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Timme S, Wendler S, Klassert TE, Saraiva JP, da Rocha UN, Wittchen M, Schramm S, Ehricht R, Monecke S, Edel B, Rödel J, Löffler B, Ramirez MS, Slevogt H, Figge MT, Tuchscherr L. Competitive inhibition and mutualistic growth in co-infections: deciphering Staphylococcus aureus-Acinetobacter baumannii interaction dynamics. ISME COMMUNICATIONS 2024; 4:ycae077. [PMID: 38962494 PMCID: PMC11221087 DOI: 10.1093/ismeco/ycae077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 06/05/2024] [Accepted: 06/06/2024] [Indexed: 07/05/2024]
Abstract
Staphylococcus aureus (Sa) and Acinetobacter baumannii (Ab) are frequently co-isolated from polymicrobial infections that are severe and refractory to therapy. Here, we apply a combination of wet-lab experiments and in silico modeling to unveil the intricate nature of the Ab/Sa interaction using both, representative laboratory strains and strains co-isolated from clinical samples. This comprehensive methodology allowed uncovering Sa's capability to exert a partial interference on Ab by the expression of phenol-soluble modulins. In addition, we observed a cross-feeding mechanism by which Sa supports the growth of Ab by providing acetoin as an alternative carbon source. This study is the first to dissect the Ab/Sa interaction dynamics wherein competitive and cooperative strategies can intertwine. Through our findings, we illuminate the ecological mechanisms supporting their coexistence in the context of polymicrobial infections. Our research not only enriches our understanding but also opens doors to potential therapeutic avenues in managing these challenging infections.
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Affiliation(s)
- Sandra Timme
- Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Friedrich Schiller University Jena, Leibniz Centre for Photonics in Infection Research (LPI), D-07743 Jena, Germany
| | - Sindy Wendler
- Institute of Medical Microbiology, Jena University Hospital, D-07740 Jena, Germany
| | - Tilman E Klassert
- Respiratory Infection Dynamics, Helmholtz Centre for Infection Research – HZI, D-38124 Braunschweig, Germany
- Department of Respiratory Medicine and Infectious Diseases, Hannover Medical School, German Center for Lung Research (DZL), BREATH, D-30625 Hannover, Germany
| | - Joao Pedro Saraiva
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, D-04318 Leipzig, Germany
| | - Ulisses Nunes da Rocha
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, D-04318 Leipzig, Germany
| | - Manuel Wittchen
- Center for Biotechnology, Bielefeld University, D-33501 Bielefeld, Germany
| | - Sareda Schramm
- Department of Biological Science, Center for Applied Biotechnology Studies, California State University, 800 N State College Blvd, Fullerton, CA 92831, United States
| | - Ralf Ehricht
- Leibniz Institute of Photonic Technology, Leibniz Centre for Photonics in Infection Research (LPI), D-07745 Jena, Germany
- Institute of Physical Chemistry, Friedrich Schiller University Jena, Leibniz Centre for Photonics in Infection Research (LPI) , D-07743 Jena, Germany
| | - Stefan Monecke
- Leibniz Institute of Photonic Technology, Leibniz Centre for Photonics in Infection Research (LPI), D-07745 Jena, Germany
- Institute for Medical Microbiology and Virology, Dresden University Hospital, Dresden, Germany
| | - Birgit Edel
- Institute of Medical Microbiology, Jena University Hospital, D-07740 Jena, Germany
| | - Jürgen Rödel
- Institute of Medical Microbiology, Jena University Hospital, D-07740 Jena, Germany
| | - Bettina Löffler
- Institute of Medical Microbiology, Jena University Hospital, D-07740 Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, D-07743 Jena, Germany
| | - Maria Soledad Ramirez
- Department of Biological Science, Center for Applied Biotechnology Studies, California State University, 800 N State College Blvd, Fullerton, CA 92831, United States
| | - Hortense Slevogt
- Respiratory Infection Dynamics, Helmholtz Centre for Infection Research – HZI, D-38124 Braunschweig, Germany
- Department of Respiratory Medicine and Infectious Diseases, Hannover Medical School, German Center for Lung Research (DZL), BREATH, D-30625 Hannover, Germany
| | - Marc Thilo Figge
- Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Friedrich Schiller University Jena, Leibniz Centre for Photonics in Infection Research (LPI), D-07743 Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, D-07743 Jena, Germany
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, D-07743 Jena, Germany
| | - Lorena Tuchscherr
- Institute of Medical Microbiology, Jena University Hospital, D-07740 Jena, Germany
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Saffer C, Timme S, Rudolph P, Figge MT. Surrogate infection model predicts optimal alveolar macrophage number for clearance of Aspergillus fumigatus infections. NPJ Syst Biol Appl 2023; 9:12. [PMID: 37037824 PMCID: PMC10086013 DOI: 10.1038/s41540-023-00272-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 02/17/2023] [Indexed: 04/12/2023] Open
Abstract
The immune system has to fight off hundreds of microbial invaders every day, such as the human-pathogenic fungus Aspergillus fumigatus. The fungal conidia can reach the lower respiratory tract, swell and form hyphae within six hours causing life-threatening invasive aspergillosis. Invading pathogens are continuously recognized and eliminated by alveolar macrophages (AM). Their number plays an essential role, but remains controversial with measurements varying by a factor greater than ten for the human lung. We here investigate the impact of the AM number on the clearance of A. fumigatus conidia in humans and mice using analytical and numerical modeling approaches. A three-dimensional to-scale hybrid agent-based model (hABM) of the human and murine alveolus allowed us to simulate millions of virtual infection scenarios, and to gain quantitative insights into the infection dynamics for varying AM numbers and infection doses. Since hABM simulations are computationally expensive, we derived and trained an analytical surrogate infection model on the large dataset of numerical simulations. This enables reducing the number of hABM simulations while still providing (i) accurate and immediate predictions on infection progression, (ii) quantitative hypotheses on the infection dynamics under healthy and immunocompromised conditions, and (iii) optimal AM numbers for combating A. fumigatus infections in humans and mice.
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Affiliation(s)
- Christoph Saffer
- Research Group Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany
| | - Sandra Timme
- Research Group Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Paul Rudolph
- Research Group Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany
| | - Marc Thilo Figge
- Research Group Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany.
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany.
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Belyaev I, Marolda A, Praetorius JP, Sarkar A, Medyukhina A, Hünniger K, Kurzai O, Thilo Figge M. Automated Characterisation of Neutrophil Activation Phenotypes in Ex Vivo Human Candida Blood Infections. Comput Struct Biotechnol J 2022; 20:2297-2308. [PMID: 35615019 PMCID: PMC9120255 DOI: 10.1016/j.csbj.2022.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 05/04/2022] [Accepted: 05/05/2022] [Indexed: 11/08/2022] Open
Abstract
Candida bloodstream infections are difficult to diagnose and treat in humans. Infection processes give rise to activation of host immune cells. Immune cell activation is reflected by characteristic cell morphology. Neutrophils exhibit distinct morphodynamics for different Candida species.
Rapid identification of pathogens is required for early diagnosis and treatment of life-threatening bloodstream infections in humans. This requirement is driving the current developments of molecular diagnostic tools identifying pathogens from human whole blood after successful isolation and cultivation. An alternative approach is to determine pathogen-specific signatures from human host immune cells that have been exposed to pathogens. We hypothesise that activated immune cells, such as neutrophils, may exhibit a characteristic behaviour — for instance in terms of their speed, dynamic cell morphology — that allows (i) identifying the type of pathogen indirectly and (ii) providing information on therapeutic efficacy. In this feasibility study, we propose a method for the quantitative assessment of static and morphodynamic features of neutrophils based on label-free time-lapse imaging data. We investigate neutrophil activation phenotypes after confrontation with fungal pathogens and isolation from a human whole-blood assay. In particular, we applied a machine learning supported approach to time-lapse microscopy data from different infection scenarios and were able to distinguish between Candida albicans and C. glabrata infection scenarios with test accuracies well above 75%, and to identify pathogen-free samples with accuracy reaching 100%. These results significantly exceed the test accuracies achieved using state-of-the-art deep neural networks to classify neutrophils by their morphodynamics.
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Forster J, Streng A, Rudolph P, Rücker V, Wallstabe J, Timme S, Pietsch F, Hartmann K, Krauthausen M, Schmidt J, Ludwig T, Gierszewski D, Jans T, Engels G, Weißbrich B, Romanos M, Dölken L, Heuschmann P, Härtel C, Gágyor I, Figge MT, Kurzai O, Liese J. Feasibility of SARS-CoV-2 Surveillance Testing Among Children and Childcare Workers at German Day Care Centers: A Nonrandomized Controlled Trial. JAMA Netw Open 2022; 5:e2142057. [PMID: 34982157 PMCID: PMC8728621 DOI: 10.1001/jamanetworkopen.2021.42057] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
IMPORTANCE Closure of day care centers has been implemented globally to contain the COVID-19 pandemic but has negative effects on children's health and psychosocial well-being. OBJECTIVE To investigate the feasibility of surveillance among children and childcare workers and to model the efficacy of surveillance on viral spread prevention. DESIGN, SETTING, AND PARTICIPANTS This nonrandomized controlled trial was conducted at 9 day care centers in Wuerzburg, Germany, from October 2020 to March 2021. Participants included children attending day care, childcare workers, and household members. Participating day care centers were assigned to different surveillance modules in a nonrandomized feasibility study. A mathematical model for SARS-CoV-2 spread in day care centers was developed to identify optimal surveillance. INTERVENTIONS Modules 1, 2, and 3 involved continuous surveillance of asymptomatic children and childcare workers by SARS-CoV-2 polymerase chain reaction testing of either midturbinate nasal swabs twice weekly (module 1) or once weekly (module 2) or self-sampled saliva samples twice weekly (module 3). Module 4 involved symptom-based, on-demand testing of children, childcare workers, and their household members by oropharyngeal swabs. All participants underwent SARS-CoV-2 antibody status testing before and after the sampling period. Questionnaires on attitudes and perception of the pandemic were administered in weeks 1, 6, and 12. Mathematical modeling was used to estimate SARS-CoV-2 spread in day care centers. MAIN OUTCOMES AND MEASURES The primary outcomes were acceptance of the respective surveillance protocols (feasibility study) and the estimated number of secondary infections (mathematical modeling). RESULTS Of 954 eligible individuals (772 children and 182 childcare workers), 592 (62%), including 442 children (median [IQR] age, 3 [2-4] years; 214 [48.6%] female) and 150 childcare workers (median [IQR] age, 29 [25-44] years; 129 [90.8%] female) participated in the surveillance. In total, 4755 tests for SARS-CoV-2 detected 2 infections (1 childcare worker and 1 adult household member). Acceptance for continuous surveillance was highest for biweekly saliva testing (150 of 221 eligible individuals [67.9%; 95% CI, 61.5%-73.7%]) compared with biweekly (51 of 117 individuals [43.6%; 95% CI, 35.0%-52.6%]) and weekly (44 of 128 individuals [34.4%; 95% CI, 26.7%-43.0%]) midturbinate swabbing (P < .001). Dropout rates were higher for midturbinate swabbing (biweekly, 11 of 62 participants [18%]; once weekly, 11 of 55 participants [20%]) than for saliva testing (6 of 156 participants [4%]). Mathematical modeling based on study and literature data identified biweekly testing of at least 50% of children and childcare workers as minimal requirements to limit secondary infections. CONCLUSIONS AND RELEVANCE In this nonrandomized controlled trial, surveillance for SARS-CoV-2 in 9 German day care centers was feasible and well accepted. Mathematical modeling estimated that testing can minimize the spread of SARS-CoV-2 in day care centers. These findings enable setup of surveillance programs to maintain institutional childcare. TRIAL REGISTRATION German Registry for Clinical Trials Identifier: DRKS00023721.
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Affiliation(s)
- Johannes Forster
- Institute for Hygiene and Microbiology, University of Wuerzburg, Wuerzburg, Germany
| | - Andrea Streng
- Department of Pediatrics, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Paul Rudolph
- Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knoell-Institute, Jena, Germany
| | - Viktoria Rücker
- Institute of Clinical Epidemiology and Biometry, University of Wuerzburg, Wuerzburg, Germany
| | - Julia Wallstabe
- Institute for Hygiene and Microbiology, University of Wuerzburg, Wuerzburg, Germany
| | - Sandra Timme
- Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knoell-Institute, Jena, Germany
| | - Franziska Pietsch
- Institute for Hygiene and Microbiology, University of Wuerzburg, Wuerzburg, Germany
| | - Katrin Hartmann
- Department of Pediatrics, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Maike Krauthausen
- Department of General Practice, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Julia Schmidt
- Institute of Clinical Epidemiology and Biometry, University of Wuerzburg, Wuerzburg, Germany
| | - Timo Ludwig
- Institute of Clinical Epidemiology and Biometry, University of Wuerzburg, Wuerzburg, Germany
| | - David Gierszewski
- Department of General Practice, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Thomas Jans
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Geraldine Engels
- Department of Pediatrics, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Benedikt Weißbrich
- Institute for Virology and Immunobiology, University of Wuerzburg, Wuerzburg, Germany
| | - Marcel Romanos
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Lars Dölken
- Institute for Virology and Immunobiology, University of Wuerzburg, Wuerzburg, Germany
| | - Peter Heuschmann
- Institute of Clinical Epidemiology and Biometry, University of Wuerzburg, Wuerzburg, Germany
- Clinical Trial Center Wuerzburg, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Christoph Härtel
- Department of Pediatrics, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Ildikó Gágyor
- Department of General Practice, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Marc Thilo Figge
- Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knoell-Institute, Jena, Germany
| | - Oliver Kurzai
- Institute for Hygiene and Microbiology, University of Wuerzburg, Wuerzburg, Germany
- Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knoell-Institute, Jena, Germany
| | - Johannes Liese
- Department of Pediatrics, University Hospital Wuerzburg, Wuerzburg, Germany
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Lehnert T, Leonhardt I, Timme S, Thomas-Rüddel D, Bloos F, Sponholz C, Kurzai O, Figge MT, Hünniger K. Ex vivo immune profiling in patient blood enables quantification of innate immune effector functions. Sci Rep 2021; 11:12039. [PMID: 34103589 PMCID: PMC8187451 DOI: 10.1038/s41598-021-91362-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 05/25/2021] [Indexed: 02/05/2023] Open
Abstract
The assessment of a patient's immune function is critical in many clinical situations. In complex clinical immune dysfunction like sepsis, which results from a loss of immune homeostasis due to microbial infection, a plethora of pro- and anti-inflammatory stimuli may occur consecutively or simultaneously. Thus, any immunomodulatory therapy would require in-depth knowledge of an individual patient's immune status at a given time. Whereas lab-based immune profiling often relies solely on quantification of cell numbers, we used an ex vivo whole-blood infection model in combination with biomathematical modeling to quantify functional parameters of innate immune cells in blood from patients undergoing cardiac surgery. These patients experience a well-characterized inflammatory insult, which results in mitigation of the pathogen-specific response patterns towards Staphylococcus aureus and Candida albicans that are characteristic of healthy people and our patients at baseline. This not only interferes with the elimination of these pathogens from blood, but also selectively augments the escape of C. albicans from phagocytosis. In summary, our model could serve as a valuable functional immune assay for recording and evaluating innate responses to infection.
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Affiliation(s)
- Teresa Lehnert
- grid.418398.f0000 0001 0143 807XResearch Group Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology ‐ Hans Knöll Institute, Jena, Germany ,grid.275559.90000 0000 8517 6224Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany
| | - Ines Leonhardt
- grid.275559.90000 0000 8517 6224Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany ,grid.418398.f0000 0001 0143 807XResearch Group Fungal Septomics, Leibniz Institute for Natural Product Research and Infection Biology ‐ Hans Knöll Institute, Jena, Germany
| | - Sandra Timme
- grid.418398.f0000 0001 0143 807XResearch Group Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology ‐ Hans Knöll Institute, Jena, Germany
| | - Daniel Thomas-Rüddel
- grid.275559.90000 0000 8517 6224Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany ,grid.275559.90000 0000 8517 6224Department of Anesthesiology and Intensive Care Medicine, Jena University Hospital, Jena, Germany
| | - Frank Bloos
- grid.275559.90000 0000 8517 6224Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany ,grid.275559.90000 0000 8517 6224Department of Anesthesiology and Intensive Care Medicine, Jena University Hospital, Jena, Germany
| | - Christoph Sponholz
- grid.275559.90000 0000 8517 6224Department of Anesthesiology and Intensive Care Medicine, Jena University Hospital, Jena, Germany
| | - Oliver Kurzai
- grid.275559.90000 0000 8517 6224Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany ,grid.418398.f0000 0001 0143 807XResearch Group Fungal Septomics, Leibniz Institute for Natural Product Research and Infection Biology ‐ Hans Knöll Institute, Jena, Germany ,grid.8379.50000 0001 1958 8658Institute for Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | - Marc Thilo Figge
- grid.418398.f0000 0001 0143 807XResearch Group Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology ‐ Hans Knöll Institute, Jena, Germany ,grid.275559.90000 0000 8517 6224Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany ,grid.9613.d0000 0001 1939 2794Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany
| | - Kerstin Hünniger
- grid.418398.f0000 0001 0143 807XResearch Group Fungal Septomics, Leibniz Institute for Natural Product Research and Infection Biology ‐ Hans Knöll Institute, Jena, Germany ,grid.8379.50000 0001 1958 8658Institute for Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
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Lehnert T, Prauße MTE, Hünniger K, Praetorius JP, Kurzai O, Figge MT. Comparative assessment of immune evasion mechanisms in human whole-blood infection assays by a systems biology approach. PLoS One 2021; 16:e0249372. [PMID: 33793643 PMCID: PMC8016326 DOI: 10.1371/journal.pone.0249372] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 03/17/2021] [Indexed: 12/26/2022] Open
Abstract
Computer simulations of mathematical models open up the possibility of assessing hypotheses generated by experiments on pathogen immune evasion in human whole-blood infection assays. We apply an interdisciplinary systems biology approach in which virtual infection models implemented for the dissection of specific immune mechanisms are combined with experimental studies to validate or falsify the respective hypotheses. Focusing on the assessment of mechanisms that enable pathogens to evade the immune response in the early time course of a whole-blood infection, the least-square error (LSE) as a measure for the quantitative agreement between the theoretical and experimental kinetics is combined with the Akaike information criterion (AIC) as a measure for the model quality depending on its complexity. In particular, we compare mathematical models with three different types of pathogen immune evasion as well as all their combinations: (i) spontaneous immune evasion, (ii) evasion mediated by immune cells, and (iii) pre-existence of an immune-evasive pathogen subpopulation. For example, by testing theoretical predictions in subsequent imaging experiments, we demonstrate that the simple hypothesis of having a subpopulation of pre-existing immune-evasive pathogens can be ruled out. Furthermore, in this study we extend our previous whole-blood infection assays for the two fungal pathogens Candida albicans and C. glabrata by the bacterial pathogen Staphylococcus aureus and calibrated the model predictions to the time-resolved experimental data for each pathogen. Our quantitative assessment generally reveals that models with a lower number of parameters are not only scored with better AIC values, but also exhibit lower values for the LSE. Furthermore, we describe in detail model-specific and pathogen-specific patterns in the kinetics of cell populations that may be measured in future experiments to distinguish and pinpoint the underlying immune mechanisms.
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Affiliation(s)
- Teresa Lehnert
- Applied Systems Biology, Leibniz Institute for Natural Product Research Infection Biology, Hans Knöll Institute (HKI), Jena, Germany
- Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany
| | - Maria T. E. Prauße
- Applied Systems Biology, Leibniz Institute for Natural Product Research Infection Biology, Hans Knöll Institute (HKI), Jena, Germany
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany
| | - Kerstin Hünniger
- Fungal Septomics, Leibniz Institute for Natural Product Research Infection Biology, Hans Knöll Institute (HKI), Jena, Germany
- Institute of Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | - Jan-Philipp Praetorius
- Applied Systems Biology, Leibniz Institute for Natural Product Research Infection Biology, Hans Knöll Institute (HKI), Jena, Germany
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany
| | - Oliver Kurzai
- Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany
- Fungal Septomics, Leibniz Institute for Natural Product Research Infection Biology, Hans Knöll Institute (HKI), Jena, Germany
- Institute of Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | - Marc Thilo Figge
- Applied Systems Biology, Leibniz Institute for Natural Product Research Infection Biology, Hans Knöll Institute (HKI), Jena, Germany
- Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany
- * E-mail:
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Survival Strategies of Pathogenic Candida Species in Human Blood Show Independent and Specific Adaptations. mBio 2020; 11:mBio.02435-20. [PMID: 33024045 PMCID: PMC7542370 DOI: 10.1128/mbio.02435-20] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
To ensure their survival, pathogens have to adapt immediately to new environments in their hosts, for example, during the transition from the gut to the bloodstream. Here, we investigated the basis of this adaptation in a group of fungal species which are among the most common causes of hospital-acquired infections, the Candida species. On the basis of a human whole-blood infection model, we studied which genes and processes are active over the course of an infection in both the host and four different Candida pathogens. Remarkably, we found that, while the human host response during the early phase of infection is predominantly uniform, the pathogens pursue largely individual strategies and each one regulates genes involved in largely disparate processes in the blood. Our results reveal that C. albicans, C. glabrata, C. parapsilosis, and C. tropicalis all have developed individual strategies for survival in the host. This indicates that their pathogenicity in humans has evolved several times independently and that genes which are central for survival in the host for one species may be irrelevant in another. Only four species, Candida albicans, C. glabrata, C. parapsilosis, and C. tropicalis, together account for about 90% of all Candida bloodstream infections and are among the most common causes of invasive fungal infections of humans. However, virulence potential varies among these species, and the phylogenetic tree reveals that their pathogenicity may have emerged several times independently during evolution. We therefore tested these four species in a human whole-blood infection model to determine, via comprehensive dual-species RNA-sequencing analyses, which fungal infection strategies are conserved and which are recent evolutionary developments. The ex vivo infection progressed from initial immune cell interactions to nearly complete killing of all fungal cells. During the course of infection, we characterized important parameters of pathogen-host interactions, such as fungal survival, types of interacting immune cells, and cytokine release. On the transcriptional level, we obtained a predominantly uniform and species-independent human response governed by a strong upregulation of proinflammatory processes, which was downregulated at later time points after most of the fungal cells were killed. In stark contrast, we observed that the different fungal species pursued predominantly individual strategies and showed significantly different global transcriptome patterns. Among other findings, our functional analyses revealed that the fungal species relied on different metabolic pathways and virulence factors to survive the host-imposed stress. These data show that adaptation of Candida species as a response to the host is not a phylogenetic trait, but rather has likely evolved independently as a prerequisite to cause human infections.
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Blickensdorf M, Timme S, Figge MT. Hybrid Agent-Based Modeling of Aspergillus fumigatus Infection to Quantitatively Investigate the Role of Pores of Kohn in Human Alveoli. Front Microbiol 2020; 11:1951. [PMID: 32903715 PMCID: PMC7438790 DOI: 10.3389/fmicb.2020.01951] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 07/24/2020] [Indexed: 12/31/2022] Open
Abstract
The healthy state of an organism is constantly threatened by external cues. Due to the daily inhalation of hundreds of particles and pathogens, the immune system needs to constantly accomplish the task of pathogen clearance in order to maintain this healthy state. However, infection dynamics are highly influenced by the peculiar anatomy of the human lung. Lung alveoli that are packed in alveolar sacs are interconnected by so called Pores of Kohn. Mainly due to the lack of in vivo methods, the role of Pores of Kohn in the mammalian lung is still under debate and partly contradicting hypotheses remain to be investigated. Although it was shown by electron microscopy that Pores of Kohn may serve as passageways for immune cells, their impact on the infection dynamics in the lung is still unknown under in vivo conditions. In the present study, we apply a hybrid agent-based infection model to quantitatively compare three different scenarios and discuss the importance of Pores of Kohn during infections of Aspergillus fumigatus. A. fumigatus is an airborne opportunistic fungus with rising incidences causing severe infections in immunocompromised patients that are associated with high mortality rates. Our hybrid agent-based model incorporates immune cell dynamics of alveolar macrophages – the resident phagocytes in the lung – as well as molecular dynamics of diffusing chemokines that attract alveolar macrophages to the site of infection. Consequently, this model allows a quantitative comparison of three different scenarios and to study the importance of Pores of Kohn. This enables us to demonstrate how passaging of alveolar macrophages and chemokine diffusion affect A. fumigatus infection dynamics. We show that Pores of Kohn alter important infection clearance mechanisms, such as the spatial distribution of macrophages and the effect of chemokine signaling. However, despite these differences, a lack of passageways for alveolar macrophages does impede infection clearance only to a minor extend. Furthermore, we quantify the importance of recruited macrophages in comparison to resident macrophages.
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Affiliation(s)
- Marco Blickensdorf
- Research Group Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany.,Faculty of Biological Sciences, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Sandra Timme
- Research Group Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Marc Thilo Figge
- Research Group Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany.,Faculty of Biological Sciences, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
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Sreekantapuram S, Lehnert T, Prauße MTE, Berndt A, Berens C, Figge MT, Jacobsen ID. Dynamic Interplay of Host and Pathogens in an Avian Whole-Blood Model. Front Immunol 2020; 11:500. [PMID: 32296424 PMCID: PMC7136455 DOI: 10.3389/fimmu.2020.00500] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 03/04/2020] [Indexed: 12/22/2022] Open
Abstract
Microbial survival in blood is an essential step toward the development of disseminated diseases and blood stream infections. For poultry, however, little is known about the interactions of host cells and pathogens in blood. We established an ex vivo chicken whole-blood infection assay as a tool to analyze interactions between host cells and three model pathogens, Escherichia coli, Staphylococcus aureus, and Candida albicans. Following a systems biology approach, we complemented the experimental measurements with functional and quantitative immune characteristics by virtual infection modeling. All three pathogens were killed in whole blood, but each to a different extent and with different kinetics. Monocytes, and to a lesser extent heterophils, associated with pathogens. Both association with host cells and transcriptional activation of genes encoding immune-associated functions differed depending on both the pathogen and the genetic background of the chickens. Our results provide first insights into quantitative interactions of three model pathogens with different immune cell populations in avian blood, demonstrating a broad spectrum of different characteristics during the immune response that depends on the pathogen and the chicken line.
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Affiliation(s)
- Sravya Sreekantapuram
- Research Group Microbial Immunology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institut, Jena, Germany
| | - Teresa Lehnert
- Research Group Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institut, Jena, Germany
| | - Maria T E Prauße
- Research Group Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institut, Jena, Germany.,Faculty of Biological Sciences, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Angela Berndt
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut, Jena, Germany
| | - Christian Berens
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut, Jena, Germany
| | - Marc Thilo Figge
- Research Group Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institut, Jena, Germany.,Faculty of Biological Sciences, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Ilse D Jacobsen
- Research Group Microbial Immunology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institut, Jena, Germany.,Faculty of Biological Sciences, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
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Blickensdorf M, Timme S, Figge MT. Comparative Assessment of Aspergillosis by Virtual Infection Modeling in Murine and Human Lung. Front Immunol 2019; 10:142. [PMID: 30804941 PMCID: PMC6370618 DOI: 10.3389/fimmu.2019.00142] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 01/17/2019] [Indexed: 01/01/2023] Open
Abstract
Aspergillus fumigatus is a ubiquitous opportunistic fungal pathogen that can cause severe infections in immunocompromised patients. Conidia that reach the lower respiratory tract are confronted with alveolar macrophages, which are the resident phagocytic cells, constituting the first line of defense. If not efficiently removed in time, A. fumigatus conidia can germinate causing severe infections associated with high mortality rates. Mice are the most extensively used model organism in research on A. fumigatus infections. However, in addition to structural differences in the lung physiology of mice and the human host, applied infection doses in animal experiments are typically orders of magnitude larger compared to the daily inhalation doses of humans. The influence of these factors, which must be taken into account in a quantitative comparison and knowledge transfer from mice to humans, is difficult to measure since in vivo live cell imaging of the infection dynamics under physiological conditions is currently not possible. In the present study, we compare A. fumigatus infection in mice and humans by virtual infection modeling using a hybrid agent-based model that accounts for the respective lung physiology and the impact of a wide range of infection doses on the spatial infection dynamics. Our computer simulations enable comparative quantification of A. fumigatus infection clearance in the two hosts to elucidate (i) the complex interplay between alveolar morphometry and the fungal burden and (ii) the dynamics of infection clearance, which for realistic fungal burdens is found to be more efficiently realized in mice compared to humans.
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Affiliation(s)
- Marco Blickensdorf
- Research Group Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University of Jena, Jena, Germany
| | - Sandra Timme
- Research Group Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University of Jena, Jena, Germany
| | - Marc Thilo Figge
- Research Group Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University of Jena, Jena, Germany
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