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Zubiria-Barrera C, Yamba LY, Klassert TE, Bos M, Ahl J, Wasserstrom L, Slevogt H, Riesbeck K. Profiling the nasopharyngeal Microbiome in patients with community-acquired pneumonia caused by Streptococcus pneumoniae: diagnostic challenges and ecological insights. Med Microbiol Immunol 2025; 214:19. [PMID: 40208342 PMCID: PMC11985632 DOI: 10.1007/s00430-025-00828-0] [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: 11/11/2024] [Accepted: 03/23/2025] [Indexed: 04/11/2025]
Abstract
Community-acquired pneumonia (CAP) is a significant health threat for adults. Although conjugate vaccines have reduced pneumococcal CAP incidence in children, Streptococcus pneumoniae-related CAP remains prevalent among older adults. The nasopharynx acts as a reservoir for S. pneumoniae, yet the interplay between this pathogen and the nasopharyngeal microbiome during and after pneumonia remains poorly understood. This study included 61 adult patients diagnosed with pneumococcal CAP and 61 matched healthy controls. An S. pneumoniae-specific PCR, urine antigen tests and bacterial cultures were performed. Nasopharyngeal swabs collected at admission and three months post-infection were analyzed for microbiome dynamics through 16 S rRNA gene amplicon sequencing. 16 S rRNA gene amplicon sequencing revealed Streptococcus spp. in the majority of all nasopharyngeal samples during infection compared to the other diagnostic test performed. While overall bacterial biomass did not differ between groups, patients exhibited higher alpha diversity (p = 0.012) and lower microbiome stability post-infection. Beta diversity analysis distinguished infection from healthy status (p = 0.002). Taxonomic analysis showed similar core microbiota across groups, but Streptococcus spp. was significantly more abundant during infection, particularly in those patients with viral co-infections. Notably, unique significant bacterial interactions were identified both during and after infection, as well as in healthy states. A negative correlation was observed between Corynebacterium and Streptococcus spp. in infected patients, suggesting a potential antagonistic interaction between these taxa. The nasopharyngeal microbiome in patients with pneumococcal CAP demonstrates persistent disruption post-infection, characterized by lower resilience three months after acute illness. Additionally, we identified specific bacterial interplays during and after infection that differed from those in healthy donors. These bacterial dynamics might play critical roles in pathogen colonization resistance and infection prevention. Thus, our findings highlight the need for further investigation into microbial interactions and potential microbiome-based therapies for respiratory infections, particularly in vulnerable populations.
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Affiliation(s)
- Cristina Zubiria-Barrera
- Department of Respiratory Medicine and Infectious Diseases, MHH, German Center for Lung Research (DZL), BREATH, Hannover, Germany.
- Respiratory Infection Dynamics Group, Helmholtz Centre for Infection Research, Braunschweig, Germany.
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Carl-Neuberg-Straße 1, 30625, Hannover, Germany.
| | - Linda Yamba Yamba
- Clinical Microbiology, Department of Translational Medicine, Faculty of Medicine, Lund University, Malmö, Sweden
- Clinical Microbiology, Infection Control and Prevention, Skåne University Hospital, Lund, Sweden
| | - Tilman E Klassert
- Department of Respiratory Medicine and Infectious Diseases, MHH, German Center for Lung Research (DZL), BREATH, Hannover, Germany
- Respiratory Infection Dynamics Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Carl-Neuberg-Straße 1, 30625, Hannover, Germany
| | - Malena Bos
- Department of Respiratory Medicine and Infectious Diseases, MHH, German Center for Lung Research (DZL), BREATH, Hannover, Germany
- Respiratory Infection Dynamics Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Carl-Neuberg-Straße 1, 30625, Hannover, Germany
| | - Jonas Ahl
- Clinical Microbiology, Department of Translational Medicine, Faculty of Medicine, Lund University, Malmö, Sweden
- Infectious Diseases, Department of Translational Medicine, Faculty of Medicine, Lund University, Malmö, Sweden
| | - Lisa Wasserstrom
- Clinical Microbiology, Department of Translational Medicine, Faculty of Medicine, Lund University, Malmö, Sweden
- Clinical Microbiology, Infection Control and Prevention, Skåne University Hospital, Lund, Sweden
| | - Hortense Slevogt
- Department of Respiratory Medicine and Infectious Diseases, MHH, German Center for Lung Research (DZL), BREATH, Hannover, Germany
- Respiratory Infection Dynamics Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Carl-Neuberg-Straße 1, 30625, Hannover, Germany
| | - Kristian Riesbeck
- Clinical Microbiology, Department of Translational Medicine, Faculty of Medicine, Lund University, Malmö, Sweden
- Clinical Microbiology, Infection Control and Prevention, Skåne University Hospital, Lund, Sweden
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Odendaal ML, Chu MLJN, Arp K, van Beveren GJ, Biesbroek G, Binkowska J, Bosch T, Groot JA, Hasrat R, Kuiling S, van Logchem EM, Parga PL, de Steenhuijsen Piters WAA, Bogaert D. Protocol for microbial profiling of low-biomass upper respiratory tract samples. STAR Protoc 2025; 6:103740. [PMID: 40198218 PMCID: PMC12008583 DOI: 10.1016/j.xpro.2025.103740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2024] [Revised: 01/31/2025] [Accepted: 03/12/2025] [Indexed: 04/10/2025] Open
Abstract
The upper respiratory tract (URT) microbiota plays a role in both acute and chronic respiratory health outcomes and consists of multiple ecologically distinct niches, all of which have low bacterial biomass. Here, we present a protocol for microbial profiling of low-biomass URT samples. We describe steps for collecting, storing, and extracting DNA. We then detail procedures for performing 16S rRNA sequencing, using an Illumina MiSeq platform, to characterize microbial communities. For complete details on the use and execution of this protocol, please refer to Odendaal et al.1.
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Affiliation(s)
- Mari-Lee Odendaal
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands; Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, the Netherlands
| | - Mei Ling J N Chu
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands; Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht, the Netherlands.
| | - Kayleigh Arp
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands; Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht, the Netherlands
| | - Gina J van Beveren
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht, the Netherlands; Spaarne Gasthuis Academy, Spaarne Gasthuis, Hoofddorp, the Netherlands
| | - Giske Biesbroek
- Department of Pediatric Immunology, Rheumatology and Infectious Diseases, Emma Children's Hospital, University Medical Center (Amsterdam UMC), Location Academic Medical Center (AMC), University of Amsterdam, Amsterdam, the Netherlands
| | - Justyna Binkowska
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - Thijs Bosch
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - James A Groot
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Raiza Hasrat
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands; Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht, the Netherlands
| | - Sjoerd Kuiling
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Elske M van Logchem
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Paula Lusarreta Parga
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - Wouter A A de Steenhuijsen Piters
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands; Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht, the Netherlands
| | - Debby Bogaert
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht, the Netherlands; Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK.
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3
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Peno C, Jagne YJ, Clerc M, Balcazar Lopez C, Armitage EP, Sallah H, Drammeh S, Senghore E, Goderski G, van Tol S, Meijer A, Ruiz-Rodriguez A, de Steenhuijsen Piters W, de Koff E, Jarju S, Lindsey BB, Camara J, Bah S, Mohammed NI, Kampmann B, Clarke E, Dockrell DH, de Silva TI, Bogaert D. Interactions between live attenuated influenza vaccine and nasopharyngeal microbiota among children aged 24-59 months in The Gambia: a phase 4, open-label, randomised controlled trial. THE LANCET. MICROBE 2025; 6:100971. [PMID: 39832517 DOI: 10.1016/j.lanmic.2024.100971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/13/2024] [Accepted: 08/02/2024] [Indexed: 01/22/2025]
Abstract
BACKGROUND Live attenuated influenza vaccines (LAIVs) alter nasopharyngeal microbiota in adults. It is poorly understood why LAIV immunogenicity varies across populations, but it could be linked to the microbiome. We aimed to investigate the interactions between intranasal immunisation with LAIV and nasopharyngeal microbiota composition in children from The Gambia. METHODS We conducted a phase 4, open-label, randomised controlled trial in Sukuta, The Gambia. Children aged 24-59 months with no underlying illness or history of respiratory illness for at least 14 days before recruitment were eligible. Participants were randomly assigned (2:1) by use of a computer-generated sequence in permuted blocks of 15, stratified by sex, to receive trivalent LAIV either on day 0 (intervention group) or after active follow-up at day 21 (control group). The investigator team was initially masked to block size and randomisation sequence; however, group allocation was later revealed to the team. Microbiome profiles were characterised from nasopharyngeal samples collected from all participants on days 0, 7, and 21 by use of 16S rRNA sequencing. The primary outcomes were the effect of LAIV on nasopharyngeal microbiome profiles on day 7 and day 21, and the association between the nasopharyngeal microbiome at baseline and LAIV-induced mucosal IgA responses at day 21, assessed with permutational ANOVA tests. Asymptomatic respiratory viral co-infection at baseline and year of recruitment (2017 or 2018) were included as covariates. This trial is registered with ClinicalTrials.gov (NCT02972957) and is closed. FINDINGS Between Feb 8 and April 12, 2017, and Jan 15 and March 28, 2018, 343 children were screened for eligibility, of whom 220 (64%) children were randomly assigned to the intervention group and 110 (32%) to the control group. 213 (97%) children in the intervention group and 108 (98%) in the control group completed the study and were included in the final analysis. Although we did not observe an independent effect of LAIV on microbial community composition at days 7 or 21, we found that LAIV had an effect dependent on the year of recruitment. LAIV affected microbial community composition in 2018 (R2 1·97% [95% CI 0·85-5·94]; p=0·037), but not in 2017 (1·23% [0·49-4·46]; p=0·091). We also found that viral co-infection at baseline had an effect on microbial composition at day 7, regardless of recruitment year (R2 1·01% [95% CI 0·28-3·01]; p=0·026). Nasopharyngeal microbial community composition at baseline had no effect on mucosal IgA responses to LAIV administration (R2 0·51% [95% CI 0·23-2·49]; p=0·46). INTERPRETATION Our findings suggest that the effect of LAIVs on nasopharyngeal microbiota composition in children is modest and temporary; therefore, LAIVs could be used as an intervention to curb influenza in children from low-income and middle-income countries, without causing long-lasting perturbations in nasopharyngeal microbiota. However, nasopharyngeal microbiota at the time of vaccination might not explain the variability observed between individuals in LAIV-induced IgA responses. FUNDING The Wellcome Trust, UK National Institute for Health Research, and Chief Scientist Office Scotland.
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Affiliation(s)
- Chikondi Peno
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Ya Jankey Jagne
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Melanie Clerc
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Carlos Balcazar Lopez
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Edwin P Armitage
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Hadijatou Sallah
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Sainabou Drammeh
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Elina Senghore
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Gabriel Goderski
- Centre for Infectious Disease Research, Diagnostics and Laboratory Surveillance, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Sophie van Tol
- Centre for Infectious Disease Research, Diagnostics and Laboratory Surveillance, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Adam Meijer
- Centre for Infectious Disease Research, Diagnostics and Laboratory Surveillance, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Alicia Ruiz-Rodriguez
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Wouter de Steenhuijsen Piters
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital-University Medical Center Utrecht, Utrecht, Netherlands
| | - Emma de Koff
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital-University Medical Center Utrecht, Utrecht, Netherlands
| | - Sheikh Jarju
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Benjamin B Lindsey
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia; Centre for International Child Health, Section of Paediatrics, Department of Medicine, Imperial College London, London, UK
| | - Janko Camara
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Sulayman Bah
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Nuredin I Mohammed
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Beate Kampmann
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia; The Vaccine Centre, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Ed Clarke
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - David H Dockrell
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Thushan I de Silva
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia; Division of Clinical Medicine, School of Medicine and Population Health, University of Sheffield, Sheffield, UK
| | - Debby Bogaert
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK; Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital-University Medical Center Utrecht, Utrecht, Netherlands.
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Baker JM, Dickson RP. The Microbiome and Pulmonary Immune Function. Clin Chest Med 2025; 46:77-91. [PMID: 39890294 DOI: 10.1016/j.ccm.2024.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2025]
Abstract
In the last decade, the lung microbiome field has matured into a promising area of translational and clinical research due to emerging evidence indicating a role for respiratory microbiota in lung immunity and pathogenesis. Here, we review recent insights pertaining to the lung microbiome's relationship with pulmonary immune function. We discuss areas of future investigation that will be essential to the development of immunomodulatory therapies targeting the respiratory microbiome.
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Affiliation(s)
- Jennifer M Baker
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA; Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Robert P Dickson
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA; Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA; Weil Institute for Critical Care Research & Innovation, Ann Arbor, MI, USA.
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5
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Tepekule B, Barcik W, Staiger WI, Bergadà-Pijuan J, Scheier T, Brülisauer L, Hall AR, Günthard HF, Hilty M, Kouyos RD, Brugger SD. Computational and in vitro evaluation of probiotic treatments for nasal Staphylococcus aureus decolonization. Proc Natl Acad Sci U S A 2025; 122:e2412742122. [PMID: 39932999 PMCID: PMC11848298 DOI: 10.1073/pnas.2412742122] [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: 06/25/2024] [Accepted: 01/07/2025] [Indexed: 02/13/2025] Open
Abstract
Despite the rising challenge of antibiotic resistance, current approaches to eradicate nasal pathobionts Staphylococcus aureus and Streptococcus pneumoniae rely on antibacterials. An alternative is the artificial inoculation of commensal bacteria, i.e., probiotic treatment, supported by the increasing evidence for commensal-mediated inhibition of pathogens. To systematically investigate the potential of this approach, we developed a quantitative framework simulating the nasal microbiome dynamics by combining mathematical modeling with longitudinal microbiota data. By inferring community parameters using 16S ribosomal RNA (rRNA) amplicon sequencing data and simulating the nasal microbial dynamics of patients colonized with S. aureus, we compared the decolonization performance of probiotic and antibiotic treatments under different assumptions on patients' community composition and susceptibility profile. To further compare the robustness of these treatments, we simulated an S. aureus challenge and quantified the recolonization probability. Through in vitro experiments using nasal swabs of adults colonized with S. aureus, we confirmed that after antibiotic treatment, recolonization of S. aureus was inhibited in samples treated with a probiotic mixture compared to the nontreated control. Our results suggest that probiotic treatment outperforms antibiotics in terms of decolonization performance, recolonization robustness, and leads to less collateral reduction in the microbiome diversity. Thus, probiotic treatment may provide a promising alternative to combat antibiotic resistance, with the additional advantage of personalized treatment options via using the patient's own metagenomic data. The combination of an in silico framework with in vitro experiments using clinical samples reported in this work is an important step forward to further investigate this alternative in clinical trials.
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Affiliation(s)
- Burcu Tepekule
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich8091, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich8057, Switzerland
| | - Weronika Barcik
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich8091, Switzerland
| | - Willy I. Staiger
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich8091, Switzerland
| | - Judith Bergadà-Pijuan
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich8091, Switzerland
| | - Thomas Scheier
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich8091, Switzerland
| | - Laura Brülisauer
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zurich, Zurich8092, Switzerland
| | - Alex R. Hall
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zurich, Zurich8092, Switzerland
| | - Huldrych F. Günthard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich8091, Switzerland
| | - Markus Hilty
- Institute for Infectious Diseases, University of Bern, Bern3001, Switzerland
| | - Roger D. Kouyos
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich8091, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich8057, Switzerland
| | - Silvio D. Brugger
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich8091, Switzerland
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Lei Y, Li M, Zhang H, Deng Y, Dong X, Chen P, Li Y, Zhang S, Li C, Wang S, Tao R. Comparative analysis of the human microbiome from four different regions of China and machine learning-based geographical inference. mSphere 2025; 10:e0067224. [PMID: 39699186 PMCID: PMC11774049 DOI: 10.1128/msphere.00672-24] [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: 08/11/2024] [Accepted: 11/22/2024] [Indexed: 12/20/2024] Open
Abstract
The human microbiome, the community of microorganisms that reside on and inside the human body, is critically important for health and disease. However, it is influenced by various factors and may vary among individuals residing in distinct geographic regions. In this study, 220 samples, consisting of sterile swabs from palmar skin and oral and nasal cavities were collected from Chinese Han individuals living in Shanghai, Chifeng, Kunming, and Urumqi, representing the geographic regions of east, northeast, southwest, and northwest China. The full-length 16S rRNA gene of the microbiota in each sample was sequenced using the PacBio single-molecule real-time sequencing platform, followed by clustering the sequences into operational taxonomic units (OTUs). The analysis revealed significant differences in microbial communities among the four regions. Cutibacterium was the most abundant bacterium in palmar samples from Shanghai and Kunming, Psychrobacter in Chifeng samples, and Psychrobacillus in Urumqi samples. Additionally, Streptococcus and Staphylococcus were the dominant bacteria in the oral and nasal cavities. Individuals from the four regions could be distinguished and predicted based on a model constructed using the random forest algorithm, with the predictive effect of palmar microbiota being better than that of oral and nasal cavities. The prediction accuracy using hypervariable regions (V3-V4 and V4-V5) was comparable with that of using the entire 16S rRNA. Overall, our study highlights the distinctiveness of the human microbiome in individuals living in these four regions. Furthermore, the microbiome can serve as a biomarker for geographic origin inference, which has immense application value in forensic science.IMPORTANCEMicrobial communities in human hosts play a significant role in health and disease, varying in species, quantity, and composition due to factors such as gender, ethnicity, health status, lifestyle, and living environment. The characteristics of microbial composition at various body sites of individuals from different regions remain largely unexplored. This study utilized single-molecule real-time sequencing technology to detect the entire 16S rRNA gene of bacteria residing in the palmar skin, oral, and nasal cavities of Han individuals from four regions in China. The composition and structure of the bacteria at these three body sites were well characterized and found to differ regionally. The results elucidate the differences in bacterial communities colonizing these body sites across different regions and reveal the influence of geographical factors on human bacteria. These findings not only contribute to a deeper understanding of the diversity and geographical distribution of human bacteria but also enrich the microbiome data of the Asian population for further studies.
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Affiliation(s)
- Yinlei Lei
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Key Laboratory of Forensic Science, Ministry of Justice, Shanghai, China
- Department of Forensic Medicine, Zunyi Medical University, Zunyi, China
| | - Min Li
- School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Han Zhang
- Institute of Forensic Science, Fudan University, Shanghai, China
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Yu Deng
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Key Laboratory of Forensic Science, Ministry of Justice, Shanghai, China
- Department of Forensic Medicine, Zunyi Medical University, Zunyi, China
| | - Xinyu Dong
- Minhang Branch of Shanghai Public Security Bureau, Shanghai, China
| | - Pengyu Chen
- Department of Forensic Medicine, Zunyi Medical University, Zunyi, China
| | - Ye Li
- Department of Forensic Medicine, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, China
| | - Suhua Zhang
- Institute of Forensic Science, Fudan University, Shanghai, China
| | - Chengtao Li
- Institute of Forensic Science, Fudan University, Shanghai, China
| | - Shouyu Wang
- Department of Forensic Medicine, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ruiyang Tao
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Key Laboratory of Forensic Science, Ministry of Justice, Shanghai, China
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7
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Besteman SB, Bogaert D, Bont L, Mejias A, Ramilo O, Weinberger DM, Dagan R. Interactions between respiratory syncytial virus and Streptococcus pneumoniae in the pathogenesis of childhood respiratory infections: a systematic review. THE LANCET. RESPIRATORY MEDICINE 2024; 12:915-932. [PMID: 38991585 DOI: 10.1016/s2213-2600(24)00148-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 03/11/2024] [Accepted: 05/03/2024] [Indexed: 07/13/2024]
Abstract
Lower respiratory tract infections, commonly caused by respiratory syncytial virus (RSV) or Streptococcus pneumoniae (pneumococcus), pose a substantial global health burden, especially in children younger than 5 years of age. A deeper understanding of the relationship between RSV and pneumococcus would aid the development of health-care approaches to disease prevention and management. We completed a systematic review to identify and assess evidence pertaining to the relationship between RSV and pneumococcus in the pathogenesis of childhood respiratory infections. We found mechanistic evidence for direct pathogen-pathogen interactions and for indirect interactions involving host modulation. We found a strong seasonal epidemiological association between these two pathogens, which was recently confirmed by a parallel decrease and a subsequent resurgence of both RSV and pneumococcus-associated disease during the COVID-19 pandemic. Importantly, we found that pneumococcal vaccination was associated with reduced RSV hospitalisations in infants, further supporting the relevance of their interaction in modulating severe disease. Overall evidence supports a broad biological and clinical interaction between pneumococcus and RSV in the pathogenesis of childhood respiratory infections. We hypothesise that the implementation of next-generation pneumococcal and RSV vaccines and monoclonal antibodies targeting RSV will act synergistically to reduce global morbidity and mortality related to childhood respiratory infections.
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Affiliation(s)
- Sjanna B Besteman
- Department of Pediatrics, Onze Lieve Vrouwe Gasthuis Ziekenhuis, Amsterdam, Netherlands
| | - Debby Bogaert
- Department of Pediatric Immunology and Infectious Diseases, University Medical Center Utrecht, Utrecht, Netherlands; Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - Louis Bont
- Department of Pediatric Immunology and Infectious Diseases, University Medical Center Utrecht, Utrecht, Netherlands
| | - Asuncion Mejias
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Octavio Ramilo
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Daniel M Weinberger
- Department of Epidemiology of Microbial Diseases and Public Health Modeling Unit, Yale School of Public Health, New Haven, CT, USA
| | - Ron Dagan
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
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8
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Mitsi E, Nikolaou E, Goncalves A, Blizard A, Hill H, Farrar M, Hyder-Wright A, Akeju O, Hamilton J, Howard A, Elterish F, Solorzano C, Robinson R, Reiné J, Collins AM, Gordon SB, Moxon RE, Weiser JN, Bogaert D, Ferreira DM. RSV and rhinovirus increase pneumococcal carriage acquisition and density, whereas nasal inflammation is associated with bacterial shedding. Cell Host Microbe 2024; 32:1608-1620.e4. [PMID: 39181126 DOI: 10.1016/j.chom.2024.07.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 06/14/2024] [Accepted: 07/29/2024] [Indexed: 08/27/2024]
Abstract
Epidemiological studies report the impact of co-infection with pneumococcus and respiratory viruses upon disease rates and outcomes, but their effect on pneumococcal carriage acquisition and bacterial load is scarcely described. Here, we assess this by combining natural viral infection with controlled human pneumococcal infection in 581 healthy adults screened for upper respiratory tract viral infection before intranasal pneumococcal challenge. Across all adults, respiratory syncytial virus (RSV) and rhinovirus asymptomatic infection confer a substantial increase in secondary infection with pneumococcus. RSV also has a major impact on pneumococcal density up to 9 days post challenge. We also study rates and kinetics of bacterial shedding through the nose and oral route in a subset. High levels of pneumococcal colonization density and nasal inflammation are strongly correlated with increased odds of nasal shedding as opposed to cough shedding. Protection against respiratory viral infections and control of pneumococcal density may contribute to preventing pneumococcal disease and reducing bacterial spread.
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Affiliation(s)
- Elena Mitsi
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford OX3 7LE, UK; Clinical Sciences Department, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK.
| | - Elissavet Nikolaou
- Clinical Sciences Department, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK; Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC 3052, Australia
| | - Andre Goncalves
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford OX3 7LE, UK; Clinical Sciences Department, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
| | - Annie Blizard
- Clinical Sciences Department, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
| | - Helen Hill
- Clinical Sciences Department, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
| | - Madlen Farrar
- Clinical Sciences Department, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
| | - Angela Hyder-Wright
- Clinical Sciences Department, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
| | - Oluwasefunmi Akeju
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford OX3 7LE, UK
| | - Josh Hamilton
- Clinical Sciences Department, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
| | - Ashleigh Howard
- Clinical Sciences Department, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
| | - Filora Elterish
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford OX3 7LE, UK
| | - Carla Solorzano
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford OX3 7LE, UK; Clinical Sciences Department, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
| | - Ryan Robinson
- Clinical Sciences Department, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
| | - Jesus Reiné
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford OX3 7LE, UK; Clinical Sciences Department, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
| | - Andrea M Collins
- Clinical Sciences Department, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
| | - Stephen B Gordon
- Clinical Sciences Department, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK; Malawi Liverpool Wellcome-Trust Programme, Queen Elizabeth Central Hospital Campus, P.O. Box 30096, Blantyre, Malawi
| | - Richard E Moxon
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford OX3 7LE, UK
| | - Jeffrey N Weiser
- Department of Microbiology, New York University School of Medicine, New York, NY 10016, USA
| | - Debby Bogaert
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK; Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Centre Utrecht, 3584 EA Utrecht, the Netherlands
| | - Daniela M Ferreira
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford OX3 7LE, UK; Clinical Sciences Department, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK.
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9
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Berni Canani R, Caminati M, Carucci L, Eguiluz-Gracia I. Skin, gut, and lung barrier: Physiological interface and target of intervention for preventing and treating allergic diseases. Allergy 2024; 79:1485-1500. [PMID: 38439599 DOI: 10.1111/all.16092] [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: 09/05/2023] [Revised: 02/21/2024] [Accepted: 02/23/2024] [Indexed: 03/06/2024]
Abstract
The epithelial barriers of the skin, gut, and respiratory tract are critical interfaces between the environment and the host, and they orchestrate both homeostatic and pathogenic immune responses. The mechanisms underlying epithelial barrier dysfunction in allergic and inflammatory conditions, such as atopic dermatitis, food allergy, eosinophilic oesophagitis, allergic rhinitis, chronic rhinosinusitis, and asthma, are complex and influenced by the exposome, microbiome, individual genetics, and epigenetics. Here, we review the role of the epithelial barriers of the skin, digestive tract, and airways in maintaining homeostasis, how they influence the occurrence and progression of allergic and inflammatory conditions, how current treatments target the epithelium to improve symptoms of these disorders, and what the unmet needs are in the identification and treatment of epithelial disorders.
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Affiliation(s)
- Roberto Berni Canani
- Department of Translational Medical Science, University of Naples Federico II, Naples, Italy
- CEINGE Advanced Biotechnologies, University of Naples Federico II, Naples, Italy
| | - Marco Caminati
- Allergy Unit and Asthma Centre, Verona Integrated University Hospital and Department of Medicine, University of Verona, Verona, Italy
| | - Laura Carucci
- Department of Translational Medical Science, University of Naples Federico II, Naples, Italy
- CEINGE Advanced Biotechnologies, University of Naples Federico II, Naples, Italy
| | - Ibon Eguiluz-Gracia
- Allergy Unit, Hospital Regional Universitario de Malága, Malaga, Spain
- Allergy Group, Biomedical Research Institute of Malaga (IBIMA)-BIONAND Platform, RICORS Inflammatory Diseases, Malaga, Spain
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10
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Lapidot R, Faits T, Ismail A, Allam M, Khumalo Z, MacLeod W, Kwenda G, Mupila Z, Nakazwe R, Segrè D, Johnson WE, Thea DM, Mwananyanda L, Gill CJ. Nasopharyngeal Dysbiosis Precedes the Development of Lower Respiratory Tract Infections in Young Infants, a Longitudinal Infant Cohort Study. Gates Open Res 2024; 6:48. [PMID: 39050991 PMCID: PMC11266592 DOI: 10.12688/gatesopenres.13561.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/24/2024] [Indexed: 07/27/2024] Open
Abstract
Background Infants suffering from lower respiratory tract infections (LRTIs) have distinct nasopharyngeal (NP) microbiome profiles that correlate with severity of disease. Whether these profiles precede the infection or are a consequence of it, is unknown. In order to answer this question, longitudinal studies are needed. Methods We conducted a retrospective analysis of NP samples collected in a longitudinal birth cohort study of Zambian mother-infant pairs. Samples were collected every two weeks from 1-week through 14-weeks of age. Ten of the infants in the cohort who developed LRTI were matched 1:3 with healthy comparators. We completed 16S rRNA gene sequencing on the samples each of these infants contributed and compared the NP microbiome of the healthy infants to infants who developed LRTI. Results The infant NP microbiome maturation was characterized by transitioning from Staphylococcus dominant to respiratory-genera dominant profiles during the first three months of life, similar to what is described in the literature. Interestingly, infants who developed LRTI had distinct NP microbiome characteristics before infection, in most cases as early as the first week of life. Their NP microbiome was characterized by the presence of Novosphingobium, Delftia, high relative abundance of Anaerobacillus, Bacillus, and low relative abundance of Dolosigranulum, compared to the healthy controls. Mothers of infants with LRTI also had low relative abundance of Dolosigranulum in their baseline samples compared to mothers of infants that did not develop an LRTI. Conclusions Our results suggest that specific characteristics of the NP microbiome precede LRTI in young infants and may be present in their mothers as well. Early dysbiosis may play a role in the causal pathway leading to LRTI or could be a marker of underlying immunological, environmental, or genetic characteristics that predispose to LRTI.
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Affiliation(s)
- Rotem Lapidot
- Pediatric Infectious Diseases, Boston Medical Center, Boston, MA, 02118, USA
- Pediatrics, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Tyler Faits
- Computational Biomedicine, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases, Johannesburg, 2131, South Africa
| | - Mushal Allam
- Sequencing Core Facility, National Institute for Communicable Diseases, Johannesburg, 2131, South Africa
| | - Zamantungwak Khumalo
- Sequencing Core Facility, National Institute for Communicable Diseases, Johannesburg, 2131, South Africa
- Department of Veterinary Tropical Diseases, University of Pretoria, Pretoria, 0002, South Africa
| | - William MacLeod
- Department of Global Health, Boston University School of Public Health, Boston, MA, 02118, USA
| | - Geoffrey Kwenda
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka, Zambia
| | | | - Ruth Nakazwe
- Department of Pathology and Microbiology, University Teaching Hospital, Lusaka, Zambia
| | - Daniel Segrè
- Bioinformatics Program and Biological Design Center, Boston University, Boston, MA, 02118, USA
- Department of Physics, Boston University, Boston, MA, 02118, USA
- Department of Biology, Boston University, Boston, MA, 02118, USA
- Department of Biomedical Engineering, Boston University, Boston, MA, 02118, USA
| | - William Evan Johnson
- Computational Biomedicine, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Donald M Thea
- Department of Global Health, Boston University School of Public Health, Boston, MA, 02118, USA
| | | | - Christopher J Gill
- Department of Global Health, Boston University School of Public Health, Boston, MA, 02118, USA
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11
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Koenen MH, de Groot RCA, de Steenhuijsen Piters WAA, Chu MLJN, Arp K, Hasrat R, de Bruijn ACJM, Estevão SC, van der Vries E, Langereis JD, Boes M, Bogaert D, van Rossum AMC, Unger WWJ, Verhagen LM. Mycoplasma pneumoniae carriage in children with recurrent respiratory tract infections is associated with a less diverse and altered microbiota. EBioMedicine 2023; 98:104868. [PMID: 37950996 PMCID: PMC10679896 DOI: 10.1016/j.ebiom.2023.104868] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 10/20/2023] [Accepted: 10/24/2023] [Indexed: 11/13/2023] Open
Abstract
BACKGROUND Mycoplasma pneumoniae is a common cause of community-acquired pneumonia in school-aged children and can be preceded by asymptomatic carriage. However, its role in recurrent respiratory tract infections is unclear. We studied the prevalence of M.pneumoniae carriage in children with recurrent respiratory infections and identified associated factors. METHODS We tested M.pneumoniae carriage by qPCR in children with recurrent infections and their healthy family members in a cross-sectional study. Serum and mucosal total and M.pneumoniae-specific antibody levels were measured by ELISA and nasopharyngeal microbiota composition was characterized by 16S-rRNA sequencing. FINDINGS Prevalence of M.pneumoniae carriage was higher in children with recurrent infections (68%) than their family members without infections (47% in siblings and 27% in parents). M.pneumoniae carriage among family members appeared to be associated with transmission within the household, likely originating from the affected child. In logistic regression corrected for age and multiple comparisons, IgA (OR 0.16 [0.06-0.37]) and total IgG deficiency (OR 0.15 [0.02-0.74]) were less prevalent in M.pneumoniae carriers (n = 78) compared to non-carriers (n = 36). In multivariable analysis, the nasopharyngeal microbiota of M.pneumoniae carriers had lower alpha diversity (OR 0.27 [0.09-0.67]) and a higher abundance of Haemophilus influenzae (OR 45.01 [2.74-1608.11]) compared to non-carriers. INTERPRETATION M.pneumoniae carriage is highly prevalent in children with recurrent infections and carriers have a less diverse microbiota with an overrepresentation of disease-associated microbiota members compared to non-carriers. Given the high prevalence of M.pneumoniae carriage and the strong association with H. influenzae, we recommend appropriate antibiotic coverage of M.pneumoniae and H. influenzae in case of suspected pneumonia in children with recurrent respiratory tract infections or their family members. FUNDING Wilhelmina Children's Hospital Research Fund, 'Christine Bader Stichting Irene KinderZiekenhuis', Sophia Scientific Research Foundation, ESPID Fellowship funded by Seqirus, Hypatia Fellowship funded by Radboudumc and The Netherlands Organisation for Health Research and Development (ZonMW VENI grant to LM Verhagen).
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Affiliation(s)
- Mischa H Koenen
- Center of Translational Immunology, UMC Utrecht, Utrecht, the Netherlands; Department of Pediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, Utrecht, the Netherlands
| | - Ruben C A de Groot
- Laboratory of Pediatrics, Division of Pediatric Infectious Diseases and Immunology, Erasmus MC University Medical Center Rotterdam - Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Wouter A A de Steenhuijsen Piters
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands; Center for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom; Department of Pediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, Utrecht, the Netherlands
| | - Mei Ling J N Chu
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands; Department of Pediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, Utrecht, the Netherlands
| | - Kayleigh Arp
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands; Department of Pediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, Utrecht, the Netherlands
| | - Raïza Hasrat
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands; Department of Pediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, Utrecht, the Netherlands
| | - Ad C J M de Bruijn
- Laboratory of Pediatrics, Division of Pediatric Infectious Diseases and Immunology, Erasmus MC University Medical Center Rotterdam - Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Silvia C Estevão
- Laboratory of Pediatrics, Division of Pediatric Infectious Diseases and Immunology, Erasmus MC University Medical Center Rotterdam - Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Erhard van der Vries
- Department of Research & Development, GD Animal Health, Deventer, the Netherlands
| | - Jeroen D Langereis
- Laboratory of Medical Immunology, Department of Laboratory Medicine, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Marianne Boes
- Center of Translational Immunology, UMC Utrecht, Utrecht, the Netherlands; Department of Pediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, Utrecht, the Netherlands
| | - Debby Bogaert
- Center for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom; Department of Pediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, Utrecht, the Netherlands
| | - Annemarie M C van Rossum
- Division of Pediatric Infectious Diseases and Immunology, Department of Pediatrics, Erasmus MC University Medical Center Rotterdam - Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Wendy W J Unger
- Laboratory of Pediatrics, Division of Pediatric Infectious Diseases and Immunology, Erasmus MC University Medical Center Rotterdam - Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Lilly M Verhagen
- Department of Pediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, Utrecht, the Netherlands; Laboratory of Medical Immunology, Department of Laboratory Medicine, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Pediatric Infectious Diseases and Immunology, Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, the Netherlands.
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12
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Paulo AC, Lança J, Almeida ST, Hilty M, Sá-Leão R. The upper respiratory tract microbiota of healthy adults is affected by Streptococcus pneumoniae carriage, smoking habits, and contact with children. MICROBIOME 2023; 11:199. [PMID: 37658443 PMCID: PMC10474643 DOI: 10.1186/s40168-023-01640-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 08/04/2023] [Indexed: 09/03/2023]
Abstract
BACKGROUND The microbiota of the upper respiratory tract is increasingly recognized as a gatekeeper of respiratory health. Despite this, the microbiota of healthy adults remains understudied. To address this gap, we investigated the composition of the nasopharyngeal and oropharyngeal microbiota of healthy adults, focusing on the effect of Streptococcus pneumoniae carriage, smoking habits, and contact with children. RESULTS Differential abundance analysis indicated that the microbiota of the oropharynx was significantly different from that of the nasopharynx (P < 0.001) and highly discriminated by a balance between the classes Negativicutes and Bacilli (AUC of 0.979). Moreover, the oropharynx was associated with a more homogeneous microbiota across individuals, with just two vs. five clusters identified in the nasopharynx. We observed a shift in the nasopharyngeal microbiota of carriers vs. noncarriers with an increased relative abundance of Streptococcus, which summed up to 30% vs. 10% in noncarriers and was not mirrored in the oropharynx. The oropharyngeal microbiota of smokers had a lower diversity than the microbiota of nonsmokers, while no differences were observed in the nasopharyngeal microbiota. In particular, the microbiota of smokers, compared with nonsmokers, was enriched (on average 16-fold) in potential pathogenic taxa involved in periodontal diseases of the genera Bacillus and Burkholderia previously identified in metagenomic studies of cigarettes. The microbiota of adults with contact with children resembled the microbiota of children. Specifically, the nasopharyngeal microbiota of these adults had, on average, an eightfold increase in relative abundance in Streptococcus sp., Moraxella catarrhalis, and Haemophilus influenzae, pathobionts known to colonize the children's upper respiratory tract, and a fourfold decrease in Staphylococcus aureus and Staphylococcus lugdunensis. CONCLUSIONS Our study showed that, in adults, the presence of S. pneumoniae in the nasopharynx is associated with a shift in the microbiota and dominance of the Streptococcus genus. Furthermore, we observed that smoking habits are associated with an increase in bacterial genera commonly linked to periodontal diseases. Interestingly, our research also revealed that adults who have regular contact with children have a microbiota enriched in pathobionts frequently carried by children. These findings collectively contribute to a deeper understanding of how various factors influence the upper respiratory tract microbiota in adults. Video Abstract.
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Affiliation(s)
- A Cristina Paulo
- Instituto de Tecnologia Química E Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
| | - João Lança
- Instituto de Tecnologia Química E Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Sónia T Almeida
- Instituto de Tecnologia Química E Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Markus Hilty
- Faculty of Medicine, Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Raquel Sá-Leão
- Instituto de Tecnologia Química E Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
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13
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Bowdish DM, Rossi L, Loeb M, Johnstone J, Schenck LP, Fontes M, Surette MG, Whelan FJ. The impact of respiratory infections and probiotic use on the nasal microbiota of frail residents in long-term care homes. ERJ Open Res 2023; 9:00212-2023. [PMID: 37753289 PMCID: PMC10518876 DOI: 10.1183/23120541.00212-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 07/19/2023] [Indexed: 09/28/2023] Open
Abstract
Background Residents in long-term care homes, who tend to be of advanced age and frail, are at increased risk of respiratory infections. The respiratory microbiota is known to change with age, but whether these changes contribute to the risk of infection is not known. Our goal was to determine how the nasal microbiota of frail older adults changes during symptoms of influenza-like illness (ILI) and how this may be impacted by enrolment in a placebo-controlled trial testing the feasibility of administering a Lactobacillus rhamnosus GG probiotic to prevent respiratory infection (2014-2017). Methods The microbiome of the nasal (mid-turbinate) of 150 residents of long-term care homes was interrogated using 16S rRNA gene sequencing. Results We identified a diverse and individualised microbiota which could be separated into nine distinct clusters based on Bray-Curtis distances. Samples collected during symptoms of ILI differed statistically from those collected pre- and post-cold and influenza season, and we observed decreased temporal stability (as measured by movement between clusters) in individuals who experienced ILI compared to those who did not. Conclusions The use of probiotics decreased ILI-induced changes to the microbiota; however, it is not clear whether this decrease is sufficient to prevent respiratory illness.
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Affiliation(s)
- Dawn M.E. Bowdish
- Department of Medicine, McMaster University, Hamilton, ON, Canada
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
- Firestone Institute for Respiratory Health, St Joseph's Healthcare Hamilton, Hamilton, ON, Canada
| | - Laura Rossi
- Department of Medicine, McMaster University, Hamilton, ON, Canada
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON, Canada
| | - Mark Loeb
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
- Department of Health Research Methods, Evidence & Impact, McMaster University, Hamilton, ON, Canada
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
| | - Jennie Johnstone
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Louis P. Schenck
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Michelle Fontes
- Department of Medicine, McMaster University, Hamilton, ON, Canada
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON, Canada
| | - Michael G. Surette
- Department of Medicine, McMaster University, Hamilton, ON, Canada
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Fiona J. Whelan
- School of Life Sciences, University of Nottingham, Nottingham, UK
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14
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Gierse LC, Meene A, Skorka S, Cuypers F, Surabhi S, Ferrero-Bordera B, Kreikemeyer B, Becher D, Hammerschmidt S, Siemens N, Urich T, Riedel K. Impact of Pneumococcal and Viral Pneumonia on the Respiratory and Intestinal Tract Microbiomes of Mice. Microbiol Spectr 2023; 11:e0344722. [PMID: 36988458 PMCID: PMC10269894 DOI: 10.1128/spectrum.03447-22] [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: 09/02/2022] [Accepted: 03/06/2023] [Indexed: 03/30/2023] Open
Abstract
With 2.56 million deaths worldwide annually, pneumonia is one of the leading causes of death. The most frequent causative pathogens are Streptococcus pneumoniae and influenza A virus. Lately, the interaction between the pathogens, the host, and its microbiome have gained more attention. The microbiome is known to promote the immune response toward pathogens; however, our knowledge on how infections affect the microbiome is still scarce. Here, the impact of colonization and infection with S. pneumoniae and influenza A virus on the structure and function of the respiratory and gastrointestinal microbiomes of mice was investigated. Using a meta-omics approach, we identified specific differences between the bacterial and viral infection. Pneumococcal colonization had minor effects on the taxonomic composition of the respiratory microbiome, while acute infections caused decreased microbial complexity. In contrast, richness was unaffected following H1N1 infection. Within the gastrointestinal microbiome, we found exclusive changes in structure and function, depending on the pathogen. While pneumococcal colonization had no effects on taxonomic composition of the gastrointestinal microbiome, increased abundance of Akkermansiaceae and Spirochaetaceae as well as decreased amounts of Clostridiaceae were exclusively found during invasive S. pneumoniae infection. The presence of Staphylococcaceae was specific for viral pneumonia. Investigation of the intestinal microbiomés functional composition revealed reduced expression of flagellin and rubrerythrin and increased levels of ATPase during pneumococcal infection, while increased amounts of acetyl coenzyme A (acetyl-CoA) acetyltransferase and enoyl-CoA transferase were unique after H1N1 infection. In conclusion, identification of specific taxonomic and functional profiles of the respiratory and gastrointestinal microbiome allowed the discrimination between bacterial and viral pneumonia. IMPORTANCE Pneumonia is one of the leading causes of death worldwide. Here, we compared the impact of bacterial- and viral-induced pneumonia on the respiratory and gastrointestinal microbiome. Using a meta-omics approach, we identified specific profiles that allow discrimination between bacterial and viral causative.
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Affiliation(s)
| | - Alexander Meene
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Sebastian Skorka
- Department of Molecular Genetics and Infection Biology, Institute for Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
| | - Fabian Cuypers
- Department of Molecular Genetics and Infection Biology, Institute for Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
| | - Surabhi Surabhi
- Department of Molecular Genetics and Infection Biology, Institute for Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
| | | | - Bernd Kreikemeyer
- Institute for Medical Microbiology, Virology and Hygiene, Rostock University Medical Centre, Rostock, Germany
| | - Dörte Becher
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Sven Hammerschmidt
- Department of Molecular Genetics and Infection Biology, Institute for Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
| | - Nikolai Siemens
- Department of Molecular Genetics and Infection Biology, Institute for Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
| | - Tim Urich
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Katharina Riedel
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
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15
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Dunne EM, Nunes MC, Slack MPE, Theilacker C, Gessner BD. Effects of pneumococcal conjugate vaccines on reducing the risk of respiratory disease associated with coronavirus infection. Pneumonia (Nathan) 2023; 15:10. [PMID: 37226198 DOI: 10.1186/s41479-023-00112-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 04/30/2023] [Indexed: 05/26/2023] Open
Abstract
Pneumococcal conjugate vaccines (PCVs) provide protection against vaccine-type pneumococcal disease in both children and adults. Growing evidence suggests that PCVs also reduce pneumonia and lower respiratory tract infections (LRTIs) more broadly, including protecting against viral-associated respiratory diseases. In this short narrative review, we highlight clinical studies investigating whether PCVs might have a role in reducing coronavirus disease, both those caused by endemic human coronaviruses (HCoVs) and severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). These studies include two randomized controlled trials assessing HCoV-associated pneumonia, one each in children and older adults, and two observational studies of PCV13 effectiveness against HCoV-associated LRTI and COVID-19 in adults. We discuss possible mechanisms for PCV protection including preventing viral pneumococcal co-infections and the possibility that pneumococci in the upper respiratory tract might modify the host immune response to SARS-CoV-2. Lastly, we identify knowledge gaps and further questions on the potential role of PCVs during the COVID-19 pandemic.
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Affiliation(s)
| | - Marta C Nunes
- Center of Excellence in Respiratory Pathogens, Hospices Civils de Lyon and Centre International de Recherche en Infectiologie (CIRI) Inserm U1111, CNRS UMR5308, ENS de Lyon, Université Claude Bernard, Lyon 1, Lyon, France
- South African Medical Research Council, Vaccines & Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mary P E Slack
- School of Medicine & Dentistry, Griffith University, Gold Coast Campus, Southport, QLD, Australia
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16
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Huang J, Xu Y. Autoimmunity: A New Focus on Nasal Polyps. Int J Mol Sci 2023; 24:ijms24098444. [PMID: 37176151 PMCID: PMC10179643 DOI: 10.3390/ijms24098444] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 04/28/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023] Open
Abstract
Chronic rhinosinusitis with nasal polyps (CRSwNP) has long been considered a benign, chronic inflammatory, and hyperplastic disease. Recent studies have shown that autoimmune-related mechanisms are involved in the pathology of nasal polyps. Activated plasma cells, eosinophils, basophils, innate type 2 lymphocytes, mast cells, and proinflammatory cytokine in polyp tissue indicate the mobilization of innate and adaptive immune pathways during polyp formation. The discovery of a series of autoantibodies further supports the autoimmune nature of nasal polyps. Local homeostasis dysregulation, infection, and chronic inflammation may trigger autoimmunity through several mechanisms, including autoantigens overproduction, microbial translocation, molecular mimicry, superantigens, activation or inhibition of receptors, bystander activation, dysregulation of Toll-Like Receptors (TLRs), epitope spreading, autoantigens complementarity. In this paper, we elaborated on the microbiome-mediated mechanism, abnormal host immunity, and genetic changes to update the role of autoimmunity in the pathogenesis of chronic rhinosinusitis with nasal polyps.
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Affiliation(s)
- Jingyu Huang
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Yu Xu
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, China
- Research Institute of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, China
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17
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Wong A, Barrero Guevara LA, Goult E, Briga M, Kramer SC, Kovacevic A, Opatowski L, Domenech de Cellès M. The interactions of SARS-CoV-2 with cocirculating pathogens: Epidemiological implications and current knowledge gaps. PLoS Pathog 2023; 19:e1011167. [PMID: 36888684 PMCID: PMC9994710 DOI: 10.1371/journal.ppat.1011167] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023] Open
Abstract
Despite the availability of effective vaccines, the persistence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) suggests that cocirculation with other pathogens and resulting multiepidemics (of, for example, COVID-19 and influenza) may become increasingly frequent. To better forecast and control the risk of such multiepidemics, it is essential to elucidate the potential interactions of SARS-CoV-2 with other pathogens; these interactions, however, remain poorly defined. Here, we aimed to review the current body of evidence about SARS-CoV-2 interactions. Our review is structured in four parts. To study pathogen interactions in a systematic and comprehensive way, we first developed a general framework to capture their major components: sign (either negative for antagonistic interactions or positive for synergistic interactions), strength (i.e., magnitude of the interaction), symmetry (describing whether the interaction depends on the order of infection of interacting pathogens), duration (describing whether the interaction is short-lived or long-lived), and mechanism (e.g., whether interaction modifies susceptibility to infection, transmissibility of infection, or severity of disease). Second, we reviewed the experimental evidence from animal models about SARS-CoV-2 interactions. Of the 14 studies identified, 11 focused on the outcomes of coinfection with nonattenuated influenza A viruses (IAVs), and 3 with other pathogens. The 11 studies on IAV used different designs and animal models (ferrets, hamsters, and mice) but generally demonstrated that coinfection increased disease severity compared with either monoinfection. By contrast, the effect of coinfection on the viral load of either virus was variable and inconsistent across studies. Third, we reviewed the epidemiological evidence about SARS-CoV-2 interactions in human populations. Although numerous studies were identified, only a few were specifically designed to infer interaction, and many were prone to multiple biases, including confounding. Nevertheless, their results suggested that influenza and pneumococcal conjugate vaccinations were associated with a reduced risk of SARS-CoV-2 infection. Finally, fourth, we formulated simple transmission models of SARS-CoV-2 cocirculation with an epidemic viral pathogen or an endemic bacterial pathogen, showing how they can naturally incorporate the proposed framework. More generally, we argue that such models, when designed with an integrative and multidisciplinary perspective, will be invaluable tools to resolve the substantial uncertainties that remain about SARS-CoV-2 interactions.
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Affiliation(s)
- Anabelle Wong
- Infectious Disease Epidemiology group, Max Planck Institute for Infection Biology, Berlin, Germany
- Institute of Public Health, Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Laura Andrea Barrero Guevara
- Infectious Disease Epidemiology group, Max Planck Institute for Infection Biology, Berlin, Germany
- Institute of Public Health, Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Elizabeth Goult
- Infectious Disease Epidemiology group, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Michael Briga
- Infectious Disease Epidemiology group, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Sarah C. Kramer
- Infectious Disease Epidemiology group, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Aleksandra Kovacevic
- Epidemiology and Modelling of Antibiotic Evasion, Institut Pasteur, Université Paris Cité, Paris, France
- Anti-infective Evasion and Pharmacoepidemiology Team, CESP, Université Paris-Saclay, Université de Versailles Saint-Quentin-en-Yvelines, INSERM U1018 Montigny-le-Bretonneux, France
| | - Lulla Opatowski
- Epidemiology and Modelling of Antibiotic Evasion, Institut Pasteur, Université Paris Cité, Paris, France
- Anti-infective Evasion and Pharmacoepidemiology Team, CESP, Université Paris-Saclay, Université de Versailles Saint-Quentin-en-Yvelines, INSERM U1018 Montigny-le-Bretonneux, France
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18
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Chow EJ, Uyeki TM, Chu HY. The effects of the COVID-19 pandemic on community respiratory virus activity. Nat Rev Microbiol 2023; 21:195-210. [PMID: 36253478 PMCID: PMC9574826 DOI: 10.1038/s41579-022-00807-9] [Citation(s) in RCA: 196] [Impact Index Per Article: 98.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/13/2022] [Indexed: 01/14/2023]
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused substantial global morbidity and deaths, leading governments to turn to non-pharmaceutical interventions to slow down the spread of infection and lessen the burden on health care systems. These policies have evolved over the course of the COVID-19 pandemic, including after the availability of COVID-19 vaccines, with regional and country-level differences in their ongoing use. The COVID-19 pandemic has been associated with changes in respiratory virus infections worldwide, which have differed between virus types. Reductions in respiratory virus infections, including by influenza virus and respiratory syncytial virus, were most notable at the onset of the COVID-19 pandemic and continued in varying degrees through subsequent waves of SARS-CoV-2 infections. The decreases in community infection burden have resulted in reduced hospitalizations and deaths associated with non-SARS-CoV-2 respiratory infections. Respiratory virus evolution relies on the maintaining of a diverse genetic pool, but evidence of genetic bottlenecking brought on by case reduction during the COVID-19 pandemic has resulted in reduced genetic diversity of some respiratory viruses, including influenza virus. By describing the differences in these changes between viral species across different geographies over the course of the COVID-19 pandemic, we may better understand the complex factors involved in community co-circulation of respiratory viruses.
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Affiliation(s)
- Eric J Chow
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Timothy M Uyeki
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Helen Y Chu
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA, USA.
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19
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Lewnard JA, Bruxvoort KJ, Hong VX, Grant LR, Jódar L, Cané A, Gessner BD, Tartof SY. Effectiveness of Pneumococcal Conjugate Vaccination Against Virus-Associated Lower Respiratory Tract Infection Among Adults: A Case-Control Study. J Infect Dis 2023; 227:498-511. [PMID: 35323906 PMCID: PMC9383607 DOI: 10.1093/infdis/jiac098] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 03/21/2022] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Interactions of Streptococcus pneumoniae with viruses feature in the pathogenesis of numerous respiratory illnesses. METHODS We undertook a case-control study among adults at Kaiser Permanente Southern California between 2015 and 2019. Case patients had diagnoses of lower respiratory tract infection (LRTI; including pneumonia or nonpneumonia LRTI diagnoses), with viral infections detected by multiplex polymerase chain reaction testing. Controls without LRTI diagnoses were matched to case patients by demographic and clinical attributes. We measured vaccine effectiveness (VE) for 13-valent (PCV13) against virus-associated LRTI by determining the adjusted odds ratio for PCV13 receipt, comparing case patients and controls. RESULTS Primary analyses included 13 856 case patients with virus-associated LRTI and 227 887 matched controls. Receipt of PCV13 was associated with a VE of 24.9% (95% confidence interval, 18.4%-30.9%) against virus-associated pneumonia and 21.5% (10.9%-30.9%) against other (nonpneumonia) virus-associated LRTIs. We estimated VEs of 26.8% (95% confidence interval, 19.9%-33.1%) and 18.6% (9.3%-27.0%) against all virus-associated LRTI episodes diagnosed in inpatient and outpatient settings, respectively. We identified statistically significant protection against LRTI episodes associated with influenza A and B viruses, endemic human coronaviruses, parainfluenza viruses, human metapneumovirus, and enteroviruses but not respiratory syncytial virus or adenoviruses. CONCLUSIONS Among adults, PCV13 conferred moderate protection against virus-associated LRTI. The impacts of pneumococcal conjugate vaccines may be mediated, in part, by effects on polymicrobial interactions between pneumococci and respiratory viruses.
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Affiliation(s)
- Joseph A Lewnard
- Division of Epidemiology, School of Public Health, University of California, Berkeley, California, USA
- Division of Infectious Diseases & Vaccinology, School of Public Health, University of California, Berkeley, California, USA
- Center for Computational Biology, College of Engineering, University of California, Berkeley, California, USA
| | - Katia J Bruxvoort
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, Alabama, USA
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, California, USA
| | - Vennis X Hong
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, California, USA
| | | | - Luis Jódar
- Pfizer Vaccines, Collegeville, Pennsylvania, USA
| | | | | | - Sara Y Tartof
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, California, USA
- Department of Health Systems Science, Kaiser Permanente Bernard J. Tyson School of Medicine, Pasadena, California, USA
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20
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Diniz MO, Mitsi E, Swadling L, Rylance J, Johnson M, Goldblatt D, Ferreira D, Maini MK. Airway-resident T cells from unexposed individuals cross-recognize SARS-CoV-2. Nat Immunol 2022; 23:1324-1329. [PMID: 36038709 PMCID: PMC9477726 DOI: 10.1038/s41590-022-01292-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 07/18/2022] [Indexed: 12/15/2022]
Abstract
T cells can contribute to clearance of respiratory viruses that cause acute-resolving infections such as SARS-CoV-2, helping to provide long-lived protection against disease. Recent studies have suggested an additional role for T cells in resisting overt infection: pre-existing cross-reactive responses were preferentially enriched in healthcare workers who had abortive infections1, and in household contacts protected from infection2. We hypothesize that such early viral control would require pre-existing cross-reactive memory T cells already resident at the site of infection; such airway-resident responses have been shown to be critical for mediating protection after intranasal vaccination in a murine model of SARS-CoV3. Bronchoalveolar lavage samples from the lower respiratory tract of healthy donors obtained before the COVID-19 pandemic revealed airway-resident, SARS-CoV-2-cross-reactive T cells, which correlated with the strength of human seasonal coronavirus immunity. We therefore demonstrate the potential to harness functional airway-resident SARS-CoV-2-reactive T cells in next-generation mucosal vaccines.
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Affiliation(s)
- Mariana O Diniz
- Division of Infection and Immunity and Institute of Immunity and Transplantation, UCL, London, UK
| | - Elena Mitsi
- Department of Clinical Science, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Leo Swadling
- Division of Infection and Immunity and Institute of Immunity and Transplantation, UCL, London, UK
| | - Jamie Rylance
- Department of Clinical Science, Liverpool School of Tropical Medicine, Liverpool, UK
| | | | | | - Daniela Ferreira
- Department of Clinical Science, Liverpool School of Tropical Medicine, Liverpool, UK.
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK.
| | - Mala K Maini
- Division of Infection and Immunity and Institute of Immunity and Transplantation, UCL, London, UK.
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21
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Audshasai T, Coles JA, Panagiotou S, Khandaker S, Scales HE, Kjos M, Baltazar M, Vignau J, Brewer JM, Kadioglu A, Yang M. Streptococcus pneumoniae Rapidly Translocate from the Nasopharynx through the Cribriform Plate to Invade the Outer Meninges. mBio 2022; 13:e0102422. [PMID: 35924840 PMCID: PMC9426477 DOI: 10.1128/mbio.01024-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 07/05/2022] [Indexed: 11/20/2022] Open
Abstract
The entry routes and translocation mechanisms of microorganisms or particulate materials into the central nervous system remain obscure We report here that Streptococcus pneumoniae (pneumococcus), or polystyrene microspheres of similar size, appear in the meninges of the dorsal cortex of mice within minutes of inhaled delivery. Recovery of viable bacteria from dissected tissue and fluorescence microscopy show that up to at least 72 h, pneumococci and microspheres were predominantly found in the outer of the two meninges: the pachymeninx. No pneumococci were found in blood or cerebrospinal fluid. Intravital imaging through the skull, aligned with flow cytometry showed recruitment and activation of LysM+ cells in the dorsal pachymeninx at 5 and 10 hours following intranasal infection. Imaging of the cribriform plate suggested that both pneumococci and microspheres entered through the foramina via an inward flow of fluid connecting the nose to the pachymeninx. Our findings bring new insight into the varied mechanisms of pneumococcal invasion of the central nervous system, but they are also pertinent to the delivery of drugs to the brain and the entry of airborne particulate matter into the cranium. IMPORTANCE Using two-photon imaging, we show that pneumococci translocate from the nasopharynx to the dorsal meninges of a mouse in the absence of any bacteria found in blood or cerebrospinal fluid. Strikingly, this takes place within minutes of inhaled delivery of pneumococci, suggesting the existence of an inward flow of fluid connecting the nasopharynx to the meninges, rather than a receptor-mediated mechanism. We also show that this process is size dependent, as microspheres of the same size as pneumococci can translocate along the same pathway, while larger size microspheres cannot. Furthermore, we describe the host response to invasion of the outer meninges. Our study provides a completely new insight into the key initial events that occur during the translocation of pneumococci directly from the nasal cavity to the meninges, with relevance to the development of intranasal drug delivery systems and the investigations of brain damage caused by inhaled air pollutants.
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Affiliation(s)
- Teerawit Audshasai
- Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
- Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
| | - Jonathan A. Coles
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Stavros Panagiotou
- Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Shadia Khandaker
- Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Hannah E. Scales
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Morten Kjos
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Murielle Baltazar
- Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Julie Vignau
- Centre de Recherche en Cancérologie et Immunologie Nantes Angers, Université de Nantes, Nantes, France
| | - James M. Brewer
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Aras Kadioglu
- Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Marie Yang
- Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
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22
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Pneumolysin boosts the neuroinflammatory response to Streptococcus pneumoniae through enhanced endocytosis. Nat Commun 2022; 13:5032. [PMID: 36028511 PMCID: PMC9418233 DOI: 10.1038/s41467-022-32624-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 08/09/2022] [Indexed: 11/08/2022] Open
Abstract
In pneumococcal meningitis, bacterial growth in the cerebrospinal fluid results in lysis, the release of toxic factors, and subsequent neuroinflammation. Exposure of primary murine glia to Streptococcus pneumoniae lysates leads to strong proinflammatory cytokine and chemokine production, blocked by inhibition of the intracellular innate receptor Nod1. Lysates enhance dynamin-dependent endocytosis, and dynamin inhibition reduces neuroinflammation, blocking ligand internalization. Here we identify the cholesterol-dependent cytolysin pneumolysin as a pro-endocytotic factor in lysates, its elimination reduces their proinflammatory effect. Only pore-competent pneumolysin enhances endocytosis in a dynamin-, phosphatidylinositol-3-kinase- and potassium-dependent manner. Endocytic enhancement is limited to toxin-exposed parts of the membrane, the effect is rapid and pneumolysin permanently alters membrane dynamics. In a murine model of pneumococcal meningitis, mice treated with chlorpromazine, a neuroleptic with a complementary endocytosis inhibitory effect show reduced neuroinflammation. Thus, the dynamin-dependent endocytosis emerges as a factor in pneumococcal neuroinflammation, and its enhancement by a cytolysin represents a proinflammatory control mechanism.
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23
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Credille B. High-Risk Cattle Management and Stocker Calf Health: Modulation of the Bovine Respiratory Microbiome from a Systems Perspective. Vet Clin North Am Food Anim Pract 2022; 38:229-243. [PMID: 35691626 DOI: 10.1016/j.cvfa.2022.03.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
Bovine respiratory disease (BRD) affects animals in all segments of the North American beef industry. The segmented nature of the beef industry results in the marketing of cattle that are considered to be at high risk of developing BRD. The microbiota is the complex microbial ecosystem that exists in and on the body of all animals. The respiratory tract has its unique microbiota that is shaped by many factors. Stress reduction, appropriate nutritional management, strategic use of vaccines, and antimicrobial administration targeted to the highest risk individuals have the potential to stabilize an inherently unstable microbial population and enhance calf health.
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Affiliation(s)
- Brent Credille
- Food Animal Health and Management Program, Department of Population Health, College of Veterinary Medicine, University of Georgia, Veterinary Medical Center, 2200 College Station Road, Athens, GA 30602, USA.
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24
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Ruiz-Rodriguez A, Lusarreta-Parga P, de Steenhuijsen Piters WAA, Koppensteiner L, Balcazar-Lopez CE, Campbell R, Dewar R, McHugh MP, Dockrell D, Templeton KE, Bogaert D. Bacterial and fungal communities in tracheal aspirates of intubated COVID-19 patients: a pilot study. Sci Rep 2022; 12:9896. [PMID: 35701442 PMCID: PMC9196859 DOI: 10.1038/s41598-022-13482-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 05/25/2022] [Indexed: 11/18/2022] Open
Abstract
Co-infections with bacterial or fungal pathogens could be associated with severity and outcome of disease in COVID-19 patients. We, therefore, used a 16S and ITS-based sequencing approach to assess the biomass and composition of the bacterial and fungal communities in endotracheal aspirates of intubated COVID-19 patients. Our method combines information on bacterial and fungal biomass with community profiling, anticipating the likelihood of a co-infection is higher with (1) a high bacterial and/or fungal biomass combined with (2) predominance of potentially pathogenic microorganisms. We tested our methods on 42 samples from 30 patients. We observed a clear association between microbial outgrowth (high biomass) and predominance of individual microbial species. Outgrowth of pathogens was in line with the selective pressure of antibiotics received by the patient. We conclude that our approach may help to monitor the presence and predominance of pathogens and therefore the likelihood of co-infections in ventilated patients, which ultimately, may help to guide treatment.
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Affiliation(s)
- Alicia Ruiz-Rodriguez
- Centre for Inflammation Research, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Paula Lusarreta-Parga
- Centre for Inflammation Research, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Wouter A A de Steenhuijsen Piters
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Lundlaan 6, 3584 EA, Utrecht, The Netherlands
| | - Lilian Koppensteiner
- Centre for Inflammation Research, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Carlos E Balcazar-Lopez
- Centre for Inflammation Research, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Robyn Campbell
- Department of Laboratory Medicine, Royal Infirmary of Edinburgh, 51 Little France Crescent, Edinburgh, EH16 4SA, UK
| | - Rebecca Dewar
- Department of Laboratory Medicine, Royal Infirmary of Edinburgh, 51 Little France Crescent, Edinburgh, EH16 4SA, UK
| | - Martin P McHugh
- Department of Laboratory Medicine, Royal Infirmary of Edinburgh, 51 Little France Crescent, Edinburgh, EH16 4SA, UK
- School of Medicine, University of St Andrews, North Haugh, St Andrews, KY16 9TF, UK
| | - David Dockrell
- Centre for Inflammation Research, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Kate E Templeton
- Department of Laboratory Medicine, Royal Infirmary of Edinburgh, 51 Little France Crescent, Edinburgh, EH16 4SA, UK
| | - Debby Bogaert
- Centre for Inflammation Research, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK.
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Lundlaan 6, 3584 EA, Utrecht, The Netherlands.
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25
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Lewnard JA, Bruxvoort KJ, Fischer H, Hong VX, Grant LR, Jódar L, Gessner BD, Tartof SY. Prevention of Coronavirus Disease 2019 Among Older Adults Receiving Pneumococcal Conjugate Vaccine Suggests Interactions Between Streptococcus pneumoniae and Severe Acute Respiratory Syndrome Coronavirus 2 in the Respiratory Tract. J Infect Dis 2022; 225:1710-1720. [PMID: 33693636 PMCID: PMC7989304 DOI: 10.1093/infdis/jiab128] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/04/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND While secondary pneumococcal pneumonia occurs less commonly after coronavirus disease 2019 (COVID-19) than after other viral infections, it remains unclear whether other interactions occur between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and Streptococcus pneumoniae. METHODS We probed potential interactions between these pathogens among adults aged ≥65 years by measuring associations of COVID-19 outcomes with pneumococcal vaccination (13-valent conjugate vaccine [PCV13] and 23-valent pneumococcal polysaccharide vaccine [PPSV23]). We estimated adjusted hazard ratios (aHRs) using Cox proportional hazards models with doubly robust inverse-propensity weighting. We assessed effect modification by antibiotic exposure to further test the biologic plausibility of a causal role for pneumococci. RESULTS Among 531 033 adults, there were 3677 COVID-19 diagnoses, leading to 1075 hospitalizations and 334 fatalities, between 1 March and 22 July 2020. Estimated aHRs for COVID-19 diagnosis, hospitalization, and mortality associated with prior PCV13 receipt were 0.65 (95% confidence interval [CI], .59-.72), 0.68 (95% CI, .57-.83), and 0.68 (95% CI, .49-.95), respectively. Prior PPSV23 receipt was not associated with protection against the 3 outcomes. COVID-19 diagnosis was not associated with prior PCV13 within 90 days following antibiotic receipt, whereas aHR estimates were 0.65 (95% CI, .50-.84) and 0.62 (95% CI, .56-.70) during the risk periods 91-365 days and >365 days, respectively, following antibiotic receipt. CONCLUSIONS Reduced risk of COVID-19 among PCV13 recipients, transiently attenuated by antibiotic exposure, suggests that pneumococci may interact with SARS-CoV-2.
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Affiliation(s)
- Joseph A Lewnard
- Division of Epidemiology, School of Public Health, University of California, Berkeley, Berkeley, California, USA
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, California, USA
- Center for Computational Biology, College of Engineering, University of California, Berkeley, Berkeley, California, USA
| | - Katia J Bruxvoort
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, California, USA
| | - Heidi Fischer
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, California, USA
| | - Vennis X Hong
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, California, USA
| | | | - Luis Jódar
- Pfizer Vaccines, Collegeville, Pennsylvania, USA
| | | | - Sara Y Tartof
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, California, USA
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26
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Goncalves P, Doisne JM, Eri T, Charbit B, Bondet V, Posseme C, Llibre A, Casrouge A, Lenoir C, Neven B, Duffy D, Fischer A, Di Santo JP, The Milieu Intérieur Consortium. Defects in mucosal immunity and nasopharyngeal dysbiosis in HSC-transplanted SCID patients with IL2RG/JAK3 deficiency. Blood 2022; 139:2585-2600. [PMID: 35157765 PMCID: PMC11022929 DOI: 10.1182/blood.2021014654] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 01/31/2022] [Indexed: 11/20/2022] Open
Abstract
Both innate and adaptive lymphocytes have critical roles in mucosal defense that contain commensal microbial communities and protect against pathogen invasion. Here we characterize mucosal immunity in patients with severe combined immunodeficiency (SCID) receiving hematopoietic stem cell transplantation (HSCT) with or without myeloablation. We confirmed that pretransplant conditioning had an impact on innate (natural killer and innate lymphoid cells) and adaptive (B and T cells) lymphocyte reconstitution in these patients with SCID and now show that this further extends to generation of T helper 2 and type 2 cytotoxic T cells. Using an integrated approach to assess nasopharyngeal immunity, we identified a local mucosal defect in type 2 cytokines, mucus production, and a selective local immunoglobulin A (IgA) deficiency in HSCT-treated SCID patients with genetic defects in IL2RG/GC or JAK3. These patients have a reduction in IgA-coated nasopharyngeal bacteria and exhibit microbial dysbiosis with increased pathobiont carriage. Interestingly, intravenous immunoglobulin replacement therapy can partially normalize nasopharyngeal immunoglobulin profiles and restore microbial communities in GC/JAK3 patients. Together, our results suggest a potential nonredundant role for type 2 immunity and/or of local IgA antibody production in the maintenance of nasopharyngeal microbial homeostasis and mucosal barrier function.
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Affiliation(s)
- Pedro Goncalves
- Institut Pasteur, Université de Paris Cité, Inserm U1223, Innate Immunity Unit, Paris, France
| | - Jean-Marc Doisne
- Institut Pasteur, Université de Paris Cité, Inserm U1223, Innate Immunity Unit, Paris, France
| | - Toshiki Eri
- Institut Pasteur, Université de Paris Cité, Inserm U1223, Innate Immunity Unit, Paris, France
| | - Bruno Charbit
- Institut Pasteur, Université de Paris Cité, Center for Translational Science, Paris, France
| | - Vincent Bondet
- Institut Pasteur, Université de Paris Cité, Translational Immunology Unit, Paris, France
| | - Celine Posseme
- Institut Pasteur, Université de Paris Cité, Translational Immunology Unit, Paris, France
| | - Alba Llibre
- Institut Pasteur, Université de Paris Cité, Translational Immunology Unit, Paris, France
| | - Armanda Casrouge
- Institut Pasteur, Université de Paris Cité, Inserm U1223, Innate Immunity Unit, Paris, France
| | - Christelle Lenoir
- Inserm Unité Mixte de Recherche 1163, Paris, France
- Imagine Institut, Université de Paris Descartes Sorbonne Paris Cité, Paris, France
| | - Bénédicte Neven
- Inserm Unité Mixte de Recherche 1163, Paris, France
- Department of Pediatric Immunology, Hematology and Rheumatology, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Darragh Duffy
- Institut Pasteur, Université de Paris Cité, Translational Immunology Unit, Paris, France
| | - Alain Fischer
- Inserm Unité Mixte de Recherche 1163, Paris, France
- Collège de France, Paris, France
| | - James P. Di Santo
- Institut Pasteur, Université de Paris Cité, Inserm U1223, Innate Immunity Unit, Paris, France
| | - The Milieu Intérieur Consortium
- Institut Pasteur, Université de Paris Cité, Inserm U1223, Innate Immunity Unit, Paris, France
- Institut Pasteur, Université de Paris Cité, Center for Translational Science, Paris, France
- Institut Pasteur, Université de Paris Cité, Translational Immunology Unit, Paris, France
- Inserm Unité Mixte de Recherche 1163, Paris, France
- Imagine Institut, Université de Paris Descartes Sorbonne Paris Cité, Paris, France
- Department of Pediatric Immunology, Hematology and Rheumatology, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France
- Collège de France, Paris, France
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Lapidot R, Faits T, Ismail A, Allam M, Khumalo Z, MacLeod W, Kwenda G, Mupila Z, Nakazwe R, Segrè D, Johnson WE, Thea DM, Mwananyanda L, Gill CJ. Nasopharyngeal Dysbiosis Precedes the Development of Lower Respiratory Tract Infections in Young Infants, a Longitudinal Infant Cohort Study. Gates Open Res 2022. [DOI: 10.12688/gatesopenres.13561.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Background: Infants suffering from lower respiratory tract infections (LRTIs) have distinct nasopharyngeal (NP) microbiome profiles that correlate with severity of disease. Whether these profiles precede the infection or a consequence of it, is unknown. In order to answer this question, longitudinal studies are needed. Methods: We conducted an analysis of a longitudinal prospective cohort study of 1,981 Zambian mother-infant pairs who underwent NP sampling from 1-week through 14-weeks of age at 2-3-week intervals. Ten of the infants in the cohort who developed LRTI were matched 1:3 with healthy comparators. We completed 16S rRNA gene sequencing on the samples each of these infants contributed, as well as from baseline samples of the infants’ mothers, and characterized the normal maturation of the healthy infant NP microbiome, compared to infants who developed LRTI. Results: The infant NP microbiome maturation was characterized by transitioning from Staphylococcus dominant to respiratory-genera dominant profiles during the first three months of life, similar to what is described in the literature. Interestingly, infants who developed LRTI had NP dysbiosis before infection, in most cases as early as the first week of life. Dysbiosis was characterized by the presence of Novosphingobium, Delftia, high relative abundance of Anaerobacillus, Bacillus, and low relative abundance of Dolosigranulum, compared to the healthy controls. Mothers of infants with LRTI also had low relative abundance of Dolosigranulum in their baseline samples compared to mothers of infants that did not develop an LRTI. Conclusions: Our results suggest that NP microbiome dysbiosis precedes LRTI in young infants and may be present in their mothers as well. Early dysbiosis may play a role in the causal pathway leading to LRTI or could be a marker of other pathogenic forces that directly lead to LRTI.
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The Immune Mechanisms of Severe Equine Asthma-Current Understanding and What Is Missing. Animals (Basel) 2022; 12:ani12060744. [PMID: 35327141 PMCID: PMC8944511 DOI: 10.3390/ani12060744] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 03/11/2022] [Accepted: 03/14/2022] [Indexed: 01/27/2023] Open
Abstract
Severe equine asthma is a chronic respiratory disease of adult horses, occurring when genetically susceptible individuals are exposed to environmental aeroallergens. This results in airway inflammation, mucus accumulation and bronchial constriction. Although several studies aimed at evaluating the genetic and immune pathways associated with the disease, the results reported are inconsistent. Furthermore, the complexity and heterogeneity of this disease bears great similarity to what is described for human asthma. Currently available studies identified two chromosome regions (ECA13 and ECA15) and several genes associated with the disease. The inflammatory response appears to be mediated by T helper cells (Th1, Th2, Th17) and neutrophilic inflammation significantly contributes to the persistence of airway inflammatory status. This review evaluates the reported findings pertaining to the genetical and immunological background of severe equine asthma and reflects on their implications in the pathophysiology of the disease whilst discussing further areas of research interest aiming at advancing treatment and prognosis of affected individuals.
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29
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Chen M, He S, Miles P, Li C, Ge Y, Yu X, Wang L, Huang W, Kong X, Ma S, Li Y, Jiang Q, Zhang W, Cao C. Nasal Bacterial Microbiome Differs Between Healthy Controls and Those With Asthma and Allergic Rhinitis. Front Cell Infect Microbiol 2022; 12:841995. [PMID: 35310838 PMCID: PMC8928226 DOI: 10.3389/fcimb.2022.841995] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 02/14/2022] [Indexed: 12/31/2022] Open
Abstract
Perturbation of the microbiome has numerous associations with the phenotypes and progression in chronic airways disease. However, the differences in the nasal microbiome in asthma and allergic rhinitis (AR) have not been defined. We examined whether the nasal microbiome would vary among different comorbidities in asthma and AR and that those differences may be associated with the severity of asthma. Nasal lavage fluid was collected from 110 participants, including 20 healthy controls, 30 subjects with AR, 30 subjects with asthma and 30 subjects with combined asthma + AR. The Asthma Control Questionnaire (ACQ-7) was used to evaluate asthma control status. Using 16S rRNA bacterial gene sequencing, we analyzed nasal microbiome in patients with asthma, AR, combined asthma + AR, and healthy controls. Bacterial diversity was analyzed in corresponding with α diversity indices (Chao and Shannon index). Compared with healthy controls, the Chao index tended to be lower in subjects with AR (P = 0.001), asthma (P = 0.001), and combined asthma + AR (P = 0.001) when compared with healthy controls. Furthermore, the Shannon index was significantly lower in subjects with asthma (P = 0.013) and comorbid asthma with AR (P = 0.004) than the control subjects. Disparity in the structure and composition of nasal bacteria were also observed among the four groups. Furthermore, patients with combined asthma + AR and isolated asthma were divided into two groups according to the level of disease control: partially or well-controlled and uncontrolled asthma. The mean relative abundance observed in the groups mentioned the genera of Pseudoflavonifractor were dominated in patients with well and partially controlled disease, in both isolated asthma and combined asthma + AR. In subjects with uncontrolled asthma and combined asthma + AR, a lower evenness and richness (Shannon index, P = 0.040) was observed in nasal microbiome composition. Importantly, lower evenness and richness in the nasal microbiome may be associated with poor disease control in combined asthma + AR. This study showed the upper airway microbiome is associated with airway inflammation disorders and the level of asthma control.
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Affiliation(s)
- Meiping Chen
- School of Medicine, Ningbo University, Ningbo, China
- Department of Respiratory and Critical Care Medicine, Ningbo First Hospital, Ningbo, China
| | - Shiyi He
- School of Medicine, Ningbo University, Ningbo, China
- Department of Respiratory and Critical Care Medicine, Ningbo First Hospital, Ningbo, China
| | - Phoebe Miles
- Faculty of Humanities and Social Sciences, University of Nottingham Ningbo, Ningbo, China
| | - Chunlin Li
- Department of Otorhinolaryngology-Head and Neck Surgery, Ningbo First Hospital, Ningbo, China
| | - Yijun Ge
- School of Medicine, Ningbo University, Ningbo, China
- Department of Respiratory and Critical Care Medicine, Ningbo First Hospital, Ningbo, China
| | - Xuechan Yu
- School of Medicine, Ningbo University, Ningbo, China
| | - Linfeng Wang
- Department of Respiratory and Critical Care Medicine, Ningbo First Hospital, Ningbo, China
| | - Weina Huang
- Department of Respiratory and Critical Care Medicine, Ningbo First Hospital, Ningbo, China
| | - Xue Kong
- Department of Respiratory and Critical Care Medicine, Ningbo First Hospital, Ningbo, China
| | - Shanni Ma
- Department of Respiratory and Critical Care Medicine, Ningbo First Hospital, Ningbo, China
| | - Yiting Li
- Department of Respiratory and Critical Care Medicine, Ningbo First Hospital, Ningbo, China
| | - Qingwen Jiang
- School of Medicine, Ningbo University, Ningbo, China
- Department of Respiratory and Critical Care Medicine, Ningbo First Hospital, Ningbo, China
| | - Wen Zhang
- Department of Respiratory and Critical Care Medicine, Ningbo First Hospital, Ningbo, China
| | - Chao Cao
- Department of Respiratory and Critical Care Medicine, Ningbo First Hospital, Ningbo, China
- *Correspondence: Chao Cao,
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30
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de Steenhuijsen Piters WAA, Watson RL, de Koff EM, Hasrat R, Arp K, Chu MLJN, de Groot PCM, van Houten MA, Sanders EAM, Bogaert D. Early-life viral infections are associated with disadvantageous immune and microbiota profiles and recurrent respiratory infections. Nat Microbiol 2022; 7:224-237. [PMID: 35058634 DOI: 10.1038/s41564-021-01043-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 12/06/2021] [Indexed: 12/17/2022]
Abstract
The respiratory tract is populated by a specialized microbial ecosystem, which is seeded during and directly following birth. Perturbed development of the respiratory microbial community in early-life has been associated with higher susceptibility to respiratory tract infections (RTIs). Given a consistent gap in time between first signs of aberrant microbial maturation and the observation of the first RTIs, we hypothesized that early-life host-microbe cross-talk plays a role in this process. We therefore investigated viral presence, gene expression profiles and nasopharyngeal microbiota from birth until 12 months of age in 114 healthy infants. We show that the strongest dynamics in gene expression profiles occurred within the first days of life, mostly involving Toll-like receptor (TLR) and inflammasome signalling. These gene expression dynamics coincided with rapid microbial niche differentiation. Early asymptomatic viral infection co-occurred with stronger interferon activity, which was related to specific microbiota dynamics following, including early enrichment of Moraxella and Haemophilus spp. These microbial trajectories were in turn related to a higher number of subsequent (viral) RTIs over the first year of life. Using a multi-omic approach, we found evidence for species-specific host-microbe interactions related to consecutive susceptibility to RTIs. Although further work will be needed to confirm causality of our findings, together these data indicate that early-life viral encounters could impact subsequent host-microbe cross-talk, which is linked to later-life infections.
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Affiliation(s)
- Wouter A A de Steenhuijsen Piters
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht, the Netherlands
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Rebecca L Watson
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Emma M de Koff
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht, the Netherlands
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
- Spaarne Gasthuis Academy, Hoofddorp and Haarlem, the Netherlands
| | - Raiza Hasrat
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht, the Netherlands
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Kayleigh Arp
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht, the Netherlands
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Mei Ling J N Chu
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht, the Netherlands
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Pieter C M de Groot
- Department of Obstetrics and Gynaecology, Spaarne Gasthuis, Hoofddorp and Haarlem, the Netherlands
| | - Marlies A van Houten
- Spaarne Gasthuis Academy, Hoofddorp and Haarlem, the Netherlands
- Department of Paediatrics, Spaarne Gasthuis, Hoofddorp and Haarlem, the Netherlands
| | - Elisabeth A M Sanders
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht, the Netherlands
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Debby Bogaert
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht, the Netherlands.
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands.
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK.
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31
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Horn KJ, Jaberi Vivar AC, Arenas V, Andani S, Janoff EN, Clark SE. Corynebacterium Species Inhibit Streptococcus pneumoniae Colonization and Infection of the Mouse Airway. Front Microbiol 2022; 12:804935. [PMID: 35082772 PMCID: PMC8784410 DOI: 10.3389/fmicb.2021.804935] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 12/03/2021] [Indexed: 12/21/2022] Open
Abstract
The stability and composition of the airway microbiome is an important determinant of respiratory health. Some airway bacteria are considered to be beneficial due to their potential to impede the acquisition and persistence of opportunistic bacterial pathogens such as Streptococcus pneumoniae. Among such organisms, the presence of Corynebacterium species correlates with reduced S. pneumoniae in both adults and children, in whom Corynebacterium abundance is predictive of S. pneumoniae infection risk. Previously, Corynebacterium accolens was shown to express a lipase which cleaves host lipids, resulting in the production of fatty acids that inhibit growth of S. pneumoniae in vitro. However, it was unclear whether this mechanism contributes to Corynebacterium-S. pneumoniae interactions in vivo. To address this question, we developed a mouse model for Corynebacterium colonization in which colonization with either C. accolens or another species, Corynebacterium amycolatum, significantly reduced S. pneumoniae acquisition in the upper airway and infection in the lung. Moreover, the lungs of co-infected mice had reduced pro-inflammatory cytokines and inflammatory myeloid cells, indicating resolution of infection-associated inflammation. The inhibitory effect of C. accolens on S. pneumoniae in vivo was mediated by lipase-dependent and independent effects, indicating that both this and other bacterial factors contribute to Corynebacterium-mediated protection in the airway. We also identified a previously uncharacterized bacterial lipase in C. amycolatum that is required for inhibition of S. pneumoniae growth in vitro. Together, these findings demonstrate the protective potential of airway Corynebacterium species and establish a new model for investigating the impact of commensal microbiota, such as Corynebacterium, on maintaining respiratory health.
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Affiliation(s)
- Kadi J. Horn
- Department of Otolaryngology Head and Neck Surgery, University of Colorado School of Medicine, Aurora, CO, United States
| | - Alexander C. Jaberi Vivar
- Department of Otolaryngology Head and Neck Surgery, University of Colorado School of Medicine, Aurora, CO, United States
- Department of Developmental Biology, Washington University in St. Louis, St. Louis, MO, United States
| | - Vera Arenas
- Department of Otolaryngology Head and Neck Surgery, University of Colorado School of Medicine, Aurora, CO, United States
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Sameer Andani
- Department of Otolaryngology Head and Neck Surgery, University of Colorado School of Medicine, Aurora, CO, United States
| | - Edward N. Janoff
- Division of Infectious Diseases, University of Colorado School of Medicine, Aurora, CO, United States
- Denver Veterans Affairs Medical Center, Aurora, CO, United States
| | - Sarah E. Clark
- Department of Otolaryngology Head and Neck Surgery, University of Colorado School of Medicine, Aurora, CO, United States
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32
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Wang J, Chai J, Zhang L, Zhang L, Yan W, Sun L, Chen Y, Sun Y, Zhao J, Chang C. Microbiota Associations with Inflammatory Pathways in Asthma. Clin Exp Allergy 2021; 52:697-705. [PMID: 34962671 DOI: 10.1111/cea.14089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/17/2021] [Accepted: 12/25/2021] [Indexed: 11/28/2022]
Abstract
BACKGROUND The airway microbiota plays an important role in asthma pathophysiology. However, the relationship between the airway microbiota and asthma phenotypes is still poorly understood. OBJECTIVE We aimed to characterize the airway microbiota in asthma patients and determine its correlation with airway inflammatory phenotypes and other phenotypic characteristics. METHODS The microbial composition of induced sputum specimens collected from asthma patients was determined using 16S rDNA gene sequencing. RESULTS Patients with asthma had a higher abundance of bacterial taxa associated with Bacteroidetes, Fusobacteria, and Proteobacteria and a reduced abundance of Firmicutes and Actinobacteria compared to healthy controls. This study classified the asthma-associated lung microbiota into three community types based on DMM models, which were defined as three pulmotypes (P1, P2, and P3). The lungs of patients with pulmotype 3 (P3) were dominated by Faecalibacterium and Bacteroides, while patients with pulmotype 1 (P1) had a greater abundance of Pasteurellaceae, Streptococcus, and Rothia. P1 patients were older (p = 0.045) and had lower blood TGF levels (P=0.028). P3 patients had fewer eosinophils (P=0.016) and more neutrophils (P=0.039) in induced sputa than P1 patients. CONCLUSIONS Differences in asthma-associated airway microbiota pulmotypes are associated with and might influence asthma, particularly inflammatory phenotypes.
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Affiliation(s)
- Juan Wang
- Department of Respiratory and Critical Care Medicine, Peking University Third Hospital, Beijing, China
| | - Jianmin Chai
- Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR, USA
| | - Linlin Zhang
- Department of Respiratory and Critical Care Medicine, Peking University Third Hospital, Beijing, China
| | - Lijiao Zhang
- Department of Respiratory and Critical Care Medicine, Peking University Third Hospital, Beijing, China
| | - Wei Yan
- Department of Respiratory and Critical Care Medicine, Peking University Third Hospital, Beijing, China
| | - Lina Sun
- Department of Respiratory and Critical Care Medicine, Peking University Third Hospital, Beijing, China
| | - Yahong Chen
- Department of Respiratory and Critical Care Medicine, Peking University Third Hospital, Beijing, China
| | - Yongchang Sun
- Department of Respiratory and Critical Care Medicine, Peking University Third Hospital, Beijing, China
| | - Jiangchao Zhao
- Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR, USA
| | - Chun Chang
- Department of Respiratory and Critical Care Medicine, Peking University Third Hospital, Beijing, China
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Flores Ramos S, Brugger SD, Escapa IF, Skeete CA, Cotton SL, Eslami SM, Gao W, Bomar L, Tran TH, Jones DS, Minot S, Roberts RJ, Johnston CD, Lemon KP. Genomic Stability and Genetic Defense Systems in Dolosigranulum pigrum, a Candidate Beneficial Bacterium from the Human Microbiome. mSystems 2021; 6:e0042521. [PMID: 34546072 PMCID: PMC8547433 DOI: 10.1128/msystems.00425-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 08/27/2021] [Indexed: 01/05/2023] Open
Abstract
Dolosigranulum pigrum is positively associated with indicators of health in multiple epidemiological studies of human nasal microbiota. Knowledge of the basic biology of D. pigrum is a prerequisite for evaluating its potential for future therapeutic use; however, such data are very limited. To gain insight into D. pigrum's chromosomal structure, pangenome, and genomic stability, we compared the genomes of 28 D. pigrum strains that were collected across 20 years. Phylogenomic analysis showed closely related strains circulating over this period and closure of 19 genomes revealed highly conserved chromosomal synteny. Gene clusters involved in the mobilome and in defense against mobile genetic elements (MGEs) were enriched in the accessory genome versus the core genome. A systematic analysis for MGEs identified the first candidate D. pigrum prophage and insertion sequence. A systematic analysis for genetic elements that limit the spread of MGEs, including restriction modification (RM), CRISPR-Cas, and deity-named defense systems, revealed strain-level diversity in host defense systems that localized to specific genomic sites, including one RM system hot spot. Analysis of CRISPR spacers pointed to a wealth of MGEs against which D. pigrum defends itself. These results reveal a role for horizontal gene transfer and mobile genetic elements in strain diversification while highlighting that in D. pigrum this occurs within the context of a highly stable chromosomal organization protected by a variety of defense mechanisms. IMPORTANCE Dolosigranulum pigrum is a candidate beneficial bacterium with potential for future therapeutic use. This is based on its positive associations with characteristics of health in multiple studies of human nasal microbiota across the span of human life. For example, high levels of D. pigrum nasal colonization in adults predicts the absence of Staphylococcus aureus nasal colonization. Also, D. pigrum nasal colonization in young children is associated with healthy control groups in studies of middle ear infections. Our analysis of 28 genomes revealed a remarkable stability of D. pigrum strains colonizing people in the United States across a 20-year span. We subsequently identified factors that can influence this stability, including genomic stability, phage predators, the role of MGEs in strain-level variation, and defenses against MGEs. Finally, these D. pigrum strains also lacked predicted virulence factors. Overall, these findings add additional support to the potential for D. pigrum as a therapeutic bacterium.
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Affiliation(s)
| | - Silvio D. Brugger
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, USA
| | - Isabel Fernandez Escapa
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
- Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, USA
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | | | - Sean L. Cotton
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
| | - Sara M. Eslami
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
| | - Wei Gao
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
- Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, USA
| | - Lindsey Bomar
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
- Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, USA
| | - Tommy H. Tran
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Dakota S. Jones
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Samuel Minot
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | - Christopher D. Johnston
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
- Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Katherine P. Lemon
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
- Division of Infectious Diseases, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Section of Infectious Diseases, Texas Children’s Hospital, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
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Xu L, Earl J, Pichichero ME. Nasopharyngeal microbiome composition associated with Streptococcus pneumoniae colonization suggests a protective role of Corynebacterium in young children. PLoS One 2021; 16:e0257207. [PMID: 34529731 PMCID: PMC8445455 DOI: 10.1371/journal.pone.0257207] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 08/25/2021] [Indexed: 01/04/2023] Open
Abstract
Streptococcus pneumoniae (Spn) is a leading respiratory tract pathogen that colonizes the nasopharynx (NP) through adhesion to epithelial cells and immune evasion. Spn actively interacts with other microbiota in NP but the nature of these interactions are incompletely understood. Using 16S rRNA gene sequencing, we analyzed the microbiota composition in the NP of children with or without Spn colonization. 96 children were included in the study cohort. 74 NP samples were analyzed when children were 6 months old and 85 NP samples were analyzed when children were 12 months old. We found several genera that correlated negatively or positively with Spn colonization, and some of these correlations appeared to be influenced by daycare attendance or other confounding factors such as upper respiratory infection (URI) or Moraxella colonization. Among these genera, Corynebacterium showed a consistent inverse relationship with Spn colonization with little influence by daycare attendance or other factors. We isolated Corynebacterium propinquum and C. pseudodiphtheriticum and found that both inhibited the growth of Spn serotype 22F strain in vitro.
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Affiliation(s)
- Lei Xu
- Center for Infectious Diseases and Immunology, Research Institute, Rochester General Hospital, Rochester, New York, United States of America
| | - Joshua Earl
- Department of Microbiology & Immunology, Centers for Genomic Sciences and Advanced Microbial Processing, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Michael E. Pichichero
- Center for Infectious Diseases and Immunology, Research Institute, Rochester General Hospital, Rochester, New York, United States of America
- * E-mail:
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35
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Fu X, Yuan Q, Zhu X, Li Y, Meng Y, Hashim JH, Hashim Z, Ali F, Zheng YW, Lai XX, Spangfort MD, Wen H, Wang L, Deng F, Hu Q, Norbäck D, Sun Y. Associations between the indoor microbiome, environmental characteristics and respiratory infections in junior high school students of Johor Bahru, Malaysia. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2021; 23:1171-1181. [PMID: 34278392 DOI: 10.1039/d1em00115a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Pathogens are commonly present in the human respiratory tract, but symptoms are varied among individuals. The interactions between pathogens, commensal microorganisms and host immune systems are important in shaping the susceptibility, development and severity of respiratory diseases. Compared to the extensive studies on the human microbiota, few studies reported the association between indoor microbiome exposure and respiratory infections. In this study, 308 students from 21 classrooms were randomly selected to survey the occurrence of respiratory infections in junior high schools of Johor Bahru, Malaysia. Vacuum dust was collected from the floor, chairs and desks of these classrooms, and high-throughput amplicon sequencing (16S rRNA and ITS) and quantitative PCR were conducted to characterize the absolute concentration of the indoor microorganisms. Fifteen bacterial genera in the classes Actinobacteria, Alphaproteobacteria, and Cyanobacteria were protectively associated with respiratory infections (p < 0.01), and these bacteria were mainly derived from the outdoor environment. Previous studies also reported that outdoor environmental bacteria were protectively associated with chronic respiratory diseases, such as asthma, but the genera identified were different between acute and chronic respiratory diseases. Four fungal genera from Ascomycota, including Devriesia, Endocarpon, Sarcinomyces and an unclassified genus from Herpotrichillaceae, were protectively associated with respiratory infections (p < 0.01). House dust mite (HDM) allergens and outdoor NO2 concentration were associated with respiratory infections and infection-related microorganisms. A causal mediation analysis revealed that the health effects of HDM and NO2 were partially or fully mediated by the indoor microorganisms. This is the first study to explore the association between environmental characteristics, microbiome exposure and respiratory infections in a public indoor environment, expanding our understanding of the complex interactions among these factors.
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Affiliation(s)
- Xi Fu
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, PR China.
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36
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Haak BW, Brands X, Davids M, Peters-Sengers H, Kullberg RFJ, van Houdt R, Hugenholtz F, Faber DR, Zaaijer HL, Scicluna BP, van der Poll T, Wiersinga WJ. Bacterial and viral respiratory tract microbiota and host characteristics in adults with lower respiratory tract infections: a case-control study. Clin Infect Dis 2021; 74:776-784. [PMID: 34156449 PMCID: PMC8906706 DOI: 10.1093/cid/ciab568] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Indexed: 01/04/2023] Open
Abstract
Background Viruses and bacteria from the nasopharynx are capable of causing community-acquired pneumonia (CAP), which can be difficult to diagnose. We aimed to investigate whether shifts in the composition of these nasopharyngeal microbial communities can be used as diagnostic biomarkers for CAP in adults. Methods We collected nasopharyngeal swabs from adult CAP patients and controls without infection in a prospective multicenter case-control study design. We generated bacterial and viral profiles using 16S ribosomal RNA gene sequencing and multiplex polymerase chain reaction (PCR), respectively. Bacterial, viral, and clinical data were subsequently used as inputs for extremely randomized trees classification models aiming to distinguish subjects with CAP from healthy controls. Results We enrolled 117 cases and 48 control subjects. Cases displayed significant beta diversity differences in nasopharyngeal microbiota (P = .016, R2 = .01) compared to healthy controls. Our extremely randomized trees classification models accurately discriminated CAP caused by bacteria (area under the curve [AUC] .83), viruses (AUC .95) or mixed origin (AUC .81) from healthy control subjects. We validated this approach using a dataset of nasopharyngeal samples from 140 influenza patients and 38 controls, which yielded highly accurate (AUC .93) separation between cases and controls. Conclusions Relative proportions of different bacteria and viruses in the nasopharynx can be leveraged to diagnose CAP and identify etiologic agent(s) in adult patients. Such data can inform the development of a microbiota-based diagnostic panel used to identify CAP patients and causative agents from nasopharyngeal samples, potentially improving diagnostic specificity, efficiency, and antimicrobial stewardship practices.
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Affiliation(s)
- Bastiaan W Haak
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, The Netherlands.,Microbiota Center Amsterdam, Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Xanthe Brands
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Mark Davids
- Microbiota Center Amsterdam, Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Hessel Peters-Sengers
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Robert F J Kullberg
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, The Netherlands.,Microbiota Center Amsterdam, Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Robin van Houdt
- Department of Virology, Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Floor Hugenholtz
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, The Netherlands.,Microbiota Center Amsterdam, Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Daniël R Faber
- Department of Internal Medicine, BovenIJ hospital, Amsterdam, The Netherlands
| | - Hans L Zaaijer
- Department of Virology, Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Brendon P Scicluna
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, The Netherlands.,Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Tom van der Poll
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, The Netherlands.,Department of Internal Medicine, Division of Infectious Diseases, Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - W Joost Wiersinga
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, The Netherlands.,Microbiota Center Amsterdam, Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, The Netherlands.,Department of Internal Medicine, Division of Infectious Diseases, Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, The Netherlands
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37
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Raya Tonetti F, Tomokiyo M, Ortiz Moyano R, Quilodrán-Vega S, Yamamuro H, Kanmani P, Melnikov V, Kurata S, Kitazawa H, Villena J. The Respiratory Commensal Bacterium Dolosigranulum pigrum 040417 Improves the Innate Immune Response to Streptococcus pneumoniae. Microorganisms 2021; 9:microorganisms9061324. [PMID: 34207076 PMCID: PMC8234606 DOI: 10.3390/microorganisms9061324] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 06/11/2021] [Accepted: 06/16/2021] [Indexed: 12/24/2022] Open
Abstract
Previously, we demonstrated that the nasal administration of Dolosigranulum pigrum 040417 differentially modulated the respiratory innate immune response triggered by the activation of Toll-like receptor 2 in infant mice. In this work, we aimed to evaluate the beneficial effects of D. pigrum 040417 in the context of Streptococcus pneumoniae infection and characterize the role of alveolar macrophages (AMs) in the immunomodulatory properties of this respiratory commensal bacterium. The nasal administration of D. pigrum 040417 to infant mice significantly increased their resistance to pneumococcal infection, differentially modulated respiratory cytokines production, and reduced lung injuries. These effects were associated to the ability of the 040417 strain to modulate AMs function. Depletion of AMs significantly reduced the capacity of the 040417 strain to improve both the reduction of pathogen loads and the protection against lung tissue damage. We also demonstrated that the immunomodulatory properties of D. pigrum are strain-specific, as D. pigrum 030918 was not able to modulate respiratory immunity or to increase the resistance of mice to an S. pneumoniae infection. These findings enhanced our knowledge regarding the immunological mechanisms involved in modulation of respiratory immunity induced by beneficial respiratory commensal bacteria and suggested that particular strains could be used as next-generation probiotics.
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Affiliation(s)
- Fernanda Raya Tonetti
- Laboratory of Immunobiotechnology, Reference Centre for Lactobacilli (CERELA-CONICET), Tucumán 4000, Argentina; (F.R.T.); (R.O.M.)
| | - Mikado Tomokiyo
- Food and Feed Immunology Group, Laboratory of Animal Food Function, Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan; (M.T.); (H.Y.); (P.K.)
- Livestock Immunology Unit, International Education and Research Center for Food and Agricultural Immunology (CFAI), Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan
| | - Ramiro Ortiz Moyano
- Laboratory of Immunobiotechnology, Reference Centre for Lactobacilli (CERELA-CONICET), Tucumán 4000, Argentina; (F.R.T.); (R.O.M.)
| | - Sandra Quilodrán-Vega
- Laboratory of Food Microbiology, Faculty of Veterinary Sciences, University of Concepción, Chillán 3780000, Chile;
| | - Hikari Yamamuro
- Food and Feed Immunology Group, Laboratory of Animal Food Function, Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan; (M.T.); (H.Y.); (P.K.)
- Livestock Immunology Unit, International Education and Research Center for Food and Agricultural Immunology (CFAI), Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan
| | - Paulraj Kanmani
- Food and Feed Immunology Group, Laboratory of Animal Food Function, Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan; (M.T.); (H.Y.); (P.K.)
| | - Vyacheslav Melnikov
- Gabrichevsky Research Institute for Epidemiology and Microbiology, 125212 Moscow, Russia;
| | - Shoichiro Kurata
- Laboratory of Molecular Genetics, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan;
| | - Haruki Kitazawa
- Food and Feed Immunology Group, Laboratory of Animal Food Function, Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan; (M.T.); (H.Y.); (P.K.)
- Livestock Immunology Unit, International Education and Research Center for Food and Agricultural Immunology (CFAI), Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan
- Correspondence: (H.K.); (J.V.)
| | - Julio Villena
- Laboratory of Immunobiotechnology, Reference Centre for Lactobacilli (CERELA-CONICET), Tucumán 4000, Argentina; (F.R.T.); (R.O.M.)
- Food and Feed Immunology Group, Laboratory of Animal Food Function, Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan; (M.T.); (H.Y.); (P.K.)
- Correspondence: (H.K.); (J.V.)
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Park DE, Higdon MM, Prosperi C, Baggett HC, Brooks WA, Feikin DR, Hammitt LL, Howie SRC, Kotloff KL, Levine OS, Madhi SA, Murdoch DR, O’Brien KL, Scott JAG, Thea DM, Antonio M, Awori JO, Baillie VL, Bunthi C, Kwenda G, Mackenzie GA, Moore DP, Morpeth SC, Mwananyanda L, Paveenkittiporn W, Ziaur Rahman M, Rahman M, Rhodes J, Sow SO, Tapia MD, Deloria Knoll M. Upper Respiratory Tract Co-detection of Human Endemic Coronaviruses and High-density Pneumococcus Associated With Increased Severity Among HIV-Uninfected Children Under 5 Years Old in the PERCH Study. Pediatr Infect Dis J 2021; 40:503-512. [PMID: 33883479 PMCID: PMC8104011 DOI: 10.1097/inf.0000000000003139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/25/2021] [Indexed: 01/08/2023]
Abstract
BACKGROUND Severity of viral respiratory illnesses can be increased with bacterial coinfection and can vary by sex, but influence of coinfection and sex on human endemic coronavirus (CoV) species, which generally cause mild to moderate respiratory illness, is unknown. We evaluated CoV and pneumococcal co-detection by sex in childhood pneumonia. METHODS In the 2011-2014 Pneumonia Etiology Research for Child Health study, nasopharyngeal and oropharyngeal (NP/OP) swabs and other samples were collected from 3981 children <5 years hospitalized with severe or very severe pneumonia in 7 countries. Severity by NP/OP detection status of CoV (NL63, 229E, OC43 or HKU1) and high-density (≥6.9 log10 copies/mL) pneumococcus (HDSpn) by real-time polymerase chain reaction was assessed by sex using logistic regression adjusted for age and site. RESULTS There were 43 (1.1%) CoV+/HDSpn+, 247 CoV+/HDSpn-, 449 CoV-/HDSpn+ and 3149 CoV-/HDSpn- cases with no significant difference in co-detection frequency by sex (range 51.2%-64.0% male, P = 0.06). More CoV+/HDSpn+ pneumonia was very severe compared with other groups for both males (13/22, 59.1% versus range 29.1%-34.7%, P = 0.04) and females (10/21, 47.6% versus 32.5%-43.5%, P = 0.009), but only male CoV+/HDSpn+ required supplemental oxygen more frequently (45.0% versus 20.6%-28.6%, P < 0.001) and had higher mortality (35.0% versus 5.3%-7.1%, P = 0.004) than other groups. For females with CoV+/HDSpn+, supplemental oxygen was 25.0% versus 24.8%-33.3% (P = 0.58) and mortality was 10.0% versus 9.2%-12.9% (P = 0.69). CONCLUSIONS Co-detection of endemic CoV and HDSpn was rare in children hospitalized with pneumonia, but associated with higher severity and mortality in males. Findings may warrant investigation of differences in severity by sex with co-detection of HDSpn and SARS-CoV-2.
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Affiliation(s)
- Daniel E. Park
- From the Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
- Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, District of Columbia
| | - Melissa M. Higdon
- From the Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Christine Prosperi
- From the Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Henry C. Baggett
- Division of Global Health Protection, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - W. Abdullah Brooks
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Bangladesh
| | - Daniel R. Feikin
- From the Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Laura L. Hammitt
- From the Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Steve R. C. Howie
- Medical Research Council Unit, Basse, The Gambia
- Department of Paediatrics, University of Auckland, New Zealand
| | - Karen L. Kotloff
- Department of Pediatrics and Department of Medicine, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland
| | - Orin S. Levine
- From the Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
- Bill & Melinda Gates Foundation, Seattle, Washington
| | - Shabir A. Madhi
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit
- Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - David R. Murdoch
- Department of Pathology and Biomedical Sciences, University of Otago
- Microbiology Unit, Canterbury Health Laboratories, Christchurch, New Zealand
| | - Katherine L. O’Brien
- From the Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - J. Anthony G. Scott
- KEMRI Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Coast, Kilifi, Kenya
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Donald M. Thea
- Department of Global Health and Development, Boston University School of Public Health, Boston, Massachusetts
| | - Martin Antonio
- Medical Research Council Unit, Basse, The Gambia
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine
- Microbiology and Infection Unit, Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Juliet O. Awori
- KEMRI Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Coast, Kilifi, Kenya
| | - Vicky L. Baillie
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit
| | - Charatdao Bunthi
- Division of Global Health Protection, Thailand Ministry of Public Health–US Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
| | - Geoffrey Kwenda
- Right to Care-Zambia
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka, Zambia
| | - Grant A. Mackenzie
- Medical Research Council Unit, Basse, The Gambia
- Murdoch Children’s Research Institute, Melbourne, Australia
- London School of Hygiene and Tropical Medicine, London, United Kingdom
- Department of Paediatrics, University of Melbourne, Australia
| | - David P. Moore
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit
- Department of Paediatrics & Child Health, Chris Hani Baragwanath Academic Hospital and University of the Witwatersrand, South Africa
| | - Susan C. Morpeth
- KEMRI Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Coast, Kilifi, Kenya
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Microbiology Laboratory, Middlemore Hospital, Counties Manukau District Health Board, Auckland, New Zealand
| | - Lawrence Mwananyanda
- Department of Global Health and Development, Boston University School of Public Health, Boston, Massachusetts
- EQUIP-Zambia, Lusaka, Zambia
| | | | - Mohammed Ziaur Rahman
- Virology Laboratory, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Bangladesh
| | - Mustafizur Rahman
- Virology Laboratory, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Bangladesh
| | - Julia Rhodes
- Division of Global Health Protection, Thailand Ministry of Public Health–US Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
| | - Samba O. Sow
- Centre pour le Développement des Vaccins (CVD-Mali), Bamako, Mali
| | - Milagritos D. Tapia
- Department of Pediatrics, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland
| | - Maria Deloria Knoll
- From the Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
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Theodosiou AA, Dorey RB, Laver JR, Cleary DW, Read RC, Jones CE. Manipulating the infant respiratory microbiomes to improve clinical outcomes: A review of the literature. J Infect 2021; 82:247-252. [PMID: 33753151 DOI: 10.1016/j.jinf.2021.03.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/12/2021] [Accepted: 03/16/2021] [Indexed: 01/01/2023]
Abstract
BACKGROUND The association between infant respiratory microbiota and disease (including respiratory tract infections and asthma) is increasingly recognised, although the mechanism remains unclear. Respiratory infections and asthma account for a large proportion of infant morbidity and mortality, so the possibility of preventing disease or modifying clinical outcomes by manipulating microbiome development warrants investigation. OBJECTIVES AND METHODS We identified studies that investigated the efficacy of live bacteria (probiotics or human challenge) or their substrates to modify respiratory colonisation or clinical outcomes in infants. ELIGIBILITY CRITERIA Interventional studies involving infants under one year of age, administration of live bacteria or their substrates, and outcome measures including bacterial colonisation, microbiome profile, or respiratory disease phenotypes. RESULTS AND LIMITATIONS Some bacterial interventions can reduce infant respiratory infections, although none have been shown to reduce asthma incidence. The literature is heterogeneous in design and quality, precluding meaningful meta-analysis. CONCLUSIONS Upper respiratory tract infant microbiome manipulation may alter outcomes in respiratory tract infection, but further well-conducted research is needed to confirm this. Improved regulation of proprietary bacterial products is essential for further progress.
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Affiliation(s)
- Anastasia A Theodosiou
- Clinical and Experimental Sciences, C level, South Academic Block, University Hospital Southampton, Tremona Road, SO166YD Southampton, United Kingdom.
| | - Robert B Dorey
- Clinical and Experimental Sciences, C level, South Academic Block, University Hospital Southampton, Tremona Road, SO166YD Southampton, United Kingdom
| | - Jay R Laver
- Clinical and Experimental Sciences, C level, South Academic Block, University Hospital Southampton, Tremona Road, SO166YD Southampton, United Kingdom
| | - David W Cleary
- Clinical and Experimental Sciences, C level, South Academic Block, University Hospital Southampton, Tremona Road, SO166YD Southampton, United Kingdom
| | - Robert C Read
- Clinical and Experimental Sciences, C level, South Academic Block, University Hospital Southampton, Tremona Road, SO166YD Southampton, United Kingdom; NIHR Southampton Clinical Research Facility and Biomedical Research Centre, University Hospital Southampton, Tremona Road, SO166YD Southampton, United Kingdom
| | - Christine E Jones
- NIHR Southampton Clinical Research Facility and Biomedical Research Centre, University Hospital Southampton, Tremona Road, SO166YD Southampton, United Kingdom; Faculty of Medicine and Institute of for Life Sciences, F level, South Academic Block, University Hospital Southampton, Tremona Road, SO166YD Southampton, United Kingdom
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40
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Weight CM, Jochems SP, Adler H, Ferreira DM, Brown JS, Heyderman RS. Insights Into the Effects of Mucosal Epithelial and Innate Immune Dysfunction in Older People on Host Interactions With Streptococcus pneumoniae. Front Cell Infect Microbiol 2021; 11:651474. [PMID: 34113578 PMCID: PMC8185287 DOI: 10.3389/fcimb.2021.651474] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 05/10/2021] [Indexed: 12/21/2022] Open
Abstract
In humans, nasopharyngeal carriage of Streptococcus pneumoniae is common and although primarily asymptomatic, is a pre-requisite for pneumonia and invasive pneumococcal disease (IPD). Together, these kill over 500,000 people over the age of 70 years worldwide every year. Pneumococcal conjugate vaccines have been largely successful in reducing IPD in young children and have had considerable indirect impact in protection of older people in industrialized country settings (herd immunity). However, serotype replacement continues to threaten vulnerable populations, particularly older people in whom direct vaccine efficacy is reduced. The early control of pneumococcal colonization at the mucosal surface is mediated through a complex array of epithelial and innate immune cell interactions. Older people often display a state of chronic inflammation, which is associated with an increased mortality risk and has been termed 'Inflammageing'. In this review, we discuss the contribution of an altered microbiome, the impact of inflammageing on human epithelial and innate immunity to S. pneumoniae, and how the resulting dysregulation may affect the outcome of pneumococcal infection in older individuals. We describe the impact of the pneumococcal vaccine and highlight potential research approaches which may improve our understanding of respiratory mucosal immunity during pneumococcal colonization in older individuals.
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Affiliation(s)
- Caroline M. Weight
- Research Department of Infection, Division of Infection and Immunity, University College London, London, United Kingdom
| | - Simon P. Jochems
- Department of Parasitology, Leiden University Medical Center, Leiden, Netherlands
| | - Hugh Adler
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Tropical and Infectious Diseases Unit, Liverpool University Hospitals National Health Service (NHS) Foundation Trust, Liverpool, United Kingdom
| | - Daniela M. Ferreira
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Jeremy S. Brown
- Respiratory Medicine, University College London, London, United Kingdom
| | - Robert S. Heyderman
- Research Department of Infection, Division of Infection and Immunity, University College London, London, United Kingdom
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Polymicrobial Interactions Operative during Pathogen Transmission. mBio 2021; 12:mBio.01027-21. [PMID: 34006664 PMCID: PMC8262881 DOI: 10.1128/mbio.01027-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Pathogen transmission is a key point not only for infection control and public health interventions but also for understanding the selective pressures in pathogen evolution. The “success” of a pathogen lies not in its ability to cause signs and symptoms of illness but in its ability to be shed from the initial hosts, survive between hosts, and then establish infection in a new host. Recent insights have shown the importance of the interaction between the pathogen and both the commensal microbiome and coinfecting pathogens on shedding, environmental survival, and acquisition of infection. Pathogens have evolved in the context of cooperation and competition with other microbes, and the roles of these cooperations and competitions in transmission can inform novel preventative and therapeutic strategies.
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de Steenhuijsen Piters WAA, Binkowska J, Bogaert D. Early Life Microbiota and Respiratory Tract Infections. Cell Host Microbe 2021; 28:223-232. [PMID: 32791114 DOI: 10.1016/j.chom.2020.07.004] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/02/2020] [Accepted: 07/07/2020] [Indexed: 12/18/2022]
Abstract
Over the last decade, it has become clear that respiratory and intestinal tract microbiota are related to pathogenesis of respiratory tract infections (RTIs). Host and environmental factors can drive respiratory microbiota maturation in early life, which in turn is related to consecutive susceptibility to RTIs. Moreover, during RTIs, including viral bronchiolitis, the local microbiome appears to play an immunomodulatory role through complex interactions, though causality has not yet been fully demonstrated. The microbiota is subsequently associated with recovery after RTIs and can be related to persistent or long-term sequelae. In this Review, we explore the epidemiological evidence supporting these associations and link to mechanistic insights. The long-term consequences of childhood RTIs and the comprehensive role of the microbiota at various stages in RTI pathogenesis call for early life preventative and therapeutic interventions to promote respiratory health.
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Affiliation(s)
- Wouter A A de Steenhuijsen Piters
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands; National Institute for Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, the Netherlands
| | - Justyna Binkowska
- University of Edinburgh Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Debby Bogaert
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands; National Institute for Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, the Netherlands; University of Edinburgh Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK.
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43
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Mettelman RC, Thomas PG. Human Susceptibility to Influenza Infection and Severe Disease. Cold Spring Harb Perspect Med 2021; 11:cshperspect.a038711. [PMID: 31964647 PMCID: PMC8091954 DOI: 10.1101/cshperspect.a038711] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Influenza viruses are a persistent threat to global human health. Increased susceptibility to infection and the risk factors associated with progression to severe influenza-related disease are determined by a multitude of viral, host, and environmental conditions. Decades of epidemiologic research have broadly defined high-risk groups, while new genomic association studies have identified specific host factors impacting an individual's response to influenza. Here, we review and highlight both human susceptibility to influenza infection and the conditions that lead to severe influenza disease.
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Affiliation(s)
- Robert C Mettelman
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
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Coleman A, Bialasiewicz S, Marsh RL, Grahn Håkansson E, Cottrell K, Wood A, Jayasundara N, Ware RS, Zaugg J, Sidjabat HE, Adams J, Ferguson J, Brown M, Roos K, Cervin A. Upper Respiratory Microbiota in Relation to Ear and Nose Health Among Australian Aboriginal and Torres Strait Islander Children. J Pediatric Infect Dis Soc 2021; 10:468-476. [PMID: 33393596 DOI: 10.1093/jpids/piaa141] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 11/06/2020] [Indexed: 01/06/2023]
Abstract
BACKGROUND We explored the nasal microbiota in Indigenous Australian children in relation to ear and nasal health. METHODS In total, 103 Indigenous Australian children aged 2-7 years (mean 4.7 years) were recruited from 2 Queensland communities. Children's ears, nose, and throats were examined and upper respiratory tract (URT) swabs collected. Clinical histories were obtained from parents/medical records. URT microbiota were characterized using culturomics with Matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) identification. Real-time PCR was used to quantify otopathogen (Haemophilus influenzae, Streptococcus pneumoniae, and Moraxella catarrhalis) loads and detect respiratory viruses. Data were analyzed using beta diversity measures, regression modeling, and a correlation network analysis. RESULTS Children with historical/current otitis media (OM) or URT infection (URTI) had higher nasal otopathogen detection and loads and rhinovirus detection compared with healthy children (all P < .04). Children with purulent rhinorrhea had higher nasal otopathogen detection and loads and rhinovirus detection (P < .04) compared with healthy children. High otopathogen loads were correlated in children with historical/current OM or URTI, whereas Corynebacterium pseudodiphtheriticum and Dolosigranulum pigrum were correlated in healthy children. CONCLUSIONS Corynebacterium pseudodiphtheriticum and D. pigrum are associated with URT and ear health. The importance of the main otopathogens in URT disease/OM was confirmed, and their role relates to co-colonization and high otopathogens loads.
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Affiliation(s)
- Andrea Coleman
- Children's Health Research Centre, The University of Queensland Centre for Clinical Research, South Brisbane, Australia
- Department of Surgery-Otolaryngology, Head and Neck Surgery, Townsville University Hospital, Townsville, Australia
| | - Seweryn Bialasiewicz
- Australian Centre for Ecogenomics, The University of Queensland, St Lucia, Australia
- Queensland Pediatric Infectious Diseases Laboratory, Queensland Children's Hospital, South Brisbane, Australia
| | - Robyn L Marsh
- Menzies School of Health Research, Charles Darwin University, Darwin, Australia
| | - Eva Grahn Håkansson
- Department of Clinical Microbiology, Umeå University and Essum AB, Umeå, Sweden
| | - Kyra Cottrell
- The University of Queensland Centre for Clinical Research, Herston, Australia
| | - Amanda Wood
- Queensland Health Deadly Ears Program, Brisbane, Australia
| | - Nadeesha Jayasundara
- Queensland Pediatric Infectious Diseases Laboratory, Queensland Children's Hospital, South Brisbane, Australia
| | - Robert S Ware
- Menzies Health Institute Queensland, Griffith University, Brisbane, Australia
| | - Julian Zaugg
- Children's Health Research Centre, The University of Queensland Centre for Clinical Research, South Brisbane, Australia
| | - Hanna E Sidjabat
- The University of Queensland Centre for Clinical Research, Herston, Australia
| | - Jasmyn Adams
- Queensland Health Deadly Ears Program, Brisbane, Australia
| | | | - Matthew Brown
- Queensland Health Deadly Ears Program, Brisbane, Australia
| | | | - Anders Cervin
- The University of Queensland Centre for Clinical Research, Herston, Australia
- Department of Otolaryngology, Head and Neck Surgery, The Royal Brisbane and Women's Hospital, Brisbane, Australia
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Sender V, Hentrich K, Henriques-Normark B. Virus-Induced Changes of the Respiratory Tract Environment Promote Secondary Infections With Streptococcus pneumoniae. Front Cell Infect Microbiol 2021; 11:643326. [PMID: 33828999 PMCID: PMC8019817 DOI: 10.3389/fcimb.2021.643326] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/01/2021] [Indexed: 01/08/2023] Open
Abstract
Secondary bacterial infections enhance the disease burden of influenza infections substantially. Streptococcus pneumoniae (the pneumococcus) plays a major role in the synergism between bacterial and viral pathogens, which is based on complex interactions between the pathogen and the host immune response. Here, we discuss mechanisms that drive the pathogenesis of a secondary pneumococcal infection after an influenza infection with a focus on how pneumococci senses and adapts to the influenza-modified environment. We briefly summarize what is known regarding secondary bacterial infection in relation to COVID-19 and highlight the need to improve our current strategies to prevent and treat viral bacterial coinfections.
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Affiliation(s)
- Vicky Sender
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Karina Hentrich
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Birgitta Henriques-Normark
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.,Clinical Microbiology, Karolinska University Hospital, Solna, Sweden
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Thibeault C, Suttorp N, Opitz B. The microbiota in pneumonia: From protection to predisposition. Sci Transl Med 2021; 13:13/576/eaba0501. [PMID: 33441423 DOI: 10.1126/scitranslmed.aba0501] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 06/30/2020] [Indexed: 12/12/2022]
Abstract
Mucosal surfaces of the upper respiratory tract and gut are physiologically colonized with their own collection of microbes, the microbiota. The normal upper respiratory tract and gut microbiota protects against pneumonia by impeding colonization by potentially pathogenic bacteria and by regulating immune responses. However, antimicrobial therapy and critical care procedures perturb the microbiota, thus compromising its function and predisposing to lung infections (pneumonia). Interindividual variations and age-related alterations in the microbiota also affect vulnerability to pneumonia. We discuss how the healthy microbiota protects against pneumonia and how host factors and medical interventions alter the microbiota, thus influencing susceptibility to pneumonia.
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Affiliation(s)
- Charlotte Thibeault
- Department of Internal Medicine/Infectious Diseases and Pulmonary Medicine, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Norbert Suttorp
- Department of Internal Medicine/Infectious Diseases and Pulmonary Medicine, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Bastian Opitz
- Department of Internal Medicine/Infectious Diseases and Pulmonary Medicine, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany.
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47
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Morton B, Jambo K, Chikaonda T, Rylance J, Henrion MY, Banda NP, Nsomba E, Gondwe J, Ferreira D, Gordon SB, MARVELS Consortium. The influence of pneumococcal conjugate vaccine-13 on nasal colonisation in a controlled human infection model of pneumococcal carriage in Malawi: a double-blinded randomised controlled trial protocol. Wellcome Open Res 2021; 6:240. [PMID: 36263101 PMCID: PMC9549377.2 DOI: 10.12688/wellcomeopenres.17172.2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/14/2022] [Indexed: 11/20/2022] Open
Abstract
Streptococcus pneumoniae is the leading cause of morbidity and mortality due to community acquired pneumonia, bacterial meningitis and bacteraemia worldwide. Pneumococcal conjugate vaccines protect against invasive disease, but are expensive to manufacture, limited in serotype coverage, associated with serotype replacement, and demonstrate reduced effectiveness against mucosal colonisation. For Malawi, nasopharyngeal carriage of vaccine-type pneumococci is common in vaccinated children despite national roll-out of 13-valent pneumococcal conjugate vaccine (PCV13) since 2011. Our team has safely transferred an established experimental human pneumococcal carriage method from Liverpool School of Tropical Medicine to the Malawi-Liverpool Wellcome Trust Clinical Research Programme, Malawi. This study will determine potential immunological mechanisms for the differential effects of PCV13 on nasal carriage between healthy Malawian and UK populations. We will conduct a double-blinded randomised controlled trial to vaccinate (1:1) participants with either PCV13 or control (normal saline). After a period of one month, participants will be inoculated with S. pneumoniae serotype 6B to experimentally induce nasal carriage using the EHPC method. Subsequently, participants will be invited for a second inoculation after one year to determine longer-term vaccine-induced immunological effects. Primary endpoint: detection of inoculated pneumococci by classical culture from nasal wash recovered from the participants after pneumococcal challenge. Secondary endpoints: local and systemic innate, humoral and cellular responses to PCV-13 with and without pneumococcal nasal carriage The primary objective of this controlled human infection model study is to determine if PCV-13 vaccination is protective against pneumococcal carriage in healthy adult Malawian volunteers. This study will help us to understand the observed differences in PCV-13 efficacy between populations and inform the design of future vaccines relevant to the Malawian population. Trial Registration: Pan African Clinical Trial Registry (REF: PACTR202008503507113).
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Affiliation(s)
- Ben Morton
- Lung Health, Malawi-Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
- Critical Care Medicine, Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK
- Department of Medicine, Queen Elizabeth Central Hospital, Blantyre, Malawi
| | - Kondwani Jambo
- Lung Health, Malawi-Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Tarsizio Chikaonda
- Lung Health, Malawi-Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Jamie Rylance
- Lung Health, Malawi-Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
- Department of Medicine, Queen Elizabeth Central Hospital, Blantyre, Malawi
| | - Marc Y.R. Henrion
- Lung Health, Malawi-Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Ndaziona Peter Banda
- Department of Medicine, Queen Elizabeth Central Hospital, Blantyre, Malawi
- College of Medicine, Malawi, Blantyre, Malawi
| | - Edna Nsomba
- Lung Health, Malawi-Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- Department of Medicine, Queen Elizabeth Central Hospital, Blantyre, Malawi
| | - Joel Gondwe
- Lung Health, Malawi-Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Daniela Ferreira
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Stephen B. Gordon
- Lung Health, Malawi-Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
- Department of Medicine, Queen Elizabeth Central Hospital, Blantyre, Malawi
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Morton B, Jambo K, Chikaonda T, Rylance J, Henrion MY, Banda NP, Nsomba E, Gondwe J, Ferreira D, Gordon SB, MARVELS Consortium. The influence of pneumococcal conjugate vaccine-13 on nasal colonisation in a controlled human infection model of pneumococcal carriage in Malawi: a double-blinded randomised controlled trial protocol. Wellcome Open Res 2021; 6:240. [PMID: 36263101 PMCID: PMC9549377 DOI: 10.12688/wellcomeopenres.17172.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2021] [Indexed: 11/20/2022] Open
Abstract
Streptococcus pneumoniae is the leading cause of morbidity and mortality due to community acquired pneumonia, bacterial meningitis and bacteraemia worldwide. Pneumococcal conjugate vaccines protect against invasive disease, but are expensive to manufacture, limited in serotype coverage, associated with serotype replacement, and demonstrate reduced effectiveness against mucosal colonisation. For Malawi, nasopharyngeal carriage of vaccine-type pneumococci is common in vaccinated children despite national roll-out of 13-valent pneumococcal conjugate vaccine (PCV13) since 2011. Our team has safely transferred an established experimental human pneumococcal carriage method from Liverpool School of Tropical Medicine to the Malawi-Liverpool Wellcome Trust Clinical Research Programme, Malawi. This study will determine potential immunological mechanisms for the differential effects of PCV13 on nasal carriage between healthy Malawian and UK populations. We will conduct a double-blinded randomised controlled trial to vaccinate (1:1) participants with either PCV13 or control (normal saline). After a period of one month, participants will be inoculated with S. pneumoniae serotype 6B to experimentally induce nasal carriage using the EHPC method. Subsequently, participants will be invited for a second inoculation after one year to determine longer-term vaccine-induced immunological effects. Primary endpoint: detection of inoculated pneumococci by classical culture from nasal wash recovered from the participants after pneumococcal challenge. Secondary endpoints: local and systemic innate, humoral and cellular responses to PCV-13 with and without pneumococcal nasal carriage The primary objective of this controlled human infection model study is to determine if PCV-13 vaccination is protective against pneumococcal carriage in healthy adult Malawian volunteers. This study will help us to understand the observed differences in PCV-13 efficacy between populations and inform the design of future vaccines relevant to the Malawian population. Trial Registration: Pan African Clinical Trial Registry (REF: PACTR202008503507113).
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Affiliation(s)
- Ben Morton
- Lung Health, Malawi-Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
- Critical Care Medicine, Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK
- Department of Medicine, Queen Elizabeth Central Hospital, Blantyre, Malawi
| | - Kondwani Jambo
- Lung Health, Malawi-Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Tarsizio Chikaonda
- Lung Health, Malawi-Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Jamie Rylance
- Lung Health, Malawi-Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
- Department of Medicine, Queen Elizabeth Central Hospital, Blantyre, Malawi
| | - Marc Y.R. Henrion
- Lung Health, Malawi-Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Ndaziona Peter Banda
- Department of Medicine, Queen Elizabeth Central Hospital, Blantyre, Malawi
- College of Medicine, Malawi, Blantyre, Malawi
| | - Edna Nsomba
- Lung Health, Malawi-Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- Department of Medicine, Queen Elizabeth Central Hospital, Blantyre, Malawi
| | - Joel Gondwe
- Lung Health, Malawi-Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Daniela Ferreira
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Stephen B. Gordon
- Lung Health, Malawi-Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
- Department of Medicine, Queen Elizabeth Central Hospital, Blantyre, Malawi
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Nasal Tissue Extraction Is Essential for Characterization of the Murine Upper Respiratory Tract Microbiota. mSphere 2020; 5:5/6/e00562-20. [PMID: 33328347 PMCID: PMC7771231 DOI: 10.1128/msphere.00562-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The nasal microbiota is composed of species that play a role in the colonization success of pathogens, including Streptococcus pneumoniae and Staphylococcus aureus. Murine models provide the ability to explore disease pathogenesis, but little is known about the natural murine nasal microbiota. Respiratory infections are a leading cause of morbidity and mortality worldwide. Bacterial pathogens often colonize the upper respiratory tract (nose or mouth) prior to causing lower respiratory infections or invasive disease. Interactions within the upper respiratory tract between colonizing bacteria and the resident microbiota could contribute to colonization success and subsequent transmission. Human carriage studies have identified associations between pathogens such as Streptococcus pneumoniae and members of the resident microbiota, although few mechanisms of competition and cooperation have been identified and would be aided by the use of animal models. Little is known about the composition of the murine nasal microbiota; thus, we set out to improve assessment, including tissue sampling, composition, and comparison between mouse sources. Nasal washes were efficient in sampling the nasopharyngeal space but barely disrupted the nasal turbinates. Nasal tissue extraction increased the yield of cultivable bacterial compared to nasal washes, revealing distinct community compositions. Experimental pneumococcal colonization led to dominance by the colonizing pathogen in the nasopharynx and nasal turbinates, but the composition of the microbiota, and interactions with resident microbes, differed depending on the sampling method. Importantly, vendor source has a large impact on microbial composition. Bacterial interactions, including cooperation and colonization resistance, depend on the biogeography of the nose and should be considered during research design of experimental colonization with pathogens. IMPORTANCE The nasal microbiota is composed of species that play a role in the colonization success of pathogens, including Streptococcus pneumoniae and Staphylococcus aureus. Murine models provide the ability to explore disease pathogenesis, but little is known about the natural murine nasal microbiota. This study established techniques to allow the exploration of the bacterial members of the nasal microbiota. The mouse nasal microbiota included traditional respiratory bacteria, including Streptococcus, Staphylococcus, and Moraxella species. Analyses were affected by different sampling methods as well as the commercial source of the mice, which should be included in future research design of infectious disease research.
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Abstract
PURPOSE OF REVIEW There has been an exponential increase in research into infant microbiome evolution, and it appears that pharyngeal microbiota are associated with clinical phenotypes (e.g. infection and asthma). Although broad consensus views are emerging, significant challenges and uncertainties remain. RECENT FINDINGS Infant pharyngeal microbiome research is limited by low biomass, high temporal diversity and lack of agreed standards for sampling, DNA sequencing and taxonomic reporting. Analysis of amplicon sequence variants and improved cost and availability of whole-genome sequencing are promising options for improving taxonomic resolution of such studies. Infant respiratory microbiomes arise, at least in part, from maternal flora (e.g. the respiratory tract and breastmilk), and are associated with environmental and clinical factors (e.g. mode of feeding and delivery, siblings, daycare attendance, birth season and antibiotic usage). Interventional research to modify the infant pharyngeal microbiota has recently been reported, using dietary supplements. SUMMARY Further work is needed to improve characterization of the infant pharyngeal microbiomes, including routes of bacterial acquisition, role of environmental factors and associations with disease phenotypes. Methodological standards are desirable to facilitate more reproducible, comparable research. Improved understanding may enable manipulation of infant pharyngeal microbiota to improve clinical outcomes.
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