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Kovacevic A, Smith DRM, Rahbé E, Novelli S, Henriot P, Varon E, Cohen R, Levy C, Temime L, Opatowski L. Exploring factors shaping antibiotic resistance patterns in Streptococcus pneumoniae during the 2020 COVID-19 pandemic. eLife 2024; 13:e85701. [PMID: 38451256 PMCID: PMC10923560 DOI: 10.7554/elife.85701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 02/12/2024] [Indexed: 03/08/2024] Open
Abstract
Non-pharmaceutical interventions implemented to block SARS-CoV-2 transmission in early 2020 led to global reductions in the incidence of invasive pneumococcal disease (IPD). By contrast, most European countries reported an increase in antibiotic resistance among invasive Streptococcus pneumoniae isolates from 2019 to 2020, while an increasing number of studies reported stable pneumococcal carriage prevalence over the same period. To disentangle the impacts of the COVID-19 pandemic on pneumococcal epidemiology in the community setting, we propose a mathematical model formalizing simultaneous transmission of SARS-CoV-2 and antibiotic-sensitive and -resistant strains of S. pneumoniae. To test hypotheses underlying these trends five mechanisms were built into the model and examined: (1) a population-wide reduction of antibiotic prescriptions in the community, (2) lockdown effect on pneumococcal transmission, (3) a reduced risk of developing an IPD due to the absence of common respiratory viruses, (4) community azithromycin use in COVID-19 infected individuals, (5) and a longer carriage duration of antibiotic-resistant pneumococcal strains. Among 31 possible pandemic scenarios involving mechanisms individually or in combination, model simulations surprisingly identified only two scenarios that reproduced the reported trends in the general population. They included factors (1), (3), and (4). These scenarios replicated a nearly 50% reduction in annual IPD, and an increase in antibiotic resistance from 20% to 22%, all while maintaining a relatively stable pneumococcal carriage. Exploring further, higher SARS-CoV-2 R0 values and synergistic within-host virus-bacteria interaction mechanisms could have additionally contributed to the observed antibiotic resistance increase. Our work demonstrates the utility of the mathematical modeling approach in unraveling the complex effects of the COVID-19 pandemic responses on AMR dynamics.
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Affiliation(s)
- Aleksandra Kovacevic
- Institut Pasteur, Université Paris Cité, Epidemiology and Modelling of Antibiotic Evasion (EMAE) unitParisFrance
- Université Paris-Saclay, Université de Versailles Saint-Quentin-en-Yvelines, Inserm U1018, CESP, Anti-infective evasion and pharmacoepidemiology teamMontigny-Le-BretonneuxFrance
| | - David RM Smith
- Institut Pasteur, Université Paris Cité, Epidemiology and Modelling of Antibiotic Evasion (EMAE) unitParisFrance
- Université Paris-Saclay, Université de Versailles Saint-Quentin-en-Yvelines, Inserm U1018, CESP, Anti-infective evasion and pharmacoepidemiology teamMontigny-Le-BretonneuxFrance
- Modélisation, épidémiologie et surveillance des risques sanitaires (MESuRS), Conservatoire national des arts et métiersParisFrance
- Health Economics Research Centre, Nuffield Department of Health, University of OxfordOxfordUnited Kingdom
| | - Eve Rahbé
- Institut Pasteur, Université Paris Cité, Epidemiology and Modelling of Antibiotic Evasion (EMAE) unitParisFrance
- Université Paris-Saclay, Université de Versailles Saint-Quentin-en-Yvelines, Inserm U1018, CESP, Anti-infective evasion and pharmacoepidemiology teamMontigny-Le-BretonneuxFrance
| | - Sophie Novelli
- Université Paris-Saclay, Université de Versailles Saint-Quentin-en-Yvelines, Inserm U1018, CESP, Anti-infective evasion and pharmacoepidemiology teamMontigny-Le-BretonneuxFrance
| | - Paul Henriot
- Modélisation, épidémiologie et surveillance des risques sanitaires (MESuRS), Conservatoire national des arts et métiersParisFrance
- PACRI unit, Institut Pasteur, Conservatoire national des arts et métiersParisFrance
| | - Emmanuelle Varon
- Centre National de Référence des Pneumocoques, Centre Hospitalier Intercommunal de CréteilCréteilFrance
| | - Robert Cohen
- Institut Mondor de Recherche Biomédicale-Groupe de Recherche Clinique Groupe d’Etude des Maladies Infectieuses Néonatales et Infantiles (IMRB-GRC GEMINI), Université Paris Est, 94000CréteilFrance
- Groupe de Pathologie Infectieuse Pédiatrique (GPIP), 06200NiceFrance
- Unité Court Séjour, Petits Nourrissons, Service de Néonatologie, Centre Hospitalier, Intercommunal de CréteilCréteilFrance
- Association Clinique et Thérapeutique Infantile du Val-de-Marne (ACTIV), 94000CréteilFrance
- Association Française de Pédiatrie Ambulatoire (AFPA), 45000OrléansFrance
| | - Corinne Levy
- Institut Mondor de Recherche Biomédicale-Groupe de Recherche Clinique Groupe d’Etude des Maladies Infectieuses Néonatales et Infantiles (IMRB-GRC GEMINI), Université Paris Est, 94000CréteilFrance
- Groupe de Pathologie Infectieuse Pédiatrique (GPIP), 06200NiceFrance
- Association Clinique et Thérapeutique Infantile du Val-de-Marne (ACTIV), 94000CréteilFrance
- Association Française de Pédiatrie Ambulatoire (AFPA), 45000OrléansFrance
| | - Laura Temime
- Modélisation, épidémiologie et surveillance des risques sanitaires (MESuRS), Conservatoire national des arts et métiersParisFrance
- PACRI unit, Institut Pasteur, Conservatoire national des arts et métiersParisFrance
| | - Lulla Opatowski
- Institut Pasteur, Université Paris Cité, Epidemiology and Modelling of Antibiotic Evasion (EMAE) unitParisFrance
- Université Paris-Saclay, Université de Versailles Saint-Quentin-en-Yvelines, Inserm U1018, CESP, Anti-infective evasion and pharmacoepidemiology teamMontigny-Le-BretonneuxFrance
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Mochan E, Sego TJ. Mathematical Modeling of the Lethal Synergism of Coinfecting Pathogens in Respiratory Viral Infections: A Review. Microorganisms 2023; 11:2974. [PMID: 38138118 PMCID: PMC10745501 DOI: 10.3390/microorganisms11122974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 12/05/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
Influenza A virus (IAV) infections represent a substantial global health challenge and are often accompanied by coinfections involving secondary viruses or bacteria, resulting in increased morbidity and mortality. The clinical impact of coinfections remains poorly understood, with conflicting findings regarding fatality. Isolating the impact of each pathogen and mechanisms of pathogen synergy during coinfections is challenging and further complicated by host and pathogen variability and experimental conditions. Factors such as cytokine dysregulation, immune cell function alterations, mucociliary dysfunction, and changes to the respiratory tract epithelium have been identified as contributors to increased lethality. The relative significance of these factors depends on variables such as pathogen types, infection timing, sequence, and inoculum size. Mathematical biological modeling can play a pivotal role in shedding light on the mechanisms of coinfections. Mathematical modeling enables the quantification of aspects of the intra-host immune response that are difficult to assess experimentally. In this narrative review, we highlight important mechanisms of IAV coinfection with bacterial and viral pathogens and survey mathematical models of coinfection and the insights gained from them. We discuss current challenges and limitations facing coinfection modeling, as well as current trends and future directions toward a complete understanding of coinfection using mathematical modeling and computer simulation.
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Affiliation(s)
- Ericka Mochan
- Department of Computational and Chemical Sciences, Carlow University, Pittsburgh, PA 15213, USA
| | - T. J. Sego
- Department of Medicine, University of Florida, Gainesville, FL 32611, USA;
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Burstein R, Althouse BM, Adler A, Akullian A, Brandstetter E, Cho S, Emanuels A, Fay K, Gamboa L, Han P, Huden K, Ilcisin M, Izzo M, Jackson ML, Kim AE, Kimball L, Lacombe K, Lee J, Logue JK, Rogers J, Chung E, Sibley TR, Van Raay K, Wenger E, Wolf CR, Boeckh M, Chu H, Duchin J, Rieder M, Shendure J, Starita LM, Viboud C, Bedford T, Englund JA, Famulare M. Interactions among 17 respiratory pathogens: a cross-sectional study using clinical and community surveillance data. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2022.02.04.22270474. [PMID: 35169816 PMCID: PMC8845514 DOI: 10.1101/2022.02.04.22270474] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Background Co-circulating respiratory pathogens can interfere with or promote each other, leading to important effects on disease epidemiology. Estimating the magnitude of pathogen-pathogen interactions from clinical specimens is challenging because sampling from symptomatic individuals can create biased estimates. Methods We conducted an observational, cross-sectional study using samples collected by the Seattle Flu Study between 11 November 2018 and 20 August 2021. Samples that tested positive via RT-qPCR for at least one of 17 potential respiratory pathogens were included in this study. Semi-quantitative cycle threshold (Ct) values were used to measure pathogen load. Differences in pathogen load between monoinfected and coinfected samples were assessed using linear regression adjusting for age, season, and recruitment channel. Results 21,686 samples were positive for at least one potential pathogen. Most prevalent were rhinovirus (33·5%), Streptococcus pneumoniae (SPn, 29·0%), SARS-CoV-2 (13.8%) and influenza A/H1N1 (9·6%). 140 potential pathogen pairs were included for analysis, and 56 (40%) pairs yielded significant Ct differences (p < 0.01) between monoinfected and co-infected samples. We observed no virus-virus pairs showing evidence of significant facilitating interactions, and found significant viral load decrease among 37 of 108 (34%) assessed pairs. Samples positive with SPn and a virus were consistently associated with increased SPn load. Conclusions Viral load data can be used to overcome sampling bias in studies of pathogen-pathogen interactions. When applied to respiratory pathogens, we found evidence of viral-SPn facilitation and several examples of viral-viral interference. Multipathogen surveillance is a cost-efficient data collection approach, with added clinical and epidemiological informational value over single-pathogen testing, but requires careful analysis to mitigate selection bias.
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Affiliation(s)
- Roy Burstein
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle WA USA
| | - Benjamin M. Althouse
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle WA USA
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle WA USA
- Department of Biology, New Mexico State University, Las Cruces, NM
| | - Amanda Adler
- Seattle Children’s Research Institute, Seattle WA USA
| | - Adam Akullian
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle WA USA
| | | | - Shari Cho
- Brotman Baty Institute for Precision Medicine, Seattle WA USA
| | - Anne Emanuels
- Department of Medicine, University of Washington, Seattle WA USA
| | - Kairsten Fay
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA USA
| | - Luis Gamboa
- Brotman Baty Institute for Precision Medicine, Seattle WA USA
| | - Peter Han
- Brotman Baty Institute for Precision Medicine, Seattle WA USA
| | - Kristen Huden
- Department of Medicine, University of Washington, Seattle WA USA
| | - Misja Ilcisin
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA USA
| | - Mandy Izzo
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle WA USA
| | | | - Ashley E. Kim
- Department of Medicine, University of Washington, Seattle WA USA
| | - Louise Kimball
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA USA
| | | | - Jover Lee
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA USA
| | | | - Julia Rogers
- Department of Medicine, University of Washington, Seattle WA USA
| | - Erin Chung
- Department of Pediatrics, University of Washington, Seattle Children’s Hospital, Seattle
| | - Thomas R. Sibley
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA USA
| | | | - Edward Wenger
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle WA USA
| | - Caitlin R. Wolf
- Department of Medicine, University of Washington, Seattle WA USA
| | - Michael Boeckh
- Department of Medicine, University of Washington, Seattle WA USA
- Brotman Baty Institute for Precision Medicine, Seattle WA USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA USA
| | - Helen Chu
- Department of Medicine, University of Washington, Seattle WA USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA USA
| | - Jeff Duchin
- Department of Medicine, University of Washington, Seattle WA USA
- Public Health Seattle & King County, Seattle WA USA
| | - Mark Rieder
- Brotman Baty Institute for Precision Medicine, Seattle WA USA
| | - Jay Shendure
- Brotman Baty Institute for Precision Medicine, Seattle WA USA
- Department of Genome Sciences, University of Washington, Seattle WA USA
- Howard Hughes Medical Institute, Seattle WA USA
| | - Lea M. Starita
- Brotman Baty Institute for Precision Medicine, Seattle WA USA
- Department of Genome Sciences, University of Washington, Seattle WA USA
| | - Cecile Viboud
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Trevor Bedford
- Brotman Baty Institute for Precision Medicine, Seattle WA USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA USA
- Howard Hughes Medical Institute, Seattle WA USA
| | - Janet A. Englund
- Seattle Children’s Research Institute, Seattle WA USA
- Brotman Baty Institute for Precision Medicine, Seattle WA USA
| | - Michael Famulare
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle WA USA
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Khorramdelazad H, Kazemi MH, Najafi A, Keykhaee M, Zolfaghari Emameh R, Falak R. Immunopathological similarities between COVID-19 and influenza: Investigating the consequences of Co-infection. Microb Pathog 2021; 152:104554. [PMID: 33157216 PMCID: PMC7607235 DOI: 10.1016/j.micpath.2020.104554] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 09/25/2020] [Accepted: 09/29/2020] [Indexed: 02/06/2023]
Abstract
Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been a global public health emergency since December 2019, and so far, more than 980,000 people (until September 24, 2020) around the world have died. SARS-CoV-2 mimics the influenza virus regarding methods and modes of transmission, clinical features, related immune responses, and seasonal coincidence. Accordingly, co-infection by these viruses is imaginable because some studies have reported several cases with SARS-CoV-2 and influenza virus co-infection. Given the importance of the mentioned co-infection and the coming influenza season, it is essential to recognize the similarities and differences between the symptoms, immunopathogenesis and treatment of SARS-CoV-2 and influenza virus. Therefore, we reviewed the virology, clinical features, and immunopathogenesis of both influenza virus and SARS-CoV-2 and evaluated outcomes in cases with SARS-CoV-2 and influenza virus co-infection.
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Affiliation(s)
- Hossein Khorramdelazad
- Department of Immunology, School of Medicine, Molecular Medicine Research Center, Research Institute of Basic Medical Sciences, Rafsanjan University of Medical Sciences, Rafsanjan, Iran; Department of Immunology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Hossein Kazemi
- Department of Immunology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran; Hematopoietic Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Alireza Najafi
- Department of Immunology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran; Immunology Research Center, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran
| | - Maryam Keykhaee
- Department of Pharmaceutical Biomaterials, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Reza Zolfaghari Emameh
- Department of Energy and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), 14965/161, Tehran, Iran
| | - Reza Falak
- Department of Immunology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran; Immunology Research Center, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran.
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5
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Bertrams W, Jung AL, Schmeck B. Modeling of Pneumonia and Acute Lung Injury: Bioinformatics, Systems Medicine, and Artificial Intelligence. SYSTEMS MEDICINE 2021. [DOI: 10.1016/b978-0-12-801238-3.11689-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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6
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Gjini E, Paupério FFS, Ganusov VV. Treatment timing shifts the benefits of short and long antibiotic treatment over infection. Evol Med Public Health 2020; 2020:249-263. [PMID: 33376597 PMCID: PMC7750949 DOI: 10.1093/emph/eoaa033] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 08/19/2020] [Indexed: 12/13/2022] Open
Abstract
Antibiotics are the major tool for treating bacterial infections. Rising antibiotic resistance, however, calls for a better use of antibiotics. While classical recommendations favor long and aggressive treatments, more recent clinical trials advocate for moderate regimens. In this debate, two axes of 'aggression' have typically been conflated: treatment intensity (dose) and treatment duration. The third dimension of treatment timing along each individual's infection course has rarely been addressed. By using a generic mathematical model of bacterial infection controlled by immune response, we examine how the relative effectiveness of antibiotic treatment varies with its timing, duration and antibiotic kill rate. We show that short or long treatments may both be beneficial depending on treatment onset, the target criterion for success and on antibiotic efficacy. This results from the dynamic trade-off between immune response build-up and resistance risk in acute, self-limiting infections, and uncertainty relating symptoms to infection variables. We show that in our model early optimal treatments tend to be 'short and strong', while late optimal treatments tend to be 'mild and long'. This suggests a shift in the aggression axis depending on the timing of treatment. We find that any specific optimal treatment schedule may perform more poorly if evaluated by other criteria, or under different host-specific conditions. Our results suggest that major advances in antibiotic stewardship must come from a deeper empirical understanding of bacterial infection processes in individual hosts. To guide rational therapy, mathematical models need to be constrained by data, including a better quantification of personal disease trajectory in humans. Lay summary: Bacterial infections are becoming more difficult to treat worldwide because bacteria are becoming resistant to the antibiotics used. Addressing this problem requires a better understanding of how treatment along with other host factors impact antibiotic resistance. Until recently, most theoretical research has focused on the importance of antibiotic dosing on antibiotic resistance, however, duration and timing of treatment remain less explored. Here, we use a mathematical model of a generic bacterial infection to study three aspects of treatment: treatment dose/efficacy (defined by the antibiotic kill rate), duration, and timing, and their impact on several infection endpoints. We show that short and long treatment success strongly depends on when treatment begins (defined by the symptom threshold), the target criterion to optimize, and on antibiotic efficacy. We find that if administered early in an infection, "strong and short" therapy performs better, while if treatment begins at higher bacterial densities, a "mild and long" course of antibiotics is favored. In the model host immune defenses are key in preventing relapses, controlling antibiotic resistant bacteria and increasing the effectiveness of moderate intervention. In order to improve rational treatments of human infections, we call for a better quantification of individual disease trajectories in bacteria-immunity space.
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Affiliation(s)
- Erida Gjini
- Mathematical Modeling of Biological Processes Laboratory, Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, Oeiras, 2780-156, Portugal
| | - Francisco F S Paupério
- Mathematical Modeling of Biological Processes Laboratory, Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, Oeiras, 2780-156, Portugal
- Departamento de Informática, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisbon, 1749-016, Portugal
| | - Vitaly V Ganusov
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA
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7
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Kanyiri CW, Luboobi L, Kimathi M. Application of Optimal Control to Influenza Pneumonia Coinfection with Antiviral Resistance. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2020; 2020:5984095. [PMID: 32256682 PMCID: PMC7091548 DOI: 10.1155/2020/5984095] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 02/01/2020] [Accepted: 02/13/2020] [Indexed: 12/30/2022]
Abstract
Influenza and pneumonia independently lead to high morbidity and mortality annually among the human population globally; however, a glaring fact is that influenza pneumonia coinfection is more vicious and it is a threat to public health. Emergence of antiviral resistance is a major impediment in the control of the coinfection. In this paper, a deterministic mathematical model illustrating the transmission dynamics of influenza pneumonia coinfection is formulated having incorporated antiviral resistance. Optimal control theory is then applied to investigate optimal strategies for controlling the coinfection using prevalence reduction and treatment as the system control variables. Pontryagin's maximum principle is used to characterize the optimal control. The derived optimality system is solved numerically using the Runge-Kutta-based forward-backward sweep method. Simulation results reveal that implementation of prevention measures is sufficient to eradicate influenza pneumonia coinfection from a given population. The prevention measures could be social distancing, vaccination, curbing mutation and reassortment, and curbing interspecies movement of the influenza virus.
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Affiliation(s)
- Caroline W. Kanyiri
- Department of Mathematics, Pan African University Institute of Basic Sciences, Technology and Innovation, P.O. Box 62000-00200, Nairobi, Kenya
| | - Livingstone Luboobi
- Institute of Mathematical Sciences, Strathmore University, P.O. Box 59857-00200, Nairobi, Kenya
| | - Mark Kimathi
- Department of Mathematics, Machakos University, P.O. Box 139-90100, Machakos, Kenya
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Abstract
The immune system is inordinately complex with many interacting components determining overall outcomes. Mathematical and computational modelling provides a useful way in which the various contributions of different immunological components can be probed in an integrated manner. Here, we provide an introductory overview and review of mechanistic simulation models. We start out by briefly defining these types of models and contrasting them to other model types that are relevant to the field of immunology. We follow with a few specific examples and then review the different ways one can use such models to answer immunological questions. While our examples focus on immune responses to infection, the overall ideas and descriptions of model uses can be applied to any area of immunology.
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Islam MM, Fernando SC, Saha R. Metabolic Modeling Elucidates the Transactions in the Rumen Microbiome and the Shifts Upon Virome Interactions. Front Microbiol 2019; 10:2412. [PMID: 31866953 PMCID: PMC6909001 DOI: 10.3389/fmicb.2019.02412] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 10/07/2019] [Indexed: 12/18/2022] Open
Abstract
The complex microbial ecosystem within the bovine rumen plays a crucial role in host nutrition, health, and environmental impact. However, little is known about the interactions between the functional entities within the system, which dictates the community structure and functional dynamics and host physiology. With the advancements in high-throughput sequencing and mathematical modeling, in silico genome-scale metabolic analysis promises to expand our understanding of the metabolic interplay in the community. In an attempt to understand the interactions between microbial species and the phages inside rumen, a genome-scale metabolic modeling approach was utilized by using key members in the rumen microbiome (a bacteroidete, a firmicute, and an archaeon) and the viral phages associated with them. Individual microbial host models were integrated into a community model using multi-level mathematical frameworks. An elaborate and heuristics-based computational procedure was employed to predict previously unknown interactions involving the transfer of fatty acids, vitamins, coenzymes, amino acids, and sugars among the community members. While some of these interactions could be inferred by the available multi-omic datasets, our proposed method provides a systemic understanding of why the interactions occur and how these affect the dynamics in a complex microbial ecosystem. To elucidate the functional role of the virome on the microbiome, local alignment search was used to identify the metabolic functions of the viruses associated with the hosts. The incorporation of these functions demonstrated the role of viral auxiliary metabolic genes in relaxing the metabolic bottlenecks in the microbial hosts and complementing the inter-species interactions. Finally, a comparative statistical analysis of different biologically significant community fitness criteria identified the variation in flux space and robustness of metabolic capacities of the community members. Our elucidation of metabolite exchange among the three members of the rumen microbiome shows how their genomic differences and interactions with the viral strains shape up a highly sophisticated metabolic interplay and explains how such interactions across kingdoms can cause metabolic and compositional shifts in the community and affect the health, nutrition, and pathophysiology of the ruminant animal.
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Affiliation(s)
- Mohammad Mazharul Islam
- Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Samodha C Fernando
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Rajib Saha
- Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, NE, United States
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Sharma-Chawla N, Stegemann-Koniszewski S, Christen H, Boehme JD, Kershaw O, Schreiber J, Guzmán CA, Bruder D, Hernandez-Vargas EA. In vivo Neutralization of Pro-inflammatory Cytokines During Secondary Streptococcus pneumoniae Infection Post Influenza A Virus Infection. Front Immunol 2019; 10:1864. [PMID: 31474978 PMCID: PMC6702285 DOI: 10.3389/fimmu.2019.01864] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 07/23/2019] [Indexed: 11/20/2022] Open
Abstract
An overt pro-inflammatory immune response is a key factor contributing to lethal pneumococcal infection in an influenza pre-infected host and represents a potential target for therapeutic intervention. However, there is a paucity of knowledge about the level of contribution of individual cytokines. Based on the predictions of our previous mathematical modeling approach, the potential benefit of IFN-γ- and/or IL-6-specific antibody-mediated cytokine neutralization was explored in C57BL/6 mice infected with the influenza A/PR/8/34 strain, which were subsequently infected with the Streptococcus pneumoniae strain TIGR4 on day 7 post influenza. While single IL-6 neutralization had no effect on respiratory bacterial clearance, single IFN-γ neutralization enhanced local bacterial clearance in the lungs. Concomitant neutralization of IFN-γ and IL-6 significantly reduced the degree of pneumonia as well as bacteremia compared to the control group, indicating a positive effect for the host during secondary bacterial infection. The results of our model-driven experimental study reveal that the predicted therapeutic value of IFN-γ and IL-6 neutralization in secondary pneumococcal infection following influenza infection is tightly dependent on the experimental protocol while at the same time paving the way toward the development of effective immune therapies.
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Affiliation(s)
- Niharika Sharma-Chawla
- Frankfurt Institute for Advanced Studies, Frankfurt am Main, Germany.,Immune Regulation Group, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany.,Infection Immunology Group, Institute of Medical Microbiology, Infection Prevention and Control, Health Immunology, Infectiology and Inflammation, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Sabine Stegemann-Koniszewski
- Immune Regulation Group, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany.,Infection Immunology Group, Institute of Medical Microbiology, Infection Prevention and Control, Health Immunology, Infectiology and Inflammation, Otto-von-Guericke University Magdeburg, Magdeburg, Germany.,Experimental Pneumology, University Hospital of Pneumology, Health Campus Immunology, Infectiology and Inflammation, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Henrike Christen
- Immune Regulation Group, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Julia D Boehme
- Immune Regulation Group, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany.,Infection Immunology Group, Institute of Medical Microbiology, Infection Prevention and Control, Health Immunology, Infectiology and Inflammation, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Olivia Kershaw
- Department of Veterinary Medicine, Institute of Veterinary Pathology, Free University Berlin, Berlin, Germany
| | - Jens Schreiber
- Experimental Pneumology, University Hospital of Pneumology, Health Campus Immunology, Infectiology and Inflammation, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Carlos A Guzmán
- Department of Vaccinology and Applied Microbiology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany.,Centre for Individualized Infection Medicine (CiiM), Hanover, Germany
| | - Dunja Bruder
- Immune Regulation Group, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany.,Infection Immunology Group, Institute of Medical Microbiology, Infection Prevention and Control, Health Immunology, Infectiology and Inflammation, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
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Pereira MC, Athanazio RA, Dalcin PDTR, Figueiredo MRFD, Gomes M, Freitas CGD, Ludgren F, Paschoal IA, Rached SZ, Maurici R. Brazilian consensus on non-cystic fibrosis bronchiectasis. ACTA ACUST UNITED AC 2019; 45:e20190122. [PMID: 31411280 PMCID: PMC6733718 DOI: 10.1590/1806-3713/e20190122] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 05/16/2019] [Indexed: 12/16/2022]
Abstract
Bronchiectasis is a condition that has been increasingly diagnosed by chest HRCT. In the literature, bronchiectasis is divided into bronchiectasis secondary to cystic fibrosis and bronchiectasis not associated with cystic fibrosis, which is termed non-cystic fibrosis bronchiectasis. Many causes can lead to the development of bronchiectasis, and patients usually have chronic airway symptoms, recurrent infections, and CT abnormalities consistent with the condition. The first international guideline on the diagnosis and treatment of non-cystic fibrosis bronchiectasis was published in 2010. In Brazil, this is the first review document aimed at systematizing the knowledge that has been accumulated on the subject to date. Because there is insufficient evidence on which to base recommendations for various treatment topics, here the decision was made to prepare an expert consensus document. The Brazilian Thoracic Association Committee on Respiratory Infections summoned 10 pulmonologists with expertise in bronchiectasis in Brazil to conduct a critical assessment of the available scientific evidence and international guidelines, as well as to identify aspects that are relevant to the understanding of the heterogeneity of bronchiectasis and to its diagnostic and therapeutic management. Five broad topics were established (pathophysiology, diagnosis, monitoring of stable patients, treatment of stable patients, and management of exacerbations). After this subdivision, the topics were distributed among the authors, who conducted a nonsystematic review of the literature, giving priority to major publications in the specific areas, including original articles, review articles, and systematic reviews. The authors reviewed and commented on all topics, producing a single final document that was approved by consensus.
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Affiliation(s)
- Mônica Corso Pereira
- . Departamento de Clínica Médica, Faculdade de Ciências Médicas, Universidade Estadual de Campinas - UNICAMP - Campinas (SP) Brasil
| | - Rodrigo Abensur Athanazio
- . Divisão de Pneumologia, Instituto do Coração - InCor - Faculdade de Medicina, Universidade de São Paulo, São Paulo (SP) Brasil
| | - Paulo de Tarso Roth Dalcin
- . Departamento de Medicina Interna, Universidade Federal do Rio Grande do Sul, Porto Alegre (RS) Brasil.,. Serviço de Pneumologia, Hospital de Clínicas de Porto Alegre, Porto Alegre (RS) Brasil
| | | | - Mauro Gomes
- . Faculdade de Ciências Médicas da Santa Casa de São Paulo, São Paulo (SP) Brasil.,. Equipe de Pneumologia, Hospital Samaritano, São Paulo (SP) Brasil
| | | | | | - Ilma Aparecida Paschoal
- . Departamento de Clínica Médica, Faculdade de Ciências Médicas, Universidade Estadual de Campinas - UNICAMP - Campinas (SP) Brasil
| | - Samia Zahi Rached
- . Divisão de Pneumologia, Instituto do Coração - InCor - Faculdade de Medicina, Universidade de São Paulo, São Paulo (SP) Brasil
| | - Rosemeri Maurici
- . Programa de Pós-Graduação em Ciências Médicas, Universidade Federal de Santa Catarina, Florianópolis (SC) Brasil
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Mortality, morbidity, and hospitalisations due to influenza lower respiratory tract infections, 2017: an analysis for the Global Burden of Disease Study 2017. THE LANCET. RESPIRATORY MEDICINE 2019; 7:69-89. [PMID: 30553848 PMCID: PMC6302221 DOI: 10.1016/s2213-2600(18)30496-x] [Citation(s) in RCA: 283] [Impact Index Per Article: 56.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 11/07/2018] [Accepted: 11/08/2018] [Indexed: 02/07/2023]
Abstract
BACKGROUND Although the burden of influenza is often discussed in the context of historical pandemics and the threat of future pandemics, every year a substantial burden of lower respiratory tract infections (LRTIs) and other respiratory conditions (like chronic obstructive pulmonary disease) are attributable to seasonal influenza. The Global Burden of Disease Study (GBD) 2017 is a systematic scientific effort to quantify the health loss associated with a comprehensive set of diseases and disabilities. In this Article, we focus on LRTIs that can be attributed to influenza. METHODS We modelled the LRTI incidence, hospitalisations, and mortality attributable to influenza for every country and selected subnational locations by age and year from 1990 to 2017 as part of GBD 2017. We used a counterfactual approach that first estimated the LRTI incidence, hospitalisations, and mortality and then attributed a fraction of those outcomes to influenza. FINDINGS Influenza LRTI was responsible for an estimated 145 000 (95% uncertainty interval [UI] 99 000-200 000) deaths among all ages in 2017. The influenza LRTI mortality rate was highest among adults older than 70 years (16·4 deaths per 100 000 [95% UI 11·6-21·9]), and the highest rate among all ages was in eastern Europe (5·2 per 100 000 population [95% UI 3·5-7·2]). We estimated that influenza LRTIs accounted for 9 459 000 (95% UI 3 709 000-22 935 000) hospitalisations due to LRTIs and 81 536 000 hospital days (24 330 000-259 851 000). We estimated that 11·5% (95% UI 10·0-12·9) of LRTI episodes were attributable to influenza, corresponding to 54 481 000 (38 465 000-73 864 000) episodes and 8 172 000 severe episodes (5 000 000-13 296 000). INTERPRETATION This comprehensive assessment of the burden of influenza LRTIs shows the substantial annual effect of influenza on global health. Although preparedness planning will be important for potential pandemics, health loss due to seasonal influenza LRTIs should not be overlooked, and vaccine use should be considered. Efforts to improve influenza prevention measures are needed. FUNDING Bill & Melinda Gates Foundation.
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13
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Handel A, Liao LE, Beauchemin CA. Progress and trends in mathematical modelling of influenza A virus infections. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.coisb.2018.08.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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14
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Corrêa RDA, Costa AN, Lundgren F, Michelin L, Figueiredo MR, Holanda M, Gomes M, Teixeira PJZ, Martins R, Silva R, Athanazio RA, da Silva RM, Pereira MC. 2018 recommendations for the management of community acquired pneumonia. J Bras Pneumol 2018; 44:405-423. [PMID: 30517341 PMCID: PMC6467584 DOI: 10.1590/s1806-37562018000000130] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 09/11/2018] [Indexed: 12/17/2022] Open
Abstract
Community-acquired pneumonia (CAP) is the leading cause of death worldwide. Despite the vast diversity of respiratory microbiota, Streptococcus pneumoniae remains the most prevalent pathogen among etiologic agents. Despite the significant decrease in the mortality rates for lower respiratory tract infections in recent decades, CAP ranks third as a cause of death in Brazil. Since the latest Guidelines on CAP from the Sociedade Brasileira de Pneumologia e Tisiologia (SBPT, Brazilian Thoracic Association) were published (2009), there have been major advances in the application of imaging tests, in etiologic investigation, in risk stratification at admission and prognostic score stratification, in the use of biomarkers, and in the recommendations for antibiotic therapy (and its duration) and prevention through vaccination. To review these topics, the SBPT Committee on Respiratory Infections summoned 13 members with recognized experience in CAP in Brazil who identified issues relevant to clinical practice that require updates given the publication of new epidemiological and scientific evidence. Twelve topics concerning diagnostic, prognostic, therapeutic, and preventive issues were developed. The topics were divided among the authors, who conducted a nonsystematic review of the literature, but giving priority to major publications in the specific areas, including original articles, review articles, and systematic reviews. All authors had the opportunity to review and comment on all questions, producing a single final document that was approved by consensus.
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Affiliation(s)
- Ricardo de Amorim Corrêa
- . Faculdade de Medicina, Universidade Federal de Minas Gerais - UFMG - Belo Horizonte (MG) Brasil
| | - Andre Nathan Costa
- . Faculdade de Medicina, Universidade de São Paulo - USP - São Paulo (SP) Brasil
| | | | - Lessandra Michelin
- . Faculdade de Medicina, Universidade de Caxias do Sul, Caxias do Sul (RS) Brasil
| | | | - Marcelo Holanda
- . Faculdade de Medicina, Universidade Federal do Ceará - UFC - Fortaleza (CE) Brasil
| | - Mauro Gomes
- . Faculdade de Ciências Médicas, Santa Casa de São Paulo, São Paulo (SP) Brasil
| | | | - Ricardo Martins
- . Faculdade de Medicina, Universidade de Brasília - UnB - Brasília (DF) Brasil
| | - Rodney Silva
- . Faculdade de Medicina, Universidade Federal do Paraná - UFPR - Curitiba (PR) Brasil
| | | | | | - Mônica Corso Pereira
- . Faculdade de Medicina, Universidade Estadual de Campinas - Unicamp - Campinas (SP) Brasil
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15
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Abstract
Influenza virus infections are a leading cause of morbidity and mortality worldwide. This is due in part to the continual emergence of new viral variants and to synergistic interactions with other viruses and bacteria. There is a lack of understanding about how host responses work to control the infection and how other pathogens capitalize on the altered immune state. The complexity of multi-pathogen infections makes dissecting contributing mechanisms, which may be non-linear and occur on different time scales, challenging. Fortunately, mathematical models have been able to uncover infection control mechanisms, establish regulatory feedbacks, connect mechanisms across time scales, and determine the processes that dictate different disease outcomes. These models have tested existing hypotheses and generated new hypotheses, some of which have been subsequently tested and validated in the laboratory. They have been particularly a key in studying influenza-bacteria coinfections and will be undoubtedly be useful in examining the interplay between influenza virus and other viruses. Here, I review recent advances in modeling influenza-related infections, the novel biological insight that has been gained through modeling, the importance of model-driven experimental design, and future directions of the field.
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Affiliation(s)
- Amber M Smith
- University of Tennessee Health Science CenterMemphisTNUSA
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16
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Opatowski L, Baguelin M, Eggo RM. Influenza interaction with cocirculating pathogens and its impact on surveillance, pathogenesis, and epidemic profile: A key role for mathematical modelling. PLoS Pathog 2018; 14:e1006770. [PMID: 29447284 PMCID: PMC5814058 DOI: 10.1371/journal.ppat.1006770] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Evidence is mounting that influenza virus interacts with other pathogens colonising or infecting the human respiratory tract. Taking into account interactions with other pathogens may be critical to determining the real influenza burden and the full impact of public health policies targeting influenza. This is particularly true for mathematical modelling studies, which have become critical in public health decision-making. Yet models usually focus on influenza virus acquisition and infection alone, thereby making broad oversimplifications of pathogen ecology. Herein, we report evidence of influenza virus interactions with bacteria and viruses and systematically review the modelling studies that have incorporated interactions. Despite the many studies examining possible associations between influenza and Streptococcus pneumoniae, Staphylococcus aureus, Haemophilus influenzae, Neisseria meningitidis, respiratory syncytial virus (RSV), human rhinoviruses, human parainfluenza viruses, etc., very few mathematical models have integrated other pathogens alongside influenza. The notable exception is the pneumococcus-influenza interaction, for which several recent modelling studies demonstrate the power of dynamic modelling as an approach to test biological hypotheses on interaction mechanisms and estimate the strength of those interactions. We explore how different interference mechanisms may lead to unexpected incidence trends and possible misinterpretation, and we illustrate the impact of interactions on public health surveillance using simple transmission models. We demonstrate that the development of multipathogen models is essential to assessing the true public health burden of influenza and that it is needed to help improve planning and evaluation of control measures. Finally, we identify the public health, surveillance, modelling, and biological challenges and propose avenues of research for the coming years.
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Affiliation(s)
- Lulla Opatowski
- Université de Versailles Saint Quentin, Institut Pasteur, Inserm, Paris, France
| | - Marc Baguelin
- London School of Hygiene & Tropical Medicine, London, United Kingdom
- Public Health England, London, United Kingdom
| | - Rosalind M. Eggo
- London School of Hygiene & Tropical Medicine, London, United Kingdom
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17
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Koch RM, Kox M, Thijs EJM, Rahamat-Langendoen JC, van de Veerdonk FL, Gerretsen J, Schloesser J, Diavatopoulos D, Rimmelzwaan GF, Netea MG, van der Hoeven JG, de Jonge MI, Pickkers P. Development of Endotoxin Tolerance Does Not Influence the Response to a Challenge with the Mucosal Live-Attenuated Influenza Vaccine in Humans In Vivo. Front Immunol 2017; 8:1600. [PMID: 29312282 PMCID: PMC5732479 DOI: 10.3389/fimmu.2017.01600] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 11/06/2017] [Indexed: 01/11/2023] Open
Abstract
Introduction The effects of bacterial infections on the response to subsequent viral infections are largely unknown. This is important to elucidate to increase insight into the pathophysiology of bacterial and viral co-infections, and to assess whether bacterial infections may influence the course of viral infections. Methods Healthy male subjects received either bacterial endotoxin [Escherichia coli-derived lipopolysaccharide (LPS), 2 ng/kg, n = 15] or placebo (n = 15) intravenously, followed by intranasal Fluenz (live-attenuated influenza vaccine) 1 week later. Results LPS administration resulted in increased plasma cytokine levels and development of endotoxin tolerance in vivo and ex vivo, illustrated by attenuated cytokine production upon rechallenge with LPS. Following Fluenz administration, infectivity for the Fluenz A/B strains was similar between the LPS-Fluenz and placebo-Fluenz groups (13/15 subjects in both groups). Also, the Fluenz-induced increase in temperature and IL-6, G-CSF and IP-10 concentrations in nasal wash were similar between both groups. Conclusion While endotoxemia profoundly attenuates the immune response upon a second LPS challenge, it does not influence the Fluenz-induced immune response. These results suggest immune suppression after bacterial infection does not alter the response to a subsequent viral infection.
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Affiliation(s)
- Rebecca M Koch
- Department of Intensive Care Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands.,Radboud Center for Infectious Diseases (RCI), Nijmegen, Netherlands
| | - Matthijs Kox
- Department of Intensive Care Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands.,Radboud Center for Infectious Diseases (RCI), Nijmegen, Netherlands
| | - Eleonora J M Thijs
- Department of Intensive Care Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Janette C Rahamat-Langendoen
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Frank L van de Veerdonk
- Radboud Center for Infectious Diseases (RCI), Nijmegen, Netherlands.,Department of Internal Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Jelle Gerretsen
- Department of Intensive Care Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands.,Radboud Center for Infectious Diseases (RCI), Nijmegen, Netherlands
| | | | - Dimitri Diavatopoulos
- Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Guus F Rimmelzwaan
- Department of Viroscience, Erasmus Medical Center, Rotterdam, Netherlands
| | - Mihai G Netea
- Radboud Center for Infectious Diseases (RCI), Nijmegen, Netherlands.,Department of Internal Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Johannes G van der Hoeven
- Department of Intensive Care Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands.,Radboud Center for Infectious Diseases (RCI), Nijmegen, Netherlands
| | - Marien I de Jonge
- Radboud Center for Infectious Diseases (RCI), Nijmegen, Netherlands.,Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Peter Pickkers
- Department of Intensive Care Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands.,Radboud Center for Infectious Diseases (RCI), Nijmegen, Netherlands
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18
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A Perfect Storm: Increased Colonization and Failure of Vaccination Leads to Severe Secondary Bacterial Infection in Influenza Virus-Infected Obese Mice. mBio 2017; 8:mBio.00889-17. [PMID: 28928207 PMCID: PMC5605935 DOI: 10.1128/mbio.00889-17] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Obesity is a risk factor for developing severe disease following influenza virus infection; however, the comorbidity of obesity and secondary bacterial infection, a serious complication of influenza virus infections, is unknown. To fill this gap in knowledge, lean and obese C57BL/6 mice were infected with a nonlethal dose of influenza virus followed by a nonlethal dose of Streptococcus pneumoniae Strikingly, not only did significantly enhanced death occur in obese coinfected mice compared to lean controls, but also high mortality was seen irrespective of influenza virus strain, bacterial strain, or timing of coinfection. This result was unexpected, given that most influenza virus strains, especially seasonal human A and B viruses, are nonlethal in this model. Both viral and bacterial titers were increased in the upper respiratory tract and lungs of obese animals as early as days 1 and 2 post-bacterial infection, leading to a significant decrease in lung function. This increased bacterial load correlated with extensive cellular damage and upregulation of platelet-activating factor receptor, a host receptor central to pneumococcal invasion. Importantly, while vaccination of obese mice against either influenza virus or pneumococcus failed to confer protection, antibiotic treatment was able to resolve secondary bacterial infection-associated mortality. Overall, secondary bacterial pneumonia could be a widespread, unaddressed public health problem in an increasingly obese population.IMPORTANCE Worldwide obesity rates have continued to increase. Obesity is associated with increased severity of influenza virus infection; however, very little is known about respiratory coinfections in this expanding, high-risk population. Our studies utilized a coinfection model to show that obesity increases mortality from secondary bacterial infection following influenza virus challenge through a "perfect storm" of host factors that lead to excessive viral and bacterial outgrowth. In addition, we found that vaccination of obese mice against either virus or bacteria failed to confer protection against coinfection, but antibiotic treatment did alleviate mortality. Combined, these results represent an understudied and imminent public health concern in a weighty portion of the global population.
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19
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Cheng YH, You SH, Lin YJ, Chen SC, Chen WY, Chou WC, Hsieh NH, Liao CM. Mathematical modeling of postcoinfection with influenza A virus and Streptococcus pneumoniae, with implications for pneumonia and COPD-risk assessment. Int J Chron Obstruct Pulmon Dis 2017; 12:1973-1988. [PMID: 28740377 PMCID: PMC5505164 DOI: 10.2147/copd.s138295] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Background The interaction between influenza and pneumococcus is important for understanding how coinfection may exacerbate pneumonia. Secondary pneumococcal pneumonia associated with influenza infection is more likely to increase respiratory morbidity and mortality. This study aimed to assess exacerbated inflammatory effects posed by secondary pneumococcal pneumonia, given prior influenza infection. Materials and methods A well-derived mathematical within-host dynamic model of coinfection with influenza A virus and Streptococcus pneumoniae (SP) integrated with dose–response relationships composed of previously published mouse experimental data and clinical studies was implemented to study potentially exacerbated inflammatory responses in pneumonia based on a probabilistic approach. Results We found that TNFα is likely to be the most sensitive biomarker reflecting inflammatory response during coinfection among three explored cytokines. We showed that the worst inflammatory effects would occur at day 7 SP coinfection, with risk probability of 50% (likely) to develop severe inflammatory responses. Our model also showed that the day of secondary SP infection had much more impact on the severity of inflammatory responses in pneumonia compared to the effects caused by initial virus titers and bacteria loads. Conclusion People and health care workers should be wary of secondary SP infection on day 7 post-influenza infection for prompt and proper control-measure implementation. Our quantitative risk-assessment framework can provide new insights into improvements in respiratory health especially, predominantly due to chronic obstructive pulmonary disease (COPD).
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Affiliation(s)
- Yi-Hsien Cheng
- Institute of Computational Comparative Medicine (ICCM), Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Shu-Han You
- National Institute of Environmental Health Sciences, National Health Research Institutes, Zhunan
| | - Yi-Jun Lin
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taipei
| | - Szu-Chieh Chen
- Department of Public Health.,Department of Family and Community Medicine, Chung Shan Medical University Hospital, Taichung
| | - Wei-Yu Chen
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Wei-Chun Chou
- National Institute of Environmental Health Sciences, National Health Research Institutes, Zhunan
| | - Nan-Hung Hsieh
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Chung-Min Liao
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taipei
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20
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Arduin H, Domenech de Cellès M, Guillemot D, Watier L, Opatowski L. An agent-based model simulation of influenza interactions at the host level: insight into the influenza-related burden of pneumococcal infections. BMC Infect Dis 2017; 17:382. [PMID: 28577533 PMCID: PMC5455134 DOI: 10.1186/s12879-017-2464-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 05/15/2017] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Host-level influenza virus-respiratory pathogen interactions are often reported. Although the exact biological mechanisms involved remain unelucidated, secondary bacterial infections are known to account for a large part of the influenza-associated burden, during seasonal and pandemic outbreaks. Those interactions probably impact the microorganisms' transmission dynamics and the influenza public health toll. Mathematical models have been widely used to examine influenza epidemics and the public health impact of control measures. However, most influenza models overlooked interaction phenomena and ignored other co-circulating pathogens. METHODS Herein, we describe a novel agent-based model (ABM) of influenza transmission during interaction with another respiratory pathogen. The interacting microorganism can persist in the population year round (endemic type, e.g. respiratory bacteria) or cause short-term annual outbreaks (epidemic type, e.g. winter respiratory viruses). The agent-based framework enables precise formalization of the pathogens' natural histories and complex within-host phenomena. As a case study, this ABM is applied to the well-known influenza virus-pneumococcus interaction, for which several biological mechanisms have been proposed. Different mechanistic hypotheses of interaction are simulated and the resulting virus-induced pneumococcal infection (PI) burden is assessed. RESULTS This ABM generates realistic data for both pathogens in terms of weekly incidences of PI cases, carriage rates, epidemic size and epidemic timing. Notably, distinct interaction hypotheses resulted in different transmission patterns and led to wide variations of the associated PI burden. Interaction strength was also of paramount importance: when influenza increased pneumococcus acquisition, 4-27% of the PI burden during the influenza season was attributable to influenza depending on the interaction strength. CONCLUSIONS This open-source ABM provides new opportunities to investigate influenza interactions from a theoretical point of view and could easily be extended to other pathogens. It provides a unique framework to generate in silico data for different scenarios and thereby test mechanistic hypotheses.
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Affiliation(s)
- Hélène Arduin
- Biostatistics, Biomathematics, Pharmacoepidemiology and Infectious Diseases, UMR1181 - Université de Versailles Saint Quentin en Yvelines, Inserm, Institut Pasteur, B2PHI Unit – Institut Pasteur, 25 rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Matthieu Domenech de Cellès
- Biostatistics, Biomathematics, Pharmacoepidemiology and Infectious Diseases, UMR1181 - Université de Versailles Saint Quentin en Yvelines, Inserm, Institut Pasteur, B2PHI Unit – Institut Pasteur, 25 rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Didier Guillemot
- Biostatistics, Biomathematics, Pharmacoepidemiology and Infectious Diseases, UMR1181 - Université de Versailles Saint Quentin en Yvelines, Inserm, Institut Pasteur, B2PHI Unit – Institut Pasteur, 25 rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Laurence Watier
- Biostatistics, Biomathematics, Pharmacoepidemiology and Infectious Diseases, UMR1181 - Université de Versailles Saint Quentin en Yvelines, Inserm, Institut Pasteur, B2PHI Unit – Institut Pasteur, 25 rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Lulla Opatowski
- Biostatistics, Biomathematics, Pharmacoepidemiology and Infectious Diseases, UMR1181 - Université de Versailles Saint Quentin en Yvelines, Inserm, Institut Pasteur, B2PHI Unit – Institut Pasteur, 25 rue du Docteur Roux, 75724 Paris Cedex 15, France
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21
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Domínguez-Hüttinger E, Boon NJ, Clarke TB, Tanaka RJ. Mathematical Modeling of Streptococcus pneumoniae Colonization, Invasive Infection and Treatment. Front Physiol 2017; 8:115. [PMID: 28303104 PMCID: PMC5332394 DOI: 10.3389/fphys.2017.00115] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 02/13/2017] [Indexed: 12/26/2022] Open
Abstract
Streptococcus pneumoniae (Sp) is a commensal bacterium that normally resides on the upper airway epithelium without causing infection. However, factors such as co-infection with influenza virus can impair the complex Sp-host interactions and the subsequent development of many life-threatening infectious and inflammatory diseases, including pneumonia, meningitis or even sepsis. With the increased threat of Sp infection due to the emergence of new antibiotic resistant Sp strains, there is an urgent need for better treatment strategies that effectively prevent progression of disease triggered by Sp infection, minimizing the use of antibiotics. The complexity of the host-pathogen interactions has left the full understanding of underlying mechanisms of Sp-triggered pathogenesis as a challenge, despite its critical importance in the identification of effective treatments. To achieve a systems-level and quantitative understanding of the complex and dynamically-changing host-Sp interactions, here we developed a mechanistic mathematical model describing dynamic interplays between Sp, immune cells, and epithelial tissues, where the host-pathogen interactions initiate. The model serves as a mathematical framework that coherently explains various in vitro and in vitro studies, to which the model parameters were fitted. Our model simulations reproduced the robust homeostatic Sp-host interaction, as well as three qualitatively different pathogenic behaviors: immunological scarring, invasive infection and their combination. Parameter sensitivity and bifurcation analyses of the model identified the processes that are responsible for qualitative transitions from healthy to such pathological behaviors. Our model also predicted that the onset of invasive infection occurs within less than 2 days from transient Sp challenges. This prediction provides arguments in favor of the use of vaccinations, since adaptive immune responses cannot be developed de novo in such a short time. We further designed optimal treatment strategies, with minimal strengths and minimal durations of antibiotics, for each of the three pathogenic behaviors distinguished by our model. The proposed mathematical framework will help to design better disease management strategies and new diagnostic markers that can be used to inform the most appropriate patient-specific treatment options.
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Affiliation(s)
- Elisa Domínguez-Hüttinger
- Department of Bioengineering, Imperial College LondonLondon, UK; Instituto de Ecología, Universidad Nacional Autónoma de MéxicoMexico City, Mexico
| | - Neville J Boon
- Department of Bioengineering, Imperial College London London, UK
| | | | - Reiko J Tanaka
- Department of Bioengineering, Imperial College London London, UK
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22
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Peripheral Leukocyte Migration in Ferrets in Response to Infection with Seasonal Influenza Virus. PLoS One 2016; 11:e0157903. [PMID: 27315117 PMCID: PMC4912066 DOI: 10.1371/journal.pone.0157903] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 06/07/2016] [Indexed: 12/31/2022] Open
Abstract
In order to better understand inflammation associated with influenza virus infection, we measured cell trafficking, via flow cytometry, to various tissues in the ferret model following infection with an A(H3N2) human seasonal influenza virus (A/Perth/16/2009). Changes in immune cells were observed in the blood, bronchoalveolar lavage fluid, and spleen, as well as lymph nodes associated with the site of infection or distant from the respiratory system. Nevertheless clinical symptoms were mild, with circulating leukocytes exhibiting rapid, dynamic, and profound changes in response to infection. Each of the biological compartments examined responded differently to influenza infection. Two days after infection, when infected ferrets showed peak fever, a marked, transient lymphopenia and granulocytosis were apparent in all infected animals. Both draining and distal lymph nodes demonstrated significant accumulation of T cells, B cells, and granulocytes at days 2 and 5 post-infection. CD8+ T cells significantly increased in spleen at days 2 and 5 post-infection; CD4+ T cells, B cells and granulocytes significantly increased at day 5. We interpret our findings as showing that lymphocytes exit the peripheral blood and differentially home to lymph nodes and tissues based on cell type and proximity to the site of infection. Monitoring leukocyte homing and trafficking will aid in providing a more detailed view of the inflammatory impact of influenza virus infection.
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Qin Z, Yang Y, Wang H, Luo J, Huang X, You J, Wang B, Li M. Role of Autophagy and Apoptosis in the Postinfluenza Bacterial Pneumonia. BIOMED RESEARCH INTERNATIONAL 2016; 2016:3801026. [PMID: 27376082 PMCID: PMC4916274 DOI: 10.1155/2016/3801026] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 04/05/2016] [Accepted: 05/16/2016] [Indexed: 12/19/2022]
Abstract
The risk of influenza A virus (IAV) is more likely caused by secondary bacterial infections. During the past decades, a great amount of studies have been conducted on increased morbidity from secondary bacterial infections following influenza and provide an increasing number of explanations for the mechanisms underlying the infections. In this paper, we first review the recent research progress that IAV infection increased susceptibility to bacterial infection. We then propose an assumption that autophagy and apoptosis manipulation are beneficial to antagonize post-IAV bacterial infection and discuss the clinical significance.
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Affiliation(s)
- Zhen Qin
- Department of Microbiology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yuan Yang
- Department of Microbiology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, China
| | - Hongren Wang
- Department of Microbiology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, China
| | - Jun Luo
- Department of Microbiology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, China
| | - Xiaojun Huang
- Department of Microbiology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, China
| | - Jiangzhou You
- Department of Microbiology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, China
| | - Baoning Wang
- Department of Microbiology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, China
| | - Mingyuan Li
- Department of Microbiology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, China
- State Key Laboratory of Oral Diseases, Sichuan University, Chengdu, Sichuan 610041, China
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Schirm S, Ahnert P, Wienhold S, Mueller-Redetzky H, Nouailles-Kursar G, Loeffler M, Witzenrath M, Scholz M. A Biomathematical Model of Pneumococcal Lung Infection and Antibiotic Treatment in Mice. PLoS One 2016; 11:e0156047. [PMID: 27196107 PMCID: PMC4873198 DOI: 10.1371/journal.pone.0156047] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 05/09/2016] [Indexed: 11/18/2022] Open
Abstract
Pneumonia is considered to be one of the leading causes of death worldwide. The outcome depends on both, proper antibiotic treatment and the effectivity of the immune response of the host. However, due to the complexity of the immunologic cascade initiated during infection, the latter cannot be predicted easily. We construct a biomathematical model of the murine immune response during infection with pneumococcus aiming at predicting the outcome of antibiotic treatment. The model consists of a number of non-linear ordinary differential equations describing dynamics of pneumococcal population, the inflammatory cytokine IL-6, neutrophils and macrophages fighting the infection and destruction of alveolar tissue due to pneumococcus. Equations were derived by translating known biological mechanisms and assuming certain response kinetics. Antibiotic therapy is modelled by a transient depletion of bacteria. Unknown model parameters were determined by fitting the predictions of the model to data sets derived from mice experiments of pneumococcal lung infection with and without antibiotic treatment. Time series of pneumococcal population, debris, neutrophils, activated epithelial cells, macrophages, monocytes and IL-6 serum concentrations were available for this purpose. The antibiotics Ampicillin and Moxifloxacin were considered. Parameter fittings resulted in a good agreement of model and data for all experimental scenarios. Identifiability of parameters is also estimated. The model can be used to predict the performance of alternative schedules of antibiotic treatment. We conclude that we established a biomathematical model of pneumococcal lung infection in mice allowing predictions regarding the outcome of different schedules of antibiotic treatment. We aim at translating the model to the human situation in the near future.
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Affiliation(s)
- Sibylle Schirm
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Peter Ahnert
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Sandra Wienhold
- Department of Internal Medicine/Infectious Diseases and Respiratory Medicine Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Holger Mueller-Redetzky
- Department of Internal Medicine/Infectious Diseases and Respiratory Medicine Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Geraldine Nouailles-Kursar
- Department of Internal Medicine/Infectious Diseases and Respiratory Medicine Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Markus Loeffler
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Martin Witzenrath
- Department of Internal Medicine/Infectious Diseases and Respiratory Medicine Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Markus Scholz
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE Research Center of Civilization Diseases, University of Leipzig, Leipzig, Germany
- * E-mail:
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Handel A, Rohani P. Crossing the scale from within-host infection dynamics to between-host transmission fitness: a discussion of current assumptions and knowledge. Philos Trans R Soc Lond B Biol Sci 2016; 370:rstb.2014.0302. [PMID: 26150668 DOI: 10.1098/rstb.2014.0302] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The progression of an infection within a host determines the ability of a pathogen to transmit to new hosts and to maintain itself in the population. While the general connection between the infection dynamics within a host and the population-level transmission dynamics of pathogens is widely acknowledged, a comprehensive and quantitative understanding that would allow full integration of the two scales is still lacking. Here, we provide a brief discussion of both models and data that have attempted to provide quantitative mappings from within-host infection dynamics to transmission fitness. We present a conceptual framework and provide examples of studies that have taken first steps towards development of a quantitative framework that scales from within-host infections to population-level fitness of different pathogens. We hope to illustrate some general themes, summarize some of the recent advances and-maybe most importantly-discuss gaps in our ability to bridge these scales, and to stimulate future research on this important topic.
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Affiliation(s)
- Andreas Handel
- Department of Epidemiology and Biostatistics, College of Public Health, University of Georgia, Athens, GA 30602, USA
| | - Pejman Rohani
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA Center for the Study of Complex Systems, University of Michigan, Ann Arbor, MI 48109, USA Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA
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Shrestha S, Foxman B, Berus J, van Panhuis WG, Steiner C, Viboud C, Rohani P. The role of influenza in the epidemiology of pneumonia. Sci Rep 2015; 5:15314. [PMID: 26486591 PMCID: PMC4614252 DOI: 10.1038/srep15314] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 09/15/2015] [Indexed: 12/25/2022] Open
Abstract
Interactions arising from sequential viral and bacterial infections play important roles in the epidemiological outcome of many respiratory pathogens. Influenza virus has been implicated in the pathogenesis of several respiratory bacterial pathogens commonly associated with pneumonia. Though clinical evidence supporting this interaction is unambiguous, its population-level effects-magnitude, epidemiological impact and variation during pandemic and seasonal outbreaks-remain unclear. To address these unknowns, we used longitudinal influenza and pneumonia incidence data, at different spatial resolutions and across different epidemiological periods, to infer the nature, timing and the intensity of influenza-pneumonia interaction. We used a mechanistic transmission model within a likelihood-based inference framework to carry out formal hypothesis testing. Irrespective of the source of data examined, we found that influenza infection increases the risk of pneumonia by ~100-fold. We found no support for enhanced transmission or severity impact of the interaction. For model-validation, we challenged our fitted model to make out-of-sample pneumonia predictions during pandemic and non-pandemic periods. The consistency in our inference tests carried out on several distinct datasets, and the predictive skill of our model increase confidence in our overall conclusion that influenza infection substantially enhances the risk of pneumonia, though only for a short period.
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Affiliation(s)
- Sourya Shrestha
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Center for the Study of Complex Systems, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Epidemiology, Johns Hopkins School of Public Health, Baltimore, MD 21205, USA
| | - Betsy Foxman
- Department of Epidemiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Joshua Berus
- Undergraduate Research Opportunity Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - Willem G. van Panhuis
- Department of Epidemiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh PA 15261, USA
| | - Claudia Steiner
- Healthcare Cost and Utilization Project, Center for Delivery, Organization and Markets, Agency for Healthcare Research and Quality, U.S. Department of Health and Human Services, Rockville, MD 20850, USA
| | - Cécile Viboud
- Division of International Epidemiology and Population Studies, National Institutes of Health, Bethesda, MD 20892, USA
| | - Pejman Rohani
- Odum School of Ecology, University of Georgia, Athens, GA 30602, USA
- Department of Infectious Diseases, School of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
- Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA
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Song JY, Nahm MH, Cheong HJ, Kim WJ. Impact of preceding flu-like illness on the serotype distribution of pneumococcal pneumonia. PLoS One 2014; 9:e93477. [PMID: 24691515 PMCID: PMC3972234 DOI: 10.1371/journal.pone.0093477] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Accepted: 03/03/2014] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Even though the pathogenicity and invasiveness of pneumococcus largely depend on capsular types, the impact of serotypes on post-viral pneumococcal pneumonia is unknown. METHODS AND FINDINGS This study was performed to evaluate the impact of capsular serotypes on the development of pneumococcal pneumonia after preceding respiratory viral infections. Patients with a diagnosis of pneumococcal pneumonia were identified. Pneumonia patients were divided into two groups (post-viral pneumococcal pneumonia versus primary pneumococcal pneumonia), and then their pneumococcal serotypes were compared. Nine hundred and nineteen patients with pneumococcal pneumonia were identified during the study period, including 327 (35.6%) cases with post-viral pneumococcal pneumonia and 592 (64.4%) cases with primary pneumococcal pneumonia. Overall, serotypes 3 and 19A were the most prevalent, followed by serotypes 19F, 6A, and 11A/11E. Although relatively uncommon (33 cases, 3.6%), infrequently colonizing invasive serotypes (4, 5, 7F/7A, 8, 9V/9A, 12F, and 18C) were significantly associated with preceding respiratory viral infections (69.7%, P<0.01). Multivariate analysis revealed several statistically significant risk factors for post-viral pneumococcal pneumonia: immunodeficiency (OR 1.66; 95% CI, 1.10-2.53), chronic lung diseases (OR 1.43; 95% CI, 1.09-1.93) and ICI serotypes (OR 4.66; 95% CI, 2.07-10.47). CONCLUSIONS Infrequently colonizing invasive serotypes would be more likely to cause pneumococcal pneumonia after preceding respiratory viral illness, particularly in patients with immunodeficiency or chronic lung diseases.
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Affiliation(s)
- Joon Young Song
- Department of Pathology, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Division of Infectious Diseases, Department of Internal Medicine, Korea University College of medicine, Seoul, Republic of Korea
| | - Moon H. Nahm
- Department of Pathology, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Department of Microbiology, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Hee Jin Cheong
- Division of Infectious Diseases, Department of Internal Medicine, Korea University College of medicine, Seoul, Republic of Korea
| | - Woo Joo Kim
- Division of Infectious Diseases, Department of Internal Medicine, Korea University College of medicine, Seoul, Republic of Korea
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