51
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Kinsella RL, Zhu DX, Harrison GA, Mayer Bridwell AE, Prusa J, Chavez SM, Stallings CL. Perspectives and Advances in the Understanding of Tuberculosis. ANNUAL REVIEW OF PATHOLOGY 2021; 16:377-408. [PMID: 33497258 DOI: 10.1146/annurev-pathol-042120-032916] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), remains a leading cause of death due to infection in humans. To more effectively combat this pandemic, many aspects of TB control must be developed, including better point of care diagnostics, shorter and safer drug regimens, and a protective vaccine. To address all these areas of need, better understanding of the pathogen, host responses, and clinical manifestations of the disease is required. Recently, the application of cutting-edge technologies to the study of Mtb pathogenesis has resulted in significant advances in basic biology, vaccine development, and antibiotic discovery. This leaves us in an exciting era of Mtb research in which our understanding of this deadly infection is improving at a faster rate than ever, and renews hope in our fight to end TB. In this review, we reflect on what is known regarding Mtb pathogenesis, highlighting recent breakthroughs that will provide leverage for the next leaps forward in the field.
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Affiliation(s)
- Rachel L Kinsella
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri 63110, USA;
| | - Dennis X Zhu
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri 63110, USA;
| | - Gregory A Harrison
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri 63110, USA;
| | - Anne E Mayer Bridwell
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri 63110, USA;
| | - Jerome Prusa
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri 63110, USA;
| | - Sthefany M Chavez
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri 63110, USA;
| | - Christina L Stallings
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri 63110, USA;
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52
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Mahmutovic A, Gillman AN, Lauksund S, Robson Moe NA, Manzi A, Storflor M, Abel Zur Wiesch P, Abel S. RESTAMP - Rate estimates by sequence-tag analysis of microbial populations. Comput Struct Biotechnol J 2021; 19:1035-1051. [PMID: 33613869 PMCID: PMC7878984 DOI: 10.1016/j.csbj.2021.01.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 01/12/2021] [Accepted: 01/14/2021] [Indexed: 12/31/2022] Open
Abstract
Microbial division rates determine the speed of mutation accumulation and thus the emergence of antimicrobial resistance. Microbial death rates are affected by antibiotic action and the immune system. Therefore, measuring these rates has advanced our understanding of host-pathogen interactions and antibiotic action. Several methods based on marker-loss or few inheritable neutral markers exist that allow estimating microbial division and death rates, each of which has advantages and limitations. Technical bottlenecks, i.e., experimental sampling events, during the experiment can distort the rate estimates and are typically unaccounted for or require additional calibration experiments. In this work, we introduce RESTAMP (Rate Estimates by Sequence Tag Analysis of Microbial Populations) as a method for determining bacterial division and death rates. This method uses hundreds of fitness neutral sequence barcodes to measure the rates and account for experimental bottlenecks at the same time. We experimentally validate RESTAMP and compare it to established plasmid loss methods. We find that RESTAMP has a number of advantages over plasmid loss or previous marker based techniques. (i) It enables to correct the distortion of rate estimates by technical bottlenecks. (ii) Rate estimates are independent of the sequence tag distribution in the starting culture allowing the use of an arbitrary number of tags. (iii) It introduces a bottleneck sensitivity measure that can be used to maximize the accuracy of the experiment. RESTAMP allows studying microbial population dynamics with great resolution over a wide dynamic range and can thus advance our understanding of host-pathogen interactions or the mechanisms of antibiotic action.
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Affiliation(s)
- Anel Mahmutovic
- Department of Pharmacy, Faculty of Health Sciences, UiT - The Arctic University of Norway, 9037 Tromsø, Norway
| | - Aaron Nicholas Gillman
- Department of Pharmacy, Faculty of Health Sciences, UiT - The Arctic University of Norway, 9037 Tromsø, Norway.,Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, PA 16802, USA
| | - Silje Lauksund
- Department of Pharmacy, Faculty of Health Sciences, UiT - The Arctic University of Norway, 9037 Tromsø, Norway
| | - Natasha-Anne Robson Moe
- Department of Pharmacy, Faculty of Health Sciences, UiT - The Arctic University of Norway, 9037 Tromsø, Norway
| | - Aime Manzi
- Department of Pharmacy, Faculty of Health Sciences, UiT - The Arctic University of Norway, 9037 Tromsø, Norway
| | - Merete Storflor
- Department of Pharmacy, Faculty of Health Sciences, UiT - The Arctic University of Norway, 9037 Tromsø, Norway.,Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, PA 16802, USA
| | - Pia Abel Zur Wiesch
- Department of Pharmacy, Faculty of Health Sciences, UiT - The Arctic University of Norway, 9037 Tromsø, Norway.,Centre for Molecular Medicine Norway, Nordic EMBL Partnership, 0318 Oslo, Norway.,Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA.,Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Sören Abel
- Department of Pharmacy, Faculty of Health Sciences, UiT - The Arctic University of Norway, 9037 Tromsø, Norway.,Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, PA 16802, USA.,Centre for Molecular Medicine Norway, Nordic EMBL Partnership, 0318 Oslo, Norway.,Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
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53
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Plumlee CR, Duffy FJ, Gern BH, Delahaye JL, Cohen SB, Stoltzfus CR, Rustad TR, Hansen SG, Axthelm MK, Picker LJ, Aitchison JD, Sherman DR, Ganusov VV, Gerner MY, Zak DE, Urdahl KB. Ultra-low Dose Aerosol Infection of Mice with Mycobacterium tuberculosis More Closely Models Human Tuberculosis. Cell Host Microbe 2021; 29:68-82.e5. [PMID: 33142108 PMCID: PMC7854984 DOI: 10.1016/j.chom.2020.10.003] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 07/21/2020] [Accepted: 09/25/2020] [Indexed: 02/02/2023]
Abstract
Tuberculosis (TB) is a heterogeneous disease manifesting in a subset of individuals infected with aerosolized Mycobacterium tuberculosis (Mtb). Unlike human TB, murine infection results in uniformly high lung bacterial burdens and poorly organized granulomas. To develop a TB model that more closely resembles human disease, we infected mice with an ultra-low dose (ULD) of between 1-3 founding bacteria, reflecting a physiologic inoculum. ULD-infected mice exhibited highly heterogeneous bacterial burdens, well-circumscribed granulomas that shared features with human granulomas, and prolonged Mtb containment with unilateral pulmonary infection in some mice. We identified blood RNA signatures in mice infected with an ULD or a conventional Mtb dose (50-100 CFU) that correlated with lung bacterial burdens and predicted Mtb infection outcomes across species, including risk of progression to active TB in humans. Overall, these findings highlight the potential of the murine TB model and show that ULD infection recapitulates key features of human TB.
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Affiliation(s)
- Courtney R Plumlee
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Fergal J Duffy
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Benjamin H Gern
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA; Department of Pediatrics, University of Washington, Seattle, WA 98109, USA
| | - Jared L Delahaye
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA; Department of Immunology, University of Washington, Seattle, WA 98109, USA
| | - Sara B Cohen
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Caleb R Stoltzfus
- Department of Immunology, University of Washington, Seattle, WA 98109, USA
| | - Tige R Rustad
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Scott G Hansen
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Michael K Axthelm
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Louis J Picker
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - John D Aitchison
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - David R Sherman
- Department of Microbiology, University of Washington, Seattle, WA 98109, USA
| | - Vitaly V Ganusov
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA
| | - Michael Y Gerner
- Department of Immunology, University of Washington, Seattle, WA 98109, USA
| | - Daniel E Zak
- Center for Infectious Disease Research, Seattle, WA 98109, USA
| | - Kevin B Urdahl
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA; Department of Pediatrics, University of Washington, Seattle, WA 98109, USA; Department of Immunology, University of Washington, Seattle, WA 98109, USA.
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54
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Vlazaki M, Price DJ, Restif O. An experimental design tool to optimize inference precision in data-driven mathematical models of bacterial infections in vivo. J R Soc Interface 2020; 17:20200717. [PMID: 33323052 DOI: 10.1098/rsif.2020.0717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The management of bacterial diseases calls for a detailed knowledge about the dynamic changes in host-bacteria interactions. Biological insights are gained by integrating experimental data with mechanistic mathematical models to infer experimentally unobservable quantities. This inter-disciplinary field would benefit from experiments with maximal information content yielding high-precision inference. Here, we present a computationally efficient tool for optimizing experimental design in terms of parameter inference in studies using isogenic-tagged strains. We study the effect of three experimental design factors: number of biological replicates, sampling timepoint selection and number of copies per tagged strain. We conduct a simulation study to establish the relationship between our optimality criterion and the size of parameter estimate confidence intervals, and showcase its application in a range of biological scenarios reflecting different dynamics patterns observed in experimental infections. We show that in low-variance systems with low killing and replication rates, predicting high-precision experimental designs is consistently achieved; higher replicate sizes and strategic timepoint selection yield more precise estimates. Finally, we address the question of resource allocation under constraints; given a fixed number of host animals and a constraint on total inoculum size per host, infections with fewer strains at higher copies per strain lead to higher-precision inference.
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Affiliation(s)
- Myrto Vlazaki
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - David J Price
- Centre for Epidemiology and Biostatistics, University of Melbourne, Grattan Street, Parkville, Victoria 3010, Australia.,The Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Melbourne, Victoria 3000, Australia
| | - Olivier Restif
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
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55
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Hicks ND, Giffen SR, Culviner PH, Chao MC, Dulberger CL, Liu Q, Stanley S, Brown J, Sixsmith J, Wolf ID, Fortune SM. Mutations in dnaA and a cryptic interaction site increase drug resistance in Mycobacterium tuberculosis. PLoS Pathog 2020; 16:e1009063. [PMID: 33253310 PMCID: PMC7738170 DOI: 10.1371/journal.ppat.1009063] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 12/15/2020] [Accepted: 10/09/2020] [Indexed: 01/26/2023] Open
Abstract
Genomic dissection of antibiotic resistance in bacterial pathogens has largely focused on genetic changes conferring growth above a single critical concentration of drug. However, reduced susceptibility to antibiotics-even below this breakpoint-is associated with poor treatment outcomes in the clinic, including in tuberculosis. Clinical strains of Mycobacterium tuberculosis exhibit extensive quantitative variation in antibiotic susceptibility but the genetic basis behind this spectrum of drug susceptibility remains ill-defined. Through a genome wide association study, we show that non-synonymous mutations in dnaA, which encodes an essential and highly conserved regulator of DNA replication, are associated with drug resistance in clinical M. tuberculosis strains. We demonstrate that these dnaA mutations specifically enhance M. tuberculosis survival during isoniazid treatment via reduced expression of katG, the activator of isoniazid. To identify DnaA interactors relevant to this phenotype, we perform the first genome-wide biochemical mapping of DnaA binding sites in mycobacteria which reveals a DnaA interaction site that is the target of recurrent mutation in clinical strains. Reconstructing clinically prevalent mutations in this DnaA interaction site reproduces the phenotypes of dnaA mutants, suggesting that clinical strains of M. tuberculosis have evolved mutations in a previously uncharacterized DnaA pathway that quantitatively increases resistance to the key first-line antibiotic isoniazid. Discovering genetic mechanisms that reduce drug susceptibility and support the evolution of high-level drug resistance will guide development of biomarkers capable of prospectively identifying patients at risk of treatment failure in the clinic.
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Affiliation(s)
- Nathan D. Hicks
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Samantha R. Giffen
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Peter H. Culviner
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Michael C. Chao
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Charles L. Dulberger
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Qingyun Liu
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Sydney Stanley
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Jessica Brown
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Jaimie Sixsmith
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Ian D. Wolf
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Sarah M. Fortune
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
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56
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Sutiwisesak R, Hicks ND, Boyce S, Murphy KC, Papavinasasundaram K, Carpenter SM, Boucau J, Joshi N, Le Gall S, Fortune SM, Sassetti CM, Behar SM. A natural polymorphism of Mycobacterium tuberculosis in the esxH gene disrupts immunodomination by the TB10.4-specific CD8 T cell response. PLoS Pathog 2020; 16:e1009000. [PMID: 33075106 PMCID: PMC7597557 DOI: 10.1371/journal.ppat.1009000] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 10/29/2020] [Accepted: 09/23/2020] [Indexed: 12/20/2022] Open
Abstract
CD8 T cells provide limited protection against Mycobacterium
tuberculosis (Mtb) infection in the mouse model. As Mtb causes
chronic infection in mice and humans, we hypothesize that Mtb impairs T cell
responses as an immune evasion strategy. TB10.4 is an immunodominant antigen in
people, nonhuman primates, and mice, which is encoded by the
esxH gene. In C57BL/6 mice, 30–50% of pulmonary CD8 T cells
recognize the TB10.44−11 epitope. However, TB10.4-specific CD8 T
cells fail to recognize Mtb-infected macrophages. We speculate that Mtb elicits
immunodominant CD8 T cell responses to antigens that are inefficiently presented
by infected cells, thereby focusing CD8 T cells on nonprotective antigens. Here,
we leverage naturally occurring polymorphisms in esxH, which
frequently occur in lineage 1 strains, to test this “decoy hypothesis”. Using
the clinical isolate 667, which contains an EsxHA10T polymorphism, we
observe a drastic change in the hierarchy of CD8 T cells. Using isogenic
Erd.EsxHA10T and Erd.EsxHWT strains, we prove that
this polymorphism alters the hierarchy of immunodominant CD8 T cell responses.
Our data are best explained by immunodomination, a mechanism by which
competition for APC leads to dominant responses suppressing subdominant
responses. These results were surprising as the variant epitope can bind to
H2-Kb and is recognized by TB10.4-specific CD8 T cells. The
dramatic change in TB10.4-specific CD8 responses resulted from increased
proteolytic degradation of A10T variant, which destroyed the
TB10.44-11epitope. Importantly, this polymorphism affected T cell
priming and recognition of infected cells. These data support a model in which
nonprotective CD8 T cells become immunodominant and suppress subdominant
responses. Thus, polymorphisms between clinical Mtb strains, and BCG or H37Rv
sequence-based vaccines could lead to a mismatch between T cells that are primed
by vaccines and the epitopes presented by infected cells. Reprograming host
immune responses should be considered in the future design of vaccines. An important question for vaccine developers is the relative potency of CD4 vs.
CD8 T cells against Mtb, as strategies differ for eliciting these different T
cell subsets. Despite robust antigen-specific pulmonary CD8 T cell responses,
CD4 T cells mediate more protection than CD8 T cells in the murine model. Most
CD8 T cells recognize a single antigen, TB10.4, which is encoded by the
esxH gene. Based on finding that
TB10.44−11-specific CD8 T cells poorly recognize Mtb-infected
macrophages, we hypothesized that Mtb evades detection by CD8 T cells and
focuses the CD8 T cell response on non-protective antigen. We termed these
antigens “decoy antigens.” To test this hypothesis, we took advantage of a
natural variant of the esxH gene, which contains an A10T
polymorphism within the TB10.44−11 epitope. This polymorphism
drastically alters the hierarchy of CD8 T cell responses elicited by Mtb. These
data suggest that immunodomination by the TB10.4 epitope acts to suppress
subdominant CD8 T cell responses to other Mtb antigens, impairing the CD8 T cell
response to other Mtb antigens, some of which might be presented by Mtb-infected
macrophages and be targets of protective immunity. Importantly, this single
amino acid polymorphism, which does not significantly alter MHC-binding or T
cell recognition, alters the half-life of the epitope and consequently, has a
profound effect on CD8 T cell priming and recognition of infected cells. These
data also provide a mechanism that could be exploited to manipulate the
hierarchy of immunodominant responses.
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Affiliation(s)
- Rujapak Sutiwisesak
- Immunology and Microbiology Program, Graduate School of Biomedical
Science, University of Massachusetts Medical School, Worcester, Massachusetts,
United States of America
- Department of Microbiology and Physiological Systems, University of
Massachusetts Medical School, Worcester, Massachusetts, United States of
America
| | - Nathan D. Hicks
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan
School of Public Health, Boston, Massachusetts, United States of
America
| | - Shayla Boyce
- Department of Microbiology and Physiological Systems, University of
Massachusetts Medical School, Worcester, Massachusetts, United States of
America
| | - Kenan C. Murphy
- Immunology and Microbiology Program, Graduate School of Biomedical
Science, University of Massachusetts Medical School, Worcester, Massachusetts,
United States of America
- Department of Microbiology and Physiological Systems, University of
Massachusetts Medical School, Worcester, Massachusetts, United States of
America
| | - Kadamba Papavinasasundaram
- Department of Microbiology and Physiological Systems, University of
Massachusetts Medical School, Worcester, Massachusetts, United States of
America
| | - Stephen M. Carpenter
- Department of Microbiology and Physiological Systems, University of
Massachusetts Medical School, Worcester, Massachusetts, United States of
America
| | - Julie Boucau
- Ragon Institute of Massachusetts General Hospital, Massachusetts
Institute of Technology and Harvard University, Cambridge, MA, United States of
America
| | - Neelambari Joshi
- Ragon Institute of Massachusetts General Hospital, Massachusetts
Institute of Technology and Harvard University, Cambridge, MA, United States of
America
| | - Sylvie Le Gall
- Ragon Institute of Massachusetts General Hospital, Massachusetts
Institute of Technology and Harvard University, Cambridge, MA, United States of
America
| | - Sarah M. Fortune
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan
School of Public Health, Boston, Massachusetts, United States of
America
| | - Christopher M. Sassetti
- Immunology and Microbiology Program, Graduate School of Biomedical
Science, University of Massachusetts Medical School, Worcester, Massachusetts,
United States of America
- Department of Microbiology and Physiological Systems, University of
Massachusetts Medical School, Worcester, Massachusetts, United States of
America
| | - Samuel M. Behar
- Immunology and Microbiology Program, Graduate School of Biomedical
Science, University of Massachusetts Medical School, Worcester, Massachusetts,
United States of America
- Department of Microbiology and Physiological Systems, University of
Massachusetts Medical School, Worcester, Massachusetts, United States of
America
- * E-mail:
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57
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Morales-Arce AY, Sabin SJ, Stone AC, Jensen JD. The population genomics of within-host Mycobacterium tuberculosis. Heredity (Edinb) 2020; 126:1-9. [PMID: 33060846 DOI: 10.1038/s41437-020-00377-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 10/02/2020] [Accepted: 10/03/2020] [Indexed: 11/09/2022] Open
Abstract
Recent progress in genomic sequencing from patient samples has allowed for the first detailed insight into the within-host genetic diversity of Mycobacterium tuberculosis (M.TB), revealing remarkably low levels of variation. While this has often been attributed to low mutation rates, other factors have been described, including resistance evolution (i.e., selective sweeps), widespread purifying and background selection, and, more recently, progeny skew. Here we review recent findings pertaining to the processes governing the evolutionary dynamics of M.TB, discuss their implications for improving our understanding of this important human pathogen, and make recommendations for future work. Significantly, this emerging evolutionary framework involving the joint estimation of demographic, selective, and reproductive processes is forming a new paradigm for the study of within-host pathogen evolution that will be widely applicable across organisms.
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Affiliation(s)
- Ana Y Morales-Arce
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA.
| | - Susanna J Sabin
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
| | - Anne C Stone
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA.,School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA
| | - Jeffrey D Jensen
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA. .,School of Life Sciences, Arizona State University, Tempe, AZ, USA.
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58
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Do chance encounters between heterogeneous cells shape the outcome of tuberculosis infections? Curr Opin Microbiol 2020; 59:72-78. [PMID: 33049596 DOI: 10.1016/j.mib.2020.08.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 08/25/2020] [Accepted: 08/27/2020] [Indexed: 12/24/2022]
Abstract
The sum of all of the interactions between single bacteria and host cells determines if an infection is cleared, controlled, or progresses at the whole host-organism level. These individual interactions have independent trajectories defined by diverse and dynamic host-cell and bacterial responses. Focusing on Mycobacterium tuberculosis infection, we discuss how advances in single-cell technologies allow investigation of heterogeneity in host-pathogen interactions and how different layers of heterogeneity in the host affect disease outcome. At late stages of infection, many single interactions co-exist and different outcomes depend on inter-granuloma and intra-granuloma heterogeneity. However, during bottleneck events involving small numbers of bacteria, random events, such as chance interactions with more or less permissive host cells, play a decisive role and may explain why some exposed individuals never develop the disease.
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59
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Auld SC, Staitieh BS. HIV and the tuberculosis "set point": how HIV impairs alveolar macrophage responses to tuberculosis and sets the stage for progressive disease. Retrovirology 2020; 17:32. [PMID: 32967690 PMCID: PMC7509826 DOI: 10.1186/s12977-020-00540-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 09/15/2020] [Indexed: 11/16/2022] Open
Abstract
As HIV has fueled a global resurgence of tuberculosis over the last several decades, there is a growing awareness that HIV-mediated impairments in both innate and adaptive immunity contribute to the heightened risk of tuberculosis in people with HIV. Since early immune responses to Mycobacterium tuberculosis (Mtb) set the stage for subsequent control or progression to active tuberculosis disease, early host-pathogen interactions following Mtb infection can be thought of as establishing a mycobacterial "set point," which we define as the mycobacterial burden at the point of adaptive immune activation. This early immune response is impaired in the context of HIV coinfection, allowing for a higher mycobacterial set point and greater likelihood of progression to active disease with greater bacterial burden. Alveolar macrophages, as the first cells to encounter Mtb in the lungs, play a critical role in containing Mtb growth and establishing the mycobacterial set point. However, a number of key macrophage functions, ranging from pathogen recognition and uptake to phagocytosis and microbial killing, are blunted in HIV coinfection. To date, research evaluating the effects of HIV on the alveolar macrophage response to Mtb has been relatively limited, particularly with regard to the critical early events that help to dictate the mycobacterial set point. A greater understanding of alveolar macrophage functions impacted by HIV coinfection will improve our understanding of protective immunity to Mtb and may reveal novel pathways amenable to intervention to improve both early immune control of Mtb and clinical outcomes for the millions of people worldwide infected with HIV.
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Affiliation(s)
- Sara C Auld
- Emory University School of Medicine, Atlanta, GA, USA.
- Rollins School of Public Health, Emory University, Atlanta, GA, USA.
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60
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Hartman AL, Nambulli S, McMillen CM, White AG, Tilston-Lunel NL, Albe JR, Cottle E, Dunn MD, Frye LJ, Gilliland TH, Olsen EL, O’Malley KJ, Schwarz MM, Tomko JA, Walker RC, Xia M, Hartman MS, Klein E, Scanga CA, Flynn JL, Klimstra WB, McElroy AK, Reed DS, Duprex WP. SARS-CoV-2 infection of African green monkeys results in mild respiratory disease discernible by PET/CT imaging and shedding of infectious virus from both respiratory and gastrointestinal tracts. PLoS Pathog 2020; 16:e1008903. [PMID: 32946524 PMCID: PMC7535860 DOI: 10.1371/journal.ppat.1008903] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/05/2020] [Accepted: 08/19/2020] [Indexed: 01/19/2023] Open
Abstract
Vaccines are urgently needed to combat the global coronavirus disease 2019 (COVID-19) pandemic, and testing of candidate vaccines in an appropriate non-human primate (NHP) model is a critical step in the process. Infection of African green monkeys (AGM) with a low passage human isolate of SARS-CoV-2 by aerosol or mucosal exposure resulted in mild clinical infection with a transient decrease in lung tidal volume. Imaging with human clinical-grade 18F-fluoro-2-deoxy-D-glucose positron emission tomography (18F-FDG PET) co-registered with computed tomography (CT) revealed pulmonary lesions at 4 days post-infection (dpi) that resolved over time. Infectious virus was shed from both respiratory and gastrointestinal (GI) tracts in all animals in a biphasic manner, first between 2-7 dpi followed by a recrudescence at 14-21 dpi. Viral RNA (vRNA) was found throughout both respiratory and gastrointestinal systems at necropsy with higher levels of vRNA found within the GI tract tissues. All animals seroconverted simultaneously for IgM and IgG, which has also been documented in human COVID-19 cases. Young AGM represent an species to study mild/subclinical COVID-19 disease and with possible insights into live virus shedding. Future vaccine evaluation can be performed in AGM with correlates of efficacy being lung lesions by PET/CT, virus shedding, and tissue viral load.
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Affiliation(s)
- Amy L. Hartman
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Infectious Diseases and Microbiology, School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Sham Nambulli
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Cynthia M. McMillen
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Infectious Diseases and Microbiology, School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Alexander G. White
- Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Natasha Louise Tilston-Lunel
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Joseph R. Albe
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Emily Cottle
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Matthew D. Dunn
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - L. James Frye
- Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Theron H. Gilliland
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Emily L. Olsen
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Katherine J. O’Malley
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Madeline M. Schwarz
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Infectious Diseases and Microbiology, School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Jaime A. Tomko
- Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Reagan C. Walker
- Division of Laboratory Animal Resources, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Mengying Xia
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Matthew S. Hartman
- Department of Radiology, Allegheny Health Network, Pittsburgh, Pennsylvania, United States of America
| | - Edwin Klein
- Division of Laboratory Animal Resources, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Charles A. Scanga
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - JoAnne L. Flynn
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - William B. Klimstra
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Anita K. McElroy
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Pediatrics, Division of Pediatric Infectious Disease, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Douglas S. Reed
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - W. Paul Duprex
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
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Ernest JP, Strydom N, Wang Q, Zhang N, Nuermberger E, Dartois V, Savic RM. Development of New Tuberculosis Drugs: Translation to Regimen Composition for Drug-Sensitive and Multidrug-Resistant Tuberculosis. Annu Rev Pharmacol Toxicol 2020; 61:495-516. [PMID: 32806997 DOI: 10.1146/annurev-pharmtox-030920-011143] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Tuberculosis (TB) kills more people than any other infectious disease. Challenges for developing better treatments include the complex pathology due to within-host immune dynamics, interpatient variability in disease severity and drug pharmacokinetics-pharmacodynamics (PK-PD), and the growing emergence of resistance. Model-informed drug development using quantitative and translational pharmacology has become increasingly recognized as a method capable of drug prioritization and regimen optimization to efficiently progress compounds through TB drug development phases. In this review, we examine translational models and tools, including plasma PK scaling, site-of-disease lesion PK, host-immune and bacteria interplay, combination PK-PD models of multidrug regimens, resistance formation, and integration of data across nonclinical and clinical phases.We propose a workflow that integrates these tools with computational platforms to identify drug combinations that have the potential to accelerate sterilization, reduce relapse rates, and limit the emergence of resistance.
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Affiliation(s)
- Jacqueline P Ernest
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California 94158, USA;
| | - Natasha Strydom
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California 94158, USA;
| | - Qianwen Wang
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California 94158, USA;
| | - Nan Zhang
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California 94158, USA;
| | - Eric Nuermberger
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
| | - Véronique Dartois
- Center for Discovery and Innovation, Hackensack Meridian School of Medicine at Seton Hall University, Nutley, New Jersey 07110, USA
| | - Rada M Savic
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California 94158, USA;
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Abstract
Lymph nodes, particularly thoracic lymph nodes, are among the most common sites of extrapulmonary tuberculosis (TB). However, Mycobacterium tuberculosis (Mtb) infection in these organs is understudied. Aside from being sites of initiation of the adaptive immune system, lymph nodes also serve as niches of Mtb growth and persistence. Mtb infection results in granuloma formation that disrupts and—if it becomes large enough—replaces the normal architecture of the lymph node that is vital to its function. In preclinical models, successful TB vaccines appear to prevent spread of Mtb from the lungs to the lymph nodes. Reactivation of latent TB can start in the lymph nodes resulting in dissemination of the bacteria to the lungs and other organs. Involvement of the lymph nodes may improve Bacille Calmette-Guerin (BCG) vaccine efficacy. Lastly, drug penetration to the lymph nodes is poor compared to blood, lung tissue, and lung granulomas. Future studies on evaluating the efficacy of vaccines and anti-TB drug treatments should include consideration of the effects on thoracic lymph nodes and not just the lungs.
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Affiliation(s)
- Sharie Keanne C. Ganchua
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Alexander G. White
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Edwin C. Klein
- Division of Laboratory Animal Resources, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - JoAnne L. Flynn
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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63
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Abstract
Understanding how Mycobacterium tuberculosis survives during antibiotic treatment is necessary to rationally devise more effective tuberculosis (TB) chemotherapy regimens. Using genome-wide mutant fitness profiling and the mouse model of TB, we identified genes that alter antibiotic efficacy specifically in the infection environment and associated several of these genes with natural genetic variants found in drug-resistant clinical isolates. These data suggest strategies for synergistic therapies that accelerate bacterial clearance, and they identify mechanisms of adaptation to drug exposure that could influence treatment outcome. Effective tuberculosis treatment requires at least 6 months of combination therapy. Alterations in the physiological state of the bacterium during infection are thought to reduce drug efficacy and prolong the necessary treatment period, but the nature of these adaptations remain incompletely defined. To identify specific bacterial functions that limit drug effects during infection, we employed a comprehensive genetic screening approach to identify mutants with altered susceptibility to the first-line antibiotics in the mouse model. We identified many mutations that increase the rate of bacterial clearance, suggesting new strategies for accelerating therapy. In addition, the drug-specific effects of these mutations suggested that different antibiotics are limited by distinct factors. Rifampin efficacy is inferred to be limited by cellular permeability, whereas isoniazid is preferentially affected by replication rate. Many mutations that altered bacterial clearance in the mouse model did not have an obvious effect on drug susceptibility using in vitro assays, indicating that these chemical-genetic interactions tend to be specific to the in vivo environment. This observation suggested that a wide variety of natural genetic variants could influence drug efficacy in vivo without altering behavior in standard drug-susceptibility tests. Indeed, mutations in a number of the genes identified in our study are enriched in drug-resistant clinical isolates, identifying genetic variants that may influence treatment outcome. Together, these observations suggest new avenues for improving therapy, as well as the mechanisms of genetic adaptations that limit it. IMPORTANCE Understanding how Mycobacterium tuberculosis survives during antibiotic treatment is necessary to rationally devise more effective tuberculosis (TB) chemotherapy regimens. Using genome-wide mutant fitness profiling and the mouse model of TB, we identified genes that alter antibiotic efficacy specifically in the infection environment and associated several of these genes with natural genetic variants found in drug-resistant clinical isolates. These data suggest strategies for synergistic therapies that accelerate bacterial clearance, and they identify mechanisms of adaptation to drug exposure that could influence treatment outcome.
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Diedrich CR, Rutledge T, Maiello P, Baranowski TM, White AG, Borish HJ, Karell P, Hopkins F, Brown J, Fortune SM, Flynn JL, Ambrose Z, Lin PL. SIV and Mycobacterium tuberculosis synergy within the granuloma accelerates the reactivation pattern of latent tuberculosis. PLoS Pathog 2020; 16:e1008413. [PMID: 32730321 PMCID: PMC7419014 DOI: 10.1371/journal.ppat.1008413] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 08/11/2020] [Accepted: 05/13/2020] [Indexed: 12/18/2022] Open
Abstract
Human immunodeficiency virus infection is the most common risk factor for severe forms of tuberculosis (TB), regardless of CD4 T cell count. Using a well-characterized cynomolgus macaque model of human TB, we compared radiographic, immunologic and microbiologic characteristics of early (subclinical) reactivation of latent M. tuberculosis (Mtb) infection among animals subsequently infected with simian immunodeficiency virus (SIV) or who underwent anti-CD4 depletion by a depletion antibody. CD4 depleted animals had significantly fewer CD4 T cells within granulomas compared to Mtb/SIV co-infected and Mtb-only control animals. After 2 months of treatment, subclinical reactivation occurred at similar rates among CD4 depleted (5 of 7 animals) and SIV infected animals (4 of 8 animals). However, SIV-induced reactivation was associated with more dissemination of lung granulomas that were permissive to Mtb growth resulting in greater bacterial burden within granulomas compared to CD4 depleted reactivators. Granulomas from Mtb/SIV animals displayed a more robust T cell activation profile (IFN-α, IFN-γ, TNF, IL-17, IL-2, IL-10, IL-4 and granzyme B) compared to CD4 depleted animals and controls though these effectors did not protect against reactivation or dissemination, but instead may be related to increased viral and/or Mtb antigens. SIV replication within the granuloma was associated with reactivation, greater overall Mtb growth and reduced Mtb killing resulting in greater overall Mtb burden. These data support that SIV disrupts protective immune responses against latent Mtb infection beyond the loss of CD4 T cells, and that synergy between SIV and Mtb occurs within granulomas.
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Affiliation(s)
- Collin R. Diedrich
- Department of Pediatrics, Children’s Hospital of Pittsburgh of the University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States of America
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Tara Rutledge
- Department of Pediatrics, Children’s Hospital of Pittsburgh of the University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States of America
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Pauline Maiello
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Tonilynn M. Baranowski
- Department of Pediatrics, Children’s Hospital of Pittsburgh of the University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States of America
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Alexander G. White
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - H. Jacob Borish
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Paul Karell
- Department of Pediatrics, Children’s Hospital of Pittsburgh of the University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States of America
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Forrest Hopkins
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Jessica Brown
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Sarah M. Fortune
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - JoAnne L. Flynn
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Zandrea Ambrose
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Philana Ling Lin
- Department of Pediatrics, Children’s Hospital of Pittsburgh of the University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States of America
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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Vlazaki M, Huber J, Restif O. Integrating mathematical models with experimental data to investigate the within-host dynamics of bacterial infections. Pathog Dis 2020; 77:5704399. [PMID: 31942996 PMCID: PMC6986552 DOI: 10.1093/femspd/ftaa001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 01/13/2020] [Indexed: 12/23/2022] Open
Abstract
Bacterial infections still constitute a major cause of mortality and morbidity worldwide. The unavailability of therapeutics, antimicrobial resistance and the chronicity of infections due to incomplete clearance contribute to this phenomenon. Despite the progress in antimicrobial and vaccine development, knowledge about the effect that therapeutics have on the host–bacteria interactions remains incomplete. Insights into the characteristics of bacterial colonization and migration between tissues and the relationship between replication and host- or therapeutically induced killing can enable efficient design of treatment approaches. Recently, innovative experimental techniques have generated data enabling the qualitative characterization of aspects of bacterial dynamics. Here, we argue that mathematical modeling as an adjunct to experimental data can enrich the biological insight that these data provide. However, due to limited interdisciplinary training, efforts to combine the two remain limited. To promote this dialogue, we provide a categorization of modeling approaches highlighting their relationship to data generated by a range of experimental techniques in the area of in vivo bacterial dynamics. We outline common biological themes explored using mathematical models with case studies across all pathogen classes. Finally, this review advocates multidisciplinary integration to improve our mechanistic understanding of bacterial infections and guide the use of existing or new therapies.
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Affiliation(s)
- Myrto Vlazaki
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, CB3 0ES, Cambridge, UK
| | - John Huber
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, CB3 0ES, Cambridge, UK
| | - Olivier Restif
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, CB3 0ES, Cambridge, UK
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66
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Ziegler CGK, Allon SJ, Nyquist SK, Mbano IM, Miao VN, Tzouanas CN, Cao Y, Yousif AS, Bals J, Hauser BM, Feldman J, Muus C, Wadsworth MH, Kazer SW, Hughes TK, Doran B, Gatter GJ, Vukovic M, Taliaferro F, Mead BE, Guo Z, Wang JP, Gras D, Plaisant M, Ansari M, Angelidis I, Adler H, Sucre JMS, Taylor CJ, Lin B, Waghray A, Mitsialis V, Dwyer DF, Buchheit KM, Boyce JA, Barrett NA, Laidlaw TM, Carroll SL, Colonna L, Tkachev V, Peterson CW, Yu A, Zheng HB, Gideon HP, Winchell CG, Lin PL, Bingle CD, Snapper SB, Kropski JA, Theis FJ, Schiller HB, Zaragosi LE, Barbry P, Leslie A, Kiem HP, Flynn JL, Fortune SM, Berger B, Finberg RW, Kean LS, Garber M, Schmidt AG, Lingwood D, Shalek AK, Ordovas-Montanes J. SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues. Cell 2020; 181:1016-1035.e19. [PMID: 32413319 PMCID: PMC7252096 DOI: 10.1016/j.cell.2020.04.035] [Citation(s) in RCA: 1708] [Impact Index Per Article: 427.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/03/2020] [Accepted: 04/20/2020] [Indexed: 02/06/2023]
Abstract
There is pressing urgency to understand the pathogenesis of the severe acute respiratory syndrome coronavirus clade 2 (SARS-CoV-2), which causes the disease COVID-19. SARS-CoV-2 spike (S) protein binds angiotensin-converting enzyme 2 (ACE2), and in concert with host proteases, principally transmembrane serine protease 2 (TMPRSS2), promotes cellular entry. The cell subsets targeted by SARS-CoV-2 in host tissues and the factors that regulate ACE2 expression remain unknown. Here, we leverage human, non-human primate, and mouse single-cell RNA-sequencing (scRNA-seq) datasets across health and disease to uncover putative targets of SARS-CoV-2 among tissue-resident cell subsets. We identify ACE2 and TMPRSS2 co-expressing cells within lung type II pneumocytes, ileal absorptive enterocytes, and nasal goblet secretory cells. Strikingly, we discovered that ACE2 is a human interferon-stimulated gene (ISG) in vitro using airway epithelial cells and extend our findings to in vivo viral infections. Our data suggest that SARS-CoV-2 could exploit species-specific interferon-driven upregulation of ACE2, a tissue-protective mediator during lung injury, to enhance infection.
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Affiliation(s)
- Carly G K Ziegler
- Program in Health Sciences & Technology, Harvard Medical School & Massachusetts Institute of Technology, Boston, MA 02115, USA; Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Graduate Program in Biophysics, Harvard University, Cambridge, MA 02138, USA
| | - Samuel J Allon
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sarah K Nyquist
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Program in Computational & Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Computer Science & Artificial Intelligence Lab, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ian M Mbano
- Africa Health Research Institute, Durban, South Africa; School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Vincent N Miao
- Program in Health Sciences & Technology, Harvard Medical School & Massachusetts Institute of Technology, Boston, MA 02115, USA; Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Constantine N Tzouanas
- Program in Health Sciences & Technology, Harvard Medical School & Massachusetts Institute of Technology, Boston, MA 02115, USA; Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Yuming Cao
- University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Ashraf S Yousif
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Julia Bals
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Blake M Hauser
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Jared Feldman
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Program in Virology, Harvard Medical School, Boston, MA 02115, USA
| | - Christoph Muus
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; John A. Paulson School of Engineering & Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Marc H Wadsworth
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Samuel W Kazer
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Travis K Hughes
- Program in Health Sciences & Technology, Harvard Medical School & Massachusetts Institute of Technology, Boston, MA 02115, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Program in Immunology, Harvard Medical School, Boston, MA 02115, USA
| | - Benjamin Doran
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA; Division of Gastroenterology, Hepatology, and Nutrition, Boston Children's Hospital, Boston, MA 02115, USA
| | - G James Gatter
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Marko Vukovic
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Faith Taliaferro
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Gastroenterology, Hepatology, and Nutrition, Boston Children's Hospital, Boston, MA 02115, USA
| | - Benjamin E Mead
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Zhiru Guo
- University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Jennifer P Wang
- University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Delphine Gras
- Aix-Marseille University, INSERM, INRA, C2VN, Marseille, France
| | - Magali Plaisant
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis, France
| | - Meshal Ansari
- Comprehensive Pneumology Center & Institute of Lung Biology and Disease, Helmholtz Zentrum München, Munich, Germany; German Center for Lung Research, Munich, Germany; Institute of Computational Biology, Helmholtz Zentrum München, Munich, Germany
| | - Ilias Angelidis
- Comprehensive Pneumology Center & Institute of Lung Biology and Disease, Helmholtz Zentrum München, Munich, Germany; German Center for Lung Research, Munich, Germany
| | - Heiko Adler
- German Center for Lung Research, Munich, Germany; Research Unit Lung Repair and Regeneration, Helmholtz Zentrum München, Munich, Germany
| | - Jennifer M S Sucre
- Division of Neonatology, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Chase J Taylor
- Divison of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Brian Lin
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Avinash Waghray
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Vanessa Mitsialis
- Division of Gastroenterology, Hepatology, and Nutrition, Boston Children's Hospital, Boston, MA 02115, USA; Division of Gastroenterology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Daniel F Dwyer
- Division of Allergy and Clinical Immunology, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Kathleen M Buchheit
- Division of Allergy and Clinical Immunology, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Joshua A Boyce
- Division of Allergy and Clinical Immunology, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Nora A Barrett
- Division of Allergy and Clinical Immunology, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Tanya M Laidlaw
- Division of Allergy and Clinical Immunology, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | | | | | - Victor Tkachev
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA; Dana Farber Cancer Institute, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Christopher W Peterson
- Stem Cell & Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Alison Yu
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA; Division of Gastroenterology and Hepatology, Seattle Children's Hospital, Seattle, WA 98145, USA
| | - Hengqi Betty Zheng
- University of Washington, Seattle, WA 98195, USA; Division of Gastroenterology and Hepatology, Seattle Children's Hospital, Seattle, WA 98145, USA
| | - Hannah P Gideon
- Department of Microbiology & Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA; Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Caylin G Winchell
- Department of Microbiology & Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA; Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA; Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Philana Ling Lin
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA; UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA; Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA
| | - Colin D Bingle
- Department of Infection, Immunity & Cardiovascular Disease, The Medical School and The Florey Institute for Host Pathogen Interactions, University of Sheffield, Sheffield, S10 2TN, UK
| | - Scott B Snapper
- Division of Gastroenterology, Hepatology, and Nutrition, Boston Children's Hospital, Boston, MA 02115, USA; Division of Gastroenterology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Jonathan A Kropski
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37240, USA; Department of Veterans Affairs Medical Center, Nashville, TN 37212, USA
| | - Fabian J Theis
- Institute of Computational Biology, Helmholtz Zentrum München, Munich, Germany
| | - Herbert B Schiller
- Comprehensive Pneumology Center & Institute of Lung Biology and Disease, Helmholtz Zentrum München, Munich, Germany; German Center for Lung Research, Munich, Germany
| | | | - Pascal Barbry
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis, France
| | - Alasdair Leslie
- Africa Health Research Institute, Durban, South Africa; School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; Department of Infection & Immunity, University College London, London, UK
| | - Hans-Peter Kiem
- Stem Cell & Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - JoAnne L Flynn
- Department of Microbiology & Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA; Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Sarah M Fortune
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Bonnie Berger
- Computer Science & Artificial Intelligence Lab, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Robert W Finberg
- University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Leslie S Kean
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA; Dana Farber Cancer Institute, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Manuel Garber
- University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Aaron G Schmidt
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Daniel Lingwood
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Alex K Shalek
- Program in Health Sciences & Technology, Harvard Medical School & Massachusetts Institute of Technology, Boston, MA 02115, USA; Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Graduate Program in Biophysics, Harvard University, Cambridge, MA 02138, USA; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Program in Computational & Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Program in Immunology, Harvard Medical School, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA.
| | - Jose Ordovas-Montanes
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Program in Immunology, Harvard Medical School, Boston, MA 02115, USA; Division of Gastroenterology, Hepatology, and Nutrition, Boston Children's Hospital, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA.
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67
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Wessler T, Joslyn LR, Borish HJ, Gideon HP, Flynn JL, Kirschner DE, Linderman JJ. A computational model tracks whole-lung Mycobacterium tuberculosis infection and predicts factors that inhibit dissemination. PLoS Comput Biol 2020; 16:e1007280. [PMID: 32433646 PMCID: PMC7239387 DOI: 10.1371/journal.pcbi.1007280] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 02/26/2020] [Indexed: 12/15/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb), the causative infectious agent of tuberculosis (TB), kills more individuals per year than any other infectious agent. Granulomas, the hallmark of Mtb infection, are complex structures that form in lungs, composed of immune cells surrounding bacteria, infected cells, and a caseous necrotic core. While granulomas serve to physically contain and immunologically restrain bacteria growth, some granulomas are unable to control Mtb growth, leading to bacteria and infected cells leaving the granuloma and disseminating, either resulting in additional granuloma formation (local or non-local) or spread to airways or lymph nodes. Dissemination is associated with development of active TB. It is challenging to experimentally address specific mechanisms driving dissemination from TB lung granulomas. Herein, we develop a novel hybrid multi-scale computational model, MultiGran, that tracks Mtb infection within multiple granulomas in an entire lung. MultiGran follows cells, cytokines, and bacterial populations within each lung granuloma throughout the course of infection and is calibrated to multiple non-human primate (NHP) cellular, granuloma, and whole-lung datasets. We show that MultiGran can recapitulate patterns of in vivo local and non-local dissemination, predict likelihood of dissemination, and predict a crucial role for multifunctional CD8+ T cells and macrophage dynamics for preventing dissemination. Tuberculosis (TB) is caused by infection with Mycobacterium tuberculosis (Mtb) and kills 3 people per minute worldwide. Granulomas, spherical structures composed of immune cells surrounding bacteria, are the hallmark of Mtb infection and sometimes fail to contain the bacteria and disseminate, leading to further granuloma growth within the lung environment. To date, the mechanisms that determine granuloma dissemination events have not been characterized. We present a computational multi-scale model of granuloma formation and dissemination within primate lungs. Our computational model is calibrated to multiple experimental datasets across the cellular, granuloma, and whole-lung scales of non-human primates. We match to both individual granuloma and granuloma-population datasets, predict likelihood of dissemination events, and predict a critical role for multifunctional CD8+ T cells and macrophage-bacteria interactions to prevent infection dissemination.
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Affiliation(s)
- Timothy Wessler
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Louis R. Joslyn
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - H. Jacob Borish
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Hannah P. Gideon
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - JoAnne L. Flynn
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Denise E. Kirschner
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail: (DEK); (JJL)
| | - Jennifer J. Linderman
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail: (DEK); (JJL)
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68
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Liu Q, Wei J, Li Y, Wang M, Su J, Lu Y, López MG, Qian X, Zhu Z, Wang H, Gan M, Jiang Q, Fu YX, Takiff HE, Comas I, Li F, Lu X, Fortune SM, Gao Q. Mycobacterium tuberculosis clinical isolates carry mutational signatures of host immune environments. SCIENCE ADVANCES 2020; 6:eaba4901. [PMID: 32524000 PMCID: PMC7259932 DOI: 10.1126/sciadv.aba4901] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 03/25/2020] [Indexed: 05/12/2023]
Abstract
Mycobacterium tuberculosis (Mtb) infection results in a spectrum of clinical and histopathologic manifestations. It has been proposed that the environmental and immune pressures associated with different contexts of infection have different consequences for the associated bacterial populations, affecting drug susceptibility and the emergence of resistance. However, there is little concrete evidence for this model. We prospectively collected sputum samples from 18 newly diagnosed and treatment-naïve patients with tuberculosis and sequenced 795 colony-derived Mtb isolates. Mutant accumulation rates varied considerably between different bacilli isolated from the same individual, and where high rates of mutation were observed, the mutational spectrum was consistent with reactive oxygen species-induced mutagenesis. Elevated bacterial mutation rates were identified in isolates from HIV-negative but not HIV-positive individuals, suggesting that they were immune-driven. These results support the model that mutagenesis of Mtb in vivo is modulated by the host environment, which could drive the emergence of variants associated with drug resistance in a host-dependent manner.
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Affiliation(s)
- Qingyun Liu
- Shanghai Public Health Clinical Center, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Medical College and School of Basic Medical Sciences, Fudan University, Shanghai, China
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Jianhao Wei
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Yawei Li
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mei Wang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Jun Su
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Yonghui Lu
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Mariana G. López
- Tuberculosis Genomic Unit, Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain
| | - Xueqin Qian
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Zhaoqin Zhu
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Haiying Wang
- Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Mingyun Gan
- Molecular Medical Center, Children’s Hospital of Fudan University, Shanghai, China
| | - Qi Jiang
- Shanghai Public Health Clinical Center, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Medical College and School of Basic Medical Sciences, Fudan University, Shanghai, China
- Shenzhen Center for Chronic Disease Control, Shenzhen, China
| | - Yun-Xin Fu
- Department of Biostatistics and Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Howard E. Takiff
- Integrated Mycobacterial Pathogenomics Unit, Institut Pasteur, Paris, France
- Nanshan Center for Chronic Disease Control, Shenzhen, China
| | - Iñaki Comas
- Tuberculosis Genomic Unit, Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain
- CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Feng Li
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Xuemei Lu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- CAS Center for Excellence in Animal Evolution and Genetics, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Sarah M. Fortune
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Qian Gao
- Shanghai Public Health Clinical Center, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Medical College and School of Basic Medical Sciences, Fudan University, Shanghai, China
- Shenzhen Center for Chronic Disease Control, Shenzhen, China
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69
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Català M, Bechini J, Tenesa M, Pérez R, Moya M, Vilaplana C, Valls J, Alonso S, López D, Cardona PJ, Prats C. Modelling the dynamics of tuberculosis lesions in a virtual lung: Role of the bronchial tree in endogenous reinfection. PLoS Comput Biol 2020; 16:e1007772. [PMID: 32433644 PMCID: PMC7239440 DOI: 10.1371/journal.pcbi.1007772] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 03/04/2020] [Indexed: 01/04/2023] Open
Abstract
Tuberculosis (TB) is an infectious disease that still causes more than 1.5 million deaths annually. The World Health Organization estimates that around 30% of the world's population is latently infected. However, the mechanisms responsible for 10% of this reserve (i.e., of the latently infected population) developing an active disease are not fully understood, yet. The dynamic hypothesis suggests that endogenous reinfection has an important role in maintaining latent infection. In order to examine this hypothesis for falsifiability, an agent-based model of growth, merging, and proliferation of TB lesions was implemented in a computational bronchial tree, built with an iterative algorithm for the generation of bronchial bifurcations and tubes applied inside a virtual 3D pulmonary surface. The computational model was fed and parameterized with computed tomography (CT) experimental data from 5 latently infected minipigs. First, we used CT images to reconstruct the virtual pulmonary surfaces where bronchial trees are built. Then, CT data about TB lesion' size and location to each minipig were used in the parameterization process. The model's outcome provides spatial and size distributions of TB lesions that successfully reproduced experimental data, thus reinforcing the role of the bronchial tree as the spatial structure triggering endogenous reinfection. A sensitivity analysis of the model shows that the final number of lesions is strongly related with the endogenous reinfection frequency and maximum growth rate of the lesions, while their mean diameter mainly depends on the spatial spreading of new lesions and the maximum radius. Finally, the model was used as an in silico experimental platform to explore the transition from latent infection to active disease, identifying two main triggering factors: a high inflammatory response and the combination of a moderate inflammatory response with a small breathing amplitude.
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Affiliation(s)
- Martí Català
- Comparative Medicine and Bioimage Centre of Catalonia (CMCiB), Fundació Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol, Badalona, Catalonia, Spain
- Departament de Física, Universitat Politècnica de Catalunya, Castelldefels, Barcelona, Catalonia, Spain
| | - Jordi Bechini
- Servei de Radiodiagnòstic, Hospital Universitari Germans Trias i Pujol, Badalona, Catalonia, Spain
| | - Montserrat Tenesa
- Servei de Radiodiagnòstic, Hospital Universitari Germans Trias i Pujol, Badalona, Catalonia, Spain
| | - Ricardo Pérez
- Servei de Radiodiagnòstic, Hospital Universitari Germans Trias i Pujol, Badalona, Catalonia, Spain
| | - Mariano Moya
- Servei de Radiodiagnòstic, Hospital Universitari Germans Trias i Pujol, Badalona, Catalonia, Spain
| | - Cristina Vilaplana
- Experimental Tuberculosis Unit, Fundació Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol, Universitat Autònoma de Barcelona, Can Ruti Campus, Edifici Mar, Badalona, Catalonia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, Madrid, Spain
| | - Joaquim Valls
- Departament de Física, Universitat Politècnica de Catalunya, Castelldefels, Barcelona, Catalonia, Spain
| | - Sergio Alonso
- Departament de Física, Universitat Politècnica de Catalunya, Castelldefels, Barcelona, Catalonia, Spain
| | - Daniel López
- Departament de Física, Universitat Politècnica de Catalunya, Castelldefels, Barcelona, Catalonia, Spain
| | - Pere-Joan Cardona
- Comparative Medicine and Bioimage Centre of Catalonia (CMCiB), Fundació Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol, Badalona, Catalonia, Spain
- Experimental Tuberculosis Unit, Fundació Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol, Universitat Autònoma de Barcelona, Can Ruti Campus, Edifici Mar, Badalona, Catalonia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, Madrid, Spain
| | - Clara Prats
- Departament de Física, Universitat Politècnica de Catalunya, Castelldefels, Barcelona, Catalonia, Spain
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70
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Bucsan AN, Mehra S, Khader SA, Kaushal D. The current state of animal models and genomic approaches towards identifying and validating molecular determinants of Mycobacterium tuberculosis infection and tuberculosis disease. Pathog Dis 2020; 77:5543892. [PMID: 31381766 PMCID: PMC6687098 DOI: 10.1093/femspd/ftz037] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Accepted: 07/25/2019] [Indexed: 12/31/2022] Open
Abstract
Animal models are important in understanding both the pathogenesis of and immunity to tuberculosis (TB). Unfortunately, we are beginning to understand that no animal model perfectly recapitulates the human TB syndrome, which encompasses numerous different stages. Furthermore, Mycobacterium tuberculosis infection is a very heterogeneous event at both the levels of pathogenesis and immunity. This review seeks to establish the current understanding of TB pathogenesis and immunity, as validated in the animal models of TB in active use today. We especially focus on the use of modern genomic approaches in these models to determine the mechanism and the role of specific molecular pathways. Animal models have significantly enhanced our understanding of TB. Incorporation of contemporary technologies such as single cell transcriptomics, high-parameter flow cytometric immune profiling, proteomics, proteomic flow cytometry and immunocytometry into the animal models in use will further enhance our understanding of TB and facilitate the development of treatment and vaccination strategies.
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Affiliation(s)
- Allison N Bucsan
- Tulane Center for Tuberculosis Research, Covington, LA, USA.,Tulane National Primate Research Center, Covington, LA, USA
| | - Smriti Mehra
- Tulane National Primate Research Center, Covington, LA, USA
| | | | - Deepak Kaushal
- Tulane Center for Tuberculosis Research, Covington, LA, USA.,Tulane National Primate Research Center, Covington, LA, USA.,Southwest National Primate Research Center, San Antonio, TX, USA.,Texas Biomedical Research Institute, San Antonio, TX, USA
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71
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Tsenova L, Singhal A. Effects of host-directed therapies on the pathology of tuberculosis. J Pathol 2020; 250:636-646. [PMID: 32108337 DOI: 10.1002/path.5407] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 02/12/2020] [Accepted: 02/24/2020] [Indexed: 12/15/2022]
Abstract
Mycobacterium tuberculosis, the causative agent of tuberculosis (TB), has co-evolved with the human immune system and utilizes multiple strategies to persist within infected cells, to hijack several immune mechanisms, and to cause severe pathology and tissue damage in the host. This delays the efficacy of current antibiotic therapy and contributes to the evolution of multi-drug-resistant strains. These challenges led to the development of the novel approach in TB treatment that involves therapeutic targeting of host immune response to control disease pathogenesis and pathogen growth, namely, host-directed therapies (HDTs). Such HDT approaches can (1) enhance the effect of antibiotics, (2) shorten treatment duration for any clinical form of TB, (3) promote development of immunological memory that could protect against relapse, and (4) ameliorate the immunopathology including matrix destruction and fibrosis associated with TB. In this review we discuss TB-HDT candidates shown to be of clinical relevance that thus could be developed to reduce pathology, tissue damage, and subsequent impairment of pulmonary function. © 2020 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Liana Tsenova
- Department of Biological Sciences, New York City College of Technology, Brooklyn, NY, USA
| | - Amit Singhal
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.,Vaccine and Infectious Disease Research Centre (VIDRC), Translational Health Science and Technology Institute (THSTI), Faridabad, India
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72
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Flynn JL. At the Interface of Microbiology and Immunology. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2020; 204:1413-1417. [PMID: 32152209 DOI: 10.4049/jimmunol.2090001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Affiliation(s)
- JoAnne L Flynn
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219
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73
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Moule MG, Cirillo JD. Mycobacterium tuberculosis Dissemination Plays a Critical Role in Pathogenesis. Front Cell Infect Microbiol 2020; 10:65. [PMID: 32161724 PMCID: PMC7053427 DOI: 10.3389/fcimb.2020.00065] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 02/07/2020] [Indexed: 12/27/2022] Open
Abstract
Mycobacterium tuberculosis is primarily a respiratory pathogen. However, 15% of infections worldwide occur at extrapulmonary sites causing additional complications for diagnosis and treatment of the disease. In addition, dissemination of M. tuberculosis out of the lungs is thought to be more than just a rare event leading to extrapulmonary tuberculosis, but rather a prerequisite step that occurs during all infections, producing secondary lesions that can become latent or productive. In this review we will cover the clinical range of extrapulmonary infections and the process of dissemination including evidence from both historical medical literature and animal experiments for dissemination and subsequent reseeding of the lungs through the lymphatic and circulatory systems. While the mechanisms of M. tuberculosis dissemination are not fully understood, we will discuss the various models that have been proposed to address how this process may occur and summarize the bacterial virulence factors that facilitate M. tuberculosis dissemination.
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Affiliation(s)
- Madeleine G. Moule
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX, United States
| | - Jeffrey D. Cirillo
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX, United States
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74
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Darrah PA, Zeppa JJ, Maiello P, Hackney JA, Wadsworth MH, Hughes TK, Pokkali S, Swanson PA, Grant NL, Rodgers MA, Kamath M, Causgrove CM, Laddy DJ, Bonavia A, Casimiro D, Lin PL, Klein E, White AG, Scanga CA, Shalek AK, Roederer M, Flynn JL, Seder RA. Prevention of tuberculosis in macaques after intravenous BCG immunization. Nature 2020; 577:95-102. [PMID: 31894150 PMCID: PMC7015856 DOI: 10.1038/s41586-019-1817-8] [Citation(s) in RCA: 344] [Impact Index Per Article: 86.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 11/11/2019] [Indexed: 12/16/2022]
Abstract
Mycobacterium tuberculosis (Mtb) is the leading cause of death from infection worldwide1. The only available vaccine, BCG (Bacillus Calmette-Guérin), is given intradermally and has variable efficacy against pulmonary tuberculosis, the major cause of mortality and disease transmission1,2. Here we show that intravenous administration of BCG profoundly alters the protective outcome of Mtb challenge in non-human primates (Macaca mulatta). Compared with intradermal or aerosol delivery, intravenous immunization induced substantially more antigen-responsive CD4 and CD8 T cell responses in blood, spleen, bronchoalveolar lavage and lung lymph nodes. Moreover, intravenous immunization induced a high frequency of antigen-responsive T cells across all lung parenchymal tissues. Six months after BCG vaccination, macaques were challenged with virulent Mtb. Notably, nine out of ten macaques that received intravenous BCG vaccination were highly protected, with six macaques showing no detectable levels of infection, as determined by positron emission tomography-computed tomography imaging, mycobacterial growth, pathology and granuloma formation. The finding that intravenous BCG prevents or substantially limits Mtb infection in highly susceptible rhesus macaques has important implications for vaccine delivery and clinical development, and provides a model for defining immune correlates and mechanisms of vaccine-elicited protection against tuberculosis.
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Affiliation(s)
- Patricia A. Darrah
- 0000 0001 2297 5165grid.94365.3dVaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD USA
| | - Joseph J. Zeppa
- 0000 0004 1936 9000grid.21925.3dDepartment of Microbiology and Molecular Genetics and Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Pauline Maiello
- 0000 0004 1936 9000grid.21925.3dDepartment of Microbiology and Molecular Genetics and Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Joshua A. Hackney
- 0000 0001 2297 5165grid.94365.3dVaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD USA
| | - Marc H. Wadsworth
- Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA USA ,0000 0001 2341 2786grid.116068.8Department of Chemistry, Institute for Medical Engineering and Sciences (IMES), MIT, Cambridge, MA USA ,grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Travis K. Hughes
- Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA USA ,0000 0001 2341 2786grid.116068.8Department of Chemistry, Institute for Medical Engineering and Sciences (IMES), MIT, Cambridge, MA USA ,grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Supriya Pokkali
- 0000 0001 2297 5165grid.94365.3dVaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD USA
| | - Phillip A. Swanson
- 0000 0001 2297 5165grid.94365.3dVaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD USA
| | - Nicole L. Grant
- 0000 0004 1936 9000grid.21925.3dDepartment of Infectious Diseases and Microbiology, University of Pittsburgh School of Public Health, Pittsburgh, PA USA
| | - Mark A. Rodgers
- 0000 0004 1936 9000grid.21925.3dDepartment of Microbiology and Molecular Genetics and Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Megha Kamath
- 0000 0001 2297 5165grid.94365.3dVaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD USA
| | - Chelsea M. Causgrove
- 0000 0004 1936 9000grid.21925.3dDepartment of Microbiology and Molecular Genetics and Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | | | | | | | - Philana Ling Lin
- 0000 0000 9753 0008grid.239553.bDepartment of Pediatrics, Children’s Hospital of the University of Pittsburgh of UPMC, Pittsburgh, PA USA
| | - Edwin Klein
- 0000 0004 1936 9000grid.21925.3dDivision of Animal Laboratory Resources, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Alexander G. White
- 0000 0004 1936 9000grid.21925.3dDepartment of Microbiology and Molecular Genetics and Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Charles A. Scanga
- 0000 0004 1936 9000grid.21925.3dDepartment of Microbiology and Molecular Genetics and Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Alex K. Shalek
- Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA USA ,0000 0001 2341 2786grid.116068.8Department of Chemistry, Institute for Medical Engineering and Sciences (IMES), MIT, Cambridge, MA USA ,grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA ,0000 0001 2341 2786grid.116068.8Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA USA
| | - Mario Roederer
- 0000 0001 2297 5165grid.94365.3dVaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD USA
| | - JoAnne L. Flynn
- 0000 0004 1936 9000grid.21925.3dDepartment of Microbiology and Molecular Genetics and Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Robert A. Seder
- 0000 0001 2297 5165grid.94365.3dVaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD USA
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Abstract
Molecular imaging is an emerging technology that enables the noninvasive visualization, characterization, and quantification of molecular events within living subjects. Positron emission tomography (PET) is a clinically available molecular imaging tool with significant potential to study pathogenesis of infections in humans. Molecular imaging is an emerging technology that enables the noninvasive visualization, characterization, and quantification of molecular events within living subjects. Positron emission tomography (PET) is a clinically available molecular imaging tool with significant potential to study pathogenesis of infections in humans. PET enables dynamic assessment of infectious processes within the same subject with high temporal and spatial resolution and obviates the need for invasive tissue sampling, which is difficult in patients and generally limited to a single time point, even in animal models. This review presents current state-of-the-art concepts on the application of molecular imaging for infectious diseases and details how PET imaging can facilitate novel insights into infectious processes, ongoing development of pathogen-specific imaging, and simultaneous in situ measurements of intralesional antimicrobial pharmacokinetics in multiple compartments, including privileged sites. Finally, the potential clinical applications of this promising technology are also discussed.
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76
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Lin PL, Flynn JL. The End of the Binary Era: Revisiting the Spectrum of Tuberculosis. THE JOURNAL OF IMMUNOLOGY 2019; 201:2541-2548. [PMID: 30348659 DOI: 10.4049/jimmunol.1800993] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 07/28/2018] [Indexed: 11/19/2022]
Abstract
Human Mycobacterium tuberculosis infection was thought to result in either active symptomatic tuberculosis (TB) or latent asymptomatic infection. It is now clear that this binary classification is insufficient to describe the myriad of infection outcomes. In active TB, symptomatic disease can be mild to severe, with a range of lung and thoracic lymph node involvement or extrapulmonary manifestations. Most humans control the infection and develop latent TB infection, with differential risks of reactivation to active TB. However, some frequently exposed persons appear to be resistant to infection, whereas others may initially become infected yet subsequently eliminate all bacilli. The immunologic factors influencing these varied outcomes are still not clear, but likely involve a range of different responses. In this article, we review the data supporting the spectrum of M. tuberculosis infection in humans as well as data in nonhuman primates that allow dissection of the immune responses leading to the varied outcomes of infection.
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Affiliation(s)
- Philana Ling Lin
- Department of Pediatrics, Children's Hospital of Pittsburgh of the University of Pittsburgh Medical Center, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224; and
| | - JoAnne L Flynn
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
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77
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Mashabela GT, de Wet TJ, Warner DF. Mycobacterium tuberculosis Metabolism. Microbiol Spectr 2019; 7:10.1128/microbiolspec.gpp3-0067-2019. [PMID: 31350832 PMCID: PMC10957194 DOI: 10.1128/microbiolspec.gpp3-0067-2019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Indexed: 02/06/2023] Open
Abstract
Mycobacterium tuberculosis is the cause of tuberculosis (TB), a disease which continues to overwhelm health systems in endemic regions despite the existence of effective combination chemotherapy and the widespread use of a neonatal anti-TB vaccine. For a professional pathogen, M. tuberculosis retains a surprisingly large proportion of the metabolic repertoire found in nonpathogenic mycobacteria with very different lifestyles. Moreover, evidence that additional functions were acquired during the early evolution of the M. tuberculosis complex suggests the organism has adapted (and augmented) the metabolic pathways of its environmental ancestor to persistence and propagation within its obligate human host. A better understanding of M. tuberculosis pathogenicity, however, requires the elucidation of metabolic functions under disease-relevant conditions, a challenge complicated by limited knowledge of the microenvironments occupied and nutrients accessed by bacilli during host infection, as well as the reliance in experimental mycobacteriology on a restricted number of experimental models with variable relevance to clinical disease. Here, we consider M. tuberculosis metabolism within the framework of an intimate host-pathogen coevolution. Focusing on recent advances in our understanding of mycobacterial metabolic function, we highlight unusual adaptations or departures from the better-characterized model intracellular pathogens. We also discuss the impact of these mycobacterial "innovations" on the susceptibility of M. tuberculosis to existing and experimental anti-TB drugs, as well as strategies for targeting metabolic pathways. Finally, we offer some perspectives on the key gaps in the current knowledge of fundamental mycobacterial metabolism and the lessons which might be learned from other systems.
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Affiliation(s)
- Gabriel T Mashabela
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DST/NRF Centre of Excellence for Biomedical TB Research, Department of Pathology and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa
- Current address: Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, University of Stellenbosch, South Africa
| | - Timothy J de Wet
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DST/NRF Centre of Excellence for Biomedical TB Research, Department of Pathology and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa
- Department of Integrative Biomedical Sciences, University of Cape Town, South Africa
| | - Digby F Warner
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DST/NRF Centre of Excellence for Biomedical TB Research, Department of Pathology and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa
- Wellcome Centre for Infectious Disease Research in Africa, University of Cape Town, South Africa
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78
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Shockey AC, Dabney J, Pepperell CS. Effects of Host, Sample, and in vitro Culture on Genomic Diversity of Pathogenic Mycobacteria. Front Genet 2019; 10:477. [PMID: 31214242 PMCID: PMC6558051 DOI: 10.3389/fgene.2019.00477] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Accepted: 05/03/2019] [Indexed: 12/16/2022] Open
Abstract
Mycobacterium tuberculosis (M. tb), an obligate human pathogen and the etiological agent of tuberculosis (TB), remains a major threat to global public health. Comparative genomics has been invaluable for monitoring the emergence and spread of TB and for gaining insight into adaptation of M. tb. Most genomic studies of M. tb are based on single bacterial isolates that have been cultured for several weeks in vitro. However, in its natural human host, M. tb comprises complex, in some cases massive bacterial populations that diversify over the course of infection and cannot be wholly represented by a single genome. Recently, enrichment via hybridization capture has been used as a rapid diagnostic tool for TB, circumventing culturing protocols and enabling the recovery of M. tb genomes directly from sputum. This method has further applicability to the study of M. tb adaptation, as it enables a higher resolution and more direct analysis of M. tb genetic diversity within hosts with TB. Here we analyzed genomic material from M. tb and Mycobacterium bovis populations captured directly from sputum and from cultured samples using metagenomic and Pool-Seq approaches. We identified effects of sampling, patient, and sample type on bacterial genetic diversity. Bacterial genetic diversity was more variable and on average higher in sputum than in culture samples, suggesting that manipulation in the laboratory reshapes the bacterial population. Using outlier analyses, we identified candidate bacterial genetic loci mediating adaptation to these distinct environments. The study of M. tb in its natural human host is a powerful tool for illuminating host pathogen interactions and understanding the bacterial genetic underpinnings of virulence.
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Affiliation(s)
- Abigail C. Shockey
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Jesse Dabney
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Caitlin S. Pepperell
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
- Department of Medicine, Division of Infectious Diseases, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
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79
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Darrah PA, DiFazio RM, Maiello P, Gideon HP, Myers AJ, Rodgers MA, Hackney JA, Lindenstrom T, Evans T, Scanga CA, Prikhodko V, Andersen P, Lin PL, Laddy D, Roederer M, Seder RA, Flynn JL. Boosting BCG with proteins or rAd5 does not enhance protection against tuberculosis in rhesus macaques. NPJ Vaccines 2019; 4:21. [PMID: 31149352 PMCID: PMC6538611 DOI: 10.1038/s41541-019-0113-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 05/03/2019] [Indexed: 12/31/2022] Open
Abstract
Tuberculosis (TB) is the leading cause of death from infection worldwide. The only approved vaccine, BCG, has variable protective efficacy against pulmonary TB, the transmissible form of the disease. Therefore, improving this efficacy is an urgent priority. This study assessed whether heterologous prime-boost vaccine regimens in which BCG priming is boosted with either (i) protein and adjuvant (M72 plus AS01E or H56 plus CAF01) delivered intramuscularly (IM), or (ii) replication-defective recombinant adenovirus serotype 5 (Ad5) expressing various Mycobacterium tuberculosis (Mtb) antigens (Ad5(TB): M72, ESAT-6/Ag85b, or ESAT-6/Rv1733/Rv2626/RpfD) administered simultaneously by IM and aerosol (AE) routes, could enhance blood- and lung-localized T-cell immunity and improve protection in a nonhuman primate (NHP) model of TB infection. Ad5(TB) vaccines administered by AE/IM routes following BCG priming elicited ~10-30% antigen-specific CD4 and CD8 T-cell multifunctional cytokine responses in bronchoalveolar lavage (BAL) but did not provide additional protection compared to BCG alone. Moreover, AE administration of an Ad5(empty) control vector after BCG priming appeared to diminish protection induced by BCG. Boosting BCG by IM immunization of M72/AS01E or H56:CAF01 elicited ~0.1-0.3% antigen-specific CD4 cytokine responses in blood with only a transient increase of ~0.5-1% in BAL; these vaccine regimens also failed to enhance BCG-induced protection. Taken together, this study shows that boosting BCG with protein/adjuvant or Ad-based vaccines using these antigens, by IM or IM/AE routes, respectively, do not enhance protection against primary infection compared with BCG alone, in the highly susceptible rhesus macaque model of tuberculosis.
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Affiliation(s)
- Patricia A Darrah
- 1Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD USA
| | - Robert M DiFazio
- 2Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Pauline Maiello
- 2Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Hannah P Gideon
- 2Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Amy J Myers
- 2Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Mark A Rodgers
- 2Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Joshua A Hackney
- 1Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD USA
| | - Thomas Lindenstrom
- 3Center for Vaccine Research, Statens Serum Institut, Copenhagen, Denmark
| | | | - Charles A Scanga
- 2Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | | | - Peter Andersen
- 3Center for Vaccine Research, Statens Serum Institut, Copenhagen, Denmark
| | - Philana Ling Lin
- 5Department of Pediatrics, Children's Hospital of the University of Pittsburgh of UPMC, Pittsburgh, PA USA
| | | | - Mario Roederer
- 1Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD USA
| | - Robert A Seder
- 1Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD USA
| | - JoAnne L Flynn
- 2Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
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80
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Barcoded Consortium Infections Resolve Cell Type-Dependent Salmonella enterica Serovar Typhimurium Entry Mechanisms. mBio 2019; 10:mBio.00603-19. [PMID: 31113898 PMCID: PMC6529635 DOI: 10.1128/mbio.00603-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Salmonella enterica serovar Typhimurium (S.Tm) is a widespread and broad-host-spectrum enteropathogen with the capacity to invade diverse cell types. Still, the molecular basis for the host cell invasion process has largely been inferred from studies of a few selected cell lines. Our work resolves the mechanisms that Salmonellae employ to invade prototypical host cell types, i.e., human epithelial, monocyte, and macrophage cells, at a previously unattainable level of temporal and quantitative precision. This highlights efficient bacterium-driven entry into innate immune cells and uncovers a type III secretion system effector module that dominates active bacterial invasion of not only epithelial cells but also monocytes and macrophages. The results are derived from a generalizable method, where we combine barcoding of the bacterial chromosome with mixed consortium infections of cultured host cells. The application of this methodology across bacterial species and infection models will provide a scalable means to address host-pathogen interactions in diverse contexts. Bacterial host cell invasion mechanisms depend on the bacterium’s virulence factors and the properties of the target cell. The enteropathogen Salmonella enterica serovar Typhimurium (S.Tm) invades epithelial cell types in the gut mucosa and a variety of immune cell types at later infection stages. The molecular mechanism(s) of host cell entry has, however, been studied predominantly in epithelial cell lines. S.Tm uses a type three secretion system (TTSS-1) to translocate effectors into the host cell cytosol, thereby sparking actin ruffle-dependent entry. The ruffles also fuel cooperative invasion by bystander bacteria. In addition, several TTSS-1-independent entry mechanisms exist, involving alternative S.Tm virulence factors, or the passive uptake of bacteria by phagocytosis. However, it remains ill-defined how S.Tm invasion mechanisms vary between host cells. Here, we developed an internally controlled and scalable method to map S.Tm invasion mechanisms across host cell types and conditions. The method relies on host cell infections with consortia of chromosomally tagged wild-type and mutant S.Tm strains, where the abundance of each strain can be quantified by qPCR or amplicon sequencing. Using this methodology, we quantified cooccurring TTSS-1-dependent, cooperative, and TTSS-1-independent invasion events in epithelial, monocyte, and macrophage cells. We found S.Tm invasion of epithelial cells and monocytes to proceed by a similar MOI-dependent mix of TTSS-1-dependent and cooperative mechanisms. TTSS-1-independent entry was more frequent in macrophages. Still, TTSS-1-dependent invasion dominated during the first minutes of interaction also with this cell type. Finally, the combined action of the SopB/SopE/SopE2 effectors was sufficient to explain TTSS-1-dependent invasion across both epithelial and phagocytic cells.
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81
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Binan L, Drobetsky EA, Costantino S. Exploiting Molecular Barcodes in High-Throughput Cellular Assays. SLAS Technol 2019; 24:298-307. [PMID: 30707854 DOI: 10.1177/2472630318824337] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Multiplexing strategies, which greatly increase the number of simultaneously measured parameters in single experiments, are now being widely implemented by both the pharmaceutical industry and academic researchers. Color has long been used to identify biological signals and, when combined with molecular barcodes, has substantially enhanced the depth of multiplexed sample characterization. Moreover, the recent advent of DNA barcodes has led to an explosion of innovative cell sequencing approaches. Novel barcoding strategies also show great promise for encoding spatial information in transcriptomic studies, and for precise assessment of molecular abundance. Both color- and DNA-based barcodes can be conveniently analyzed with either a microscope or a cytometer, or via DNA sequencing. Here we review the basic principles of several technologies used to create barcodes and detail the type of samples that can be identified with such tags.
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Affiliation(s)
- Loïc Binan
- 1 Research Center of the Maisonneuve-Rosemont Hospital, Montreal, QC, Canada.,2 Department of Ophthalmology, Université de Montréal, Montreal, QC, Canada
| | - Elliot A Drobetsky
- 1 Research Center of the Maisonneuve-Rosemont Hospital, Montreal, QC, Canada.,3 Department of Medicine & Molecular Biology Program, University of Montreal, Montreal, QC, Canada
| | - Santiago Costantino
- 1 Research Center of the Maisonneuve-Rosemont Hospital, Montreal, QC, Canada.,2 Department of Ophthalmology, Université de Montréal, Montreal, QC, Canada
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82
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An explant technique for high-resolution imaging and manipulation of mycobacterial granulomas. Nat Methods 2018; 15:1098-1107. [PMID: 30504889 PMCID: PMC6312189 DOI: 10.1038/s41592-018-0215-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 10/10/2018] [Indexed: 12/31/2022]
Abstract
A central and critical structure in tuberculosis, the mycobacterial granuloma consists of highly organized immune cells, including macrophages that drive granuloma formation through a characteristic epithelioid transformation. Difficulties in imaging within intact animals as well as the inherent caveats of in vitro assembly models have severely limited the study and experimental manipulation of mature granulomas. Here we describe a new ex vivo granuloma culture technique, wherein mature, fully organized granulomas are microdissected and maintained in three-dimensional culture. This approach, in which granulomas retain key bacterial and host characteristics, enables high-resolution microscopy of granuloma macrophage dynamics, including epithelioid macrophage motility and granuloma consolidation. Through mass spectrometry, we find active production of key phosphotidylinositol species identified previously in human granulomas. We describe a method to transfect isolated granulomas, enabling genetic manipulation. In addition, we provide proof-of-concept for host-directed small molecule screens, identifying PKC signaling as an important regulator of granuloma macrophage organization.
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83
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Preexisting Simian Immunodeficiency Virus Infection Increases Susceptibility to Tuberculosis in Mauritian Cynomolgus Macaques. Infect Immun 2018; 86:IAI.00565-18. [PMID: 30224552 DOI: 10.1128/iai.00565-18] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 09/10/2018] [Indexed: 01/01/2023] Open
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis, is the leading cause of death among human immunodeficiency virus (HIV)-positive patients. The precise mechanisms by which HIV impairs host resistance to a subsequent M. tuberculosis infection are unknown. We modeled this coinfection in Mauritian cynomolgus macaques (MCM) using simian immunodeficiency virus (SIV) as an HIV surrogate. We infected seven MCM with SIVmac239 intrarectally and 6 months later coinfected them via bronchoscope with ∼10 CFU of M. tuberculosis Another eight MCM were infected with M. tuberculosis alone. TB progression was monitored by clinical parameters, by culturing bacilli in gastric and bronchoalveolar lavages, and by serial [18F]fluorodeoxyglucose (FDG) positron emission tomography/computed tomography (PET/CT) imaging. The eight MCM infected with M. tuberculosis alone displayed dichotomous susceptibility to TB, with four animals reaching humane endpoint within 13 weeks and four animals surviving >19 weeks after M. tuberculosis infection. In stark contrast, all seven SIV+ animals exhibited rapidly progressive TB following coinfection and all reached humane endpoint by 13 weeks. Serial PET/CT imaging confirmed dichotomous outcomes in MCM infected with M. tuberculosis alone and marked susceptibility to TB in all SIV+ MCM. Notably, imaging revealed a significant increase in TB granulomas between 4 and 8 weeks after M. tuberculosis infection in SIV+ but not in SIV-naive MCM and implies that SIV impairs the ability of animals to contain M. tuberculosis dissemination. At necropsy, animals with preexisting SIV infection had more overall pathology, increased bacterial loads, and a trend towards more extrapulmonary disease than animals infected with M. tuberculosis alone. We thus developed a tractable MCM model in which to study SIV-M. tuberculosis coinfection and demonstrate that preexisting SIV dramatically diminishes the ability to control M. tuberculosis coinfection.
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84
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Ganchua SKC, Cadena AM, Maiello P, Gideon HP, Myers AJ, Junecko BF, Klein EC, Lin PL, Mattila JT, Flynn JL. Lymph nodes are sites of prolonged bacterial persistence during Mycobacterium tuberculosis infection in macaques. PLoS Pathog 2018; 14:e1007337. [PMID: 30383808 PMCID: PMC6211753 DOI: 10.1371/journal.ppat.1007337] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 09/13/2018] [Indexed: 02/07/2023] Open
Abstract
Tuberculosis is commonly considered a chronic lung disease, however, extrapulmonary infection can occur in any organ. Even though lymph nodes (LN) are among the most common sites of extrapulmonary Mycobacterium tuberculosis (Mtb) infection, and thoracic LNs are frequently infected in humans, bacterial dynamics and the effect of Mtb infection in LN structure and function is relatively unstudied. We surveyed thoracic LNs from Mtb-infected cynomolgus and rhesus macaques analyzing PET CT scans, bacterial burden, LN structure and immune function. FDG avidity correlated with the presence of live bacteria in LNs at necropsy. Lymph nodes have different trajectories (increasing, maintaining, decreasing in PET activity over time) even within the same animal. Rhesus macaques are more susceptible to Mtb infection than cynomolgus macaques and this is in part due to more extensive LN pathology. Here, we show that Mtb grows to the same level in cynomolgus and rhesus macaque LNs, however, cynomolgus macaques control Mtb at later time points post-infection while rhesus macaques do not. Notably, compared to lung granulomas, LNs are generally poor at killing Mtb, even with drug treatment. Granulomas that form in LNs lack B cell-rich tertiary lymphoid structures, disrupt LN structure by pushing out T cells and B cells, introduce large numbers of macrophages that can serve as niches for Mtb, and destroy normal vasculature. Our data support that LNs are not only sites of antigen presentation and immune activation during infection, but also serve as important sites for persistence of significant numbers of Mtb bacilli. Since tuberculosis is commonly considered a chronic lung disease, most studies in tuberculosis focus on the lungs while lymph nodes are almost always depicted only as sites of antigen presentation and immune activation. However, lymph nodes are among the most frequently infected sites of Mycobacterium tuberculosis (Mtb) aside from the lungs. The effect of Mtb infection and how lymph nodes respond to Mtb infection is currently unknown. To investigate this, we examined the lymph nodes of two macaque species, cynomolgus and rhesus macaques, at different time points after Mtb infection. We found that overall lymph nodes are not effective killers of Mtb; the lymph nodes of rhesus macaques being less effective at killing Mtb than cynomolgus macaques. Mtb infection also resulted in the destruction of the lymph node structure and this was associated with increased bacterial burden. After a short course of anti-TB drug therapy, the reduction in bacterial burden was lower in lymph nodes compared to lung granulomas. Our data show that aside from being sites of antigen presentation and immune activation, lymph nodes are also niches of Mtb growth and persistence.
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Affiliation(s)
- Sharie Keanne C. Ganchua
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Anthony M. Cadena
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Pauline Maiello
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Hannah P. Gideon
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Amy J. Myers
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Beth F. Junecko
- Department of Infectious Disease and Microbiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania, United States of America
| | - Edwin C. Klein
- Division of Laboratory Animal Resources, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Philana Ling Lin
- Department of Pediatrics, Children’s Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States of America
| | - Joshua T. Mattila
- Department of Infectious Disease and Microbiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania, United States of America
| | - JoAnne L. Flynn
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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85
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Abstract
Tuberculosis kills more people worldwide than any other single infectious disease agent, a threat made more dire by the spread of drug-resistant strains of Mycobacterium tuberculosis (Mtb). Development of new vaccines capable of preventing TB disease and new Mtb infection are an essential component of the strategy to combat the TB epidemic. Accordingly, the WHO considers the development of new TB vaccines a major public health priority. In October 2017, the WHO convened a consultation with global leaders in the TB vaccine development field to emphasize the WHO commitment to this effort and to facilitate creative approaches to the discovery and development of TB vaccine candidates. This review summarizes the presentations at this consultation, updated with scientific literature references, and includes discussions of the public health need for a TB vaccine; the status of efforts to develop vaccines to replace or potentiate BCG in infants and develop new TB vaccines for adolescents and adults; strategies being employed to diversify vaccine platforms; and new animal models being developed to facilitate TB vaccine development. A perspective on the status of these efforts from the major funders and organizational contributors also is included. This presentation highlights the extraordinary progress being made to develop new TB vaccines and provided a clear picture of the exciting development pathways that are being explored.
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Affiliation(s)
| | | | - Johan Vekemans
- Initiative for Vaccine Research, World Health Organization, Geneva, Switzerland
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86
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Abstract
Tuberculosis kills more people worldwide than any other single infectious disease agent, a threat made more dire by the spread of drug-resistant strains of Mycobacterium tuberculosis (Mtb). Development of new vaccines capable of preventing TB disease and new Mtb infection are an essential component of the strategy to combat the TB epidemic. Accordingly, the WHO considers the development of new TB vaccines a major public health priority. In October 2017, the WHO convened a consultation with global leaders in the TB vaccine development field to emphasize the WHO commitment to this effort and to facilitate creative approaches to the discovery and development of TB vaccine candidates. This review summarizes the presentations at this consultation, updated with scientific literature references, and includes discussions of the public health need for a TB vaccine; the status of efforts to develop vaccines to replace or potentiate BCG in infants and develop new TB vaccines for adolescents and adults; strategies being employed to diversify vaccine platforms; and new animal models being developed to facilitate TB vaccine development. A perspective on the status of these efforts from the major funders and organizational contributors also is included. This presentation highlights the extraordinary progress being made to develop new TB vaccines and provided a clear picture of the exciting development pathways that are being explored.
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Affiliation(s)
| | | | - Johan Vekemans
- Initiative for Vaccine Research, World Health Organization, Geneva, Switzerland
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87
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Cadena AM, Ma Y, Ding T, Bryant M, Maiello P, Geber A, Lin PL, Flynn JL, Ghedin E. Profiling the airway in the macaque model of tuberculosis reveals variable microbial dysbiosis and alteration of community structure. MICROBIOME 2018; 6:180. [PMID: 30301469 PMCID: PMC6178261 DOI: 10.1186/s40168-018-0560-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 09/20/2018] [Indexed: 05/04/2023]
Abstract
BACKGROUND The specific interactions of Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), and the lung microbiota in infection are entirely unexplored. Studies in cancer and other infectious diseases suggest that there are important exchanges occurring between host and microbiota that influence the immunological landscape. This can result in alterations in immune regulation and inflammation both locally and systemically. To assess whether Mtb infection modifies the lung microbiome, and identify changes in microbial abundance and diversity as a function of pulmonary inflammation, we compared infected and uninfected lung lobe washes collected serially from 26 macaques by bronchoalveolar lavage over the course of infection. RESULTS We found that Mtb induced an initial increase in lung microbial diversity at 1 month post infection that normalized by 5 months of infection across all macaques. Several core genera showed global shifts from baseline and throughout infection. Moreover, we identified several specific taxa normally associated with the oral microbiome that increased in relative abundance in the lung following Mtb infection, including SR1, Aggregatibacter, Leptotrichia, Prevotella, and Campylobacter. On an individual macaque level, we found significant heterogeneity in both the magnitude and duration of change within the lung microbial community that was unrelated to lung inflammation and lobe involvement as seen by positron emission tomography/computed tomography (PET/CT) imaging. By comparing microbial interaction networks pre- and post-infection using the predictive algorithm SPIEC-EASI, we observe that extra connections are gained by Actinomycetales, the order containing Mtb, in spite of an overall reduction in the number of interactions of the whole community post-infection, implicating Mtb-driven ecological reorganization within the lung. CONCLUSIONS This study is the first to probe the dynamic interplay between Mtb and host microbiota longitudinally and in the macaque lung. Our findings suggest that Mtb can alter the microbial landscape of infected lung lobes and that these interactions induce dysbiosis that can disrupt oral-airway boundaries, shift overall lung diversity, and modulate specific microbial relationships. We also provide evidence that this effect is heterogeneous across different macaques. Overall, however, the changes to the airway microbiota after Mtb infection were surprisingly modest, despite a range of Mtb-induced pulmonary inflammation in this cohort of macaques.
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Affiliation(s)
- Anthony M Cadena
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Present address: Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Yixuan Ma
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, USA
| | - Tao Ding
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, USA
| | - MacKenzie Bryant
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Present address: Department of Pediatrics, University of California, San Diego School of Medicine, La Jolla, California, USA
| | - Pauline Maiello
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Adam Geber
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, USA
| | - Philana Ling Lin
- Department of Pediatrics, Children's Hospital of Pittsburgh of University of Pittsburgh Medical Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - JoAnne L Flynn
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
| | - Elodie Ghedin
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, USA.
- College of Global Public Health, New York University, New York, NY, USA.
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88
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Cadena AM, Hopkins FF, Maiello P, Carey AF, Wong EA, Martin CJ, Gideon HP, DiFazio RM, Andersen P, Lin PL, Fortune SM, Flynn JL. Concurrent infection with Mycobacterium tuberculosis confers robust protection against secondary infection in macaques. PLoS Pathog 2018; 14:e1007305. [PMID: 30312351 PMCID: PMC6200282 DOI: 10.1371/journal.ppat.1007305] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 10/24/2018] [Accepted: 09/13/2018] [Indexed: 02/03/2023] Open
Abstract
For many pathogens, including most targets of effective vaccines, infection elicits an immune response that confers significant protection against reinfection. There has been significant debate as to whether natural Mycobacterium tuberculosis (Mtb) infection confers protection against reinfection. Here we experimentally assessed the protection conferred by concurrent Mtb infection in macaques, a robust experimental model of human tuberculosis (TB), using a combination of serial imaging and Mtb challenge strains differentiated by DNA identifiers. Strikingly, ongoing Mtb infection provided complete protection against establishment of secondary infection in over half of the macaques and allowed near sterilizing bacterial control for those in which a secondary infection was established. By contrast, boosted BCG vaccination reduced granuloma inflammation but had no impact on early granuloma bacterial burden. These findings are evidence of highly effective concomitant mycobacterial immunity in the lung, which may inform TB vaccine design and development.
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Affiliation(s)
- Anthony M. Cadena
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Forrest F. Hopkins
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Pauline Maiello
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Allison F. Carey
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Eileen A. Wong
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Constance J. Martin
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Hannah P. Gideon
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Robert M. DiFazio
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | | | - Philana Ling Lin
- Department of Pediatrics, Children’s Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States of America
| | - Sarah M. Fortune
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, United States of America
| | - JoAnne L. Flynn
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
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89
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Koch A, Cox H, Mizrahi V. Drug-resistant tuberculosis: challenges and opportunities for diagnosis and treatment. Curr Opin Pharmacol 2018; 42:7-15. [PMID: 29885623 PMCID: PMC6219890 DOI: 10.1016/j.coph.2018.05.013] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Revised: 05/11/2018] [Accepted: 05/21/2018] [Indexed: 01/01/2023]
Abstract
With an estimated incidence of 490000 cases in 2016, multidrug resistant tuberculosis (TB), against which key first-line anti-tuberculars are less efficacious, presents major challenges for global health. Poor treatment outcomes coupled with a yawning treatment gap between those in need of second-line therapy and those who receive it, underscore the urgent need for new approaches to tackle the scourge of drug-resistant TB. Against this background, significant progress has been made in understanding the complex biology of TB drug resistance and disease pathogenesis, and in establishing a pipeline for delivering new drugs and drug combinations. In this review, we highlight the challenges of drug-resistant TB and the ways in which new advances could be harnessed to improve treatment outcomes.
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Affiliation(s)
- Anastasia Koch
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DST/NRF Centre of Excellence for Biomedical TB Research and Wellcome Centre for Clinical Infectious Diseases Research in Africa, University of Cape Town, South Africa; Institute of Infectious Disease and Molecular Medicine and Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Helen Cox
- Institute of Infectious Disease and Molecular Medicine and Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Valerie Mizrahi
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DST/NRF Centre of Excellence for Biomedical TB Research and Wellcome Centre for Clinical Infectious Diseases Research in Africa, University of Cape Town, South Africa; Institute of Infectious Disease and Molecular Medicine and Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, South Africa.
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90
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Olive AJ, Sassetti CM. Tolerating the Unwelcome Guest; How the Host Withstands Persistent Mycobacterium tuberculosis. Front Immunol 2018; 9:2094. [PMID: 30258448 PMCID: PMC6143787 DOI: 10.3389/fimmu.2018.02094] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 08/24/2018] [Indexed: 12/20/2022] Open
Abstract
Our understanding of the host response to infections has historically focused on “resistance” mechanisms that directly control pathogen replication. However, both pathogen effectors and antimicrobial immune pathways have the capacity to damage host tissue, and the ability to tolerate these insults can also be critical for host survival. These “tolerance” mechanisms may be equally as important as resistance to prevent disease in the context of a persistent infection, such as tuberculosis, when resistance mechanisms are ineffective and the pathogen persists in the tissue for long periods. Host tolerance encompasses a wide range of strategies, many of which involve regulation of the inflammatory response. Here we will examine general strategies used by macrophages and T cells to promote tolerance in the context of tuberculosis, and focus on pathways, such as regulation of inflammasome activation, that are emerging as common mediators of tolerance.
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Affiliation(s)
- Andrew J Olive
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
| | - Christopher M Sassetti
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, United States
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91
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Tanner L, Denti P, Wiesner L, Warner DF. Drug permeation and metabolism in Mycobacterium tuberculosis: Prioritising local exposure as essential criterion in new TB drug development. IUBMB Life 2018; 70:926-937. [PMID: 29934964 PMCID: PMC6129860 DOI: 10.1002/iub.1866] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 04/11/2018] [Accepted: 04/11/2018] [Indexed: 12/22/2022]
Abstract
Anti-tuberculosis (TB) drugs possess diverse abilities to penetrate the different host tissues and cell types in which infecting Mycobacterium tuberculosis bacilli are located during active disease. This is important since there is increasing evidence that the respective "lesion-penetrating" properties of the front-line TB drugs appear to correlate well with their specific activity in standard combination therapy. In turn, these observations suggest that rational efforts to discover novel treatment-shortening drugs and drug combinations should incorporate knowledge about the comparative abilities of both existing and experimental anti-TB agents to access bacilli in defined physiological states at different sites of infection, as well as avoid elimination by efflux or inactivation by host or bacterial metabolism. However, while there is a fundamental requirement to understand the mode of action and pharmacological properties of any current or experimental anti-TB agent within the context of the obligate human host, this is complex and, until recently, has been severely limited by the available methodologies and models. Here, we discuss advances in analytical models and technologies which have enabled investigations of drug metabolism and pharmacokinetics (DMPK) for new TB drug development. In particular, we consider the potential to shift the focus of traditional pharmacokinetic-pharmacodynamic analyses away from plasma to a more specific "site of action" drug exposure as an essential criterion for drug development and the design of dosing strategies. Moreover, in summarising approaches to determine DMPK data for the "unit of infection" comprising host macrophage and intracellular bacillus, we evaluate the potential benefits of including these analyses at an early stage in the preclinical drug development algorithm. © 2018 IUBMB Life, 70(9):926-937, 2018.
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Affiliation(s)
- Lloyd Tanner
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, Department of Pathology and Institute of Infectious Disease & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory, South Africa
- Division of Clinical Pharmacology, Department of Medicine, Faculty of Health Sciences, University of Cape Town, Observatory, South Africa
| | - Paolo Denti
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, Department of Pathology and Institute of Infectious Disease & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory, South Africa
| | - Lubbe Wiesner
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, Department of Pathology and Institute of Infectious Disease & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory, South Africa
| | - Digby F. Warner
- Division of Clinical Pharmacology, Department of Medicine, Faculty of Health Sciences, University of Cape Town, Observatory, South Africa
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92
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Cicchese JM, Evans S, Hult C, Joslyn LR, Wessler T, Millar JA, Marino S, Cilfone NA, Mattila JT, Linderman JJ, Kirschner DE. Dynamic balance of pro- and anti-inflammatory signals controls disease and limits pathology. Immunol Rev 2018; 285:147-167. [PMID: 30129209 PMCID: PMC6292442 DOI: 10.1111/imr.12671] [Citation(s) in RCA: 145] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Immune responses to pathogens are complex and not well understood in many diseases, and this is especially true for infections by persistent pathogens. One mechanism that allows for long-term control of infection while also preventing an over-zealous inflammatory response from causing extensive tissue damage is for the immune system to balance pro- and anti-inflammatory cells and signals. This balance is dynamic and the immune system responds to cues from both host and pathogen, maintaining a steady state across multiple scales through continuous feedback. Identifying the signals, cells, cytokines, and other immune response factors that mediate this balance over time has been difficult using traditional research strategies. Computational modeling studies based on data from traditional systems can identify how this balance contributes to immunity. Here we provide evidence from both experimental and mathematical/computational studies to support the concept of a dynamic balance operating during persistent and other infection scenarios. We focus mainly on tuberculosis, currently the leading cause of death due to infectious disease in the world, and also provide evidence for other infections. A better understanding of the dynamically balanced immune response can help shape treatment strategies that utilize both drugs and host-directed therapies.
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Affiliation(s)
- Joseph M. Cicchese
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Stephanie Evans
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Caitlin Hult
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Louis R. Joslyn
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Timothy Wessler
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Jess A. Millar
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Simeone Marino
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Nicholas A. Cilfone
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Joshua T. Mattila
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Denise E. Kirschner
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
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93
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Gregg RW, Maiello P, Borish HJ, Coleman MT, Reed DS, White AG, Flynn JL, Lin PL. Spatial and temporal evolution of lung granulomas in a cynomolgus macaque model of Mycobacterium tuberculosis infection. RADIOLOGY OF INFECTIOUS DISEASES (BEIJING, CHINA) 2018; 5:110-117. [PMID: 35128020 DOI: 10.1016/j.jrid.2018.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
BACKGROUND Little is known about granuloma progression of Mycobacterium tuberculosis infection in humans. Using serial positron emission tomography and computed tomography (PET/CT) of an animal model that recapitulates human infection with M. tuberculosis, we are able to track lung granulomas. OBJECTIVE We characterized the spatial and temporal pattern of granuloma formation during primary infection and reactivation. METHODS Serial PET/CT was performed on cynomolgus macaques (n = 28) during primary and reactivation M. tuberculosis infection. Distances between granulomas during the first six weeks post infection ("primary" granulomas) were compared to new granulomas that developed afterwards ("secondary" granulomas) using nearest neighbor analysis during primary infection, reactivation and between different routes of infection. RESULTS Secondary granulomas developed within 2 cm of a primary granuloma within the same lung lobe with 80% probability during the course of primary infection, and this same pattern was observed during reactivation of latent infection after immune suppression. Using a logistic growth function, we were able to predict the maximum number of granulomas that would develop over the course of infection with good correlation (R2 = 0.96). CONCLUSION These data provide important insights into the dynamic patterns of bacterial dissemination during the earliest phases of primary infection and reactivation tuberculosis.
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Affiliation(s)
- Robert W Gregg
- Department of Chemical Engineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Pauline Maiello
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - H Jacob Borish
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - M Teresa Coleman
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Douglas S Reed
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA, USA
| | - Alexander G White
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - JoAnne L Flynn
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Philana Ling Lin
- Department of Pediatrics, Children's Hospital of Pittsburgh of University of Pittsburgh Medical Center, Pittsburgh, PA, USA
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94
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Hicks ND, Yang J, Zhang X, Zhao B, Grad YH, Liu L, Ou X, Chang Z, Xia H, Zhou Y, Wang S, Dong J, Sun L, Zhu Y, Zhao Y, Jin Q, Fortune SM. Clinically prevalent mutations in Mycobacterium tuberculosis alter propionate metabolism and mediate multidrug tolerance. Nat Microbiol 2018; 3:1032-1042. [PMID: 30082724 PMCID: PMC6233875 DOI: 10.1038/s41564-018-0218-3] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 07/09/2018] [Indexed: 01/09/2023]
Abstract
The global epidemic of drug-resistant tuberculosis is a catastrophic example of how antimicrobial resistance is undermining the public health gains made possible by combination drug therapy. Recent evidence points to unappreciated bacterial factors that accelerate the emergence of drug resistance. In a genome-wide association study of Mycobacterium tuberculosis isolates from China, we find mutations in the gene encoding the transcription factor prpR enriched in drug-resistant strains. prpR mutations confer conditional drug tolerance to three of the most effective classes of antibiotics by altering propionyl-CoA metabolism. prpR-mediated drug tolerance is carbon-source dependent, and while readily detectable during infection of human macrophages, is not captured by standard susceptibility testing. These data define a previously unrecognized and clinically prevalent class of M. tuberculosis variants that undermine antibiotic efficacy and drive drug resistance.
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Affiliation(s)
- Nathan D Hicks
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jian Yang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Centre for Tuberculosis, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaobing Zhang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Centre for Tuberculosis, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Bing Zhao
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yonatan H Grad
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Liguo Liu
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Centre for Tuberculosis, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xichao Ou
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zhili Chang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Centre for Tuberculosis, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hui Xia
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yang Zhou
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Shengfen Wang
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jie Dong
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Centre for Tuberculosis, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lilian Sun
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Centre for Tuberculosis, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yafang Zhu
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Centre for Tuberculosis, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yanlin Zhao
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
| | - Qi Jin
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Centre for Tuberculosis, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Sarah M Fortune
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA.
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95
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Cohen SB, Gern BH, Delahaye JL, Adams KN, Plumlee CR, Winkler JK, Sherman DR, Gerner MY, Urdahl KB. Alveolar Macrophages Provide an Early Mycobacterium tuberculosis Niche and Initiate Dissemination. Cell Host Microbe 2018; 24:439-446.e4. [PMID: 30146391 DOI: 10.1016/j.chom.2018.08.001] [Citation(s) in RCA: 299] [Impact Index Per Article: 49.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 05/03/2018] [Accepted: 07/18/2018] [Indexed: 01/15/2023]
Abstract
Mycobacterium tuberculosis (Mtb) infection is initiated in the distal airways, but the bacteria ultimately disseminate to the lung interstitium. Although various cell types, including alveolar macrophages (AM), neutrophils, and permissive monocytes, are known to be infected with Mtb, the initially infected cells as well as those that mediate dissemination from the alveoli to the lung interstitium are unknown. In this study, using a murine infection model, we reveal that early, productive Mtb infection occurs almost exclusively within airway-resident AM. Thereafter Mtb-infected, but not uninfected, AM localize to the lung interstitium through mechanisms requiring an intact Mtb ESX-1 secretion system. Relocalization of infected AM precedes Mtb uptake by recruited monocyte-derived macrophages and neutrophils. This dissemination process is driven by non-hematopoietic host MyD88/interleukin-1 receptor inflammasome signaling. Thus, interleukin-1-mediated crosstalk between Mtb-infected AM and non-hematopoietic cells promotes pulmonary Mtb infection by enabling infected cells to disseminate from the alveoli to the lung interstitium.
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Affiliation(s)
- Sara B Cohen
- Center for Infectious Disease Research, 307 Westlake Avenue North, Suite #500, Seattle, WA 98109, USA
| | - Benjamin H Gern
- Center for Infectious Disease Research, 307 Westlake Avenue North, Suite #500, Seattle, WA 98109, USA; Department of Pediatrics, Division of Infectious Diseases, University of Washington School of Medicine and Seattle Children's Hospital, Seattle, WA 98195, USA
| | - Jared L Delahaye
- Center for Infectious Disease Research, 307 Westlake Avenue North, Suite #500, Seattle, WA 98109, USA; Department of Immunology, University of Washington School of Medicine, Seattle, WA 98109, USA
| | - Kristin N Adams
- Center for Infectious Disease Research, 307 Westlake Avenue North, Suite #500, Seattle, WA 98109, USA
| | - Courtney R Plumlee
- Center for Infectious Disease Research, 307 Westlake Avenue North, Suite #500, Seattle, WA 98109, USA
| | - Jessica K Winkler
- Center for Infectious Disease Research, 307 Westlake Avenue North, Suite #500, Seattle, WA 98109, USA
| | - David R Sherman
- Center for Infectious Disease Research, 307 Westlake Avenue North, Suite #500, Seattle, WA 98109, USA; Department of Global Health, University of Washington, Seattle, WA 98195, USA
| | - Michael Y Gerner
- Department of Immunology, University of Washington School of Medicine, Seattle, WA 98109, USA
| | - Kevin B Urdahl
- Center for Infectious Disease Research, 307 Westlake Avenue North, Suite #500, Seattle, WA 98109, USA; Department of Pediatrics, Division of Infectious Diseases, University of Washington School of Medicine and Seattle Children's Hospital, Seattle, WA 98195, USA; Department of Immunology, University of Washington School of Medicine, Seattle, WA 98109, USA.
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96
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Blanc L, Sarathy JP, Alvarez Cabrera N, O'Brien P, Dias-Freedman I, Mina M, Sacchettini J, Savic RM, Gengenbacher M, Podell BK, Prideaux B, Ioerger T, Dick T, Dartois V. Impact of immunopathology on the antituberculous activity of pyrazinamide. J Exp Med 2018; 215:1975-1986. [PMID: 30018074 PMCID: PMC6080910 DOI: 10.1084/jem.20180518] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 05/15/2018] [Accepted: 06/28/2018] [Indexed: 12/21/2022] Open
Abstract
In the 1970s, inclusion of pyrazinamide (PZA) in the drug regimen of tuberculosis (TB) patients for the first 2 mo achieved a drastic reduction of therapy duration. Until now, however, the mechanisms underlying PZA's unique contribution to efficacy have remained controversial, and animal efficacy data vary across species. To understand how PZA kills bacterial populations present in critical lung lesion compartments, we first characterized a rabbit model of active TB, showing striking similarities in lesion types and fates to nonhuman primate models deemed the most appropriate surrogates of human TB. We next employed this model with lesion-centric molecular and bacteriology readouts to demonstrate that PZA exhibits potent activity against Mycobacterium tuberculosis residing in difficult-to-sterilize necrotic lesions. Our data also indicate that PZA is slow acting, suggesting that PZA administration beyond the first 2 mo may accelerate the cure. In conclusion, we provide a pharmacodynamic explanation for PZA's treatment-shortening effect and deliver new tools to dissect the contribution of immune response versus drug at the lesion level.
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Affiliation(s)
- Landry Blanc
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ
| | - Jansy Passiflora Sarathy
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ
| | - Nadine Alvarez Cabrera
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ
| | - Paul O'Brien
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ
| | - Isabela Dias-Freedman
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ
| | - Marizel Mina
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ
| | - James Sacchettini
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX
| | - Radojka M Savic
- Department of Bioengineering and Therapeutic Sciences, Schools of Pharmacy and Medicine, University of California, San Francisco, San Francisco, CA
| | - Martin Gengenbacher
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ
| | - Brendan K Podell
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO
| | - Brendan Prideaux
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ
| | - Thomas Ioerger
- Department of Computer Science, Texas A&M University, College Station, TX
| | - Thomas Dick
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ
- Department of Medicine, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ
| | - Véronique Dartois
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ
- Department of Medicine, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ
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97
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Malherbe ST, Kleynhans L, Walzl G. The potential of imaging tools as correlates of infection and disease for new TB vaccine development. Semin Immunol 2018; 39:73-80. [PMID: 29914653 DOI: 10.1016/j.smim.2018.06.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Accepted: 06/07/2018] [Indexed: 12/17/2022]
Abstract
The development of an improved vaccine to stimulate an effective response against Mycobacterium tuberculosis (MTB) infection and disease will be a major breakthrough in the fight against TB. A lack of tools to adequately track the progression or resolution of events in TB pathogenesis that occur at bacterial loads below the threshold for culture in human samples seriously hampers vaccine development and evaluation. In this review we discuss recent studies that use new imaging applications, modalities and analysis techniques to provide insight into the dynamic processes of MTB infection and disease that are challenging to monitor. These include early infection, the spectrum of latency and subclinical disease, the paucibacillary state induced by treatment, and events leading to recurrence, including relapse.
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Affiliation(s)
- Stephanus T Malherbe
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Léanie Kleynhans
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Gerhard Walzl
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.
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98
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Qian X, Nguyen DT, Lyu J, Albers AE, Bi X, Graviss EA. Risk factors for extrapulmonary dissemination of tuberculosis and associated mortality during treatment for extrapulmonary tuberculosis. Emerg Microbes Infect 2018; 7:102. [PMID: 29872046 PMCID: PMC5988830 DOI: 10.1038/s41426-018-0106-1] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 04/15/2018] [Accepted: 04/29/2018] [Indexed: 01/28/2023]
Abstract
Many environmental, host, and microbial characteristics have been recognized as risk factors for dissemination of extrapulmonary tuberculosis (EPTB). However, there are few population-based studies investigating the association between the primary sites of tuberculosis (TB) infection and mortality during TB treatment. De-identified population-based surveillance data of confirmed TB patients reported from 2009 to 2015 in Texas, USA, were analyzed. Regression analyses were used to determine the risk factors for EPTB, as well as its subsite distribution and mortality. We analyzed 7007 patients with exclusively pulmonary TB, 1259 patients with exclusively EPTB, and 894 EPTB patients with reported concomitant pulmonary involvement. Age ≥45 years, female gender, human immunodeficiency virus (HIV)-positive status, and end-stage renal disease (ESRD) were associated with EPTB. ESRD was associated with the most clinical presentations of EPTB other than meningeal and genitourinary TB. Patients age ≥45 years had a disproportionately high rate of bone TB, while foreign-born patients had increased pleural TB and HIV+ patients had increased meningeal TB. Age ≥45 years, HIV+ status, excessive alcohol use within the past 12 months, ESRD, and abnormal chest radiographs were independent risk factors for EPTB mortality during TB treatment. The epidemiologic risk factors identified by multivariate analyses provide new information that may be useful to health professionals in managing patients with EPTB.
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Affiliation(s)
- Xu Qian
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical University, Wenzhou, P. R. China
- Center for Precision Biomedicine, Institute of Molecular Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
- People's Hospital of Hangzhou Medical College, Hangzhou, P. R. China
| | - Duc T Nguyen
- Houston Methodist Research Institute, Houston, TX, USA
| | - Jianxin Lyu
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical University, Wenzhou, P. R. China
- People's Hospital of Hangzhou Medical College, Hangzhou, P. R. China
| | - Andreas E Albers
- Department of Otorhinolaryngology, Head and Neck Surgery, Berlin Institute of Health, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Campus Benjamin Franklin, Berlin, Germany
| | - Xiaohong Bi
- Center for Precision Biomedicine, Institute of Molecular Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
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99
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Logsdon MM, Aldridge BB. Stable Regulation of Cell Cycle Events in Mycobacteria: Insights From Inherently Heterogeneous Bacterial Populations. Front Microbiol 2018; 9:514. [PMID: 29619019 PMCID: PMC5871693 DOI: 10.3389/fmicb.2018.00514] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 03/06/2018] [Indexed: 11/24/2022] Open
Abstract
Model bacteria, such as E. coli and B. subtilis, tightly regulate cell cycle progression to achieve consistent cell size distributions and replication dynamics. Many of the hallmark features of these model bacteria, including lateral cell wall elongation and symmetric growth and division, do not occur in mycobacteria. Instead, mycobacterial growth is characterized by asymmetric polar growth and division. This innate asymmetry creates unequal birth sizes and growth rates for daughter cells with each division, generating a phenotypically heterogeneous population. Although the asymmetric growth patterns of mycobacteria lead to a larger variation in birth size than typically seen in model bacterial populations, the cell size distribution is stable over time. Here, we review the cellular mechanisms of growth, division, and cell cycle progression in mycobacteria in the face of asymmetry and inherent heterogeneity. These processes coalesce to control cell size. Although Mycobacterium smegmatis and Mycobacterium bovis Bacillus Calmette-Guérin (BCG) utilize a novel model of cell size control, they are similar to previously studied bacteria in that initiation of DNA replication is a key checkpoint for cell division. We compare the regulation of DNA replication initiation and strategies used for cell size homeostasis in mycobacteria and model bacteria. Finally, we review the importance of cellular organization and chromosome segregation relating to the physiology of mycobacteria and consider how new frameworks could be applied across the wide spectrum of bacterial diversity.
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Affiliation(s)
- Michelle M Logsdon
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, United States.,Department of Molecular Microbiology, Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, MA, United States
| | - Bree B Aldridge
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, United States.,Department of Molecular Microbiology, Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, MA, United States.,Department of Biomedical Engineering, Tufts University School of Engineering, Medford, MA, United States
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100
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Ravimohan S, Kornfeld H, Weissman D, Bisson GP. Tuberculosis and lung damage: from epidemiology to pathophysiology. Eur Respir Rev 2018; 27:27/147/170077. [PMID: 29491034 PMCID: PMC6019552 DOI: 10.1183/16000617.0077-2017] [Citation(s) in RCA: 222] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 10/28/2017] [Indexed: 12/12/2022] Open
Abstract
A past history of pulmonary tuberculosis (TB) is a risk factor for long-term respiratory impairment. Post-TB lung dysfunction often goes unrecognised, despite its relatively high prevalence and its association with reduced quality of life. Importantly, specific host and pathogen factors causing lung impairment remain unclear. Host immune responses probably play a dominant role in lung damage, as excessive inflammation and elevated expression of lung matrix-degrading proteases are common during TB. Variability in host genes that modulate these immune responses may determine the severity of lung impairment, but this hypothesis remains largely untested. In this review, we provide an overview of the epidemiological literature on post-TB lung impairment and link it to data on the pathogenesis of lung injury from the perspective of dysregulated immune responses and immunogenetics. Host factors driving lung injury in TB likely contribute to variable patterns of pulmonary impairment after TBhttp://ow.ly/a3of30hBsxB
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Affiliation(s)
- Shruthi Ravimohan
- Dept of Medicine, Division of Infectious Diseases, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Hardy Kornfeld
- Dept of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Drew Weissman
- Dept of Medicine, Division of Infectious Diseases, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Gregory P Bisson
- Dept of Medicine, Division of Infectious Diseases, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.,Dept of Biostatistics and Epidemiology, Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
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