging to 12 SITs with at least 100 isolates each. Lineage 1 and Lineage 3 made up 67% of all isolates, although a lineage could not be assigned for 16% of isolates. Lineage 1 isolates were most common in Southern, Western and Eastern India, and Lineage 3 was most common in Northern and Central India. The RULE, CBN and KBBN lineage prediction algorithms from the TB-lineage tools performed variably, with the correct lineage predicted correctly for only 64% of patterns with known lineage. Using a consensus definition, 64% of the 1359 isolates with unknown lineage were assigned to Lineage 1, and 14% each were assigned to Lineages 3 and 4. With these lineage assignments, 80% of all isolates belonged to either Lineage 1 or Lineage 3. CONCLUSION Our findings indicate significant M. tuberculosis diversity in India. The documentation of 1056 orphan and unreported patterns indicate that this diversity is under-represented in global databases.
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Affiliation(s)
- Husain Poonawala
- National Institute for Research in Tuberculosis, Chetpet, Chennai 600031, India; Institute of Public Health, Banashankari, Bangalore 560070, India.
| | - Narender Kumar
- Department of Medicine, University of Cambridge, Hills Rd, Cambridge CB2 0QQ, United Kingdom
| | - Sharon J Peacock
- Department of Medicine, University of Cambridge, Hills Rd, Cambridge CB2 0QQ, United Kingdom.
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van Leeuwen LM, Versteegen P, Zaharie SD, van Elsland SL, Jordaan A, Streicher EM, Warren RM, van der Kuip M, van Furth AM. Bacterial Genotyping of Central Nervous System Tuberculosis in South Africa: Heterogenic Mycobacterium tuberculosis Infection and Predominance of Lineage 4. J Clin Microbiol 2019; 57:e00415-19. [PMID: 31189579 PMCID: PMC6663911 DOI: 10.1128/jcm.00415-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 05/30/2019] [Indexed: 12/20/2022] Open
Abstract
Tuberculous meningitis (TBM), the most severe extrapulmonary manifestation of tuberculosis, is caused by the pathogen Mycobacterium tuberculosis The M. tuberculosis complex includes seven lineages, all described to harbor a unique geographical dissemination pattern and clinical presentation. In this study, we set out to determine whether a certain M. tuberculosis lineage demonstrated tropism to cause TBM in patients from Cape Town, South Africa. DNA was extracted from formalin-fixed paraffin-embedded central nervous system (CNS) tissue from a unique neuropathological cohort of 83 TBM patients, collected between 1975 and 2012. M. tuberculosis lineages 1, 2, 3, and 4 were determined using an allele-specific PCR and Sanger sequencing. Of the 83 patient specimens tested, bacterial characterization could be performed on 46 specimens (55%). M. tuberculosis lineage 4 was present in 26 patient specimens (56%), and non-lineage 4 was identified in 10 cases (22%). Moreover, genomic heterogeneity was detected in the CNS specimens of 7 adults and 3 children. We could show that infection of the CNS is not restricted to a single M. tuberculosis lineage and that even young children with rapid progression of disease can harbor more than one M. tuberculosis lineage in the CNS.
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Affiliation(s)
- L M van Leeuwen
- Department of Pediatric Infectious Diseases and Immunology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | - P Versteegen
- Department of Pediatric Infectious Diseases and Immunology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | - S D Zaharie
- Department of Anatomical Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - S L van Elsland
- Department of Paediatrics and Child Health, Tygerberg Hospital, Stellenbosch University, Cape Town, South Africa
| | - A Jordaan
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, DST-NRF Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - E M Streicher
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, DST-NRF Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - R M Warren
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, DST-NRF Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - M van der Kuip
- Department of Pediatric Infectious Diseases and Immunology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | - A M van Furth
- Department of Pediatric Infectious Diseases and Immunology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
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Phylogenetic Analysis of Mycobacterium tuberculosis Strains in Wales by Use of Core Genome Multilocus Sequence Typing To Analyze Whole-Genome Sequencing Data. J Clin Microbiol 2019; 57:JCM.02025-18. [PMID: 30944195 DOI: 10.1128/jcm.02025-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 03/27/2019] [Indexed: 01/08/2023] Open
Abstract
An inability to standardize the bioinformatic data produced by whole-genome sequencing (WGS) has been a barrier to its widespread use in tuberculosis phylogenetics. The aim of this study was to carry out a phylogenetic analysis of tuberculosis in Wales, United Kingdom, using Ridom SeqSphere software for core genome multilocus sequence typing (cgMLST) analysis of whole-genome sequencing data. The phylogenetics of tuberculosis in Wales have not previously been studied. Sixty-six Mycobacterium tuberculosis isolates (including 42 outbreak-associated isolates) from south Wales were sequenced using an Illumina platform. Isolates were assigned to principal genetic groups, single nucleotide polymorphism (SNP) cluster groups, lineages, and sublineages using SNP-calling protocols. WGS data were submitted to the Ridom SeqSphere software for cgMLST analysis and analyzed alongside 179 previously lineage-defined isolates. The data set was dominated by the Euro-American lineage, with the sublineage composition being dominated by T, X, and Haarlem family strains. The cgMLST analysis successfully assigned 58 isolates to major lineages, and the results were consistent with those obtained by traditional SNP mapping methods. In addition, the cgMLST scheme was used to resolve an outbreak of tuberculosis occurring in the region. This study supports the use of a cgMLST method for standardized phylogenetic assignment of tuberculosis isolates and for outbreak resolution and provides the first insight into Welsh tuberculosis phylogenetics, identifying the presence of the Haarlem sublineage commonly associated with virulent traits.
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Guthrie JL, Marchand-Austin A, Cronin K, Lam K, Pyskir D, Kong C, Jorgensen D, Rodrigues M, Roth D, Tang P, Cook VJ, Johnston J, Jamieson FB, Gardy JL. Universal genotyping reveals province-level differences in the molecular epidemiology of tuberculosis. PLoS One 2019; 14:e0214870. [PMID: 30943250 PMCID: PMC6447219 DOI: 10.1371/journal.pone.0214870] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 03/21/2019] [Indexed: 11/21/2022] Open
Abstract
OBJECTIVES Compare the molecular epidemiology of tuberculosis (TB) between two large Canadian provinces-Ontario and British Columbia (BC)-to identify genotypic clusters within and across both provinces, allowing for an improved understanding of genotype data and providing context to more accurately identify clusters representing local transmission. DESIGN We compared 24-locus Mycobacterial Interspersed Repetitive Units-Variable Number of Tandem Repeats (MIRU-VNTR) genotyping for 3,314 Ontario and 1,602 BC clinical Mycobacterium tuberculosis isolates collected from 2008 through 2014. Laboratory data for each isolate was linked to case-level records to obtain clinical and demographic data. RESULTS The demographic characteristics of persons with TB varied between provinces, most notably in the proportion of persons born outside Canada, which was reflected in the large number of unique genotypes (n = 3,461). The proportion of clustered isolates was significantly higher in BC. Substantial clustering amongst non-Lineage 4 TB strains was observed within and across the provinces. Only two large clusters (≥10 cases/cluster) representing within province transmission had interprovincial genotype matches. CONCLUSION We recommend expanding analysis of shared genotypes to include neighbouring jurisdictions, and implementing whole genome sequencing to improve identification of TB transmission, recognize outbreaks, and monitor changing trends in TB epidemiology.
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Affiliation(s)
- Jennifer L. Guthrie
- School of Population and Public Health, University of British Columbia, Vancouver, Canada
- Public Health Ontario, Toronto, Canada
| | | | - Kirby Cronin
- Public Health Ontario, Toronto, Canada
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Karen Lam
- Public Health Ontario, Toronto, Canada
| | | | - Clare Kong
- British Columbia Centre for Disease Control, Public Health Laboratory, Vancouver, Canada
| | - Danielle Jorgensen
- British Columbia Centre for Disease Control, Public Health Laboratory, Vancouver, Canada
| | - Mabel Rodrigues
- British Columbia Centre for Disease Control, Public Health Laboratory, Vancouver, Canada
| | - David Roth
- British Columbia Centre for Disease Control, Vancouver, Canada
| | - Patrick Tang
- British Columbia Centre for Disease Control, Public Health Laboratory, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Victoria J. Cook
- British Columbia Centre for Disease Control, Vancouver, Canada
- Respiratory Medicine, University of British Columbia, Vancouver, Canada
| | - James Johnston
- British Columbia Centre for Disease Control, Vancouver, Canada
- Respiratory Medicine, University of British Columbia, Vancouver, Canada
| | - Frances B. Jamieson
- Public Health Ontario, Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Jennifer L. Gardy
- School of Population and Public Health, University of British Columbia, Vancouver, Canada
- British Columbia Centre for Disease Control, Vancouver, Canada
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Woodman M, Haeusler IL, Grandjean L. Tuberculosis Genetic Epidemiology: A Latin American Perspective. Genes (Basel) 2019; 10:genes10010053. [PMID: 30654542 PMCID: PMC6356704 DOI: 10.3390/genes10010053] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 01/09/2019] [Accepted: 01/11/2019] [Indexed: 11/16/2022] Open
Abstract
There are an estimated 10 million new cases of tuberculosis worldwide annually, with 282,000 new or relapsed cases each year reported from the Americas. With improvements in genome sequencing technology, it is now possible to study the genetic diversity of tuberculosis with much greater resolution. Although tuberculosis bacteria do not engage in horizontal gene transfer, the genome is far more variable than previously thought. The study of genome-wide variation in tuberculosis has improved our understanding of the evolutionary origins of tuberculosis, the arrival of tuberculosis in Latin America, the genetic determinants of drug resistance, and lineage-specific associations with important clinical phenotypes. This article reviews what is known about the arrival of tuberculosis in Latin America, the genetic diversity of tuberculosis in Latin America, and the genotypic determinants of clinical phenotypes.
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Affiliation(s)
- Marc Woodman
- Institute of Child Health, University College London, London WC1N 3JH, UK.
| | - Ilsa L Haeusler
- Institute of Child Health, University College London, London WC1N 3JH, UK.
| | - Louis Grandjean
- Institute of Child Health, University College London, London WC1N 3JH, UK.
- Department of Medicine, Imperial College London, London W2 1NY, UK.
- Great Ormond Street Hospital, Institute of Child Health, University College London, London WC1N 3JH, UK.
- Laboratorio de Investigacion y Desarollo, Universidad Peruana Cayetano Heredia, Av. Honorio Delgado 430, San Martin de Porres 15102, Lima, Peru.
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25
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Varghese B, Enani M, Alrajhi A, Al Johani S, Albarak A, Althawadi S, Elkhizzi N, AlGhafli H, Shoukri M, Al-Hajoj S. Impact of Mycobacterium tuberculosis complex lineages as a determinant of disease phenotypes from an immigrant rich moderate tuberculosis burden country. Respir Res 2018; 19:259. [PMID: 30587190 PMCID: PMC6307224 DOI: 10.1186/s12931-018-0966-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 12/16/2018] [Indexed: 02/04/2023] Open
Abstract
Background Growing evidences suggested that the Mycobacterium tuberculosis complex (MTBC) lineages can determine the clinical outcome of pulmonary and extra-pulmonary tuberculosis. However, limited data only available revealing such association of bacterial genotypes and clinical phenotypes from immigrant rich countries. Methods A multicenter study has been carried out on a collection of 2092 (1003 extrapulmonary and 1089 pulmonary) MTBC isolates. Genotyping of all the isolates were carried out by spoligotyping and 24 loci based MIRU-VNTR typing. Results Demographically domination of young Saudi nationals (61.4%) and men (61.2%) were found in this cohort. Lymph nodes (62.4%) and gastrointestinal sites (16.7%) were the most common anatomical sites of infection. The predominant lineages were Delhi/CAS (26.9%), EAI (14.2%) and Ghana (9.9%). Mycobacterium africanum type I and II were reported for the first time in the country among extrapulmonary cases. ‘Ancestral’ lineages M.bovis (OR-5.22; 95% CI-2.23-8.22, p- < 0.001) and Delhi/CAS (OR-0.57; 95% CI-0.411-0.734, p- < 0.001) were directly associated with lymph node tuberculosis and gastrointestinal tuberculosis (M. bovis-OR-0.33; 95% CI-0.085-0.567, p-0.001 and Delhi/CAS-OR-1.87; 95% CI-1.22-2.53, p- < 0.001) respectively. Among the ‘Modern’ lineages, EAI showed significant association to central nervous system tuberculosis (OR-1.98; 95% CI-0.76-3.19, p-0.04) and Uganda-I to gastrointestinal tuberculosis (OR-2.41; 95% CI-0.77-4.06, p-0.02). Conclusions The findings substantially contribute to the emerging evidences that MTBC lineages influence disease phenotypes and epidemiological consequences. Electronic supplementary material The online version of this article (10.1186/s12931-018-0966-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bright Varghese
- Department of Infection and Immunity, MBC-03, King Faisal Specialist Hospital and Research Centre, Post Box # 3354, Riyadh, 11211, Saudi Arabia
| | - Mushira Enani
- Medical Specialties Department, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Abdulrahman Alrajhi
- Department of Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Sameera Al Johani
- Department of Microbiology, King Abdul Aziz Medical City, Riyadh, Saudi Arabia
| | - Ali Albarak
- Department of Medicine, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Sahar Althawadi
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Noura Elkhizzi
- Department of Microbiology, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Hawra AlGhafli
- Department of Infection and Immunity, MBC-03, King Faisal Specialist Hospital and Research Centre, Post Box # 3354, Riyadh, 11211, Saudi Arabia
| | - Mohammed Shoukri
- National Biotechnology Centre, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Sahal Al-Hajoj
- Department of Infection and Immunity, MBC-03, King Faisal Specialist Hospital and Research Centre, Post Box # 3354, Riyadh, 11211, Saudi Arabia.
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Barreira-Silva P, Torrado E, Nebenzahl-Guimaraes H, Kallenius G, Correia-Neves M. Aetiopathogenesis, immunology and microbiology of tuberculosis. Tuberculosis (Edinb) 2018. [DOI: 10.1183/2312508x.10020917] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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27
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Tram TTB, Nhung HN, Vijay S, Hai HT, Thu DDA, Ha VTN, Dinh TD, Ashton PM, Hanh NT, Phu NH, Thwaites GE, Thuong NTT. Virulence of Mycobacterium tuberculosis Clinical Isolates Is Associated With Sputum Pre-treatment Bacterial Load, Lineage, Survival in Macrophages, and Cytokine Response. Front Cell Infect Microbiol 2018; 8:417. [PMID: 30538956 PMCID: PMC6277702 DOI: 10.3389/fcimb.2018.00417] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 11/12/2018] [Indexed: 12/12/2022] Open
Abstract
It is uncertain whether differences in Mycobacterium tuberculosis (Mtb) virulence defined in vitro influence clinical tuberculosis pathogenesis, transmission, and mortality. We primarily used a macrophage lysis model to characterize the virulence of Mtb isolates collected from 153 Vietnamese adults with pulmonary tuberculosis. The virulence phenotypes were then investigated for their relationship with sputum bacterial load, bacterial lineages, bacterial growth, and cytokine responses in macrophages. Over 6 days of infection, 34 isolates (22.2%) showed low virulence (< 5% macrophages lysed), 46 isolates (30.1%) showed high virulence (≥90% lysis of macrophages), and 73 isolates (47.7%) were of intermediate virulence (5–90% macrophages lysed). Highly virulent isolates were associated with an increased bacterial load in patients' sputum before anti-tuberculosis therapy (P = 0.02). Isolate-dependent virulence phenotype was consistent in both THP-1 and human monocyte-derived macrophages. High virulence isolates survived better and replicated in macrophages one hundred fold faster than those with low virulence. Macrophages infected with high virulence isolates produced lower concentrations of TNF-α and IL-6 (P = 0.002 and 0.0005, respectively), but higher concentration of IL-1β (P = 5.1 × 10−5) compared to those infected with low virulence isolates. High virulence was strongly associated with East Asian/Beijing lineage [P = 0.002, Odd ratio (OR) = 4.32, 95% confident intervals (CI) 1.68–11.13]. The association between virulence phenotypes, bacterial growth, and proinflammatory cytokines in macrophages suggest the suppression of certain proinflammatory cytokines (TNF-α and IL-6) but not IL-1β allows better intracellular survival of highly virulent Mtb. This could result in rapid macrophage lysis and higher bacterial load in sputum of patients infected with high virulence isolates, which may contribute to the pathogenesis and success of the Beijing lineage.
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Affiliation(s)
- Trinh T B Tram
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Hoang N Nhung
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Srinivasan Vijay
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Hoang T Hai
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Do D A Thu
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Vu T N Ha
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Tran D Dinh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Philip M Ashton
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Nguyen T Hanh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nguyen H Phu
- Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Guy E Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
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Mekonnen A, Merker M, Collins JM, Addise D, Aseffa A, Petros B, Ameni G, Niemann S. Molecular epidemiology and drug resistance patterns of Mycobacterium tuberculosis complex isolates from university students and the local community in Eastern Ethiopia. PLoS One 2018; 13:e0198054. [PMID: 30222743 PMCID: PMC6141063 DOI: 10.1371/journal.pone.0198054] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 08/30/2018] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Previous studies suggest the burden of pulmonary tuberculosis (PTB) in Ethiopia may be greater in university students relative to the overall population. However, little is known about the transmission dynamics of PTB among students and members of the communities surrounding university campuses in Eastern Ethiopia. METHODS A cross sectional study was conducted in Eastern Ethiopia among prevalent culture-confirmed PTB cases from university students (n = 36) and community members diagnosed at one of four hospitals (n = 152) serving the surrounding area. Drug susceptibility testing (DST) was performed on Mycobacterium tuberculosis complex (MTBC) isolates using BD Bactec MGIT 960 and molecular genotyping was performed using spoligotyping and 24-loci MIRU-VNTR. MTBC strains with Identical genotyping patterns were assigned to molecular clusters as surrogate marker for recent transmission and further contact tracing was initiated among clustered patients. RESULTS Among all study participants, four MTBC lineages and 11 sub-lineages were identified, with Ethiopia_3 (Euro-American lineage) being most common sub-lineage (29.4%) in both cohorts and associated with strain clustering (P = 0.016). We further identified 13 (8.1%) strains phylogenetically closely related to Ethiopia_3 but with a distinct Spoligotyping pattern and designated as Ethiopia_4. The clustering rate of MTBC strains was 52.9% for university students and 66.7% for community members with a Recent Transmission Index (RTI) of 17.6% and 48.4%, respectively. Female gender, urban residence, and new TB cases were significantly associated with strain clustering (P<0.05). Forty-eight (30%) of the study participants were resistant to one or more first line anti TB drugs, three patients were classified as multidrug resistant (MDR). CONCLUSION We found evidence for recent transmission of PTB among Ethiopian university students and the local community in Eastern Ethiopia, mainly linked to strains classified as Ethiopia_3 sub lineage. Drug resistance didn't have a major impact on recent transmission but comprehensive molecular surveillance in combination with drug resistance profiling of MTBC strains is desirable to better characterize TB transmission dynamics in high risk congregate living environments such as university campuses and guide regional TB control programs.
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Affiliation(s)
- Abiyu Mekonnen
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Matthias Merker
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Jeffrey M. Collins
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Desalegn Addise
- Ethiopian National Tuberculosis Reference laboratory, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Abraham Aseffa
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Beyene Petros
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Gobena Ameni
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Partner Site Borstel, Borstel, Germany
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Incipient and Subclinical Tuberculosis: a Clinical Review of Early Stages and Progression of Infection. Clin Microbiol Rev 2018; 31:31/4/e00021-18. [PMID: 30021818 DOI: 10.1128/cmr.00021-18] [Citation(s) in RCA: 303] [Impact Index Per Article: 50.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Tuberculosis (TB) is the leading infectious cause of mortality worldwide, due in part to a limited understanding of its clinical pathogenic spectrum of infection and disease. Historically, scientific research, diagnostic testing, and drug treatment have focused on addressing one of two disease states: latent TB infection or active TB disease. Recent research has clearly demonstrated that human TB infection, from latent infection to active disease, exists within a continuous spectrum of metabolic bacterial activity and antagonistic immunological responses. This revised understanding leads us to propose two additional clinical states: incipient and subclinical TB. The recognition of incipient and subclinical TB, which helps divide latent and active TB along the clinical disease spectrum, provides opportunities for the development of diagnostic and therapeutic interventions to prevent progression to active TB disease and transmission of TB bacilli. In this report, we review the current understanding of the pathogenesis, immunology, clinical epidemiology, diagnosis, treatment, and prevention of both incipient and subclinical TB, two emerging clinical states of an ancient bacterium.
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30
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Chae H, Shin SJ. Importance of differential identification of Mycobacterium tuberculosis strains for understanding differences in their prevalence, treatment efficacy, and vaccine development. J Microbiol 2018; 56:300-311. [PMID: 29721826 DOI: 10.1007/s12275-018-8041-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 02/14/2018] [Accepted: 02/14/2018] [Indexed: 01/28/2023]
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains a serious global health problem in the 21st century because of its high mortality. Mtb is an extremely successful human-adapted pathogen that displays a multifactorial ability to control the host immune response and to evade killing by drugs, resulting in the breakdown of BCG vaccine-conferred anti-TB immunity and development of multidrug-resistant (MDR) and extensively drug-resistant (XDR) Mtb. Although genetic components of the genomes of the Mtb complex strains are highly conserved, showing over 99% similarity to other bacterial genera, recently accumulated evidence suggests that the genetic diversity of the Mtb complex strains has implications for treatment outcomes, development of MDR/XDR Mtb, BCG vaccine efficacy, transmissibility, and epidemiological outbreaks. Thus, new insights into the pathophysiological features of the Mtb complex strains are required for development of novel vaccines and for control of MDR/XDR Mtb infection, eventually leading to refinement of treatment regimens and the health care system. Many studies have focused on the differential identification of Mtb complex strains belonging to different lineages because of differences in their virulence and geographical dominance. In this review, we discuss the impact of differing genetic characteristics among Mtb complex strains on vaccine efficacy, treatment outcome, development of MDR/XDR Mtb strains, and epidemiological outbreaks by focusing on the best-adapted human Mtb lineages. We further explore the rationale for differential identification of Mtb strains for more effective control of TB in clinical and laboratory settings by scrutinizing current diagnostic methods.
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Affiliation(s)
- Hansong Chae
- Department of Microbiology, Institute for Immunology and Immunological Diseases, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Sung Jae Shin
- Department of Microbiology, Institute for Immunology and Immunological Diseases, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.
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31
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Ma Y, Zhang Y, Zhao Y, Wang X, Lin Y, Ma A. Expression of autophagy-related genes in cerebrospinal fluid of patients with tuberculous meningitis. Exp Ther Med 2018; 15:4671-4676. [PMID: 29805485 PMCID: PMC5952066 DOI: 10.3892/etm.2018.5999] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 12/11/2017] [Indexed: 12/21/2022] Open
Abstract
The expression of autophagy-related genes in cerebrospinal fluid of patients with tuberculous meningitis (TBM) and their clinical significance in patients with TBM was investigated. Sixty patients with TBM (observation group) and twenty healthy volunteers during the same period (control group) were selected and the cerebrospinal fluid was collected. The expression levels of p62, Beclin1 and LC3-II genes in cerebrospinal fluid were detected via semi-quantitative reverse transcription-polymerase chain reaction and patients in observation group were divided into high expression and normal or low expression group on the basis of LC3-II expression levels. On the other hand, the contents of inflammatory factors interleukin-6, −10 (IL-6, −10), and tumor necrosis factor-α (TNF-α) were detected using the enzyme-linked immunosorbent assay kit. The mRNA levels of p62, Beclin1 and LC3-II in cerebrospinal fluid of patients in observation were significantly higher than those in the control group (P<0.01). TUNEL assay showed that the apoptosis level of cerebro-spinal fluid in high expression was obviously lower than that in normal or low expression group (P<0.01); the content of IL-6 and TNF-α in cerebrospinal fluid in high expression was significantly lower than those in normal or low expression group (P<0.01); the content of IL-10 in cerebrospinal fluid in high expression was obviously higher than that in normal or low expression group (P<0.01). Correlation analysis revealed that LC3-II was positively correlated with IL-10, but negatively correlated with IL-6 and TNF-α. The mRNA levels of p62, Beclin1 and LC3-II in cerebrospinal fluid of patients with TBM are increased, there is a correlation between expression levels of autophagy-related genes and inflammatory factors, and the high expression of autophagy-related genes may have a protective effect on patients with TBM.
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Affiliation(s)
- Yunbo Ma
- Department of Preventive Medicine, Linyi People's Hospital, Linyi, Shandong 276034, P.R. China
| | - Yongxia Zhang
- Department of Emergency, Linyi People's Hospital, Linyi, Shandong 276034, P.R. China
| | - Yanyan Zhao
- Department of Clinical Laboratory, Linyi People's Hospital, Linyi, Shandong 276034, P.R. China
| | - Xianhua Wang
- School of Public Health, Qingdao University, Qingdao, Shandong 266021, P.R. China
| | - Yuefu Lin
- Department of Preventive Medicine, Linyi People's Hospital, Linyi, Shandong 276034, P.R. China
| | - Aiguo Ma
- School of Public Health, Qingdao University, Qingdao, Shandong 266021, P.R. China
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Faksri K, Xia E, Ong RTH, Tan JH, Nonghanphithak D, Makhao N, Thamnongdee N, Thanormchat A, Phurattanakornkul A, Rattanarangsee S, Ratanajaraya C, Suriyaphol P, Prammananan T, Teo YY, Chaiprasert A. Comparative whole-genome sequence analysis of Mycobacterium tuberculosis isolated from tuberculous meningitis and pulmonary tuberculosis patients. Sci Rep 2018; 8:4910. [PMID: 29559684 PMCID: PMC5861094 DOI: 10.1038/s41598-018-23337-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 03/02/2018] [Indexed: 12/25/2022] Open
Abstract
Tuberculous meningitis (TBM) is a severe form of tuberculosis with a high mortality rate. The factors associated with TBM pathogenesis are still unclear. Using comparative whole-genome sequence analysis we compared Mycobacterium tuberculosis (Mtb) isolates from cerebrospinal fluid of TBM cases (n = 73) with those from sputum of pulmonary tuberculosis (PulTB) patients (n = 220) from Thailand. The aim of this study was to seek genetic variants of Mtb associated with TBM. Regardless of Mtb lineage, we found 242 variants that were common to all TBM isolates. Among these variants, 28 were missense SNPs occurring mainly in the pks genes (involving polyketide synthesis) and the PE/PPE gene. Six lineage-independent SNPs were commonly found in TBM isolates, two of which were missense SNPs in Rv0532 (PE_PGRS6). Structural variant analysis revealed that PulTB isolates had 14 genomic regions containing 2-3-fold greater read depth, indicating higher copy number variants and half of these genes belonged to the PE/PPE gene family. Phylogenetic analysis revealed only two small clusters of TBM clonal isolates without support from epidemiological data. This study reported genetic variants of Mtb commonly found in TBM patients compared to PulTB patients. Variants associated with TBM disease warrant further investigation.
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Affiliation(s)
- Kiatichai Faksri
- Department of Microbiology Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand. .,Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, 40002, Thailand.
| | - Eryu Xia
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, 119077, Singapore
| | - Rick Twee-Hee Ong
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, 119077, Singapore
| | - Jun Hao Tan
- Duke-NUS Medical School, National University of Singapore, Singapore, 119077, Singapore
| | - Ditthawat Nonghanphithak
- Department of Microbiology Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand.,Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Nampueng Makhao
- Drug Resistant Tuberculosis Laboratory, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Nongnard Thamnongdee
- Drug Resistant Tuberculosis Laboratory, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Arirat Thanormchat
- Drug Resistant Tuberculosis Laboratory, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Arisa Phurattanakornkul
- Drug Resistant Tuberculosis Laboratory, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Somcharn Rattanarangsee
- Drug Resistant Tuberculosis Laboratory, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Chate Ratanajaraya
- Drug Resistant Tuberculosis Laboratory, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Prapat Suriyaphol
- Bioinformatics and Data Management for Research Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Therdsak Prammananan
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Ministry of Science and Technology, Pathum Thani, 12120, Thailand
| | - Yik-Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, 119077, Singapore.,NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, 119077, Singapore.,Genome Institute of Singapore, Singapore, 138672, Singapore.,Department of Statistics and Applied Probability, National University of Singapore, Singapore, 119077, Singapore.,Life Sciences Institute, National University of Singapore, Singapore, 119077, Singapore
| | - Angkana Chaiprasert
- Drug Resistant Tuberculosis Laboratory, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand.
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Carey AF, Rock JM, Krieger IV, Chase MR, Fernandez-Suarez M, Gagneux S, Sacchettini JC, Ioerger TR, Fortune SM. TnSeq of Mycobacterium tuberculosis clinical isolates reveals strain-specific antibiotic liabilities. PLoS Pathog 2018; 14:e1006939. [PMID: 29505613 PMCID: PMC5854444 DOI: 10.1371/journal.ppat.1006939] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 03/15/2018] [Accepted: 02/13/2018] [Indexed: 01/25/2023] Open
Abstract
Once considered a phenotypically monomorphic bacterium, there is a growing body of work demonstrating heterogeneity among Mycobacterium tuberculosis (Mtb) strains in clinically relevant characteristics, including virulence and response to antibiotics. However, the genetic and molecular basis for most phenotypic differences among Mtb strains remains unknown. To investigate the basis of strain variation in Mtb, we performed genome-wide transposon mutagenesis coupled with next-generation sequencing (TnSeq) for a panel of Mtb clinical isolates and the reference strain H37Rv to compare genetic requirements for in vitro growth across these strains. We developed an analytic approach to identify quantitative differences in genetic requirements between these genetically diverse strains, which vary in genomic structure and gene content. Using this methodology, we found differences between strains in their requirements for genes involved in fundamental cellular processes, including redox homeostasis and central carbon metabolism. Among the genes with differential requirements were katG, which encodes the activator of the first-line antitubercular agent isoniazid, and glcB, which encodes malate synthase, the target of a novel small-molecule inhibitor. Differences among strains in their requirement for katG and glcB predicted differences in their response to these antimicrobial agents. Importantly, these strain-specific differences in antibiotic response could not be predicted by genetic variants identified through whole genome sequencing or by gene expression analysis. Our results provide novel insight into the basis of variation among Mtb strains and demonstrate that TnSeq is a scalable method to predict clinically important phenotypic differences among Mtb strains.
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Affiliation(s)
- Allison F. Carey
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Jeremy M. Rock
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Inna V. Krieger
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Michael R. Chase
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Marta Fernandez-Suarez
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Sebastien Gagneux
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - James C. Sacchettini
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Thomas R. Ioerger
- Department of Computer Science, Texas A&M University, College Station, Texas, United States of America
- * E-mail: (SMF); (TRI)
| | - Sarah M. Fortune
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- * E-mail: (SMF); (TRI)
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34
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Shaping the niche in macrophages: Genetic diversity of the M. tuberculosis complex and its consequences for the infected host. Int J Med Microbiol 2017; 308:118-128. [PMID: 28969988 DOI: 10.1016/j.ijmm.2017.09.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 09/09/2017] [Accepted: 09/11/2017] [Indexed: 12/12/2022] Open
Abstract
Pathogenic mycobacteria of the Mycobacterium tuberculosis complex (MTBC) have co-evolved with their individual hosts and are able to transform the hostile environment of the macrophage into a permissive cellular habitat. The impact of MTBC genetic variability has long been considered largely unimportant in TB pathogenesis. Members of the MTBC can now be distinguished into three major phylogenetic groups consisting of 7 phylogenetic lineages and more than 30 so called sub-lineages/subgroups. MTBC genetic diversity indeed influences the transmissibility and virulence of clinical MTBC isolates as well as the immune response and the clinical outcome. Here we review the genetic diversity and epidemiology of MTBC strains and describe the current knowledge about the host immune response to infection with MTBC clinical isolates using human and murine experimental model systems in vivo and in vitro. We discuss the role of innate cytokines in detail and portray two in our group recently developed approaches to characterize the intracellular niches of MTBC strains. Characterizing the niches and deciphering the strategies of MTBC strains to transform an antibacterial effector cell into a permissive cellular habitat offers the opportunity to identify strain- and lineage-specific key factors which may represent targets for novel antimicrobial or host directed therapies for tuberculosis.
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35
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Golla V, Snow K, Mandalakas AM, Schaaf HS, Du Preez K, Hesseling AC, Seddon JA. The impact of drug resistance on the risk of tuberculosis infection and disease in child household contacts: a cross sectional study. BMC Infect Dis 2017; 17:593. [PMID: 28851285 PMCID: PMC5576070 DOI: 10.1186/s12879-017-2668-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 08/03/2017] [Indexed: 11/10/2022] Open
Abstract
Background The relative fitness of organisms causing drug-susceptible (DS) and multidrug-resistant (MDR) tuberculosis (TB) is unclear. We compared the risk of TB infection and TB disease in young child household contacts of adults with confirmed DS-TB and MDR-TB. Methods In this cross-sectional analysis we included data from two community-based contact cohort investigation studies conducted in parallel in Cape Town, South Africa. Children <5 years of age with household exposure to an infectious TB case were included between August 2008 to June 2011. Children completed investigation for TB infection (tuberculin skin test) and TB disease (symptom evaluation, chest radiograph, bacteriology) in both studies using standard approaches. The impact of MDR-TB exposure on each covariate of TB infection and TB disease was assessed using univariable and multivariable logistic regression. Results Of 538 children included, 312 had DS-TB and 226 had MDR-TB exposure. 107 children with DS-TB exposure had TB infection (34.3%) vs. 101 (44.7%) of children with MDR-TB exposure (adjusted Odds Ratio [aOR]: 2.05; 95% confidence interval [CI]: 1.34–3.12). A total of 15 (6.6%) MDR-TB vs. 27 (8.7%) DS-TB child contacts had TB disease at enrolment (aOR: 0.43; 95% CI: 0.19–0.97). Conclusions Our results suggest a higher risk of TB infection in child contacts with household MDR-TB vs. DS-TB exposure, but a lower risk of TB disease. Although potentially affected by residual confounding or selection bias, our results are consistent with the hypothesis of impaired virulence in MDR-TB strains in this setting.
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Affiliation(s)
- Vera Golla
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, 8000, Cape Town, South Africa
| | - Kathryn Snow
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Anna M Mandalakas
- Global TB Program, Department of Pediatrics, Baylor College of Medicine, Houston, USA
| | - H Simon Schaaf
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, 8000, Cape Town, South Africa
| | - Karen Du Preez
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, 8000, Cape Town, South Africa
| | - Anneke C Hesseling
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, 8000, Cape Town, South Africa.
| | - James A Seddon
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, 8000, Cape Town, South Africa. .,Centre for International Child Health, Department of Paediatrics, Imperial College London, Norfolk Place, London, W2 1PG, UK.
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36
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Zhou Y, van den Hof S, Wang S, Pang Y, Zhao B, Xia H, Anthony R, Ou X, Li Q, Zheng Y, Song Y, Zhao Y, van Soolingen D. Association between genotype and drug resistance profiles of Mycobacterium tuberculosis strains circulating in China in a national drug resistance survey. PLoS One 2017; 12:e0174197. [PMID: 28333978 PMCID: PMC5363926 DOI: 10.1371/journal.pone.0174197] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 03/06/2017] [Indexed: 11/19/2022] Open
Abstract
We describe the population structure of a representative collection of 3,133 Mycobacterium tuberculosis isolates, collected within the framework of a national resistance survey from 2007 in China. Genotyping data indicate that the epidemic strains in China can be divided into seven major complexes, of which 92% belonged to the East Asian (mainly Beijing strains) or the Euro-American lineage. The epidemic Beijing strains in China are closely related to the Beijing B0/W148 strain earlier described in Russia and a large cluster of these strains has spread national wide. The density of Beijing strains is high in the whole of China (average 70%), but the highest prevalence was found North of the Yellow river. The Euro-American lineage consists of three sublineages (sublineage_1, 2, and 3) and is more prevalent in the South. Beijing lineage showed the highest cluster rate of 48% and a significantly higher level of resistance to rifampicin (14%, p<0.001), ethambutol (9%, p = 0.001), and ofloxacin (5%, p = 0.011). Within the Euro-American Lineage, sublineage_3 revealed the highest cluster rate (28%) and presented a significantly elevated level of resistance to streptomycin (44%, p<0.001). Our findings suggest that standardised treatment in this region may have contributed to the successful spread of certain strains: sublineage_3 in the Euro-American lineage may have thrived when streptomycin was used without rifampicin for treatment, while later under DOTS based treatment, in which rifampicin plays a key role, Beijing lineage appears to be spreading.
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Affiliation(s)
- Yang Zhou
- Chinese Centre for Disease Control and Prevention, Changping district, Beijing, China, P.R
| | - Susan van den Hof
- KNCV Tuberculosis Foundation, CC The Hague, The Netherlands
- Department of Global Health, Amsterdam Medical Center, Pietersbergweg 17, BM Amsterdam, The Netherlands
| | - Shengfen Wang
- Chinese Centre for Disease Control and Prevention, Changping district, Beijing, China, P.R
| | - Yu Pang
- Chinese Centre for Disease Control and Prevention, Changping district, Beijing, China, P.R
| | - Bing Zhao
- Chinese Centre for Disease Control and Prevention, Changping district, Beijing, China, P.R
| | - Hui Xia
- Chinese Centre for Disease Control and Prevention, Changping district, Beijing, China, P.R
| | - Richard Anthony
- National Institute for Public Health and the Environment, the Netherlands,BA Bilthoven, The Netherlands
| | - Xichao Ou
- Chinese Centre for Disease Control and Prevention, Changping district, Beijing, China, P.R
| | - Qiang Li
- Chinese Centre for Disease Control and Prevention, Changping district, Beijing, China, P.R
| | - Yang Zheng
- Chinese Centre for Disease Control and Prevention, Changping district, Beijing, China, P.R
| | - Yuanyuan Song
- Chinese Centre for Disease Control and Prevention, Changping district, Beijing, China, P.R
| | - Yanlin Zhao
- Chinese Centre for Disease Control and Prevention, Changping district, Beijing, China, P.R
| | - Dick van Soolingen
- National Institute for Public Health and the Environment, the Netherlands,BA Bilthoven, The Netherlands
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37
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Tientcheu LD, Koch A, Ndengane M, Andoseh G, Kampmann B, Wilkinson RJ. Immunological consequences of strain variation within the Mycobacterium tuberculosis complex. Eur J Immunol 2017; 47:432-445. [PMID: 28150302 PMCID: PMC5363233 DOI: 10.1002/eji.201646562] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 01/26/2017] [Accepted: 01/31/2017] [Indexed: 11/11/2022]
Abstract
In 2015, there were an estimated 10.4 million new cases of tuberculosis (TB) globally, making it one of the leading causes of death due to an infectious disease. TB is caused by members of the Mycobacterium tuberculosis complex (MTBC), with human disease resulting from infection by M. tuberculosis sensu stricto and M. africanum. Recent progress in genotyping techniques, in particular the increasing availability of whole genome sequence data, has revealed previously under appreciated levels of genetic diversity within the MTBC. Several studies have shown that this genetic diversity may translate into differences in TB transmission, clinical manifestations of disease, and host immune responses. This suggests the existence of MTBC genotype‐dependent host–pathogen interactions which may influence the outcome of infection and progression of disease. In this review, we highlight the studies demonstrating differences in innate and adaptive immunological outcomes consequent on MTBC genetic diversity, and discuss how these differences in immune response might influence the development of TB vaccines, diagnostics and new therapies.
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Affiliation(s)
- Leopold D Tientcheu
- Vaccines and Immunity Theme, Medical Research Council Unit, The Gambia, Banjul, The Gambia.,Department of Biochemistry, Faculty of Science, University of Yaoundé 1, Yaoundé, Cameroon
| | - Anastasia Koch
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine and Department of Medicine, University of Cape Town, Observatory, Republic of South Africa
| | - Mthawelenga Ndengane
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine and Department of Medicine, University of Cape Town, Observatory, Republic of South Africa
| | - Genevieve Andoseh
- Department of Biochemistry, Faculty of Science, University of Yaoundé 1, Yaoundé, Cameroon
| | - Beate Kampmann
- Vaccines and Immunity Theme, Medical Research Council Unit, The Gambia, Banjul, The Gambia.,Department of Medicine, Imperial College, London, United Kingdom
| | - Robert J Wilkinson
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine and Department of Medicine, University of Cape Town, Observatory, Republic of South Africa.,Department of Medicine, Imperial College, London, United Kingdom.,The Francis Crick Institute, London, United Kingdom
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38
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MARCO variants are associated with phagocytosis, pulmonary tuberculosis susceptibility and Beijing lineage. Genes Immun 2016; 17:419-425. [PMID: 27853145 PMCID: PMC5133378 DOI: 10.1038/gene.2016.43] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 10/14/2016] [Accepted: 10/17/2016] [Indexed: 11/22/2022]
Abstract
Macrophage receptor with collagenous structure (MARCO) has an important role in the phagocytosis of Mycobacterium tuberculosis (M. tuberculosis). We hypothesized that MARCO polymorphisms are associated with phagocytosis, tuberculosis (TB) disease susceptibility and presentation, and infecting lineage. We used a human cellular model to examine how MARCO genotype mediates the immune response; a case–control study to investigate tuberculosis host genetic susceptibility; and a host–pathogen genetic analysis to study host–pathogen interactions. Two MARCO heterozygous (AG) genotypes (single-nucleotide polymorphisms rs2278589 and rs6751745) were associated with impaired phagocytosis of M. tuberculosis trehalose 6,6'-dimycolate-cord factor and β-glucan-coated beads in macrophages. The heterozygous genotypes of rs2278589 and rs6751745 were also associated with increased risk of pulmonary TB (PTB; rs2278589, P=0.001, odds ratio (OR)=1.6; rs6751745, P=0.009, OR=1.4), and with severe chest X-ray abnormalities (P=0.007, OR=1.6). These two genotypes were also associated with the Beijing lineage (rs2278589, P=0.001, OR=1.7; rs6751745, P=0.01, OR=1.5). Together, these results suggest that MARCO polymorphisms may regulate phagocytosis of M. tuberculosis and susceptibility and severity of PTB. They also suggest MARCO genotype and Beijing strains may interact to increase the risk of PTB.
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39
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Gurjav U, Outhred AC, Jelfs P, McCallum N, Wang Q, Hill-Cawthorne GA, Marais BJ, Sintchenko V. Whole Genome Sequencing Demonstrates Limited Transmission within Identified Mycobacterium tuberculosis Clusters in New South Wales, Australia. PLoS One 2016; 11:e0163612. [PMID: 27737005 PMCID: PMC5063377 DOI: 10.1371/journal.pone.0163612] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 09/12/2016] [Indexed: 11/18/2022] Open
Abstract
Australia has a low tuberculosis incidence rate with most cases occurring among recent immigrants. Given suboptimal cluster resolution achieved with 24-locus mycobacterium interspersed repetitive unit (MIRU-24) genotyping, the added value of whole genome sequencing was explored. MIRU-24 profiles of all Mycobacterium tuberculosis culture-confirmed tuberculosis cases diagnosed between 2009 and 2013 in New South Wales (NSW), Australia, were examined and clusters identified. The relatedness of cases within the largest MIRU-24 clusters was assessed using whole genome sequencing and phylogenetic analyses. Of 1841 culture-confirmed TB cases, 91.9% (1692/1841) had complete demographic and genotyping data. East-African Indian (474; 28.0%) and Beijing (470; 27.8%) lineage strains predominated. The overall rate of MIRU-24 clustering was 20.1% (340/1692) and was highest among Beijing lineage strains (35.7%; 168/470). One Beijing and three East-African Indian (EAI) clonal complexes were responsible for the majority of observed clusters. Whole genome sequencing of the 4 largest clusters (30 isolates) demonstrated diverse single nucleotide polymorphisms (SNPs) within identified clusters. All sequenced EAI strains and 70% of Beijing lineage strains clustered by MIRU-24 typing demonstrated distinct SNP profiles. The superior resolution provided by whole genome sequencing demonstrated limited M. tuberculosis transmission within NSW, even within identified MIRU-24 clusters. Routine whole genome sequencing could provide valuable public health guidance in low burden settings.
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Affiliation(s)
- Ulziijargal Gurjav
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia
- Centre for Infectious Diseases and Microbiology–Public Health, Westmead Hospital, Sydney, Australia
| | - Alexander C. Outhred
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia
- Children's Hospital at Westmead, Sydney, Australia
| | - Peter Jelfs
- Centre for Infectious Diseases and Microbiology–Public Health, Westmead Hospital, Sydney, Australia
- NSW Mycobacterium Reference Laboratory, Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research–Pathology West, Sydney, Australia
| | - Nadine McCallum
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia
- Centre for Infectious Diseases and Microbiology–Public Health, Westmead Hospital, Sydney, Australia
| | - Qinning Wang
- Centre for Infectious Diseases and Microbiology–Public Health, Westmead Hospital, Sydney, Australia
| | - Grant A. Hill-Cawthorne
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia
- School of Public Health and Westmead Institute for Medical Research, The University of Sydney, Sydney, Australia
| | - Ben J. Marais
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia
- Children's Hospital at Westmead, Sydney, Australia
| | - Vitali Sintchenko
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia
- Centre for Infectious Diseases and Microbiology–Public Health, Westmead Hospital, Sydney, Australia
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40
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Beardsley J, Denning DW, Chau NV, Yen NTB, Crump JA, Day JN. Estimating the burden of fungal disease in Vietnam. Mycoses 2016; 58 Suppl 5:101-6. [PMID: 26449514 PMCID: PMC4606745 DOI: 10.1111/myc.12382] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 04/14/2015] [Accepted: 05/02/2015] [Indexed: 12/18/2022]
Abstract
Data regarding the prevalence of fungal infections in Vietnam are limited yet they are likely to occur more frequently as increasingly sophisticated healthcare creates more iatrogenic risk factors. In this study, we sought to estimate baseline incidence and prevalence of selected serious fungal infections for the year 2012. We made estimates with a previously described actuarial method, using reports on the incidence and prevalence of various established risk factors for fungal infections from Vietnam, or similar environments, supplemented by personal communications. Global data were used if local data were unavailable. We estimated 2 352 748 episodes of serious fungal infection occurred in Vietnam in 2012. Frequent conditions included recurrent vaginal candidiasis (3893/100 000 women annually), tinea capitis (457/100 000 annually) and chronic pulmonary aspergillosis (61/100 000/5 year period). We estimated 140 cases of cryptococcal meningitis, 206 of penicilliosis and 608 of Pneumocystis jirovecii pneumonia. This is the first summary of Vietnamese fungal infections. The majority of severe disease is due to Aspergillus species, driven by the high prevalence of pulmonary tuberculosis. The AIDS epidemic highlights opportunistic infections, such as penicilliosis and cryptococcosis, which may complicate immunosuppressive treatments. These estimates provide a useful indication of disease prevalence to inform future research and resource allocation but should be verified by further epidemiological approaches.
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Affiliation(s)
- J Beardsley
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - D W Denning
- The National Aspergillosis Centre, The University of Manchester, Manchester, UK
| | - N V Chau
- Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - N T B Yen
- Pham Ngoc Thach Hospital, Ho Chi Minh City, Vietnam
| | - J A Crump
- Centre for International Health, University of Otago, Dunedin, New Zealand
| | - J N Day
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Wellcome Trust Intermediate Fellow, London, UK
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Coker OO, Chaiprasert A, Ngamphiw C, Tongsima S, Regmi SM, Clark TG, Ong RTH, Teo YY, Prammananan T, Palittapongarnpim P. Genetic signatures of Mycobacterium tuberculosis Nonthaburi genotype revealed by whole genome analysis of isolates from tuberculous meningitis patients in Thailand. PeerJ 2016; 4:e1905. [PMID: 27114869 PMCID: PMC4841212 DOI: 10.7717/peerj.1905] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 03/16/2016] [Indexed: 01/27/2023] Open
Abstract
Genome sequencing plays a key role in understanding the genetic diversity of Mycobacterium tuberculosis (M.tb). The genotype-specific character of M. tb contributes to tuberculosis severity and emergence of drug resistance. Strains of M. tb complex can be classified into seven lineages. The Nonthaburi (NB) genotype, belonging to the Indo-Oceanic lineage (lineage 1), has a unique spoligotype and IS6110-RFLP pattern but has not previously undergone a detailed whole genome analysis. In addition, there is not much information available on the whole genome analysis of M. tb isolates from tuberculous meningitis (TBM) patients in public databases. Isolates CSF3053, 46-5069 and 43-13838 of NB genotype were obtained from the cerebrospinal fluids of TBM Thai patients in Siriraj Hospital, Bangkok. The whole genomes were subjected to high throughput sequencing. The sequence data of each isolate were assembled into draft genome. The sequences were also aligned to reference genome, to determine genomic variations. Single nucleotide polymorphisms (SNPs) were obtained and grouped according to the functions of the genes containing them. They were compared with SNPs from 1,601 genomes, representing the seven lineages of M. tb complex, to determine the uniqueness of NB genotype. Susceptibility to first-line, second-line and other antituberculosis drugs were determined and related to the SNPs previously reported in drug-resistant related genes. The assembled genomes have an average size of 4,364,461 bp, 4,154 genes, 48 RNAs and 64 pseudogenes. A 500 base pairs deletion, which includes ppe50, was found in all isolates. RD239, specific for members of Indo Oceanic lineage, and RD147c were identified. A total of 2,202 SNPs were common to the isolates and used to classify the NB strains as members of sublineage 1.2.1. Compared with 1,601 genomes from the seven lineages of M. tb complex, mutation G2342203C was found novel to the isolates in this study. Three mutations (T28910C, C1180580T and C152178T) were found only in Thai NB isolates, including isolates from previous study. Although drug susceptibility tests indicated pan-susceptibility, non-synonymous SNPs previously reported to be associated with resistance to anti-tuberculous drugs; isoniazid, ethambutol, and ethionamide were identified in all the isolates. Non-synonymous SNPs were found in virulence genes such as the genes playing roles in apoptosis inhibition and phagosome arrest. We also report polymorphisms in essential genes, efflux pumps associated genes and genes with known epitopes. The analysis of the TBM isolates and the availability of the variations obtained will provide additional resources for global comparison of isolates from pulmonary tuberculosis and TBM. It will also contribute to the richness of genomic databases towards the prediction of antibiotic resistance, level of virulence and of origin of infection.
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Affiliation(s)
- Olabisi Oluwabukola Coker
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University , Bangkok , Thailand
| | - Angkana Chaiprasert
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University , Bangkok , Thailand
| | - Chumpol Ngamphiw
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency , Pathum Thani , Thailand
| | - Sissades Tongsima
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency , Pathum Thani , Thailand
| | - Sanjib Mani Regmi
- Department of Microbiology, Gandaki Medical College , Pokhara Kaski , Nepal
| | - Taane G Clark
- Faculty of Epidemiology and Population Health, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, University of London , London , United Kingdom
| | - Rick Twee Hee Ong
- Saw Swee Hock School of Public Health, National University of Singapore , Singapore
| | - Yik-Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore , Singapore
| | - Therdsak Prammananan
- Tuberculosis Research Laboratory, Medical Molecular Biology Research Unit, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency , Pathum Thani , Thailand
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Zhao LL, Xiao TY, Sun Q, Liu HC, Zhao XQ, Jiang Y, Li GL, Zeng CY, Wan KL. Mutations in lysX as the new and reliable markers for tuberculosis Beijing and modern Beijing strains. Tuberculosis (Edinb) 2015; 97:33-7. [PMID: 26980493 DOI: 10.1016/j.tube.2015.12.006] [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: 11/04/2015] [Revised: 12/16/2015] [Accepted: 12/20/2015] [Indexed: 10/22/2022]
Abstract
Genotyping results and DNA sequencing analysis of 235 Mycobacterium tuberculosis (M. tuberculosis) isolates from China indicated that mutations at codon 995 (Pro CCG to Pro CCA) and 701 (Ile ATT to Thr ACT) in lysX gene (Rv1640c), are specific markers for Beijing and modern Beijing strains, respectively. This observation was also confirmed by 24 genomes of M. tuberculosis strains from other countries. Moreover, a simple and fast multiplex allele-specific PCR (MAS-PCR) method for detecting mutations at codon 995 and 701 in lysX has been established and used to screen 235 DNA samples obtained from M. tuberculosis isolates. In all cases, Beijing and modern Beijing strains were identified correctly.
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Affiliation(s)
- Li-li Zhao
- State Key Laboratory for Infectious Diseases Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Tong-yang Xiao
- State Key Laboratory for Infectious Diseases Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Qing Sun
- State Key Laboratory for Infectious Diseases Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; Department of Medicine, Hunan Traditional Chinese Medical College, Zhuzhou 412012, China
| | - Hai-can Liu
- State Key Laboratory for Infectious Diseases Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Xiu-qin Zhao
- State Key Laboratory for Infectious Diseases Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Yi Jiang
- State Key Laboratory for Infectious Diseases Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Gui-lian Li
- State Key Laboratory for Infectious Diseases Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Chun-yan Zeng
- Hulunbeier People's Hospital, Hulunbeier 021000, China
| | - Kang-lin Wan
- State Key Laboratory for Infectious Diseases Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; Department of Medicine, Hunan Traditional Chinese Medical College, Zhuzhou 412012, China.
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Hu Y, Mathema B, Zhao Q, Zheng X, Li D, Jiang W, Wang W, Xu B. Comparison of the socio-demographic and clinical features of pulmonary TB patients infected with sub-lineages within the W-Beijing and non-Beijing Mycobacterium tuberculosis. Tuberculosis (Edinb) 2015; 97:18-25. [PMID: 26980491 DOI: 10.1016/j.tube.2015.11.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 11/24/2015] [Accepted: 11/26/2015] [Indexed: 10/22/2022]
Abstract
BACKGROUND Highly lethal outbreaks of multidrug-resistant (MDR) and extensively drug-resistant (XDR) tuberculosis are increasing. Mycobacterium tuberculosis variant Beijing family and its members is regarded as a successful clone of M. tuberculosis that is associated with drug resistance in China. Understanding the genetic characteristics and molecular mechanism of drug resistant tuberculosis within Beijing family may help to clarify its origin and evolutionary history and the driving forces behind its emergence and current dissemination. METHODS Totally of 1222 Mycobacterium tuberculosis isolates were recovered from patients in six counties of two provinces in eastern China within 2010/2012. Strain lineage and its major subgroups were studied respectively by using Spoligotyping and MIRU-VNTR. The 1st-line drug susceptibility was analyzed by proportional method and 2nd-line drug susceptibility was determined by the HAINs MTBDRsl test. The genetic characterization of drug resistance was analyzed by sequencing the previously reported genes and loci associated with drug resistance together with the multiple genotyping including MIRU-VNTR, Spoligotyping and LSP genotyping. RESULTS Of the 1222 Mtb isolates, 298 (24.4%) were resistant to 1st-line drug and 73 (5.9%) were simultaneously resistant to INH and RIF namely MDR-TB. Respectively 23.8% of 1st-line drug resistant TB and 12.0% of the drug susceptible TB contained the mutation associated with 2nd-line drugs by HAINs test. The Spoligotyping of 1222 Mtb isolates revealed the 967 (79.1%) of the isolates belonged to the W-Beijing family. Within W-Beijing family, 78.8% MDR-TB were observed in the isolates with simultaneous deletion of RD105 and RD207, with sub-lineage 181 accounting for 75% of MDR-TB. Analysis of 24 MIRU-VNTR loci revealed that 88.2% (15/17) of MDR and extensively drug resistant (XDR) clustered isolates were sub-lineage 181. CONCLUSIONS Sublineage 181 might have the capacity to spread throughout the general community in rural China. This is the first report on the extensive association of sub-lineage 181 with MDR TB and possibly pre-XDR TB and XDR TB. It is important to monitor sublineage 181 to verify its heightened transmission and understand its importance in the global MDR-TB and XDR-TB epidemics.
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Affiliation(s)
- Yi Hu
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China; Key Laboratory of Public Health Safety (Fudan University), Ministry of Education, China.
| | - Barun Mathema
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, USA.
| | - Qi Zhao
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China; Key Laboratory of Public Health Safety (Fudan University), Ministry of Education, China
| | - Xubin Zheng
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China; Key Laboratory of Public Health Safety (Fudan University), Ministry of Education, China.
| | - Dange Li
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China; Key Laboratory of Public Health Safety (Fudan University), Ministry of Education, China.
| | - Weili Jiang
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China; Key Laboratory of Public Health Safety (Fudan University), Ministry of Education, China.
| | - Weibing Wang
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China; Key Laboratory of Public Health Safety (Fudan University), Ministry of Education, China
| | - Biao Xu
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China; Key Laboratory of Public Health Safety (Fudan University), Ministry of Education, China.
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Korma W, Mihret A, Hussien J, Anthony R, Lakew M, Aseffa A. Clinical, molecular and drug sensitivity pattern of mycobacterial isolates from extra-pulmonary tuberculosis cases in Addis Ababa, Ethiopia. BMC Infect Dis 2015; 15:456. [PMID: 26503529 PMCID: PMC4623242 DOI: 10.1186/s12879-015-1177-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2014] [Accepted: 10/05/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In conjunction with the spread of HIV infection, tuberculosis (TB) remains a major cause of illness and death worldwide. The Ethiopian national report reveals that extra pulmonary tuberculosis is on the rise and that case detection rate is exceeding that of smear positive or negative cases in many parts of the country. Different studies indicated that host and/or pathogen related factors are associated with the rise of extra pulmonary cases. However, the reason for this is not clearly known in our setting. METHODS Specimens were taken from clinically suspected extra pulmonary patients and confirmed by cytology, histopathology and culture. Deletion typing and Spoligotyping was utilized to identify the strains. The isolates were then assigned to lineage using conformal Bayesian network (rules model) algorithm and dendrograms were drawn using UPGMA methods. In addition, drug sensitivity test was done using the indirect proportion and 24 well plate methods. RESULTS Out of the 200 clinically suspected extra pulmonary tuberculosis patients, 106 (53 %) were between 15 and 35 years of age and 167 (83.5 %) were new while 33 (16.5 %) were retreatment cases. The culture yield was 29.5 % (59). Of these only one was M. bovis and 58 were M. tuberculosis strains with 31 different spoligotype patterns grouped into seven clusters. The largest cluster (ST53) comprised 12 (20.3 %) isolates. There was higher clustering of CAS isolates in TBLN than in any other form of extra pulmonary tuberculosis cases. Resistance to rifampicin was higher (22 %) than that for INH, STM and EMB (8.1 %, 5 % and 3 % respectively). Out of the 37 isolates tested for resistance, only 2 isolates were resistant for both STM and INH and no MDR strain was found. CONCLUSIONS There is an ongoing active recent transmission among extra pulmonary tuberculosis in the study areas as shown by the presence of clusters. Although no MDR case was observed, there is a risk of emergence of MDR as noted from the high proportion of resistance to rifampicin. Detailed study at population level is recommended to monitor its trend.
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Affiliation(s)
- Workneh Korma
- Institute of Biotechnology, Addis Ababa University, P.O. Box 62720, Addis Ababa, Ethiopia. .,Armauer Hansen Research Institute, P.O.Box 1105, Addis Ababa, Ethiopia.
| | - Adane Mihret
- Armauer Hansen Research Institute, P.O.Box 1105, Addis Ababa, Ethiopia.
| | - Jemal Hussien
- Armauer Hansen Research Institute, P.O.Box 1105, Addis Ababa, Ethiopia.
| | - Richard Anthony
- Royal Tropical Institute, Meibergdreef 39, 1105 AZ, Amsterdam, The Netherlands.
| | - Mekuria Lakew
- Department of Microbial, Cellular and Molecular, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia.
| | - Abraham Aseffa
- Armauer Hansen Research Institute, P.O.Box 1105, Addis Ababa, Ethiopia.
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45
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Han SJ, Song T, Cho YJ, Kim JS, Choi SY, Bang HE, Chun J, Bai GH, Cho SN, Shin SJ. Complete genome sequence of Mycobacterium tuberculosis K from a Korean high school outbreak, belonging to the Beijing family. Stand Genomic Sci 2015; 10:78. [PMID: 26473025 PMCID: PMC4606834 DOI: 10.1186/s40793-015-0071-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 10/08/2015] [Indexed: 01/04/2023] Open
Abstract
Mycobacterium tuberculosis K, a member of the Beijing family, was first identified in 1999 as the most prevalent genotype in South Korea among clinical isolates of M. tuberculosis from high school outbreaks. M. tuberculosis K is an aerobic, non-motile, Gram-positive, and non-spore-forming rod-shaped bacillus. A transmission electron microscopy analysis displayed an abundance of lipid bodies in the cytosol. The genome of the M. tuberculosis K strain was sequenced using two independent sequencing methods (Sanger and Illumina). Here, we present the genomic features of the 4,385,518-bp-long complete genome sequence of M. tuberculosis K (one chromosome, no plasmid, and 65.59 % G + C content) and its annotation, which consists of 4194 genes (3447 genes with predicted functions), 48 RNA genes (3 rRNA and 45 tRNA) and 261 genes with peptide signals.
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Affiliation(s)
- Seung Jung Han
- Department of Microbiology, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea.,Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, South Korea
| | - Taeksun Song
- Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, South Korea
| | - Yong-Joon Cho
- ChunLab Inc., Seoul National University, Seoul, South Korea
| | - Jong-Seok Kim
- Department of Microbiology, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea.,Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, South Korea
| | - Soo Young Choi
- Department of Microbiology, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea
| | - Hye-Eun Bang
- ChunLab Inc., Seoul National University, Seoul, South Korea
| | - Jongsik Chun
- ChunLab Inc., Seoul National University, Seoul, South Korea
| | - Gill-Han Bai
- Korean Institute of Tuberculosis, Korean National Tuberculosis Association, Osong, South Korea
| | - Sang-Nae Cho
- Department of Microbiology, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea.,Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, South Korea
| | - Sung Jae Shin
- Department of Microbiology, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea.,Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, South Korea
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Bonnet J, Boudot C, Courtioux B. Overview of the Diagnostic Methods Used in the Field for Human African Trypanosomiasis: What Could Change in the Next Years? BIOMED RESEARCH INTERNATIONAL 2015; 2015:583262. [PMID: 26504815 PMCID: PMC4609347 DOI: 10.1155/2015/583262] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 06/19/2015] [Accepted: 07/02/2015] [Indexed: 11/18/2022]
Abstract
Sleeping sickness is a parasitic infection caused by two species of trypanosomes (Trypanosoma brucei gambiense and rhodesiense), transmitted by the tsetse fly. The disease eventually affects the central nervous system, resulting in severe neurological symptoms. Without treatment, death is inevitable. During the first stage of the disease, infected patients are mildly symptomatic and early detection of infection allows safer treatment (administered on an outpatient basis) which can avoid death; routine screening of the exposed population is necessary, especially in areas of high endemicity. The current therapeutic treatment of this disease, especially in stage 2, can cause complications and requires a clinical surveillance for several days. A good stage diagnosis of the disease is the cornerstone for delivering the adequate treatment. The task faced by the medical personnel is further complicated by the lack of support from local health infrastructure, which is at best weak, but often nonexistent. Therefore it is crucial to look for new more efficient technics for the diagnosis of stage which are also best suited to use in the field, in areas not possessing high-level health facilities. This review, after an overview of the disease, summarizes the current diagnosis procedures and presents the advances in the field.
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Affiliation(s)
- Julien Bonnet
- INSERM, U1094, Tropical Neuroepidemiology, Limoges, France
- UMR_S 1094, Tropical Neuroepidemiology, Institute of Neuroepidemiology and Tropical Neurology, Université de Limoges, CNRS FR 3503 GEIST, 87000 Limoges, France
| | - Clotilde Boudot
- INSERM, U1094, Tropical Neuroepidemiology, Limoges, France
- UMR_S 1094, Tropical Neuroepidemiology, Institute of Neuroepidemiology and Tropical Neurology, Université de Limoges, CNRS FR 3503 GEIST, 87000 Limoges, France
| | - Bertrand Courtioux
- INSERM, U1094, Tropical Neuroepidemiology, Limoges, France
- UMR_S 1094, Tropical Neuroepidemiology, Institute of Neuroepidemiology and Tropical Neurology, Université de Limoges, CNRS FR 3503 GEIST, 87000 Limoges, France
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Beijing clades of Mycobacterium tuberculosis are associated with differential survival in HIV-negative Russian patients. INFECTION GENETICS AND EVOLUTION 2015; 36:517-523. [PMID: 26319998 DOI: 10.1016/j.meegid.2015.08.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 08/01/2015] [Accepted: 08/23/2015] [Indexed: 11/24/2022]
Abstract
We conducted a prospective study to establish factors associated with survival in tuberculosis patients in Russia including social, clinical and pathogen-related genetic parameters. Specifically we wished to determine whether different strains/clades of the Beijing lineage exerted a differential effect of survival. HIV-negative culture-confirmed cases were recruited during 2008-2010 across Samara Oblast and censored in December 2011. Molecular characterization was performed by a combination of spoligotyping, multilocus VNTR typing and whole genome sequencing (WGS). We analyzed 2602 strains and detected a high prevalence of Beijing family (n=1933; 74%) represented largely by two highly homogenous dominant clades A (n=794) and B (n=402) and non-A/non-B (n=737). Multivariable analysis of 1366 patients with full clinical and genotyping data showed that multi- and extensive drug resistance (HR=1.86; 95%CI: 1.52, 2.28 and HR=2.19; 95%CI: 1.55, 3.11) had the largest impact on survival. In addition older age, extensive lung damage, shortness of breath, treatment in the past and alcohol abuse reduced survival time. After adjustment for clinical and demographic predictors there was evidence that clades A and B combined were associated with poorer survival than other Beijing strains (HR=0.48; 95%CI 0.34, 0.67). All other pathogen-related factors (polymorphisms in genes plcA, plcB, plcC, lipR, dosT and pks15/1) had no effect on survival. In conclusion, drug resistance exerted the greatest effect on survival of TB patients. Nevertheless we provide evidence for the independent biological effect on survival of different Beijing family strains even within the same defined geographical population. Better understanding of the role of different strain factors in active disease and their influence on outcome is essential.
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Zinserling VA, Svistunov VV, Karev VE, Semenova NY. [Morphological diagnosis of tuberculosis under present-day conditions]. Arkh Patol 2015; 77:3-9. [PMID: 26226775 DOI: 10.17116/patol20157733-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The paper presents general statistical data on morbidity and mortality rates of tuberculosis, which show positive trends in recent years, with exception of those of its concurrence with HIV infection. The tasks of the morphological diagnosis of tuberculosis are divided into 4 groups: 1) to refine approaches to detecting mycobacteria in tissues; 2) to optimize the postmortem diagnosis of tuberculosis; 3) to optimize the lifetime differential diagnosis of tuberculosis and to develop methods for predicting its course; 4) to study the pathogenesis of tuberculosis from the standpoint of modern views on an infectious process. The data suggesting that the tissue forms of mycobacteria, the types of inflammatory responses, and the specific features of the pathogenesis of tuberculosis call for further investigations are given. To establish the real role of nontuberculous mycobacteria, to study the likelihood that the patient will be superinfected with other M. tuberculosis genotypes, and to elaborate a uniform (clinical, pathogenetic, and morphological) classification of tuberculosis should be also regarded as the most important tasks in its morphological examination.
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Affiliation(s)
- V A Zinserling
- Laboratory of Pathomorphology, Saint Petersburg Research Institute of Phthisiopulmonology; Department of Pathology, Medical Faculty, Saint Petersburg University; Center for Infectious Diseases, S.P. Botkin Infectious Diseases Hospital
| | - V V Svistunov
- Laboratory of Pathomorphology, Saint Petersburg Research Institute of Phthisiopulmonology; Department of Pathoanatomy, Irkutsk State Medical University
| | - V E Karev
- Laboratory of Pathomorphology, Research Institute of Childhood Infections
| | - N Yu Semenova
- Laboratory of Pathomorphology, Saint Petersburg Research Institute of Phthisiopulmonology
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Nakiyingi L, Nonyane BAS, Ssengooba W, Kirenga BJ, Nakanjako D, Lubega G, Byakika-Kibwika P, Joloba ML, Ellner JJ, Dorman SE, Mayanja-Kizza H, Manabe YC. Predictors for MTB Culture-Positivity among HIV-Infected Smear-Negative Presumptive Tuberculosis Patients in Uganda: Application of New Tuberculosis Diagnostic Technology. PLoS One 2015. [PMID: 26222142 PMCID: PMC4519276 DOI: 10.1371/journal.pone.0133756] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Background The existing World Health Organization diagnostic algorithms for smear-negative TB perform poorly in HIV-infected individuals. New TB diagnostics such as urine TB lipoarabinomannan (LAM) could improve the accuracy and reduce delays in TB diagnosis in HIV-infected smear-negative presumptive TB. We sought to determine predictors for MTB culture-positivity among these patients. Methods This study was nested into a prospective evaluation of HIV-infected outpatients and inpatients clinically suspected to have TB who were screened by smear-microscopy on two spot sputum samples. Data on socio-demographics, clinical symptoms, antiretroviral therapy, CXR, CD4 count, mycobacterial sputum and blood cultures and TB-LAM were collected. Logistic regression and conditional inference tree analysis were used to determine the most predictive indicators for MTB culture-positivity. Results Of the 418 smear-negative participants [female, 64%; median age (IQR) 32 (28-39) years, median CD4 106 (IQR 22 - 298) cells/mm3], 96/418 (23%) were sputum and/ or blood culture-positive for Mycobacterium tuberculosis (MTB) complex. Abnormal CXR (aOR 3.68, 95% CI 1.76- 7.71, p=0.001) and positive urine TB-LAM (aOR 6.21, 95% CI 3.14-12.27, p< 0.001) were significantly associated with MTB culture-positivity. Previous TB treatment (aOR 0.41, 95% CI 0.17-0.99, p=0.049) reduced the likelihood of a positive MTB culture. A conditional inference tree analysis showed that positive urine TB-LAM and abnormal CXR were the most predictive indicators of MTB culture-positivity. A combination of urine TB-LAM test and CXR had sensitivity and specificity of 50% and 86.1% respectively overall, and 70.8% and 84.1% respectively among those with CD4<100 cells/mm3. Conclusions A positive urine TB-LAM test and an abnormal CXR significantly predict MTB culture-positivity among smear-negative HIV-infected presumptive TB patients while previous TB treatment reduces the likelihood of a positive MTB culture. Validation studies to assess the performance of diagnostic algorithms that include urine TB-LAM in the diagnosis of smear-negative TB in HIV-infected individuals are warranted.
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Affiliation(s)
- Lydia Nakiyingi
- Infectious Diseases Institute, Makerere University College of Health Sciences, Kampala, Uganda
- Department of Medicine, School of Medicine, Makerere University College of Heath Sciences, Kampala, Uganda
- * E-mail:
| | - Bareng A. S. Nonyane
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Willy Ssengooba
- Department of Medical Microbiology, Makerere University College of Heath Sciences, Kampala, Uganda
| | - Bruce J. Kirenga
- Department of Medicine, School of Medicine, Makerere University College of Heath Sciences, Kampala, Uganda
| | - Damalie Nakanjako
- Infectious Diseases Institute, Makerere University College of Health Sciences, Kampala, Uganda
- Department of Medicine, School of Medicine, Makerere University College of Heath Sciences, Kampala, Uganda
| | - Gloria Lubega
- Infectious Diseases Institute, Makerere University College of Health Sciences, Kampala, Uganda
| | - Pauline Byakika-Kibwika
- Infectious Diseases Institute, Makerere University College of Health Sciences, Kampala, Uganda
- Department of Medicine, School of Medicine, Makerere University College of Heath Sciences, Kampala, Uganda
| | - Moses L. Joloba
- Department of Medical Microbiology, Makerere University College of Heath Sciences, Kampala, Uganda
| | - Jerry J. Ellner
- Boston Medical Center, Boston University School of Medicine, Boston, MA, United States of America
| | - Susan E. Dorman
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Harriet Mayanja-Kizza
- Department of Medicine, School of Medicine, Makerere University College of Heath Sciences, Kampala, Uganda
| | - Yukari C. Manabe
- Infectious Diseases Institute, Makerere University College of Health Sciences, Kampala, Uganda
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
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Correlates between models of virulence for Mycobacterium tuberculosis among isolates of the Central Asian lineage: a case for lysozyme resistance testing? Infect Immun 2015; 83:2213-23. [PMID: 25776753 DOI: 10.1128/iai.03080-14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 03/09/2015] [Indexed: 12/30/2022] Open
Abstract
Virulence factors (VFs) contribute to the emergence of new human Mycobacterium tuberculosis strains, are lineage dependent, and are relevant to the development of M. tuberculosis drugs/vaccines. VFs were sought within M. tuberculosis lineage 3, which has the Central Asian (CAS) spoligotype. Three isolates were selected from clusters previously identified as dominant in London, United Kingdom. Strain-associated virulence was studied in guinea pig, monocyte-derived macrophage, and lysozyme resistance assays. Whole-genome sequencing, single nucleotide polymorphism (SNP) analysis, and a literature review contributed to the identification of SNPs of interest. The animal model revealed borderline differences in strain-associated pathogenicity. Ex vivo, isolate C72 exhibited statistically significant differences in intracellular growth relative to C6 and C14. SNP candidates inducing lower fitness levels included 123 unique nonsynonymous SNPs, including three located in genes (lysX, caeA, and ponA2) previously identified as VFs in the laboratory-adapted reference strain H37Rv and shown to confer lysozyme resistance. C72 growth was most affected by lysozyme in vitro. A BLAST search revealed that all three SNPs of interest (C35F, P76Q, and P780R) also occurred in Tiruvallur, India, and in Uganda. Unlike C72, however, no single isolate identified through BLAST carried all three SNPs simultaneously. CAS isolates representative of three medium-sized human clusters demonstrated differential outcomes in models commonly used to estimate strain-associated virulence, supporting the idea that virulence varies within, not just across, M. tuberculosis lineages. Three VF SNPs of interest were identified in two additional locations worldwide, which suggested independent selection and supported a role for these SNPs in virulence. The relevance of lysozyme resistance to strain virulence remains to be established.
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