1
|
Asare-Baah M, Séraphin MN, Salmon-Trejo LAT, Johnston L, Dominique L, Ashkin D, Vaddiparti K, Kwara A, Maurelli AT, Lauzardo M. Effects of the Beijing genotype on latent tuberculosis infection, TB disease risk, and clustering of TB cases. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 123:105648. [PMID: 39059734 DOI: 10.1016/j.meegid.2024.105648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 07/22/2024] [Accepted: 07/23/2024] [Indexed: 07/28/2024]
Abstract
BACKGROUND The Beijing genotype of Mycobacterium tuberculosis (Mtb) has sparked debate regarding its virulence and transmissibility. This study contributes to this discussion by assessing its effect on the risk of latent tuberculosis infection (LTBI), active tuberculosis (TB) disease among contacts, and clustering of known TB cases. METHODS We conducted a retrospective cohort study using the records of 4457 culture-confirmed TB patients and their contacts (20,448) reported to the Florida Department of Health between 2009 and 2023. Univariate and multivariate analyses were used to evaluate the effect of the Beijing strain on LTBI, active TB risk among contacts, and case clustering. RESULTS Our study revealed no significant difference in transmissibility between the Beijing and non-Beijing genotypes among contacts. LTBI prevalence was 19.9%, slightly higher in non-Beijing than Beijing genotypes (20.2% vs. 15.5%, p < 0.001). The prevalence of active TB was 1.8%, with no significant difference between the Beijing and non-Beijing genotypes (1.4% vs. 1.8%, p = 0.296). Increased LTBI risk was associated with older age, male sex, Hispanic ethnicity, multidrug-resistant TB exposure, household exposure, and a longer exposure duration. Active TB risk was higher for males, HIV-positive individuals, and contacts with more prolonged exposure to index cases. The Beijing genotype was associated with increased TB case clustering (aOR = 1.98, 95%CI: 1.53, 2.55, p < 0.001) as compared to the non-Beijing genotypes. US birthplace (aOR = 2.75, 95%CI: 2.37, 3.19, p < 0.001), pulmonary disease (aOR = 1.27, 95%CI: 1.04, 1.56, p < 0.020), cavitary TB (aOR = 1.25, 95% CI: 1.08, 1.44, p < 0.003), previous year alcohol use (aOR = 1.68, 95%CI: 1.38, 2.04, p < 0.001), and recreational drug use (aOR = 1.32, 95%CI: 1.04, 1.67, p < 0.024) were also associated with an increased risk of TB case clustering. CONCLUSION While the Beijing genotype did not increase the risk of LTBI or active TB among contacts, it showed a higher tendency for case clustering. Hence, interventions should prioritize populations where this genotype is prevalent.
Collapse
Affiliation(s)
- Michael Asare-Baah
- Department of Epidemiology, University of Florida, College of Public Health and Health Professions, College of Medicine, 2004 Mowry Road, PO Box 100231, Gainesville, FL 32610, United States; Emerging Pathogens Institute, University of Florida, 2055 Mowry Road, PO Box 100009, Gainesville, FL 32610, United States
| | - Marie Nancy Séraphin
- Emerging Pathogens Institute, University of Florida, 2055 Mowry Road, PO Box 100009, Gainesville, FL 32610, United States; Division of Infectious Diseases and Global Medicine, University of Florida, College of Medicine, 2055 Mowry Road, PO Box 103600, Gainesville, FL 32610, United States
| | - LaTweika A T Salmon-Trejo
- Division of Infectious Diseases and Global Medicine, University of Florida, College of Medicine, 2055 Mowry Road, PO Box 103600, Gainesville, FL 32610, United States; Institute of Public Health, Florida A & M University, Tallahassee, FL, United States
| | - Lori Johnston
- Florida Department of Health, Bureau of Tuberculosis Control, 4052 Bald Cypress Way, Bin A-20, Tallahassee, FL 32399, United States
| | - Lina Dominique
- Florida Department of Health, Bureau of Tuberculosis Control, 4052 Bald Cypress Way, Bin A-20, Tallahassee, FL 32399, United States
| | - David Ashkin
- Florida Department of Health, Bureau of Tuberculosis Control, 4052 Bald Cypress Way, Bin A-20, Tallahassee, FL 32399, United States
| | - Krishna Vaddiparti
- Department of Epidemiology, University of Florida, College of Public Health and Health Professions, College of Medicine, 2004 Mowry Road, PO Box 100231, Gainesville, FL 32610, United States
| | - Awewura Kwara
- Department of Medicine, University of Florida, College of Medicine, Gainesville, FL, USA; Medical Service, North Florida South Georgia Veterans Health System, Gainesville, FL, USA
| | - Anthony T Maurelli
- Emerging Pathogens Institute, University of Florida, 2055 Mowry Road, PO Box 100009, Gainesville, FL 32610, United States; Department of Environmental and Global Health, University of Florida, Gainesville, FL 32610, USA
| | - Michael Lauzardo
- Emerging Pathogens Institute, University of Florida, 2055 Mowry Road, PO Box 100009, Gainesville, FL 32610, United States; Division of Infectious Diseases and Global Medicine, University of Florida, College of Medicine, 2055 Mowry Road, PO Box 103600, Gainesville, FL 32610, United States.
| |
Collapse
|
2
|
Ocampo JC, Alzate JF, Barrera LF, Baena A. Tuberculosis Severity Predictive Model Using Mtb Variants and Serum Biomarkers in a Colombian Cohort of APTB Patients. Biomedicines 2023; 11:3110. [PMID: 38137331 PMCID: PMC10740695 DOI: 10.3390/biomedicines11123110] [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: 09/11/2023] [Revised: 10/27/2023] [Accepted: 11/04/2023] [Indexed: 12/24/2023] Open
Abstract
Currently, tuberculosis (TB) is a bacterial infection caused by Mycobacterium tuberculosis (Mtb) that primarily affects the lungs. The severity of active pulmonary TB (APTB) is an important determinant of transmission, morbidity, mortality, disease experience, and treatment outcomes. Several publications have shown a high prevalence of disabling complications in individuals who have had severe APTB. Furthermore, certain strains of Mtb were associated with more severe disease outcomes. The use of biomarkers to predict severe APTB patients who are candidates for host-directed therapies, due to the high risk of developing post-tuberculous lung disease (PTLD), has not yet been implemented in the management of TB patients. We followed 108 individuals with APTB for 6 months using clinical tools, flow cytometry, and whole-genome sequencing (WGS). The median age of the study population was 26.5 years, and the frequency of women was 53.7%. In this study, we aimed to identify biomarkers that could help us to recognize individuals with APTB and improve our understanding of the immunopathology in these individuals. In this study, we conducted a follow-up on the treatment progress of 121 cases of APTB. The follow-up process commenced at the time of diagnosis (T0), continued with a control visit at 2 months (T2), and culminated in an exit appointment at 6 months following the completion of medical treatment (T6). People classified with severe APTB showed significantly higher levels of IL-6 (14.7 pg/mL; p < 0.05) compared to those with mild APTB (7.7 pg/mL) at T0. The AUCs for the ROC curves and the Matthews correlation coefficient values (MCC) demonstrate correlations ranging from moderate to very strong. We conducted WGS on 88 clinical isolates of Mtb, and our analysis revealed a total of 325 genes with insertions and deletions (Indels) within their coding regions when compared to the Mtb H37Rv reference genome. The pattern of association was found between serum levels of CHIT1 and the presence of Indels in Mtb isolates from patients with severe APTB. A key finding in our study was the high levels of CHIT1 in severe APTB patients. We identified a biomarker profile (IL-6, IFN-γ, IL-33, and CHIT1) that allows us to identify individuals with severe APTB, as well as the identification of a panel of polymorphisms (125) in clinical isolates of Mtb from individuals with severe APTB. Integrating these findings into a predictive model of severity would show promise for the management of APTB patients in the future, to guide host-directed therapy and reduce the prevalence of PTLD.
Collapse
Affiliation(s)
- Juan C. Ocampo
- Grupo de Inmunología Celular e Inmunogenética (GICIG), Universidad de Antioquia (UdeA), Medellín 050010, Colombia; (J.C.O.); (L.F.B.)
| | - Juan F. Alzate
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia (UdeA), Medellín 050010, Colombia;
- Centro Nacional de Secuenciación Genómica (CNSG), Facultad de Medicina, Universidad de Antioquia (UdeA), Medellín 050010, Colombia
| | - Luis F. Barrera
- Grupo de Inmunología Celular e Inmunogenética (GICIG), Universidad de Antioquia (UdeA), Medellín 050010, Colombia; (J.C.O.); (L.F.B.)
- Instituto de Investigaciones Médicas, Universidad de Antioquia (UdeA), Medellín 050010, Colombia
| | - Andres Baena
- Grupo de Inmunología Celular e Inmunogenética (GICIG), Universidad de Antioquia (UdeA), Medellín 050010, Colombia; (J.C.O.); (L.F.B.)
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia (UdeA), Medellín 050010, Colombia;
| |
Collapse
|
3
|
Mokrousov I, Vinogradova T, Dogonadze M, Zabolotnykh N, Vyazovaya A, Vitovskaya M, Solovieva N, Ariel B. A multifaceted interplay between virulence, drug resistance, and the phylogeographic landscape of Mycobacterium tuberculosis. Microbiol Spectr 2023; 11:e0139223. [PMID: 37768091 PMCID: PMC10581221 DOI: 10.1128/spectrum.01392-23] [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: 03/31/2023] [Accepted: 08/06/2023] [Indexed: 09/29/2023] Open
Abstract
Latin-American Mediterranean (LAM) family is one of the most significant and global genotypes of Mycobacterium tuberculosis. Here, we used the murine model to study the virulence and lethality of the genetically and epidemiologically distinct LAM strains. The pathobiological characteristics of the four LAM strains (three drug resistant and one drug susceptible) and the susceptible reference strain H37Rv were studied in the C57BL/6 mouse model. The whole-genome sequencing was performed using the HiSeq Illumina platform, followed by bioinformatics and phylogenetic analysis. The susceptible strain H37Rv showed the highest virulence. Drug-susceptible LAM strain (spoligotype SIT264) was more virulent than three multidrug-resistant (MDR) strains (SIT252, SIT254, and SIT266). All three MDR isolates were low lethal, while the susceptible isolate and H37Rv were moderately/highly lethal. Putting the genomic, phenotypic, and virulence features of the LAM strains/spoligotypes in the context of their dynamic phylogeography over 20 years reveals three types of relationships between virulence, resistance, and transmission. First, the most virulent and more lethal drug-susceptible SIT264 increased its circulation in parts of Russia. Second, moderately virulent and pre-XDR SIT266 was prevalent in Belarus and continues to be visible in North-West Russia. Third, the low virulent and MDR strain SIT252 previously considered as emerging has disappeared from the population. These findings suggest that strain virulence impacts the transmission, irrespective of drug resistance properties. The increasing circulation of susceptible but more virulent and lethal strains implies that personalized TB treatment should consider not only resistance but also the virulence of the infecting M. tuberculosis strains. IMPORTANCE The study is multidisciplinary and investigates the epidemically/clinically important and global lineage of Mycobacterium tuberculosis, named Latin-American-Mediterranean (LAM), yet insufficiently studied with regard to its pathobiology. We studied different LAM strains (epidemic vs endemic and resistant vs susceptible) in the murine model and using whole-genome analysis. We also collected long-term, 20-year data on their prevalence in Eurasia. The findings are both expected and unexpected. (i) We observe that a drug-susceptible but highly virulent strain increased its prevalence. (ii) By contrast, the multidrug-resistant (MDR) but low-virulent, low-lethal strain (that we considered as emerging 15 years ago) has almost disappeared. (iii) Finally, an intermediate case is the MDR strain with moderate virulence that continues to circulate. We conclude that (i) the former and latter strains are the most hazardous and require close epidemiological monitoring, and (ii) personalized TB treatment should consider not only drug resistance but also the virulence of the infecting strains and development of anti-virulence drugs is warranted.
Collapse
Affiliation(s)
- Igor Mokrousov
- St. Petersburg Pasteur Institute, St. Petersburg, Russia
| | - Tatiana Vinogradova
- St. Petersburg Pasteur Institute, St. Petersburg, Russia
- St. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia
| | - Marine Dogonadze
- St. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia
| | - Natalia Zabolotnykh
- St. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia
| | - Anna Vyazovaya
- St. Petersburg Pasteur Institute, St. Petersburg, Russia
| | - Maria Vitovskaya
- St. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia
| | - Natalia Solovieva
- St. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia
| | - Boris Ariel
- St. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia
| |
Collapse
|
4
|
Maladan Y, Safari D, Parikesit AA. Structural dynamics insights into the M306L, M306V, and D1024N mutations in Mycobacterium tuberculosis inducing resistance to ethambutol. Genomics Inform 2023; 21:e32. [PMID: 37813628 PMCID: PMC10584647 DOI: 10.5808/gi.23019] [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: 03/27/2023] [Revised: 05/18/2023] [Accepted: 08/07/2023] [Indexed: 10/11/2023] Open
Abstract
Resistance to anti-tuberculosis drugs, especially ethambutol (EMB), has been widely reported worldwide. EMB resistance is caused by mutations in the embB gene, which encodes the arabinosyl transferase enzyme. This study aimed to detect mutations in the embB gene of Mycobacterium tuberculosis from Papua and to evaluate their impact on the effectiveness of EMB. We analyzed 20 samples of M. tuberculosis culture that had undergone whole-genome sequencing, of which 19 samples were of sufficient quality for further bioinformatics analysis. Mutation analysis was performed using TBProfiler, which identified M306L, M306V, D1024N, and E378A mutations. In sample TB035, the M306L mutation was present along with E378A. The binding affinity of EMB to arabinosyl transferase was calculated using AutoDock Vina. The molecular docking results revealed that all mutants demonstrated an increased binding affinity to EMB compared to the native protein (-0.948 kcal/mol). The presence of the M306L mutation, when coexisting with E378A, resulted in a slight increase in binding affinity compared to the M306L mutation alone. The molecular dynamics simulation results indicated that the M306L, M306L + E378A, M306V, and E378A mutants decreased protein stability. Conversely, the D1024N mutant exhibited stability comparable to the native protein. In conclusion, this study suggests that the M306L, M306L + E378A, M306V, and E378A mutations may contribute to EMB resistance, while the D1024N mutation may be consistent with continued susceptibility to EMB.
Collapse
Affiliation(s)
- Yustinus Maladan
- Eijkman Research Center for Molecular Biology, The National Research and Innovation Agency, Cibinong, Bogor 16911, Indonesia
| | - Dodi Safari
- Eijkman Research Center for Molecular Biology, The National Research and Innovation Agency, Cibinong, Bogor 16911, Indonesia
| | - Arli Aditya Parikesit
- Department of Bioinformatics, School of Life Sciences, Indonesia International Institute for Life Sciences (I3L), Jakarta 13210, Indonesia
| |
Collapse
|
5
|
Jonas D, Kirby M, Schenkel AR, Dangelmayr G. Modeling of adaptive immunity uncovers disease tolerance mechanisms. J Theor Biol 2023; 568:111498. [PMID: 37100114 DOI: 10.1016/j.jtbi.2023.111498] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 03/03/2023] [Accepted: 04/17/2023] [Indexed: 04/28/2023]
Abstract
When an organism is challenged with a pathogen a cascade of events unfolds. The innate immune system rapidly mounts a preliminary nonspecific defense, while the acquired immune system slowly develops microbe-killing specialists. These responses cause inflammation, and along with the pathogen cause direct and indirect tissue damage, which anti-inflammatory mediators seek to temper. This interplay of systems is credited for maintaining homeostasis but may produce unexpected results such as disease tolerance. Tolerance is characterized by the persistence of pathogen and damage mitigation, where the relevant mechanisms are poorly understood. In this work we develop an ordinary differential equations model of the immune response to infection in order to identify key components in tolerance. Bifurcation analysis uncovers health, immune- and pathogen-mediated death clinical outcomes dependent on pathogen growth rate. We demonstrate that decreasing the inflammatory response to damage and increasing the strength of the immune system gives rise to a region in which limit cycles, or periodic solutions, are the only biological trajectories. We then describe areas of parameter space corresponding to disease tolerance by varying immune cell decay, pathogen removal, and lymphocyte proliferation rates.
Collapse
Affiliation(s)
- Daniel Jonas
- Colorado State University, Department of Mathematics, Fort Collins, CO, United States.
| | - Michael Kirby
- Colorado State University, Department of Mathematics, Fort Collins, CO, United States; Colorado State University, Department of Computer Science, Fort Collins, CO, United States
| | - Alan R Schenkel
- Colorado State University Department of Microbiology, Immunology, and Pathology, Fort Collins, CO, United States
| | - Gerhard Dangelmayr
- Colorado State University, Department of Mathematics, Fort Collins, CO, United States
| |
Collapse
|
6
|
Rajwani R, Galata C, Lee AWT, So PK, Leung KSS, Tam KKG, Shehzad S, Ng TTL, Zhu L, Lao HY, Chan CTM, Leung JSL, Lee LK, Wong KC, Yam WC, Siu GKH. A multi-omics investigation into the mechanisms of hyper-virulence in Mycobacterium tuberculosis. Virulence 2022; 13:1088-1100. [PMID: 35791449 PMCID: PMC9262360 DOI: 10.1080/21505594.2022.2087304] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Clinical manifestations of tuberculosis range from asymptomatic infection to a life-threatening disease such as tuberculous meningitis (TBM). Recent studies showed that the spectrum of disease severity could be related to genetic diversity among clinical strains of Mycobacterium tuberculosis (Mtb). Certain strains are reported to preferentially invade the central nervous system, thus earning the label “hypervirulent strains”.However, specific genetic mutations that accounted for enhanced mycobacterial virulence are still unknown. We previously identified a set of 17 mutations in a hypervirulent Mtb strain that was from TBM patient and exhibited significantly better intracellular survivability. These mutations were also commonly shared by a cluster of globally circulating hyper-virulent strains. Here, we aimed to validate the impact of these hypervirulent-specific mutations on the dysregulation of gene networks associated with virulence in Mtb via multi-omic analysis. We surveyed transcriptomic and proteomic differences between the hyper-virulent and low-virulent strains using RNA-sequencing and label-free quantitative LC-MS/MS approach, respectively. We identified 25 genes consistently differentially expressed between the strains at both transcript and protein level, regardless the strains were growing in a nutrient-rich or a physiologically relevant multi-stress condition (acidic pH, limited nutrients, nitrosative stress, and hypoxia). Based on integrated genomic-transcriptomic and proteomic comparisons, the hypervirulent-specific mutations in FadE5 (g. 295,746 C >T), Rv0178 (p. asp150glu), higB (p. asp30glu), and pip (IS6110-insertion) were linked to deregulated expression of the respective genes and their functionally downstream regulons. The result validated the connections between mutations, gene expression, and mycobacterial pathogenicity, and identified new possible virulence-associated pathways in Mtb.
Collapse
Affiliation(s)
- Rahim Rajwani
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, Hong Kong, China
| | - Chala Galata
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, Hong Kong, China
| | - Annie Wing Tung Lee
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, Hong Kong, China
| | - Pui-Kin So
- University Research Facility in Life Sciences, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Kenneth Siu Sing Leung
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Kingsley King Gee Tam
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Sheeba Shehzad
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, Hong Kong, China
| | - Timothy Ting Leung Ng
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, Hong Kong, China
| | - Li Zhu
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, Hong Kong, China
| | - Hiu Yin Lao
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, Hong Kong, China
| | - Chloe Toi-Mei Chan
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, Hong Kong, China
| | - Jake Siu-Lun Leung
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, Hong Kong, China
| | - Lam-Kwong Lee
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, Hong Kong, China
| | - Kin Chung Wong
- Department of Clinical Pathology, United Christian Hospital, Hong Kong Special Administrative Region, China
| | - Wing Cheong Yam
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Gilman Kit-Hang Siu
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, Hong Kong, China
| |
Collapse
|
7
|
Zha BS, Desvignes L, Fergus TJ, Cornelius A, Cheng TY, Moody DB, Ernst JD. Bacterial Strain-Dependent Dissociation of Cell Recruitment and Cell-to-Cell Spread in Early M. tuberculosis Infection. mBio 2022; 13:e0133222. [PMID: 35695454 PMCID: PMC9239178 DOI: 10.1128/mbio.01332-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 05/16/2022] [Indexed: 11/20/2022] Open
Abstract
In the initial stage of respiratory infection, Mycobacterium tuberculosis traverses from alveolar macrophages to phenotypically diverse monocyte-derived phagocytes and neutrophils in the lung parenchyma. Here, we compare the in vivo kinetics of early bacterial growth and cell-to-cell spread of two strains of M. tuberculosis: a lineage 2 strain, 4334, and the widely studied lineage 4 strain H37Rv. Using flow cytometry, live cell sorting of phenotypic subsets, and quantitation of bacteria in cells of the distinct subsets, we found that 4334 induces less leukocyte influx into the lungs but demonstrates earlier population expansion and cell-to-cell spread. The earlier spread of 4334 to recruited cells, including monocyte-derived dendritic cells, is accompanied by earlier and greater magnitude of CD4+ T cell activation. The results provide evidence that strain-specific differences in interactions with lung leukocytes can shape adaptive immune responses in vivo. IMPORTANCE Tuberculosis is a leading infectious disease killer worldwide and is caused by Mycobacterium tuberculosis. After exposure to M. tuberculosis, outcomes range from apparent elimination to active disease. Early innate immune responses may contribute to differences in outcomes, yet it is not known how bacterial strains alter the early dynamics of innate immune and T cell responses. We infected mice with distinct strains of M. tuberculosis and discovered striking differences in innate cellular recruitment, cell-to-cell spread of bacteria in the lungs, and kinetics of initiation of antigen-specific CD4 T cell responses. We also found that M. tuberculosis can spread beyond alveolar macrophages even before a large influx of inflammatory cells. These results provide evidence that distinct strains of M. tuberculosis can exhibit differential kinetics in cell-to-cell spread which is not directly linked to early recruitment of phagocytes but is subsequently linked to adaptive immune responses.
Collapse
Affiliation(s)
- B. Shoshana Zha
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of California, San Francisco, California, USA
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, California, USA
| | - Ludovic Desvignes
- Department of Medicine, New York University School of Medicine, New York, New York, USA
| | - Tawania J. Fergus
- Department of Medicine, New York University School of Medicine, New York, New York, USA
| | - Amber Cornelius
- Department of Medicine, New York University School of Medicine, New York, New York, USA
| | - Tan-Yun Cheng
- Division of Rheumatology, Immunity and Inflammation, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - D. Branch Moody
- Division of Rheumatology, Immunity and Inflammation, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Joel D. Ernst
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, California, USA
| |
Collapse
|
8
|
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.
Collapse
|
9
|
Tong J, Meng L, Bei C, Liu Q, Wang M, Yang T, Takiff HE, Zhang S, Gao Q, Wang C, Yan B. Modern Beijing sublineage of Mycobacterium tuberculosis shift macrophage into a hyperinflammatory status. Emerg Microbes Infect 2022; 11:715-724. [PMID: 35125072 PMCID: PMC8890550 DOI: 10.1080/22221751.2022.2037395] [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] [Indexed: 11/05/2022]
Abstract
The high prevalence of the modern Beijing sublineage of Mycobacterium tuberculosis may be related to increased virulence, although the responsible mechanisms remain poorly understood. We previously described enhanced triacylglycerol accumulation in modern Beijing strains. Here we show that modern Beijing strains grow faster in vitro and trigger a vigorous immune response and pronounced macrophage infiltration. Transcriptomic analysis of bone marrow derived macrophages infected with modern Beijing lineage strains revealed a significant enrichment of infection, cholesterol homeostasis and amino acid metabolic pathways. The upregulation of proinflammatory / bactericidal cytokines was confirmed by RT–PCR analysis, which is also in consistent with the reduced bacterial burden in modern strains infected macrophages. These results suggest that modern Beijing strains elicit a hyperinflammatory response which might indicate a stronger virulence and contribute to their extensive global prevalence.
Collapse
Affiliation(s)
- Jingfeng Tong
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College and Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Lu Meng
- The Center for Microbes, Development and Health, Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences/University of Chinese Academy of Sciences, Shanghai, China
| | - Cheng Bei
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College and Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Qingyun Liu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College and Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.,Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Min Wang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - TingTing Yang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College and Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Howard E Takiff
- Department of Tuberculosis Control and Prevention, Shenzhen Nanshan Centre for Chronic Disease Control, Shenzhen, China.,Instituto Venezolano de Investigaciones Cientificas, Caracas, Venezuela
| | - Shuye Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Qian Gao
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College and Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Chuan Wang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College and Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Bo Yan
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| |
Collapse
|
10
|
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.
Collapse
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
| |
Collapse
|
11
|
Vinogradova T, Dogonadze M, Zabolotnykh N, Badleeva M, Yarusova I, Vyazovaya A, Gerasimova A, Zhdanova S, Vitovskaya M, Solovieva N, Pasechnik O, Ogarkov O, Mokrousov I. Extremely lethal and hypervirulent Mycobacterium tuberculosis strain cluster emerging in Far East, Russia. Emerg Microbes Infect 2021; 10:1691-1701. [PMID: 34380361 PMCID: PMC8381949 DOI: 10.1080/22221751.2021.1967704] [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] [Indexed: 11/29/2022]
Abstract
Mycobacterium tuberculosis strains of the early ancient sublineage of the Beijing genotype are mostly drug susceptible and mainly circulate in East Asia. We have recently discovered two clusters of this sublineage emerging in the Asian part of Russia (VNTR-defined 1071-32 and 14717-15 types) and, to our surprise, both were strongly MDR/XDR-associated. Here, we evaluated their pathogenic features. The clinical isolates and reference laboratory strain H37Rv were investigated in the C57BL/6 mouse model to assess their virulence and lethality properties. The BACTEC MGIT 960 system was used to study the in vitro growth characteristics. In the murine model, strains 396 (14717-15-cluster, from Buryatia, Far East) and 6691 (1071-32-cluster, from Omsk, Siberia) demonstrated contrasting properties. The 396-infected group had significantly higher mortality, more weight loss, higher bacterial burden, and more severe lung pathology. Furthermore, compared to the previously published data on other Russian epidemic Beijing strains (B0/W148, CAO, Central Asian Russian), strain 396 demonstrated the highest mortality. Under the in vitro growth experiment, cluster 14717-15 isolates had significantly shorter lag-phase. To conclude, low-virulent MDR strain 6691 belongs to the Beijing 1071-32-cluster widespread across FSU countries but at low prevalence. This corresponds to common expectation that multiple drug resistance mutations reduce fitness and virulence. In contrast, highly lethal and hypervirulent MDR strain 396 represents an intriguing Beijing 14717-15 cluster predominant only in Buryatia, Far East (16%), sporadically found beyond it, but not forming clusters of transmission. Further in-depth study of this most virulent Russian Beijing cluster is warranted.
Collapse
Affiliation(s)
- Tatiana Vinogradova
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, St. Petersburg, Russia.,Laboratory of Experimental Tuberculosis and New Medical Technologies, St. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia
| | - Marine Dogonadze
- Bacteriology Laboratory, St. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia
| | - Natalia Zabolotnykh
- Laboratory of Experimental Tuberculosis and New Medical Technologies, St. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia
| | - Maria Badleeva
- Department of Infectious Diseases, Buryat State University, Ulan-Ude, Buryatia, Russia
| | - Irina Yarusova
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, St. Petersburg, Russia.,Bacteriology Laboratory, Clinical Anti-tuberculosis Dispensary, Omsk, Russia
| | - Anna Vyazovaya
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, St. Petersburg, Russia
| | - Alena Gerasimova
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, St. Petersburg, Russia
| | - Svetlana Zhdanova
- Department of Epidemiology and Microbiology, Scientific Centre of the Family Health and Human Reproduction Problems, Irkutsk, Russia
| | - Maria Vitovskaya
- Laboratory of Experimental Tuberculosis and New Medical Technologies, St. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia
| | - Natalia Solovieva
- Bacteriology Laboratory, St. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia
| | - Oksana Pasechnik
- Department of Public Health, Omsk State Medical University, Omsk, Russia
| | - Oleg Ogarkov
- Department of Epidemiology and Microbiology, Scientific Centre of the Family Health and Human Reproduction Problems, Irkutsk, Russia
| | - Igor Mokrousov
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, St. Petersburg, Russia
| |
Collapse
|
12
|
Yang HJ, Wang D, Wen X, Weiner DM, Via LE. One Size Fits All? Not in In Vivo Modeling of Tuberculosis Chemotherapeutics. Front Cell Infect Microbiol 2021; 11:613149. [PMID: 33796474 PMCID: PMC8008060 DOI: 10.3389/fcimb.2021.613149] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 02/08/2021] [Indexed: 12/11/2022] Open
Abstract
Tuberculosis (TB) remains a global health problem despite almost universal efforts to provide patients with highly effective chemotherapy, in part, because many infected individuals are not diagnosed and treated, others do not complete treatment, and a small proportion harbor Mycobacterium tuberculosis (Mtb) strains that have become resistant to drugs in the standard regimen. Development and approval of new drugs for TB have accelerated in the last 10 years, but more drugs are needed due to both Mtb's development of resistance and the desire to shorten therapy to 4 months or less. The drug development process needs predictive animal models that recapitulate the complex pathology and bacterial burden distribution of human disease. The human host response to pulmonary infection with Mtb is granulomatous inflammation usually resulting in contained lesions and limited bacterial replication. In those who develop progressive or active disease, regions of necrosis and cavitation can develop leading to lasting lung damage and possible death. This review describes the major vertebrate animal models used in evaluating compound activity against Mtb and the disease presentation that develops. Each of the models, including the zebrafish, various mice, guinea pigs, rabbits, and non-human primates provides data on number of Mtb bacteria and pathology resolution. The models where individual lesions can be dissected from the tissue or sampled can also provide data on lesion-specific bacterial loads and lesion-specific drug concentrations. With the inclusion of medical imaging, a compound's effect on resolution of pathology within individual lesions and animals can also be determined over time. Incorporation of measurement of drug exposure and drug distribution within animals and their tissues is important for choosing the best compounds to push toward the clinic and to the development of better regimens. We review the practical aspects of each model and the advantages and limitations of each in order to promote choosing a rational combination of them for a compound's development.
Collapse
Affiliation(s)
- Hee-Jeong Yang
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research (DIR), National Institute of Allergy and Infectious Disease (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Decheng Wang
- Medical College, China Three Gorges University, Yichang, China.,Institute of Infection and Inflammation, China Three Gorges University, Yichang, China
| | - Xin Wen
- Medical College, China Three Gorges University, Yichang, China.,Institute of Infection and Inflammation, China Three Gorges University, Yichang, China
| | - Danielle M Weiner
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research (DIR), National Institute of Allergy and Infectious Disease (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States.,Tuberculosis Imaging Program, DIR, NIAID, NIH, Bethesda, MD, United States
| | - Laura E Via
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research (DIR), National Institute of Allergy and Infectious Disease (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States.,Tuberculosis Imaging Program, DIR, NIAID, NIH, Bethesda, MD, United States.,Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| |
Collapse
|
13
|
Verma D, Chan ED, Ordway DJ. The double-edged sword of Tregs in M tuberculosis, M avium, and M absessus infection. Immunol Rev 2021; 301:48-61. [PMID: 33713043 DOI: 10.1111/imr.12959] [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: 12/07/2020] [Revised: 01/24/2021] [Accepted: 01/25/2021] [Indexed: 12/12/2022]
Abstract
Immunity against different Mycobacteria species targeting the lung requires distinctly different pulmonary immune responses for bacterial clearance. Many parameters of acquired and regulatory immune responses differ quantitatively and qualitatively from immunity during infection with Mycobacteria species. Nontuberculosis Mycobacteria species (NTM) Mycobacterium avium- (M avium), Mycobacterium abscessus-(M abscessus), and the Mycobacteria species Mycobacterium tuberculosis-(Mtb). Herein, we discuss the potential implications of acquired and regulatory immune responses in the context of animal and human studies, as well as future directions for efforts to treat Mycobacteria diseases.
Collapse
Affiliation(s)
- Deepshikha Verma
- Mycobacteria Research Laboratory, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Edward D Chan
- Department of Medicine, Rocky Mountain Regional Veterans Affairs Medical Center, Denver, CO, USA.,Departments of Medicine and Academic Affairs, National Jewish Health, Denver, CO, USA.,Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Denver, CO, USA
| | - Diane J Ordway
- Mycobacteria Research Laboratory, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| |
Collapse
|
14
|
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.
Collapse
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
| |
Collapse
|
15
|
Uddin MKM, Rahman A, Ather MF, Ahmed T, Rahman SMM, Ahmed S, Banu S. Distribution and Frequency of rpoB Mutations Detected by Xpert MTB/RIF Assay Among Beijing and Non-Beijing Rifampicin Resistant Mycobacterium tuberculosis Isolates in Bangladesh. Infect Drug Resist 2020; 13:789-797. [PMID: 32210593 PMCID: PMC7073589 DOI: 10.2147/idr.s240408] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 02/07/2020] [Indexed: 12/19/2022] Open
Abstract
Background Rifampicin resistance (RR) is a key indicator of multidrug-resistant tuberculosis (MDR-TB) and 95% of the RR is associated with the mutation in the 81-bp rifampicin resistance determining region (RRDR) of the rpoB gene of Mycobacterium tuberculosis complex (MTBC). The Xpert MTB/RIF (Xpert) assay uses five overlapping molecular beacon probes (A-E) complementary to RRDR region that detect MTBC and mutations associated with RR. The objective of the study was to investigate the distribution and frequency of mutations detected by Xpert assay among Beijing and non-Beijing RR-TB isolates. Methods A total of 205 randomly selected RR-TB specimens detected by Xpert assay were included in this study. A portion of specimens was further subjected to culture, MTBDRplus test and the positive culture isolates were genotyped by spoligotyping. Results We found that the most frequent mutation occurred at probe E (S531L) binding region in both Beijing and non-Beijing isolates (61.9% and 66.9%, respectively). The Beijing family had higher mutation rates than non-Beijing (19.0% vs 12.4%) at probe B (D516V) while the non-Beijing family had higher mutations at probe D (H526D or H526Y) than the Beijing (13.2% vs 10.7%) family. Mutations at probes Aand C were less common in both Beijing and non-Beijing isolates. There was no significant difference (P=0.36) in the occurrence of mutations at different probes between Beijing and non-Beijing isolates. Conclusions The study results revealed that the most frequent mutation occurs in the region of probe E and the least common mutations at probe A and C among both Beijing and non-Beijing RR-TB cases. This first insight into the probe mutation variation and frequencies among the RR-TB cases in Bangladesh forms the baseline information for further investigation.
Collapse
Affiliation(s)
| | - Arfatur Rahman
- Infectious Diseases Division, icddr,b, Dhaka, Bangladesh.,Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus), Parkville VIC 3052, Australia
| | - Md Fahim Ather
- Infectious Diseases Division, icddr,b, Dhaka, Bangladesh
| | - Tanvir Ahmed
- Infectious Diseases Division, icddr,b, Dhaka, Bangladesh
| | | | - Shahriar Ahmed
- Infectious Diseases Division, icddr,b, Dhaka, Bangladesh
| | - Sayera Banu
- Infectious Diseases Division, icddr,b, Dhaka, Bangladesh
| |
Collapse
|
16
|
Subbarao S, Sanchez-Garrido J, Krishnan N, Shenoy AR, Robertson BD. Genetic and pharmacological inhibition of inflammasomes reduces the survival of Mycobacterium tuberculosis strains in macrophages. Sci Rep 2020; 10:3709. [PMID: 32111888 PMCID: PMC7048741 DOI: 10.1038/s41598-020-60560-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 02/13/2020] [Indexed: 12/15/2022] Open
Abstract
Mycobacterium tuberculosis infection causes high rates of morbidity and mortality. Host-directed therapy may enhance the immune response, reduce tissue damage and shorten treatment duration. The inflammasome is integral to innate immune responses but over-activation has been described in tuberculosis (TB) pathology and TB-immune reconstitution syndrome. Here we explore how clinical isolates differentially activate the inflammasome and how inflammasome inhibition can lead to enhanced bacterial clearance. Wild-type, Nlrp3−/−/Aim2−/−, Casp1/11−/− and Asc−/− murine bone-marrow derived macrophages (BMDMs) were infected with laboratory strain M. tuberculosis H37Rv or clinical isolates from various lineages. Inflammasome activation and bacterial numbers were measured, and pharmacological inhibition of NLRP3 was achieved using MCC950. Clinical isolates of M. tuberculosis differed in their ability to activate inflammasomes. Beijing isolates had contrasting effects on IL-1β and caspase-1 activation, but all clinical isolates induced lower IL-1β release than H37Rv. Our studies suggest the involvement of NLRP3, AIM2 and an additional unknown sensor in IL-1β maturation. Pharmacological blockade of NLRP3 with MCC950 reduced bacterial survival, and combined treatment with the antimycobacterial drug rifampicin enhanced the effect. Modulating the inflammasome is an attractive adjunct to current anti-mycobacterial therapy that warrants further investigation.
Collapse
Affiliation(s)
- Sathyavani Subbarao
- MRC Centre for Molecular Bacteriology and Infection, Department of Infectious Disease, Flowers Building, Imperial College London, London, SW7 2AZ, UK
| | - Julia Sanchez-Garrido
- MRC Centre for Molecular Bacteriology and Infection, Department of Infectious Disease, Flowers Building, Imperial College London, London, SW7 2AZ, UK
| | - Nitya Krishnan
- MRC Centre for Molecular Bacteriology and Infection, Department of Infectious Disease, Flowers Building, Imperial College London, London, SW7 2AZ, UK
| | - Avinash R Shenoy
- MRC Centre for Molecular Bacteriology and Infection, Department of Infectious Disease, Flowers Building, Imperial College London, London, SW7 2AZ, UK.
| | - Brian D Robertson
- MRC Centre for Molecular Bacteriology and Infection, Department of Infectious Disease, Flowers Building, Imperial College London, London, SW7 2AZ, UK.
| |
Collapse
|
17
|
Cardona P, Cardona PJ. Regulatory T Cells in Mycobacterium tuberculosis Infection. Front Immunol 2019; 10:2139. [PMID: 31572365 PMCID: PMC6749097 DOI: 10.3389/fimmu.2019.02139] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 08/27/2019] [Indexed: 12/11/2022] Open
Abstract
Anti-inflammatory regulatory T cells have lately attracted attention as part of the immune response to Mycobacterium tuberculosis infection, where they counterbalance the protective but pro-inflammatory immune response mediated by Th17 cells and especially by the better-known Th1 cells. In chronic infectious diseases there is a delicate balance between pro- and anti-inflammatory responses. While Th1 and Th17 are needed in order to control infection by Mycobacterium tuberculosis, the inflammatory onset can ultimately become detrimental for the host. In this review, we assess current information on the controversy over whether counterbalancing regulatory T cells are promoting pathogen growth or protecting the host.
Collapse
Affiliation(s)
- Paula Cardona
- Unitat de Tuberculosi Experimental, Fundació Institut Germans Trias i Pujol, CIBER Enfermedades Respiratorias, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Pere-Joan Cardona
- Unitat de Tuberculosi Experimental, Fundació Institut Germans Trias i Pujol, CIBER Enfermedades Respiratorias, Universitat Autònoma de Barcelona, Badalona, Spain
| |
Collapse
|
18
|
Wampande EM, Naniima P, Mupere E, Kateete DP, Malone LL, Stein CM, Mayanja-Kizza H, Gagneux S, Boom WH, Joloba ML. Genetic variability and consequence of Mycobacterium tuberculosis lineage 3 in Kampala-Uganda. PLoS One 2019; 14:e0221644. [PMID: 31498808 PMCID: PMC6733460 DOI: 10.1371/journal.pone.0221644] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 08/12/2019] [Indexed: 11/30/2022] Open
Abstract
Background Limited data existed exclusively describing Mycobacterium tuberculosis lineage 3 (MTB-L3), sub-lineages, and clinical manifestations in Kampala, Uganda. This study sought to elucidate the circulating MTB-L3 sub-lineages and their corresponding clinical phenotypes. Method A total of 141 M. tuberculosis isolates were identified as M. tuberculosis lineage 3 using Single nucleotide polymorphism (SNP) marker analysis method. To ascertain the sub-lineages/sub-strains within the M. tuberculosis lineage 3, the direct repeat (DR) loci for all the isolates was examined for sub-lineage specific signatures as described in the SITVIT2 database. The infecting sub-strains were matched with patients’ clinical and demographic characteristics to identify any possible association. Result The data showed 3 sub-lineages circulating with CAS 1 Delhi accounting for 55% (77/141), followed by CAS 1-Kili 16% (22/141) and CAS 2/CAS 8% (12/141). Remaining isolates 21% (30/141) were unclassifiable. To explore whether the sub-lineages differ in their ability to cause increased severe disease, we used extent of lung involvement as a proxy for severe disease. Multivariable analysis showed no association between M. tuberculosis lineage 3 sub-lineages with severe disease. The risk factors associated with severe disease include having a positive smear (OR = 9.384; CI 95% = 2.603–33.835), HIV (OR = 0.316; CI 95% = 0.114–0.876), lymphadenitis (OR = 0. 171; CI 95% = 0.034–0.856) and a BCG scar (OR = 0.295; CI 95% = 0.102–0.854). Conclusion In Kampala, Uganda, there are three sub-lineages of M. tuberculosis lineage 3 that cause disease of comparable severity with CAS-Dehli as the most prevalent. Having HIV, lymphadenitis, a BCG scar and a smear negative status is associated with reduced severe disease.
Collapse
Affiliation(s)
- Eddie M. Wampande
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
- Department of Veterinary Medicine, Clinical and Comparative medicine, College of Veterinary Medicine, Animal Resources and Bio Security, Makerere University, Kampala, Uganda
| | - Peter Naniima
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Ezekiel Mupere
- Department of Pediatrics and Child Health College of Health Sciences, Makerere University, Kampala, Uganda
| | - David P. Kateete
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - LaShaunda L. Malone
- Uganda-Case Western Reserve University Research Collaboration, Kampala, Uganda
- Tuberculosis Research Unit, School of Medicine, Case Western Reserve University and University Hospitals of Cleveland, Cleveland, OH, Uinted States of America
| | - Catherine M. Stein
- Tuberculosis Research Unit, School of Medicine, Case Western Reserve University and University Hospitals of Cleveland, Cleveland, OH, Uinted States of America
- Department of Population and Quantitative Health Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, Uinted States of America
| | | | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - W. Henry Boom
- Tuberculosis Research Unit, School of Medicine, Case Western Reserve University and University Hospitals of Cleveland, Cleveland, OH, Uinted States of America
| | - Moses L. Joloba
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
- * E-mail:
| |
Collapse
|
19
|
Rutaihwa LK, Menardo F, Stucki D, Gygli SM, Ley SD, Malla B, Feldmann J, Borrell S, Beisel C, Middelkoop K, Carter EJ, Diero L, Ballif M, Jugheli L, Reither K, Fenner L, Brites D, Gagneux S. Multiple Introductions of Mycobacterium tuberculosis Lineage 2–Beijing Into Africa Over Centuries. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00112] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
20
|
Pan D, Palittapongarnpim P, Chaiprasert A, Lin M, Lin D, Long X, Huang L, Qin H, McNeil E, Lan R, Qiu X, Chongsuvivatwong V. Infectivity of Mycobacterium tuberculosis Genotypes and Outcome of Contact Investigation in Classroom in Guangxi, China. BIOMED RESEARCH INTERNATIONAL 2019; 2019:3980658. [PMID: 31111051 PMCID: PMC6487147 DOI: 10.1155/2019/3980658] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 03/05/2019] [Indexed: 12/02/2022]
Abstract
OBJECTIVE To evaluate the infectivity of Mycobacterium tuberculosis (M.tb) genotypes of index cases in the classroom of adolescent schools in Guangxi, China. METHODS Adolescent school tuberculosis (TB) contact investigations were conducted for all reported index TB cases from November 2016 to December 2017 in Guangxi, China. Genotypes of index cases and contact cases were identified by 15-loci mycobacterial interspersed repetitive units-variable number tandem repeat and spoligotyping. Outcome variable was 5 levels' order of tuberculin skin test (TST) results to new active TB [0-5 mm, 6-9 mm, 10-14 mm, ≥ 15 mm (without TB), and ≥15 mm (with TB)]. Multivariate ordered logistic regression analysis was performed to evaluate the independent effect of genotypes of index case on contact screening outcome. RESULTS Beijing genotype occurred more commonly in female index patients. One genotypic cluster of two index cases and one cluster of two contact cases were detected. The association between infectivity of Beijing genotype of index cases and outcome of contact investigation was statistically significant in univariate analysis but no so after adjustment for characteristics of contacts and sex of index cases (P value=0.057). Female index cases increased the chance for TB infection/being active TB among contacts (ordinal odds ratio = 1.39, 95% confidence interval: 1.21, 1.60). Contacts who studied in the middle school, who with non-Han ethnicity and who without BCG scar had increased risk for TB infection/being active TB. CONCLUSION There was not enough evidence from our data to support that Beijing strains were more infective than non-Beijing strains in TB transmission in school setting.
Collapse
Affiliation(s)
- Dongxiang Pan
- School of Public Health, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Prasit Palittapongarnpim
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, 10700, Thailand
- National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Angkana Chaiprasert
- Office of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Mei Lin
- Department of Tuberculosis Prevention and Control, Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Nanning, Guangxi, 530021, China
| | - Dingwen Lin
- Department of Tuberculosis Prevention and Control, Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Nanning, Guangxi, 530021, China
| | - Xi Long
- School of Public Health, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Liwen Huang
- Department of Tuberculosis Prevention and Control, Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Nanning, Guangxi, 530021, China
| | - Huifang Qin
- Department of Tuberculosis Prevention and Control, Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Nanning, Guangxi, 530021, China
| | - Edward McNeil
- Epidemiology Unit, Faculty of Medicine, Prince of Songkla University, Hatyai, Songkhla, 90110, Thailand
| | - Rushu Lan
- Department of Tuberculosis Prevention and Control, Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Nanning, Guangxi, 530021, China
| | - Xiaoqiang Qiu
- School of Public Health, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | | |
Collapse
|
21
|
Mantilla Galindo A, Ocampo M, Patarroyo MA. Experimental models used in evaluating anti-tuberculosis vaccines: the latest advances in the field. Expert Rev Vaccines 2019; 18:365-377. [PMID: 30773949 DOI: 10.1080/14760584.2019.1583558] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
INTRODUCTION Tuberculosis is an infectious disease which is caused by bacilli from the M. tuberculosis complex. The Mycobacterium bovis Bacillus Calmette-Guérin vaccine is currently available as a prophylactic tool for preventing the disease; it has been shown to be efficient in preventing disseminated forms of tuberculosis during early ages; however, its efficiency is limited in areas where individuals have had prior exposure to environmental mycobacteria, and its efficacy decreases with a host's age. AREAS COVERED Following a comprehensive search of the available literature, this review describes some of the most frequently used animal models, the most frequently used methods for evaluating efficacy in animal models and some in vitro strategies as alternatives for evaluating vaccines. EXPERT OPINION Identifying the animal models used up to now for evaluating vaccines during their development stages, their characteristics and limitations, as well as knowledge regarding strategies for evaluating promising vaccine candidate efficacy, will ensure more efficient, reliable and reproducible pre-clinical trials. Although much of the knowledge accrued to date concerning vaccine effectiveness against tuberculosis has been based on animal models, it is clear that large questions still need to be resolved and that extrapolation of such efficacy to humans has yet to be achieved.
Collapse
Affiliation(s)
| | - Marisol Ocampo
- b Basic Sciences Department, School of Medicine and Health Sciences , Universidad del Rosario , Bogotá , Colombia.,c Department of Tuberculosis and Molecular Biology , Fundación Instituto de Inmunología de Colombia (FIDIC) , Bogotá , Colombia
| | - Manuel Alfonso Patarroyo
- b Basic Sciences Department, School of Medicine and Health Sciences , Universidad del Rosario , Bogotá , Colombia.,c Department of Tuberculosis and Molecular Biology , Fundación Instituto de Inmunología de Colombia (FIDIC) , Bogotá , Colombia
| |
Collapse
|
22
|
Cheng G, Hussain T, Sabir N, Ni J, Li M, Zhao D, Zhou X. Comparative Study of the Molecular Basis of Pathogenicity of M. bovis Strains in a Mouse Model. Int J Mol Sci 2018; 20:ijms20010005. [PMID: 30577452 PMCID: PMC6337294 DOI: 10.3390/ijms20010005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 12/17/2018] [Accepted: 12/18/2018] [Indexed: 12/14/2022] Open
Abstract
It is widely accepted that different strains of Mycobacterium tuberculosis have variable degrees of pathogenicity and induce different immune responses in infected hosts. Similarly, different strains of Mycobacterium bovis have been identified but there is a lack of information regarding the degree of pathogenicity of these strains and their ability to provoke host immune responses. Therefore, in the current study, we used a mouse model to evaluate various factors involved in the severity of disease progression and the induction of immune responses by two strains of M. bovis isolated from cattle. Mice were infected with both strains of M. bovis at different colony-forming unit (CFU) via inhalation. Gross and histological findings revealed more severe lesions in the lung and spleen of mice infected with M. bovis N strain than those infected with M. bovis C68004 strain. In addition, high levels of interferon-γ (IFN-γ), interleukin-17 (IL-17), and IL-22 production were observed in the serum samples of mice infected with M. bovis N strain. Comparative genomic analysis showed the existence of 750 single nucleotide polymorphisms and 145 small insertions/deletions between the two strains. After matching with the Virulence Factors Database, mutations were found in 29 genes, which relate to 17 virulence factors. Moreover, we found an increased number of virulent factors in M. bovis N strain as compared to M. bovis C68004 strain. Taken together, our data reveal that variation in the level of pathogenicity is due to the mutation in the virulence factors of M. bovis N strain. Therefore, a better understanding of the mechanisms of mutation in the virulence factors will ultimately contribute to the development of new strategies for the control of M. bovis infection.
Collapse
Affiliation(s)
- Guangyu Cheng
- State Key Laboratories for Agrobiotechnology, Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China.
| | - Tariq Hussain
- State Key Laboratories for Agrobiotechnology, Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China.
| | - Naveed Sabir
- State Key Laboratories for Agrobiotechnology, Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China.
| | - Jiamin Ni
- State Key Laboratories for Agrobiotechnology, Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China.
| | - Miaoxuan Li
- State Key Laboratories for Agrobiotechnology, Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China.
| | - Deming Zhao
- State Key Laboratories for Agrobiotechnology, Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China.
| | - Xiangmei Zhou
- State Key Laboratories for Agrobiotechnology, Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China.
| |
Collapse
|
23
|
DNA markers for tuberculosis diagnosis. Tuberculosis (Edinb) 2018; 113:139-152. [PMID: 30514496 DOI: 10.1016/j.tube.2018.09.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 09/23/2018] [Accepted: 09/27/2018] [Indexed: 02/07/2023]
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis complex (MTBC), is an infectious disease with more than 10.4 million cases and 1.7 million deaths reported worldwide in 2016. The classical methods for detection and differentiation of mycobacteria are: acid-fast microscopy (Ziehl-Neelsen staining), culture, and biochemical methods. However, the microbial phenotypic characterization is time-consuming and laborious. Thus, fast, easy, and sensitive nucleic acid amplification tests (NAATs) have been developed based on specific DNA markers, which are commercially available for TB diagnosis. Despite these developments, the disease remains uncontrollable. The identification and differentiation among MTBC members with the use of NAATs remains challenging due, among other factors, to the high degree of homology within the members and mutations, which hinders the identification of specific target sequences in the genome with potential impact in the diagnosis and treatment outcomes. In silico methods provide predictive identification of many new target genes/fragments/regions that can specifically be used to identify species/strains, which have not been fully explored. This review focused on DNA markers useful for MTBC detection, species identification and antibiotic resistance determination. The use of DNA targets with new technological approaches will help to develop NAATs applicable to all levels of the health system, mainly in low resource areas, which urgently need customized methods to their specific conditions.
Collapse
|
24
|
Zaychikova MV, Mikheecheva NE, Belay YO, Alekseeva MG, Melerzanov AV, Danilenko VN. Single nucleotide polymorphisms of Beijing lineage Mycobacterium tuberculosis toxin-antitoxin system genes: Their role in the changes of protein activity and evolution. Tuberculosis (Edinb) 2018; 112:11-19. [PMID: 30205962 DOI: 10.1016/j.tube.2018.06.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 06/07/2018] [Accepted: 06/09/2018] [Indexed: 11/26/2022]
Abstract
The article investigates SNP in genes of toxin-antitoxin systems type II in Mycobacterium tuberculosis Beijing lineage strains and their possible role in the development and formation of new sublineages. We established the catalog of SNPs in 142 TA systems genes in 1349 sequenced genomes of the M. tuberculosis Beijing lineage. Based on the catalog, 15 new sublineages were identified as part of Beijing lineages by non-synonymous SNP in 21 genes of TA systems. We discovered three toxin genes with mutations specific for epidemiologically dangerous sublineages Beijing-modern (vapC37 A46G, vapC38 T143C) and Beijing-B0/W148 (vapC12 A95G). We proved the functional significance of these polymorphisms by cloning these genes wild-type and with marker mutations for the Beijing lineage vapC12 (A95G), vapC37 (A46G), vapC38 (T143C). In vitro study of their activities revealed effect of mutations on the RNase activity of toxin proteins. Mutations in vapC37 and vapC38 decreased toxin activity, and mutation in the vapC12 increased it. We cloned the toxin vapC37 gene of Mycobacterium smegmatis mc2 155 in both allelic variants: without mutation and with A46G mutation, specific for the Beijing-modern lineage. It was shown that this mutation leads to a loss of toxicity.
Collapse
Affiliation(s)
- M V Zaychikova
- Vavilov Institute of General Genetics, Gubkina Str. 3, Moscow, 119333, Russian Federation.
| | - N E Mikheecheva
- Vavilov Institute of General Genetics, Gubkina Str. 3, Moscow, 119333, Russian Federation; Moscow Institute of Physics and Technology, 9 Institutskiy per, Dolgoprudny, Moscow Region, 141701, Russian Federation.
| | - Y O Belay
- Vavilov Institute of General Genetics, Gubkina Str. 3, Moscow, 119333, Russian Federation.
| | - M G Alekseeva
- Vavilov Institute of General Genetics, Gubkina Str. 3, Moscow, 119333, Russian Federation.
| | - A V Melerzanov
- Moscow Institute of Physics and Technology, 9 Institutskiy per, Dolgoprudny, Moscow Region, 141701, Russian Federation.
| | - V N Danilenko
- Vavilov Institute of General Genetics, Gubkina Str. 3, Moscow, 119333, Russian Federation.
| |
Collapse
|
25
|
Shanley CA, Henao-Tamayo MI, Bipin C, Mugasimangalam R, Verma D, Ordway DJ, Streicher EM, Orme IM. Biology of clinical strains of Mycobacterium tuberculosis with varying levels of transmission. Tuberculosis (Edinb) 2018; 109:123-133. [PMID: 29559116 PMCID: PMC5884417 DOI: 10.1016/j.tube.2018.02.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 02/06/2018] [Accepted: 02/08/2018] [Indexed: 12/14/2022]
Abstract
Transmission of Mycobacterium tuberculosis bacilli from one individual to another is the basis of the disease process. While considerable emphasis has been placed on the role of host mechanisms of resistance in establishing or preventing new infection, far less has been expended on understanding possible factors operative at the bacterial level. In this study we established a panel of clinical isolates of M. tuberculosis strains obtained from the Western Cape region of South Africa, each of which had been carefully tracked in terms of their degree of transmission in the community. Each of the panel were used to infect guinea pigs with 15-20 bacilli by aerosol exposure and the course of the infection then determined. Strains with different degrees of transmission could not be distinguished in terms of their capacity to grow in the main target organs of infected animals. However, rather surprisingly, while strains with no evidence of transmission [NOT] in general caused moderate to severe lung damage, this parameter in animals infected with highly transmitted [HT] strains was mostly mild. In terms of TH1 immunity these signals were strongest in these latter animals, as was IL-17 gene expression, whereas minimal signals for regulatory molecules including IL-10 and FoxP3 were seen across the entire panel. In terms of T cell numbers, responses of both CD4 and CD8 were both far faster and far higher in animals infected with the HT strains. At the gene expression level we observed a major three-fold difference [both up and down] between NOT and HT strains, but in terms of proteins of key interest only a few [including PD-L1 and HIF-3] showed major differences between the two groups. Overall, it was apparent that NOT strains were far more inflammatory that HT strains, and appeared to trigger a much larger number of genes, possibly explaining the observed damage to the lungs and progressive pathology. In contrast, the HT strains, while equally virulent, were more immunogenic and developed much stronger T cell responses, while keeping lung damage to a minimum. Hence, in terms of trying to explain the capacity of these strains to cause transmission, these results are clearly paradoxical.
Collapse
Affiliation(s)
- Crystal A Shanley
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Marcela I Henao-Tamayo
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Chand Bipin
- Genotypic Technology Ltd, Bangalore, Karnataka, India
| | | | - Deepshika Verma
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Diane J Ordway
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Elizabeth M Streicher
- Biomedical Sciences, University of Stellenbosch, Tygerberg, Western Cape, South Africa
| | - Ian M Orme
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA.
| |
Collapse
|
26
|
Stein CM, Sausville L, Wejse C, Sobota RS, Zetola NM, Hill PC, Boom WH, Scott WK, Sirugo G, Williams SM. Genomics of human pulmonary tuberculosis: from genes to pathways. CURRENT GENETIC MEDICINE REPORTS 2017; 5:149-166. [PMID: 29805915 DOI: 10.1007/s40142-017-0130-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Purpose of review Tuberculosis (TB), caused by Mycobacterium tuberculosis (MTB), remains a major public health threat globally. Several lines of evidence support a role for host genetic factors in resistance/susceptibility to TB disease and MTB infection. However, results across candidate gene and genome-wide association studies (GWAS) are largely inconsistent, so a cohesive genetic model underlying TB risk has not emerged. Recent Findings Despite the difficulties in identifying consistent genetic associations, genetic studies of TB and MTB infection have revealed a few well-documented loci. These well validated genes are presented in this review, but there remains a large gap in how these genes translate into better understanding of TB. To address this, we present a pathway based extension of standard association analyses, seeding the results with the best validated genes from candidate gene and GWAS studies. Summary Several pathways were significantly enriched using pathway analyses that may help to explain population patterns of TB risk. In conclusion, we advocate for novel approaches to the study of host genetic analysis of TB that extend traditional association approaches.
Collapse
Affiliation(s)
- Catherine M Stein
- Department of Population and Quantitative Health Sciences, Cleveland, OH.,Tuberculosis Research Unit, Case Western Reserve University, Cleveland, OH
| | - Lindsay Sausville
- Department of Population and Quantitative Health Sciences, Cleveland, OH
| | - Christian Wejse
- Dept of Infectious Diseases/Center for Global Health, Aarhus University, Aarhus, Denmark
| | - Rafal S Sobota
- The Ken and Ruth Davee Department of Neurology, Northwestern University, Chicago, IL
| | - Nicola M Zetola
- Division of Infectious Diseases, University of Pennsylvania, Philadelphia, PA 19104, USA.,Botswana-UPenn Partnership, Gaborone, Botswana.,Department of Medicine, University of Botswana, Gaborone, Botswana
| | - Philip C Hill
- Centre for International Health, University of Otago, Dunedin, New Zealand
| | - W Henry Boom
- Tuberculosis Research Unit, Case Western Reserve University, Cleveland, OH
| | - William K Scott
- Department of Human Genetics and Genomics, University of Miami School of Medicine, Miami, FL
| | - Giorgio Sirugo
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Scott M Williams
- Department of Population and Quantitative Health Sciences, Cleveland, OH
| |
Collapse
|
27
|
Séraphin MN, Doggett R, Johnston L, Zabala J, Gerace AM, Lauzardo M. Association between Mycobacterium tuberculosis lineage and site of disease in Florida, 2009-2015. INFECTION GENETICS AND EVOLUTION 2017; 55:366-371. [PMID: 28993293 DOI: 10.1016/j.meegid.2017.10.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 10/01/2017] [Accepted: 10/03/2017] [Indexed: 01/05/2023]
Abstract
BACKGROUND Mycobacterium tuberculosis is characterized into four global lineages with strong geographical restriction. To date one study in the United States has investigated M. tuberculosis lineage association with tuberculosis (TB) disease presentation (extra-pulmonary versus pulmonary). We update this analysis using recent (2009-2015) data from the State of Florida to measure lineage association with pulmonary TB, the infectious form of the disease. METHODS M. tuberculosis lineage was assigned based on the spacer oligonucleotide typing (spoligotyping) patterns. TB disease site was defined as exclusively pulmonary or extra-pulmonary. We used ORs to measure the association between M. tuberculosis lineages and pulmonary compared to extra-pulmonary TB. The final multivariable model was adjusted for patient socio-demographics, HIV and diabetes status. RESULTS We analyzed 3061 cases, 83.4% were infected with a Euro-American lineage, 8.4% Indo-Oceanic and 8.2% East-Asian lineage. The majority of the cases (86.0%) were exclusively pulmonary. Compared to the Indo-Oceanic lineage, infection with a Euro-American (AOR=1.87, 95% CI: 1.21, 2.91) or an East-Asian (AOR=2.11, 95% CI: 1.27, 3.50) lineage favored pulmonary disease compared to extra-pulmonary. In a sub-analysis among pulmonary cases, strain lineage was not associated with sputum smear positive status, indicating that the observed association with pulmonary disease is independent of host contagiousness. CONCLUSION As an obligate pathogen, M. tuberculosis' fitness is directly correlated to its transmission potential. In this analysis, we show that M. tuberculosis lineage is associated with pulmonary disease presentation. This association may explain the predominance in a region of certain lineages compared to others.
Collapse
Affiliation(s)
- Marie Nancy Séraphin
- Division of Infectious Diseases and Global Medicine, University of Florida, College of Medicine, 2055 Mowry Road, P.O. Box 103600, Gainesville, FL 32610, USA; Emerging Pathogen Institute, University of Florida, 2055 Mowry Road, P.O. Box 100009, Gainesville, FL 32610, USA.
| | - Richard Doggett
- Florida Department of Health, Bureau of Public Health Laboratories, 1217 N. Pearl Street, Jacksonville, FL, 32202, USA.
| | - Lori Johnston
- Florida Department of Health, Bureau of Tuberculosis Control, 4052 Bald Cypress Way, Bin A-20, Tallahassee, FL 32399.
| | - Jose Zabala
- Florida Department of Health, Bureau of Tuberculosis Control, 4052 Bald Cypress Way, Bin A-20, Tallahassee, FL 32399.
| | - Alexandra M Gerace
- Division of Infectious Diseases and Global Medicine, University of Florida, College of Medicine, 2055 Mowry Road, P.O. Box 103600, Gainesville, FL 32610, USA; Emerging Pathogen Institute, University of Florida, 2055 Mowry Road, P.O. Box 100009, Gainesville, FL 32610, USA.
| | - Michael Lauzardo
- Division of Infectious Diseases and Global Medicine, University of Florida, College of Medicine, 2055 Mowry Road, P.O. Box 103600, Gainesville, FL 32610, USA; Emerging Pathogen Institute, University of Florida, 2055 Mowry Road, P.O. Box 100009, Gainesville, FL 32610, USA.
| |
Collapse
|
28
|
Nebenzahl-Guimaraes H, van Laarhoven A, Farhat MR, Koeken VACM, Mandemakers JJ, Zomer A, van Hijum SAFT, Netea MG, Murray M, van Crevel R, van Soolingen D. Transmissible Mycobacterium tuberculosis Strains Share Genetic Markers and Immune Phenotypes. Am J Respir Crit Care Med 2017; 195:1519-1527. [PMID: 27997216 DOI: 10.1164/rccm.201605-1042oc] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
RATIONALE Successful transmission of tuberculosis depends on the interplay of human behavior, host immune responses, and Mycobacterium tuberculosis virulence factors. Previous studies have been focused on identifying host risk factors associated with increased transmission, but the contribution of specific genetic variations in mycobacterial strains themselves are still unknown. OBJECTIVES To identify mycobacterial genetic markers associated with increased transmissibility and to examine whether these markers lead to altered in vitro immune responses. METHODS Using a comprehensive tuberculosis registry (n = 10,389) and strain collection in the Netherlands, we identified a set of 100 M. tuberculosis strains either least or most likely to be transmitted after controlling for host factors. We subjected these strains to whole-genome sequencing and evolutionary convergence analysis, and we repeated this analysis in an independent validation cohort. We then performed immunological experiments to measure in vitro cytokine production and neutrophil responses to a subset of the original strains with or without the identified mutations associated with increased transmissibility. MEASUREMENTS AND MAIN RESULTS We identified the loci espE, PE-PGRS56, Rv0197, Rv2813-2814c, and Rv2815-2816c as targets of convergent evolution among transmissible strains. We validated four of these regions in an independent set of strains, and we demonstrated that mutations in these targets affected in vitro monocyte and T-cell cytokine production, neutrophil reactive oxygen species release, and apoptosis. CONCLUSIONS In this study, we identified genetic markers in convergent evolution of M. tuberculosis toward enhanced transmissibility in vivo that are associated with altered immune responses in vitro.
Collapse
Affiliation(s)
- Hanna Nebenzahl-Guimaraes
- 1 National Institute for Public Health and the Environment, Bilthoven, the Netherlands.,2 Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal.,3 ICVS/3B's Research Group, PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Arjan van Laarhoven
- 4 Department of Internal Medicine and Radboud Center for Infectious Diseases
| | - Maha R Farhat
- 5 Pulmonary and Critical Care Division, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | | | | | - Aldert Zomer
- 7 Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, and.,8 Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Sacha A F T van Hijum
- 7 Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, and
| | - Mihai G Netea
- 4 Department of Internal Medicine and Radboud Center for Infectious Diseases
| | - Megan Murray
- 9 Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts; and.,10 Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts
| | - Reinout van Crevel
- 4 Department of Internal Medicine and Radboud Center for Infectious Diseases
| | - Dick van Soolingen
- 1 National Institute for Public Health and the Environment, Bilthoven, the Netherlands.,11 Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, the Netherlands
| |
Collapse
|
29
|
Pan XL, Zhang CL, Nakajima C, Fu J, Shao CX, Zhao LN, Cui JY, Jiao N, Fan CL, Suzuki Y, Hattori T, Li D, Ling H. A quantitative and efficient approach to select MIRU-VNTR loci based on accumulation of the percentage differences of strains for discriminating divergent Mycobacterium tuberculosis sublineages. Emerg Microbes Infect 2017; 6:e68. [PMID: 28745309 PMCID: PMC5567172 DOI: 10.1038/emi.2017.58] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 05/11/2017] [Accepted: 06/04/2017] [Indexed: 11/09/2022]
Abstract
Although several optimal mycobacterial interspersed repetitive units-variable number tandem repeat (MIRU-VNTR) loci have been suggested for genotyping homogenous Mycobacterium tuberculosis, including the Beijing genotype, a more efficient and convenient selection strategy for identifying optimal VNTR loci is needed. Here 281 M. tuberculosis isolates were analyzed. Beijing genotype and non-Beijing genotypes were identified, as well as Beijing sublineages, according to single nucleotide polymorphisms. A total of 22 MIRU-VNTR loci were used for genotyping. To efficiently select optimal MIRU-VNTR loci, we established accumulations of percentage differences (APDs) between the strains among the different genotypes. In addition, we constructed a minimum spanning tree for clustering analysis of the VNTR profiles. Our findings showed that eight MIRU-VNTR loci displayed disparities in h values of ≥0.2 between the Beijing genotype and non-Beijing genotype isolates. To efficiently discriminate Beijing and non-Beijing genotypes, an optimal VNTR set was established by adding loci with APDs ranging from 87.2% to 58.8%, resulting in the construction of a nine-locus set. We also found that QUB11a is a powerful locus for separating ST10s (including ST10, STF and STCH1) and ST22s (including ST22 and ST8) strains, whereas a combination of QUB11a, QUB4156, QUB18, Mtub21 and QUB26 could efficiently discriminate Beijing sublineages. Our findings suggested that two nine-locus sets were not only efficient for distinguishing the Beijing genotype from non-Beijing genotype strains, but were also suitable for sublineage genotyping with different discriminatory powers. These results indicate that APD represents a quantitative and efficient approach for selecting MIRU-VNTR loci to discriminate between divergent M. tuberculosis sublineages.
Collapse
Affiliation(s)
- Xin-Ling Pan
- Department of Microbiology, Wu Lien-Teh Institute, Harbin Medical University, Heilongjiang Provincial Key Laboratory of Infection and Immunity, Key Laboratory of Pathogen Biology, Harbin 150081, China
| | - Chun-Lei Zhang
- Department of Clinical Laboratory, Harbin Chest Hospital, Harbin 150081, China
| | - Chie Nakajima
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo 0010020, Japan.,The Global Station for Zoonosis Control, Hokkaido University Global Institution for Collaborative Research and Education, Sapporo 0600808, Japan
| | - Jin Fu
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150026, China
| | - Chang-Xia Shao
- Department of Microbiology, Wu Lien-Teh Institute, Harbin Medical University, Heilongjiang Provincial Key Laboratory of Infection and Immunity, Key Laboratory of Pathogen Biology, Harbin 150081, China
| | - Li-Na Zhao
- Department of Clinical Laboratory, Harbin Chest Hospital, Harbin 150081, China
| | - Jia-Yi Cui
- Department of Microbiology, Wu Lien-Teh Institute, Harbin Medical University, Heilongjiang Provincial Key Laboratory of Infection and Immunity, Key Laboratory of Pathogen Biology, Harbin 150081, China
| | - Na Jiao
- Department of Clinical Laboratory, Harbin Chest Hospital, Harbin 150081, China
| | - Chang-Long Fan
- Department of Clinical Laboratory, Harbin Chest Hospital, Harbin 150081, China
| | - Yasuhiko Suzuki
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo 0010020, Japan.,The Global Station for Zoonosis Control, Hokkaido University Global Institution for Collaborative Research and Education, Sapporo 0600808, Japan
| | - Toshio Hattori
- Graduate School of Health Science Studies, Kibi International University, Takahashi 7168508, Japan
| | - Di Li
- Department of Microbiology, Wu Lien-Teh Institute, Harbin Medical University, Heilongjiang Provincial Key Laboratory of Infection and Immunity, Key Laboratory of Pathogen Biology, Harbin 150081, China
| | - Hong Ling
- Department of Microbiology, Wu Lien-Teh Institute, Harbin Medical University, Heilongjiang Provincial Key Laboratory of Infection and Immunity, Key Laboratory of Pathogen Biology, Harbin 150081, China
| |
Collapse
|
30
|
Abstract
Tuberculosis (TB) remains the most deadly bacterial infectious disease worldwide. Its treatment and control are threatened by increasing numbers of multidrug-resistant (MDR) or nearly untreatable extensively drug-resistant (XDR) strains. New concepts are therefore urgently needed to understand the factors driving the TB epidemics and the spread of different strain populations, especially in association with drug resistance. Classical genotyping and, more recently, whole-genome sequencing (WGS) revealed that the world population of tubercle bacilli is more diverse than previously thought. Several major phylogenetic lineages can be distinguished, which are associated with their sympatric host population. Distinct clonal (sub)populations can even coexist within infected patients. WGS is now used as the ultimate approach for differentiating clinical isolates and for linking phenotypic to genomic variation from lineage to strain levels. Multiple lines of evidence indicate that the genetic diversity of TB strains translates into pathobiological consequences, and key molecular mechanisms probably involved in differential pathoadaptation of some main lineages have recently been identified. Evidence also accumulates on molecular mechanisms putatively fostering the emergence and rapid expansion of particular MDR and XDR strain groups in some world regions. However, further integrative studies will be needed for complete elucidation of the mechanisms that allow the pathogen to infect its host, acquire multidrug resistance, and transmit so efficiently. Such knowledge will be key for the development of the most effective new diagnostics, drugs, and vaccination strategies.
Collapse
|
31
|
Abstract
Immunity against Mycobacterium tuberculosis requires a balance between adaptive immune responses to constrain bacterial replication and the prevention of potentially damaging immune activation. Regulatory T (Treg) cells express the transcription factor Foxp3+ and constitute an essential counterbalance of inflammatory Th1 responses and are required to maintain immune homeostasis. The first reports describing the presence of Foxp3-expressing CD4+ Treg cells in tuberculosis (TB) emerged in 2006. Different Treg cell subsets, most likely specialized for different tissues and microenvironments, have been shown to expand in both human TB and animal models of TB. Recently, additional functional roles for Treg cells have been demonstrated during different stages and spectrums of TB disease. Foxp3+ regulatory cells can quickly expand during early infection and impede the onset of cellular immunity and persist during chronic TB infection. Increased frequencies of Treg cells have been associated with a detrimental outcome of active TB, and may be dependent on the M. tuberculosis strain, animal model, local environment, and the stage of infection. Some investigations also suggest that Treg cells are required together with effector T cell responses to obtain reduced pathology and sterilizing immunity. In this review, we will first provide an overview of the regulatory cells and mechanisms that control immune homeostasis. Then, we will review what is known about the phenotype and function of Treg cells from studies in human TB and experimental animal models of TB. We will discuss the potential role of Treg cells in the progression of TB disease and the relevance of this knowledge for future efforts to prevent, modulate, and treat TB.
Collapse
|
32
|
Abstract
This article describes the nature of the host response to Mycobacterium tuberculosis in the mouse and guinea pig models of infection. It describes the great wealth of information obtained from the mouse model, reflecting the general availability of immunological reagents, as well as genetic manipulations of the mouse strains themselves. This has led to a good understanding of the nature of the T-cell response to the infection, as well as an appreciation of the complexity of the response involving multiple cytokine- and chemokine-mediated systems. As described here and elsewhere, we have a growing understanding of how multiple CD4-positive T-cell subsets are involved, including regulatory T cells, TH17 cells, as well as the subsequent emergence of effector and central memory T-cell subsets. While, in contrast, our understanding of the host response in the guinea pig model is less advanced, considerable strides have been made in the past decade in terms of defining the basis of the immune response, as well as a better understanding of the immunopathologic process. This model has long been the gold standard for vaccine testing, and more recently is being revisited as a model for testing new drug regimens (bedaquiline being the latest example).
Collapse
|
33
|
Abstract
Faithful replication and maintenance of the genome are essential to the ability of any organism to survive and propagate. For an obligate pathogen such as Mycobacterium tuberculosis that has to complete successive cycles of transmission, infection, and disease in order to retain a foothold in the human population, this requires that genome replication and maintenance must be accomplished under the metabolic, immune, and antibiotic stresses encountered during passage through variable host environments. Comparative genomic analyses have established that chromosomal mutations enable M. tuberculosis to adapt to these stresses: the emergence of drug-resistant isolates provides direct evidence of this capacity, so too the well-documented genetic diversity among M. tuberculosis lineages across geographic loci, as well as the microvariation within individual patients that is increasingly observed as whole-genome sequencing methodologies are applied to clinical samples and tuberculosis (TB) disease models. However, the precise mutagenic mechanisms responsible for M. tuberculosis evolution and adaptation are poorly understood. Here, we summarize current knowledge of the machinery responsible for DNA replication in M. tuberculosis, and discuss the potential contribution of the expanded complement of mycobacterial DNA polymerases to mutagenesis. We also consider briefly the possible role of DNA replication-in particular, its regulation and coordination with cell division-in the ability of M. tuberculosis to withstand antibacterial stresses, including host immune effectors and antibiotics, through the generation at the population level of a tolerant state, or through the formation of a subpopulation of persister bacilli-both of which might be relevant to the emergence and fixation of genetic drug resistance.
Collapse
|
34
|
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.
Collapse
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
| |
Collapse
|
35
|
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.
Collapse
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
| |
Collapse
|
36
|
Biological and Epidemiological Consequences of MTBC Diversity. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1019:95-116. [PMID: 29116631 DOI: 10.1007/978-3-319-64371-7_5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Tuberculosis is caused by different groups of bacteria belonging to the Mycobacterium tuberculosis complex (MTBC). The combined action of human factors, environmental conditions and bacterial virulence determine the extent and form of human disease. MTBC virulence is a composite of different clinical phenotypes such as transmission rate and disease severity among others. Clinical phenotypes are also influenced by cellular and immunological phenotypes. MTBC phenotypes are determined by the genotype, therefore finding genotypes responsible for clinical phenotypes would allow discovering MTBC virulence factors. Different MTBC strains display different cellular and clinical phenotypes. Strains from Lineage 5 and Lineage 6 are metabolically different, grow slower, and are less virulent. Also, at least certain groups of Lineage 2 and Lineage 4 strains are more virulent in terms of disease severity and human-to-human transmission. Because phenotypic differences are ultimately caused by genotypic differences, different genomic loci have been related to various cellular and clinical phenotypes. However, defining the impact of specific bacterial genomic loci on virulence when other bacterial determinants, human and environmental factors are also impacting the phenotype would contribute to a better knowledge of tuberculosis virulence and ultimately benefit tuberculosis control.
Collapse
|
37
|
Shiratori B, Zhao J, Okumura M, Chagan-Yasutan H, Yanai H, Mizuno K, Yoshiyama T, Idei T, Ashino Y, Nakajima C, Suzuki Y, Hattori T. Immunological Roles of Elevated Plasma Levels of Matricellular Proteins in Japanese Patients with Pulmonary Tuberculosis. Int J Mol Sci 2016; 18:ijms18010019. [PMID: 28025511 PMCID: PMC5297654 DOI: 10.3390/ijms18010019] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 12/16/2016] [Accepted: 12/16/2016] [Indexed: 01/17/2023] Open
Abstract
Elevated matricellular proteins (MCPs), including osteopontin (OPN) and galectin-9 (Gal-9), were observed in the plasma of patients with Manila-type tuberculosis (TB) previously. Here, we quantified plasma OPN, Gal-9, and soluble CD44 (sCD44) by enzyme-linked immunosorbent assay (ELISA), and another 29 cytokines by Luminex assay in 36 patients with pulmonary TB, six subjects with latent tuberculosis (LTBI), and 19 healthy controls (HCs) from Japan for a better understanding of the roles of MCPs in TB. All TB subjects showed positive results of enzyme-linked immunospot assays (ELISPOTs). Spoligotyping showed that 20 out of 36 Mycobacterium tuberculosis (MTB) strains belong to the Beijing type. The levels of OPN, Gal-9, and sCD44 were higher in TB (positivity of 61.1%, 66.7%, and 63.9%, respectively) than in the HCs. Positive correlations between OPN and Gal-9, between OPN and sCD44, and negative correlation between OPN and ESAT-6-ELISPOT response, between chest X-ray severity score of cavitary TB and ESAT-6-ELISPOT response were observed. Instead of OPN, Gal-9, and sCD44, cytokines G-CSF, GM-CSF, IFN-α, IFN-γ, IL-12p70, and IL-1RA levels were higher in Beijing MTB-infected patients. These findings suggest immunoregulatory, rather than inflammatory, effect of MCPs and can advance the understanding of the roles of MCPs in the context of TB pathology.
Collapse
Affiliation(s)
- Beata Shiratori
- Division of Disaster-Related Infectious Diseases, International Research Institute of Disaster Science, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan.
| | - Jingge Zhao
- Division of Disaster-Related Infectious Diseases, International Research Institute of Disaster Science, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan.
| | - Masao Okumura
- Department of Respiratory Medicine, Fukujuji Hospital, Japan Anti-Tuberculosis Association, 3-1-24 Matsuyama, Kiyose, Tokyo 204-8533, Japan.
| | - Haorile Chagan-Yasutan
- Division of Disaster-Related Infectious Diseases, International Research Institute of Disaster Science, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan.
| | - Hideki Yanai
- Department of Clinical Laboratory, Fukujuji Hospital, Japan Anti-Tuberculosis Association, 3-1-2 4 Matsuyama, Kiyose, Tokyo 204-8533, Japan.
| | - Kazue Mizuno
- Department of Clinical Laboratory, Fukujuji Hospital, Japan Anti-Tuberculosis Association, 3-1-2 4 Matsuyama, Kiyose, Tokyo 204-8533, Japan.
| | - Takashi Yoshiyama
- Department of Respiratory Medicine, Fukujuji Hospital, Japan Anti-Tuberculosis Association, 3-1-24 Matsuyama, Kiyose, Tokyo 204-8533, Japan.
| | - Tadashi Idei
- Department of Clinical Laboratory, Fukujuji Hospital, Japan Anti-Tuberculosis Association, 3-1-2 4 Matsuyama, Kiyose, Tokyo 204-8533, Japan.
| | - Yugo Ashino
- Division of Disaster-Related Infectious Diseases, International Research Institute of Disaster Science, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan.
| | - Chie Nakajima
- Division of Global Epidemiology, Research Center for Zoonosis Control, Hokkaido University, North 20, West 10, Kita-ku, Sapporo, Hokkaido 001-0020, Japan.
| | - Yasuhiko Suzuki
- Division of Global Epidemiology, Research Center for Zoonosis Control, Hokkaido University, North 20, West 10, Kita-ku, Sapporo, Hokkaido 001-0020, Japan.
| | - Toshio Hattori
- Department of Health Science and Social Welfare, Kibi International University, 8 Igamachi, Takahashi 716-8508, Japan.
| |
Collapse
|
38
|
de Keijzer J, Mulder A, de Ru AH, van Soolingen D, van Veelen PA. Parallel reaction monitoring of clinical Mycobacterium tuberculosis lineages reveals pre-existent markers of rifampicin tolerance in the emerging Beijing lineage. J Proteomics 2016; 150:9-17. [PMID: 27576137 DOI: 10.1016/j.jprot.2016.08.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Revised: 05/05/2016] [Accepted: 08/25/2016] [Indexed: 11/30/2022]
Abstract
The spread of multidrug resistant Mycobacterium tuberculosis is one of the major challenges in tuberculosis control. In Eurasia, the spread of multidrug resistant tuberculosis is driven by the M. tuberculosis Beijing genotype. In this study, we examined whether selective advantages are present in the proteome of Beijing isolates that contribute to the emergence of this genotype. To this end, we compared the proteome of M. tuberculosis Beijing to that of M. tuberculosis H37Rv, both in the presence and absence of the first-line antibiotic rifampicin. During rifampicin exposure, both M. tuberculosis genotypes express proteins belonging to the DosR dormancy regulon, which induces a metabolically hypoactive-, drug tolerant phenotype. However, these markers of rifampicin tolerance were already more abundant in the M. tuberculosis Beijing isolate prior to drug exposure. To determine whether the a priori high abundance of specific proteins contribute to the formation of antibiotic resistance in M. tuberculosis Beijing, we quantified the abundance of 33 selected proteins in 27 clinical isolates from the five most common M. tuberculosis lineages using parallel reaction monitoring. The observed pre-existing high abundance of dormancy proteins in Beijing strains provides an evolutionary advantage that allows these strains to persist for prolonged periods during rifampicin treatment. SIGNIFICANCE M. tuberculosis is the leading cause of death by a bacterial infection worldwide. Treatment-regimen to eradicate this pathogen make use of the first-line antibiotic rifampicin, which is considered to be the cornerstone of modern day anti-tuberculosis treatment. Despite the potency of rifampicin, there is an increasing occurrence of rifampicin resistant mutants in a specific cluster of M. tuberculosis, the Beijing genotype. Using both a data dependent acquisition and a targeted proteomic approach we identified markers of rifampicin tolerance to be high abundant in members of the M. tuberculosis Beijing genotype, already prior drug exposure. The identification of this M. tuberculosis Beijing specific trait will contribute to improved diagnostics and treatment of M. tuberculosis.
Collapse
Affiliation(s)
- Jeroen de Keijzer
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center (LUMC), Leiden, 2300, RC, The Netherlands.
| | - Arnout Mulder
- Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Bilthoven, 3720, BA, The Netherlands
| | - Arnoud H de Ru
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center (LUMC), Leiden, 2300, RC, The Netherlands; Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), Leiden, 2300, RC, The Netherlands
| | - Dick van Soolingen
- Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Bilthoven, 3720, BA, The Netherlands; Departments of Pulmonary Diseases and Medical Microbiology, Radboud University Medical Center, Nijmegen, 6500, HB, The Netherlands
| | - Peter A van Veelen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center (LUMC), Leiden, 2300, RC, The Netherlands; Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), Leiden, 2300, RC, The Netherlands
| |
Collapse
|
39
|
Ben-Kahla I, Al-Hajoj S. Drug-resistant tuberculosis viewed from bacterial and host genomes. Int J Antimicrob Agents 2016; 48:353-60. [PMID: 27566907 DOI: 10.1016/j.ijantimicag.2016.07.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Revised: 06/26/2016] [Accepted: 07/15/2016] [Indexed: 12/14/2022]
Abstract
The outcome of infection with Mycobacterium tuberculosis (MTB) is largely influenced by the host-pathogen interaction in which both the human host and the MTB genetic backgrounds play an important role. Whether this interaction also influences the selection and expansion of drug-resistant MTB strains is the primary focus of this review. We first outline the main and recent findings regarding MTB determinants implicated in the development of drug resistance. Second, we examine data regarding human genetic factors that may play a role in TB drug resistance. We highlight interesting openings for TB research and therapy.
Collapse
Affiliation(s)
- Imen Ben-Kahla
- Mycobacteriology Section, Department of Infection and Immunity, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Sahal Al-Hajoj
- Mycobacteriology Section, Department of Infection and Immunity, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia.
| |
Collapse
|
40
|
Wiens KE, Ernst JD. The Mechanism for Type I Interferon Induction by Mycobacterium tuberculosis is Bacterial Strain-Dependent. PLoS Pathog 2016; 12:e1005809. [PMID: 27500737 PMCID: PMC4976988 DOI: 10.1371/journal.ppat.1005809] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Accepted: 07/13/2016] [Indexed: 12/30/2022] Open
Abstract
Type I interferons (including IFNαβ) are innate cytokines that may contribute to pathogenesis during Mycobacterium tuberculosis (Mtb) infection. To induce IFNβ, Mtb must gain access to the host cytosol and trigger stimulator of interferon genes (STING) signaling. A recently proposed model suggests that Mtb triggers STING signaling through bacterial DNA binding cyclic GMP-AMP synthase (cGAS) in the cytosol. The aim of this study was to test the generalizability of this model using phylogenetically distinct strains of the Mtb complex (MTBC). We infected bone marrow derived macrophages with strains from MTBC Lineages 2, 4 and 6. We found that the Lineage 6 strain induced less IFNβ, and that the Lineage 2 strain induced more IFNβ, than the Lineage 4 strain. The strains did not differ in their access to the host cytosol and IFNβ induction by each strain required both STING and cGAS. We also found that the three strains shed similar amounts of bacterial DNA. Interestingly, we found that the Lineage 6 strain was associated with less mitochondrial stress and less mitochondrial DNA (mtDNA) in the cytosol compared with the Lineage 4 strain. Treating macrophages with a mitochondria-specific antioxidant reduced cytosolic mtDNA and inhibited IFNβ induction by the Lineage 2 and 4 strains. We also found that the Lineage 2 strain did not induce more mitochondrial stress than the Lineage 4 strain, suggesting that additional pathways contribute to higher IFNβ induction. These results indicate that the mechanism for IFNβ by Mtb is more complex than the established model suggests. We show that mitochondrial dynamics and mtDNA contribute to IFNβ induction by Mtb. Moreover, we show that the contribution of mtDNA to the IFNβ response varies by MTBC strain and that additional mechanisms exist for Mtb to induce IFNβ.
Collapse
Affiliation(s)
- Kirsten E. Wiens
- Department of Pathology, New York University School of Medicine, New York, New York, United States of America
- Division of Infectious Disease, Department of Medicine, New York University School of Medicine, New York, New York, United States of America
| | - Joel D. Ernst
- Department of Pathology, New York University School of Medicine, New York, New York, United States of America
- Division of Infectious Disease, Department of Medicine, New York University School of Medicine, New York, New York, United States of America
- Department of Microbiology, New York University School of Medicine, New York, New York, United States of America
- * E-mail:
| |
Collapse
|
41
|
Henao-Tamayo MI, Obregón-Henao A, Arnett K, Shanley CA, Podell B, Orme IM, Ordway DJ. Effect of bacillus Calmette-Guérin vaccination on CD4+Foxp3+ T cells during acquired immune response to Mycobacterium tuberculosis infection. J Leukoc Biol 2016; 99:605-17. [PMID: 26590147 PMCID: PMC4787291 DOI: 10.1189/jlb.4a0614-308rr] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 09/14/2015] [Accepted: 10/27/2015] [Indexed: 12/13/2022] Open
Abstract
Increasing information has shown that many newly emerging strains of Mycobacterium tuberculosis, including the highly prevalent and troublesome Beijing family of strains, can potently induce the emergence of Foxp3(+)CD4 Tregs Although the significance of this is still not fully understood, we have previously provided evidence that the emergence of this population can significantly ablate the protective effect of BCG vaccination, causing progressive fatal disease in the mouse model. However, whether the purpose of this response is to control inflammation or to directly dampen the acquired immune response is still unclear. In the present study, we have shown, using both cell depletion and adoptive transfer strategies, that Tregs can have either properties. Cell depletion resulted in a rapid, but transient, decrease in the lung bacterial load, suggesting release or temporary re-expansion of effector immunity. Transfer of Tregs into Rag2(-/-)or marked congenic mice worsened the disease course and depressed cellular influx of effector T cells into the lungs. Tregs from infected donors seemed to preferentially depress the inflammatory response and granulocytic influx. In contrast, those from BCG-vaccinated and then challenged donors seemed more focused on depression of acquired immunity. These qualitative differences might be related to increasing knowledge reflecting the plasticity of the Treg response.
Collapse
Affiliation(s)
- Marcela I Henao-Tamayo
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins CO, USA
| | - Andres Obregón-Henao
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins CO, USA
| | - Kimberly Arnett
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins CO, USA
| | - Crystal A Shanley
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins CO, USA
| | - Brendan Podell
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins CO, USA
| | - Ian M Orme
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins CO, USA
| | - Diane J Ordway
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins CO, USA
| |
Collapse
|
42
|
Culture-positive Pediatric Tuberculosis in Toronto, Ontario: Sources of Infection and Relationship of Birthplace and Mycobacterial Lineage to Phenotype. Pediatr Infect Dis J 2016; 35:13-8. [PMID: 26379168 DOI: 10.1097/inf.0000000000000915] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
BACKGROUND Few data relate Mycobacterium tuberculosis (Mtb) lineage and disease phenotype in the pediatric population or examine the contribution of travel to the tuberculosis (TB)-endemic country in North America. We examined clinical, demographic and Mtb genotype data from patients with TB who were treated in Toronto between 2002 and 2012. METHODS Consecutive Mtb culture-positive, pediatric patients were included. Clinical data were collected from a prospectively populated clinical database. Mtb case isolate genotypes were identified using Mycobacterial Interspersed Repetitive Units-Variable Number Tandem Repeat (MIRU-VNTR) and spoligotyping and were categorized into phylogeographic lineages for analysis. RESULTS The 77 patients included 30.4% of all culture-positive pediatric TB cases in Ontario from 2002 to 2012. Seventy-six (99%) patients were first or second generation Canadians. Foreign-born patients were more likely to have extrathoracic disease [odds ratios (OR) = 3.0; 95% confidence interval (CI): 1.04-8.71; P < 0.05] and less likely to have a genotype match in the Public Health Ontario Laboratories database [OR = 0.32 (95% CI: 0.11-0.90); P < 0.05] than Canadian-born patients. For those without a known TB contact, Canadian-born patients were more likely to have travelled to a TB-endemic country [OR = 13.0 (95% CI: 2.5-78.5); P < 0.001]. Extrathoracic disease was less likely in patients infected with the East Asian Mtb lineage [OR = 0.1 (95% CI: 0.01-0.9); P < 0.05] and more likely in those infected with the Indo-Oceanic Mtb lineage [OR = 5.4 (95% CI: 1.5-19.2); P < 0.05]. CONCLUSIONS Travel to TB-endemic countries likely plays an important part in the etiology of pediatric TB infection and disease, especially in Canadian-born children. Mtb lineage seems to contribute to disease phenotype in children as it has been described in adults.
Collapse
|
43
|
Wampande EM, Mupere E, Jaganath D, Nsereko M, Mayanja HK, Eisenach K, Boom WH, Gagneux S, Joloba ML. Distribution and transmission of Mycobacterium tuberculosis complex lineages among children in peri-urban Kampala, Uganda. BMC Pediatr 2015; 15:140. [PMID: 26424324 PMCID: PMC4588907 DOI: 10.1186/s12887-015-0455-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 09/14/2015] [Indexed: 11/15/2022] Open
Abstract
Background To gain insight into the transmission of tuberculosis (TB) in peri-urban Kampala-Uganda, we performed a household contact study using children as a surrogate for recent transmission of Mycobacterium tuberculosis (MTB). Using this approach, we sought to understand M. tuberculosis complex (MTBC) lineage diversity, distribution and how these relate to TB transmission to exposed children. Method MTBC isolates from children aged ≤ 15 years, collected from 2002 to 2010 in a household-contact study, were analyzed using a LightCycler RT-PCR SNP genotyping assay (LRPS). The resultant genotypic data was used to determine associations between MTBC lineage and the children’s clinical and epidemiological characteristics. Results and discussion Of the 761 children surveyed, 9 % (69/761) had culture-positive TB an estimate in the range of global childhood TB; of these 71 % (49/69) were infected with an MTBC strain of the “Uganda family”, 17 % (12/69) infected with MTBC lineage 4 strains other than MTBC Uganda family and 12 % (8/69) infected with MTBC lineage 3, thereby disproportionately causing TB in the study area. Overall the data showed no correlation between the MTBC lineages studied and transmission (OR = 0.304; P-value = 0.251; CI: 95 %; 0.039-2.326) using children a proxy for TB transmission. Conclusions Our findings indicate that MTBC Uganda family strains are the main cause of TB in children in peri-urban Kampala. Furthermore, MTBC lineages did not differ in their transmissibility to children.
Collapse
Affiliation(s)
- Eddie M Wampande
- Department of Medical Microbiology, College of Health Sciences, Makerere University, P.O box 7072, Kampala, Uganda. .,Department of Bio-molecular Resources and Biolab Sciences, College of Veterinary Medicine, Animal Resources and Bio Security, Makerere University, Kampala, Uganda.
| | - Ezekiel Mupere
- Department of Pediatrics and Child Health College of Health Sciences, Makerere University, Kampala, Uganda.
| | - Devan Jaganath
- The Johns Hopkins School of medicine, Department of Pediatricss, Baltimore, USA.
| | - Mary Nsereko
- Uganda-Case Western Reserve University Research Collaboration, Kampala, Uganda.
| | - Harriet K Mayanja
- Uganda-Case Western Reserve University Research Collaboration, Kampala, Uganda. .,Department of Medicine College of Health Sciences, Makerere University, Kampala, Uganda.
| | - Kathleen Eisenach
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA.
| | - W Henry Boom
- Uganda-Case Western Reserve University Research Collaboration, Kampala, Uganda. .,Tuberculosis Research Unit, School of Medicine, Case Western Reserve University and University Hospitals of Cleveland, Cleveland, Ohio, USA.
| | - Sebastien Gagneux
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland. .,University of Basel, Basel, Switzerland.
| | - Moses L Joloba
- Department of Medical Microbiology, College of Health Sciences, Makerere University, P.O box 7072, Kampala, Uganda. .,Uganda-Case Western Reserve University Research Collaboration, Kampala, Uganda.
| | | |
Collapse
|
44
|
Whole genome sequencing identifies circulating Beijing-lineage Mycobacterium tuberculosis strains in Guatemala and an associated urban outbreak. Tuberculosis (Edinb) 2015; 95:810-816. [PMID: 26542222 PMCID: PMC4672993 DOI: 10.1016/j.tube.2015.09.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 08/22/2015] [Accepted: 09/05/2015] [Indexed: 12/15/2022]
Abstract
Limited data are available regarding the molecular epidemiology of Mycobacterium tuberculosis (Mtb) strains circulating in Guatemala. Beijing-lineage Mtb strains have gained prevalence worldwide and are associated with increased virulence and drug resistance, but there have been only a few cases reported in Central America. Here we report the first whole genome sequencing of Central American Beijing-lineage strains of Mtb. We find that multiple Beijing-lineage strains, derived from independent founding events, are currently circulating in Guatemala, but overall still represent a relatively small proportion of disease burden. Finally, we identify a specific Beijing-lineage outbreak centered on a poor neighborhood in Guatemala City.
Collapse
|
45
|
Yuan L, Mi L, Li Y, Zhang H, Zheng F, Li Z. Genotypic characteristics of Mycobacterium tuberculosis circulating in Xinjiang, China. Infect Dis (Lond) 2015; 48:108-15. [DOI: 10.3109/23744235.2015.1087649] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Li Yuan
- Department of Immunology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei
- Department of Immunology, Medical College, Shihezi University, Xinjiang, China
| | - Ligu Mi
- Department of Immunology, Medical College, Shihezi University, Xinjiang, China
| | - Yongxiang Li
- Department of Immunology, Medical College, Shihezi University, Xinjiang, China
| | - Hui Zhang
- Department of Immunology, Medical College, Shihezi University, Xinjiang, China
| | - Fang Zheng
- Department of Immunology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei
| | - Zhuoya Li
- Department of Immunology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei
| |
Collapse
|
46
|
Henao-Tamayo M, Shanley CA, Verma D, Zilavy A, Stapleton MC, Furney SK, Podell B, Orme IM. The Efficacy of the BCG Vaccine against Newly Emerging Clinical Strains of Mycobacterium tuberculosis. PLoS One 2015; 10:e0136500. [PMID: 26368806 PMCID: PMC4569086 DOI: 10.1371/journal.pone.0136500] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 08/04/2015] [Indexed: 01/15/2023] Open
Abstract
To date, most new vaccines against Mycobacterium tuberculosis, including new recombinant versions of the current BCG vaccine, have usually been screened against the laboratory strains H37Rv or Erdman. In this study we took advantage of our recent work in characterizing an increasingly large panel of newly emerging clinical isolates [from the United States or from the Western Cape region of South Africa], to determine to what extent vaccines would protect against these [mostly high virulence] strains. We show here that both BCG Pasteur and recombinant BCG Aeras-422 [used here as a good example of the new generation BCG vaccines] protected well in both mouse and guinea pig low dose aerosol infection models against the majority of clinical isolates tested. However, Aeras-422 was not effective in a long term survival assay compared to BCG Pasteur. Protection was very strongly expressed against all of the Western Cape strains tested, reinforcing our viewpoint that any attempt at boosting BCG would be very difficult to achieve statistically. This observation is discussed in the context of the growing argument made by others that the failure of a recent vaccine trial disqualifies the further use of animal models to predict vaccine efficacy. This viewpoint is in our opinion completely erroneous, and that it is the fitness of prevalent strains in the trial site area that is the centrally important factor, an issue that is not being addressed by the field.
Collapse
Affiliation(s)
- Marcela Henao-Tamayo
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Crystal A Shanley
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Deepshikha Verma
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Andrew Zilavy
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Margaret C Stapleton
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Synthia K Furney
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Brendan Podell
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Ian M Orme
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| |
Collapse
|
47
|
Marcus SA, Steinberg H, Talaat AM. Protection by novel vaccine candidates, Mycobacterium tuberculosis ΔmosR and ΔechA7, against challenge with a Mycobacterium tuberculosis Beijing strain. Vaccine 2015; 33:5633-5639. [PMID: 26363381 DOI: 10.1016/j.vaccine.2015.08.084] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 08/07/2015] [Accepted: 08/28/2015] [Indexed: 11/18/2022]
Abstract
Mycobacterium tuberculosis, the etiological agent of tuberculosis (TB), infects over two billion people, claiming around 1.5 million lives annually. The only vaccine approved for clinical use against this disease is the Bacillus Calmette-Guérin (BCG) vaccine. Unfortunately, BCG has limited efficacy against the adult, pulmonary form of tuberculosis. This vaccine was developed from M. bovis with antigen expression and host specificity that differ from M. tuberculosis. To address these problems, we have designed two novel, live attenuated vaccine (LAV) candidates on an M. tuberculosis background: ΔmosR and ΔechA7. These targeted genes are important to M. tuberculosis pathogenicity during infection. To examine the efficacy of these strains, C57BL/6 mice were vaccinated subcutaneously with either LAV, BCG, or PBS. Both LAV strains persisted up to 16 weeks in the spleens or lungs of vaccinated mice, while eliciting minimal pathology prior to challenge. Following challenge with a selected, high virulence M. tuberculosis Beijing strain, protection was notably greater for both groups of LAV vaccinated animals as compared to BCG at both 30 and 60 days post-challenge. Additionally, vaccination with either ΔmosR or ΔechA7 elicited an immune response similar to BCG. Although these strains require further development to meet safety standards, this first evidence of protection by these two new, live attenuated vaccine candidates shows promise.
Collapse
Affiliation(s)
- Sarah A Marcus
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Howard Steinberg
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Adel M Talaat
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Food Hygiene and Control, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt.
| |
Collapse
|
48
|
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.
Collapse
|
49
|
Persistent Infection by a Mycobacterium tuberculosis Strain That Was Theorized To Have Advantageous Properties, as It Was Responsible for a Massive Outbreak. J Clin Microbiol 2015; 53:3423-9. [PMID: 26269618 DOI: 10.1128/jcm.01405-15] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 08/01/2015] [Indexed: 01/21/2023] Open
Abstract
The strains involved in tuberculosis outbreaks are considered highly virulent and transmissible. We analyzed the case of a patient in Madrid, Spain, who was persistently infected over an 8-year period by the same Beijing Mycobacterium tuberculosis strain. The strain was responsible for a severe outbreak on Gran Canaria Island. The case provides us with a unique opportunity to challenge our assumptions about M. tuberculosis Beijing strains. No clinical/radiological findings consistent with a virulent strain were documented, and the in vitro growth rate of the strain in macrophages was only moderate. No secondary cases stemming from this prolonged active case were detected in the host population. The strain did not acquire resistance mutations, despite constant treatment interruptions, and it remained extremely stable, as demonstrated by the lack of single-nucleotide-polymorphism (SNP)-based differences between the sequential isolates. Our data suggest that the general assumption about M. tuberculosis Beijing strains having advantageous properties (in terms of virulence, transmissibility, and the tendency to acquire mutations and resistance) is not always accurate.
Collapse
|
50
|
Witney AA, Gould KA, Arnold A, Coleman D, Delgado R, Dhillon J, Pond MJ, Pope CF, Planche TD, Stoker NG, Cosgrove CA, Butcher PD, Harrison TS, Hinds J. Clinical application of whole-genome sequencing to inform treatment for multidrug-resistant tuberculosis cases. J Clin Microbiol 2015; 53:1473-83. [PMID: 25673793 PMCID: PMC4400773 DOI: 10.1128/jcm.02993-14] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 02/06/2015] [Indexed: 01/29/2023] Open
Abstract
The treatment of drug-resistant tuberculosis cases is challenging, as drug options are limited, and the existing diagnostics are inadequate. Whole-genome sequencing (WGS) has been used in a clinical setting to investigate six cases of suspected extensively drug-resistant Mycobacterium tuberculosis (XDR-TB) encountered at a London teaching hospital between 2008 and 2014. Sixteen isolates from six suspected XDR-TB cases were sequenced; five cases were analyzed in a clinically relevant time frame, with one case sequenced retrospectively. WGS identified mutations in the M. tuberculosis genes associated with antibiotic resistance that are likely to be responsible for the phenotypic resistance. Thus, an evidence base was developed to inform the clinical decisions made around antibiotic treatment over prolonged periods. All strains in this study belonged to the East Asian (Beijing) lineage, and the strain relatedness was consistent with the expectations from the case histories, confirming one contact transmission event. We demonstrate that WGS data can be produced in a clinically relevant time scale some weeks before drug sensitivity testing (DST) data are available, and they actively help clinical decision-making through the assessment of whether an isolate (i) has a particular resistance mutation where there are absent or contradictory DST results, (ii) has no further resistance markers and therefore is unlikely to be XDR, or (iii) is identical to an isolate of known resistance (i.e., a likely transmission event). A small number of discrepancies between the genotypic predictions and phenotypic DST results are discussed in the wider context of the interpretation and reporting of WGS results.
Collapse
Affiliation(s)
- Adam A Witney
- Institute for Infection and Immunity, St. George's University of London, London, United Kingdom
| | - Katherine A Gould
- Institute for Infection and Immunity, St. George's University of London, London, United Kingdom
| | - Amber Arnold
- Clinical Infection Unit, St. George's Healthcare NHS Trust, London, United Kingdom
| | - David Coleman
- Institute for Infection and Immunity, St. George's University of London, London, United Kingdom
| | - Rachel Delgado
- Department of Microbiology, St. George's Healthcare NHS Trust, London, United Kingdom
| | - Jasvir Dhillon
- Institute for Infection and Immunity, St. George's University of London, London, United Kingdom
| | - Marcus J Pond
- Institute for Infection and Immunity, St. George's University of London, London, United Kingdom
| | - Cassie F Pope
- Department of Microbiology, St. George's Healthcare NHS Trust, London, United Kingdom
| | - Tim D Planche
- Institute for Infection and Immunity, St. George's University of London, London, United Kingdom Department of Microbiology, St. George's Healthcare NHS Trust, London, United Kingdom
| | - Neil G Stoker
- Institute for Infection and Immunity, St. George's University of London, London, United Kingdom
| | - Catherine A Cosgrove
- Institute for Infection and Immunity, St. George's University of London, London, United Kingdom Clinical Infection Unit, St. George's Healthcare NHS Trust, London, United Kingdom
| | - Philip D Butcher
- Institute for Infection and Immunity, St. George's University of London, London, United Kingdom
| | - Thomas S Harrison
- Institute for Infection and Immunity, St. George's University of London, London, United Kingdom Clinical Infection Unit, St. George's Healthcare NHS Trust, London, United Kingdom
| | - Jason Hinds
- Institute for Infection and Immunity, St. George's University of London, London, United Kingdom
| |
Collapse
|