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Zhang Q, Song J, Wu H, Wang L, Zhuo G, Li H, He S, Pan Y, Liu G. Intratumoral microbiota associates with systemic immune inflammation state in nasopharyngeal carcinoma. Int Immunopharmacol 2024; 141:112984. [PMID: 39173404 DOI: 10.1016/j.intimp.2024.112984] [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: 05/24/2024] [Revised: 07/07/2024] [Accepted: 08/16/2024] [Indexed: 08/24/2024]
Abstract
BACKGROUND The nasopharynx serves as a crucial niche for the microbiome of the upper respiratory tract. However, the association between the intratumoral microbiota and host systemic inflammation and immune status in nasopharyngeal carcinoma (NPC) remain uncertain. METHODS We performed 5R 16S rDNA sequencing on NPC tissue samples, followed by diversity analysis, LEfSe differential analysis, and KEGG functional prediction. The analyses were based on indices such as AISI, SIRI, PAR, PLR, and NAR. Correlation analyses between microbes and these indices were performed to identify microbes associated with inflammation and immune status. Additionally, regression analysis based on tumor TNM stage was performed to identify key microbes linked to tumor progression. The head and neck squamous cell carcinoma (HNSC) transcriptome and the paired HNSC microbiome data from TCGA were utilized to validate the analyses. RESULTS The Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes were the most enriched phyla in NPC tissues. Microbes within these phyla demonstrated high sensitivity to changes in host systemic inflammation and immune status. Proteobacteria and Firmicutes showed significant differences between inflammation groups. Actinobacteria varied specifically with platelet-related inflammatory indices, and Bacteroidetes genera exhibited significant differences between NAR groups. Corynebacterium and Brevundimonas significantly impacted the T stage of tumors, with a high load of Corynebacterium within tumors associated with a better prognosis CONCLUSION: Our analysis indicates that Proteobacteria play a crucial role in the inflammatory state of NPC, while Bacteroidetes are more sensitive to the tumor immune status.
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Affiliation(s)
- Qian Zhang
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430071, China
| | - Jiangqin Song
- Department of Laboratory Medicine, The First People's Hospital of Tianmen City, Tianmen, Hubei 431700, China
| | - Huiqing Wu
- Department of Radiology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430071, China
| | - Liping Wang
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430071, China
| | - Guangzheng Zhuo
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430071, China
| | - Huashun Li
- Department of Pathology, The First People's Hospital of Tianmen City, Tianmen, Hubei 431700, China
| | - Siyu He
- Department of Laboratory Medicine, The First People's Hospital of Tianmen City, Tianmen, Hubei 431700, China
| | - Yunbao Pan
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430071, China; Hubei Engineering Center for Infectious Disease Prevention, Control and Treatment, Wuhan, China.
| | - Guohong Liu
- Department of Radiology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430071, China.
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Konovalovas A, Armalytė J, Klimkaitė L, Liveikis T, Jonaitytė B, Danila E, Bironaitė D, Mieliauskaitė D, Bagdonas E, Aldonytė R. Human nasal microbiota shifts in healthy and chronic respiratory disease conditions. BMC Microbiol 2024; 24:150. [PMID: 38678223 PMCID: PMC11055347 DOI: 10.1186/s12866-024-03294-5] [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: 11/30/2023] [Accepted: 04/04/2024] [Indexed: 04/29/2024] Open
Abstract
BACKGROUND An increasing number of studies investigate various human microbiotas and their roles in the development of diseases, maintenance of health states, and balanced signaling towards the brain. Current data demonstrate that the nasal microbiota contains a unique and highly variable array of commensal bacteria and opportunistic pathogens. However, we need to understand how to harness current knowledge, enrich nasal microbiota with beneficial microorganisms, and prevent pathogenic developments. RESULTS In this study, we have obtained nasal, nasopharyngeal, and bronchoalveolar lavage fluid samples from healthy volunteers and patients suffering from chronic respiratory tract diseases for full-length 16 S rRNA sequencing analysis using Oxford Nanopore Technologies. Demographic and clinical data were collected simultaneously. The microbiome analysis of 97 people from Lithuania suffering from chronic inflammatory respiratory tract disease and healthy volunteers revealed that the human nasal microbiome represents the microbiome of the upper airways well. CONCLUSIONS The nasal microbiota of patients was enriched with opportunistic pathogens, which could be used as indicators of respiratory tract conditions. In addition, we observed that a healthy human nasal microbiome contained several plant- and bee-associated species, suggesting the possibility of enriching human nasal microbiota via such exposures when needed. These candidate probiotics should be investigated for their modulating effects on airway and lung epithelia, immunogenic properties, neurotransmitter content, and roles in maintaining respiratory health and nose-brain interrelationships.
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Affiliation(s)
- Aleksandras Konovalovas
- Life Sciences Center, Institute of Biosciences, Vilnius University, Vilnius, Lithuania
- State Research Institute Centre for Innovative Medicine, Vilnius, Lithuania
| | - Julija Armalytė
- Life Sciences Center, Institute of Biosciences, Vilnius University, Vilnius, Lithuania.
| | - Laurita Klimkaitė
- Life Sciences Center, Institute of Biosciences, Vilnius University, Vilnius, Lithuania
| | - Tomas Liveikis
- Life Sciences Center, Institute of Biosciences, Vilnius University, Vilnius, Lithuania
| | - Brigita Jonaitytė
- Clinic of Chest Diseases, Immunology, and Allergology, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Edvardas Danila
- Clinic of Chest Diseases, Immunology, and Allergology, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
- Centre of Pulmonology and Allergology, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania
| | - Daiva Bironaitė
- State Research Institute Centre for Innovative Medicine, Vilnius, Lithuania
| | | | - Edvardas Bagdonas
- State Research Institute Centre for Innovative Medicine, Vilnius, Lithuania
| | - Rūta Aldonytė
- State Research Institute Centre for Innovative Medicine, Vilnius, Lithuania.
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Zelasko S, Swaney MH, Sandstrom S, Davenport TC, Seroogy CM, Gern JE, Kalan LR, Currie CR. Upper respiratory microbial communities of healthy populations are shaped by niche and age. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.14.589416. [PMID: 38645133 PMCID: PMC11030450 DOI: 10.1101/2024.04.14.589416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Background Alterations in upper respiratory microbiomes have been implicated in shaping host health trajectories, including by limiting mucosal pathogen colonization. However, limited comparative studies of respiratory microbiome development and functioning across age groups have been performed. Herein, we perform shotgun metagenomic sequencing paired with pathogen inhibition assays to elucidate differences in nasal and oral microbiome composition and functioning across healthy 24-month-old infant (n=229) and adult (n=100) populations. Results We find that beta diversity of nasal and oral microbiomes varies with age, with nasal microbiomes showing greater population-level variation compared to oral microbiomes. Infant microbiome alpha diversity was significantly lower across nasal samples and higher in oral samples, relative to adults. Accordingly, we demonstrate significant differences in genus- and species-level composition of microbiomes between sites and age groups. Antimicrobial resistome patterns likewise varied across body sites, with oral microbiomes showing higher resistance gene abundance compared to nasal microbiomes. Biosynthetic gene clusters encoding specialized metabolite production were found in higher abundance across infant oral microbiomes, relative to adults. Investigation of pathogen inhibition revealed greater inhibition of gram-negative and gram-positive bacteria by oral commensals, while nasal isolates had higher antifungal activity. Conclusions In summary, we identify significant differences in the microbial communities inhabiting nasal and oral cavities of healthy infants relative to adults. These findings inform our understanding of the interactions impacting respiratory microbiome composition and functioning, with important implications for host health across the lifespan.
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Affiliation(s)
- Susan Zelasko
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Mary Hannah Swaney
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Shelby Sandstrom
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Timothy C. Davenport
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Christine M. Seroogy
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - James E. Gern
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Lindsay R. Kalan
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- M.G. DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Cameron R. Currie
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- M.G. DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
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Ortmann J, Heise JK, Janzen I, Jenniches F, Kemmling Y, Frömke C, Castell S. Suitability and user acceptance of the eResearch system "Prospective Monitoring and Management App (PIA)"-The example of an epidemiological study on infectious diseases. PLoS One 2023; 18:e0279969. [PMID: 36595548 PMCID: PMC9810156 DOI: 10.1371/journal.pone.0279969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 12/19/2022] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND The eResearch system "Prospective Monitoring and Management App (PIA)" allows researchers to implement questionnaires on any topic and to manage biosamples. Currently, we use PIA in the longitudinal study ZIFCO (Integrated DZIF Infection Cohort within the German National Cohort) in Hannover (Germany) to investigate e.g. associations of risk factors and infectious diseases. Our aim was to assess user acceptance and compliance to determine suitability of PIA for epidemiological research on transient infectious diseases. METHODS ZIFCO participants used PIA to answer weekly questionnaires on health status and report spontaneous onset of symptoms. In case of symptoms of a respiratory infection, the app requested participants to self-sample a nasal swab for viral analysis. To assess user acceptance, we implemented the System Usability Scale (SUS) and fitted a linear regression model on the resulting score. For investigation of compliance with submitting the weekly health questionnaires, we used a logistic regression model with binomial response. RESULTS We analyzed data of 313 participants (median age 52.5 years, 52.4% women). An average SUS of 72.0 reveals good acceptance of PIA. Participants with a higher technology readiness score at the beginning of study participation also reported higher user acceptance. Overall compliance with submitting the weekly health questionnaires showed a median of 55.7%. Being female, of younger age and being enrolled for a longer time decreased the odds to respond. However, women over 60 had a higher chance to respond than women under 60, while men under 40 had the highest chance to respond. Compliance with nasal swab self-sampling was 77.2%. DISCUSSION Our findings show that PIA is suitable for the use in epidemiologic studies with regular short questionnaires. Still, we will focus on user engagement and gamification for the further development of PIA to help incentivize regular and long-term participation.
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Affiliation(s)
- Julia Ortmann
- Department for Epidemiology, Helmholtz Centre for Infection Research, Brunswick, Lower Saxony, Germany
| | - Jana-Kristin Heise
- Department for Epidemiology, Helmholtz Centre for Infection Research, Brunswick, Lower Saxony, Germany
- German Centre of Infection Research (DZIF), Brunswick, Lower Saxony, Germany
| | - Irina Janzen
- Department for Epidemiology, Helmholtz Centre for Infection Research, Brunswick, Lower Saxony, Germany
| | - Felix Jenniches
- Department for Epidemiology, Helmholtz Centre for Infection Research, Brunswick, Lower Saxony, Germany
| | - Yvonne Kemmling
- Department for Epidemiology, Helmholtz Centre for Infection Research, Brunswick, Lower Saxony, Germany
| | - Cornelia Frömke
- Hannover University of Applied Sciences and Arts, Hanover, Lower Saxony, Germany
| | - Stefanie Castell
- Department for Epidemiology, Helmholtz Centre for Infection Research, Brunswick, Lower Saxony, Germany
- German Centre of Infection Research (DZIF), Brunswick, Lower Saxony, Germany
- * E-mail:
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5
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Costantini C, Nunzi E, Romani L. From the nose to the lungs: the intricate journey of airborne pathogens amidst commensal bacteria. Am J Physiol Cell Physiol 2022; 323:C1036-C1043. [PMID: 36036448 PMCID: PMC9529274 DOI: 10.1152/ajpcell.00287.2022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The recent COVID-19 pandemic has dramatically brought the pitfalls of airborne pathogens to the attention of the scientific community. Not only viruses but also bacteria and fungi may exploit air transmission to colonize and infect potential hosts and be the cause of significant morbidity and mortality in susceptible populations. The efforts to decipher the mechanisms of pathogenicity of airborne microbes have brought to light the delicate equilibrium that governs the homeostasis of mucosal membranes. The microorganisms already thriving in the permissive environment of the respiratory tract represent a critical component of this equilibrium and a potent barrier to infection by means of direct competition with airborne pathogens or indirectly via modulation of the immune response. Moving down the respiratory tract, physicochemical and biological constraints promote site-specific expansion of microbes that engage in cross talk with the local immune system to maintain homeostasis and promote protection. In this review, we critically assess the site-specific microbial communities that an airborne pathogen encounters in its hypothetical travel along the respiratory tract and discuss the changes in the composition and function of the microbiome in airborne diseases by taking fungal and SARS-CoV-2 infections as examples. Finally, we discuss how technological and bioinformatics advancements may turn microbiome analysis into a valuable tool in the hands of clinicians to predict the risk of disease onset, the clinical course, and the response to treatment of individual patients in the direction of personalized medicine implementation.
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Affiliation(s)
- Claudio Costantini
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Emilia Nunzi
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Luigina Romani
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
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Tamanai-Shacoori Z, Le Gall-David S, Moussouni F, Sweidan A, Polard E, Bousarghin L, Jolivet-Gougeon A. SARS-CoV-2 and Prevotella spp.: friend or foe? A systematic literature review. J Med Microbiol 2022; 71. [PMID: 35511246 DOI: 10.1099/jmm.0.001520] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
During this global pandemic of the COVID-19 disease, a lot of information has arisen in the media and online without scientific validation, and among these is the possibility that this disease could be aggravated by a secondary bacterial infection such as Prevotella, as well as the interest or not in using azithromycin, a potentially active antimicrobial agent. The aim of this study was to carry out a systematic literature review, to prove or disprove these allegations by scientific arguments. The search included Medline, PubMed, and Pubtator Central databases for English-language articles published 1999-2021. After removing duplicates, a total of final eligible studies (n=149) were selected. There were more articles showing an increase of Prevotella abundance in the presence of viral infection like that related to Human Immunodeficiency Virus (HIV), Papillomavirus (HPV), Herpesviridae and respiratory virus, highlighting differences according to methodologies and patient groups. The arguments for or against the use of azithromycin are stated in light of the results of the literature, showing the role of intercurrent factors, such as age, drug consumption, the presence of cancer or periodontal diseases. However, clinical trials are lacking to prove the direct link between the presence of Prevotella spp. and a worsening of COVID-19, mainly those using azithromycin alone in this indication.
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Affiliation(s)
- Zohreh Tamanai-Shacoori
- Univ Rennes, INSERM, INRAE, CHU Rennes, Institut NUMECAN (Nutrition Metabolisms and Cancer), F-35000 Rennes, France
| | - Sandrine Le Gall-David
- Univ Rennes, INSERM, INRAE, CHU Rennes, Institut NUMECAN (Nutrition Metabolisms and Cancer), F-35000 Rennes, France
| | - Fouzia Moussouni
- Univ Rennes, INSERM, INRAE, CHU Rennes, Institut NUMECAN (Nutrition Metabolisms and Cancer), F-35000 Rennes, France
| | - Alaa Sweidan
- Laboratory of Microbiology, Department of Life and Earth Sciences, Faculty of Sciences, Lebanese University, Hadath Campus, Beirut, Lebanon
| | - Elisabeth Polard
- Teaching Hospital Rennes, Service de Pharmacovigilance, F-35033 Rennes, France
| | - Latifa Bousarghin
- Univ Rennes, INSERM, INRAE, CHU Rennes, Institut NUMECAN (Nutrition Metabolisms and Cancer), F-35000 Rennes, France
| | - Anne Jolivet-Gougeon
- Univ Rennes, INSERM, INRAE, CHU Rennes, Institut NUMECAN (Nutrition Metabolisms and Cancer), F-35000 Rennes, France
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7
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A High-Risk Profile for Invasive Fungal Infections Is Associated with Altered Nasal Microbiota and Niche Determinants. Infect Immun 2022; 90:e0004822. [PMID: 35311544 DOI: 10.1128/iai.00048-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
It is becoming increasingly clear that the communities of microorganisms that populate the surfaces exposed to the external environment, termed microbiota, are key players in the regulation of pathogen-host cross talk affecting the onset as well as the outcome of infectious diseases. We have performed a multicenter, prospective, observational study in which nasal and oropharyngeal swabs were collected for microbiota predicting the risk of invasive fungal infections (IFIs) in patients with hematological malignancies. Here, we demonstrate that the nasal and oropharyngeal microbiota are different, although similar characteristics differentiate high-risk from low-risk samples at both sites. Indeed, similar to previously published results on the oropharyngeal microbiota, high-risk samples in the nose were characterized by low diversity, a loss of beneficial bacteria, and an expansion of potentially pathogenic taxa, in the presence of reduced levels of tryptophan (Trp). At variance with oropharyngeal samples, however, low Trp levels were associated with defective host-derived kynurenine production, suggesting reduced tolerance mechanisms at the nasal mucosal surface. This was accompanied by reduced levels of the chemokine interleukin-8 (IL-8), likely associated with a reduced recruitment of neutrophils and impaired fungal clearance. Thus, the nasal and pharyngeal microbiomes of hematological patients provide complementary information that could improve predictive tools for the risk of IFI in hematological patients.
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8
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Pharyngeal Microbial Signatures Are Predictive of the Risk of Fungal Pneumonia in Hematologic Patients. Infect Immun 2021; 89:e0010521. [PMID: 33782152 DOI: 10.1128/iai.00105-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The ability to predict invasive fungal infections (IFI) in patients with hematological malignancies is fundamental for successful therapy. Although gut dysbiosis is known to occur in hematological patients, whether airway dysbiosis also contributes to the risk of IFI has not been investigated. Nasal and oropharyngeal swabs were collected for functional microbiota characterization in 173 patients with hematological malignancies recruited in a multicenter, prospective, observational study and stratified according to the risk of developing IFI. A lower microbial richness and evenness were found in the pharyngeal microbiota of high-risk patients that were associated with a distinct taxonomic and metabolic profile. A murine model of IFI provided biologic plausibility for the finding that loss of protective anaerobes, such as Clostridiales and Bacteroidetes, along with an apparent restricted availability of tryptophan, is causally linked to the risk of IFI in hematologic patients and indicates avenues for antimicrobial stewardship and metabolic reequilibrium in IFI.
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Eisele M, Pohontsch NJ, Scherer M. Strategies in Primary Care to Face the SARS-CoV-2 / COVID-19 Pandemic: An Online Survey. Front Med (Lausanne) 2021; 8:613537. [PMID: 34150788 PMCID: PMC8206267 DOI: 10.3389/fmed.2021.613537] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 05/10/2021] [Indexed: 01/12/2023] Open
Abstract
Background: Primary care plays a key role in pandemics like the SARS-CoV-2 pandemic in 2020. We aimed to investigate the challenges faced and the solutions implemented in primary care. Methods: One hundred and twenty-one general practitioners in Germany completed the online survey. We used open questions to examine challenges experienced and solutions implemented during the early pandemic and chose qualitative content analysis to extract and describe the meaning of the answers. We derived deductive categories from the research questions and formed inductive categories during the material reviews. Results: Main challenges were: insufficient information, lack of protective equipment, need to restructure practice procedures and insufficient individual and structural pandemic preparedness, resulting in secondary challenges: fear of infection, impaired patient care, aggravated steering of patients, difficult cooperation with external entities and a not viable hygiene concept advised by authorities. Strategies to address these challenges included establishing regular team-meetings to develop new solutions, focusing on few reliable sources of information, working in alternating shifts, increasing telemedicine, establishing window and open-air practices and building networks with other health care providers. Respondents criticized the lack of consideration of their experiences in planning pandemic measures within primary care. Conclusions: General practitioners successfully applied pragmatic and creative strategies in their practices during the early phase of the pandemic. Among these, communication within and between practices emerged as a key strategy. These strategies should be provided with pandemic preparedness plans. The lacking consideration of the primary care providers' experiences in planning and implementing pandemic measures needs to be addressed by stakeholders.
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Affiliation(s)
- Marion Eisele
- Department of General Practice and Primary Care, Center for Psychosocial Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Nadine Janis Pohontsch
- Department of General Practice and Primary Care, Center for Psychosocial Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Martin Scherer
- Department of General Practice and Primary Care, Center for Psychosocial Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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10
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Kronbichler A, Harrison EM, Wagner J. Nasal microbiome research in ANCA-associated vasculitis: Strengths, limitations, and future directions. Comput Struct Biotechnol J 2020; 19:415-423. [PMID: 33489010 PMCID: PMC7804347 DOI: 10.1016/j.csbj.2020.12.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/22/2020] [Accepted: 12/22/2020] [Indexed: 12/11/2022] Open
Abstract
The human nasal microbiome is characterized by biodiversity and undergoes changes during the span of life. In granulomatosis with polyangiitis (GPA), the persistent nasal colonization by Staphylococcus aureus (S. aureus) assessed by culture-based detection methods has been associated with increased relapse frequency. Different research groups have characterized the nasal microbiome in patients with GPA and found that patients have a distinct nasal microbiome compared to controls, but the reported results between studies differed. In order to increase comparability, there is a need to standardize patient selection, sample preparation, and analytical methodology; particularly as low biomass samples like those obtained by nasal swabbing are impacted by reagent contamination. Optimization in obtaining a sample and processing with the inclusion of critical controls is needed for consistent comparative studies. Ongoing studies will analyze the nasal microbiome in GPA in a longitudinal way and the results will inform whether or not targeted antimicrobial management in a clinical trial should be pursued or not. This review focuses on the proposed role of S. aureus in GPA, the (healthy) nasal microbiome, findings in the first pilot studies in GPA, and will discuss future strategies.
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Affiliation(s)
- Andreas Kronbichler
- Department of Internal Medicine IV (Nephrology and Hypertension), Medical University Innsbruck, Innsbruck, Austria
- Department of Medicine, University of Cambridge, CB2 0QQ, United Kingdom
- Corresponding author at: Department of Internal Medicine IV (Nephrology and Hypertension), Medical University Innsbruck, Innsbruck, Austria.
| | - Ewan M. Harrison
- Department of Medicine, University of Cambridge, CB2 0QQ, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CD10 1SA, United Kingdom
- Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Worts Causeway, Cambridge CB1 8RN, United Kingdom
| | - Josef Wagner
- Victorian Infectious Diseases Reference Laboratory, The Peter Doherty Institute for Infection and Immunity, Royal Melbourne Hospital, Victoria, Australia
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Adeniji AA. 'Self-collected upper respiratory tract swabs for COVID-19 test': A feasible way to increase overall testing rate and conserve resources in South Africa. Afr J Prim Health Care Fam Med 2020; 12:e1-e4. [PMID: 32501019 PMCID: PMC7300941 DOI: 10.4102/phcfm.v12i1.2445] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 04/21/2020] [Indexed: 02/03/2023] Open
Abstract
Disparity in the testing rate of SARS-CoV-2 amongst different countries and regions is a very big challenge in understanding the COVID-19 pandemic. Although some developed countries have a very high testing rate and subsequently a high number of confirmed cases, less developed countries have a low testing rate and an illusive positivity rate. Collection of the upper respiratory specimen is not often comfortable. The discomfort could be accompanied with epistaxis and headache in some patients. The trained personnel taking the swab is forced to protect self with personal protective equipment (PPE) to avoid infections that may result from the patient due to provoked cough, sneezing and spitting. This study looks into an efficient means of increasing the testing rate for COVID 19 without compromising the quality. A literature review was conducted on the different modalities of collecting upper respiratory specimens and assessing the efficacy of samples collected using different methods in terms of the laboratory yield of different pathogens. Self-collection of upper respiratory tract specimen for diagnostic purposes is not new. Studies have demonstrated that trained staff-collected nasal swabs are not in any way superior to self-collected or parent-assisted swabs. The laboratory yield of different specimens is not determined by who took the sample but by the anatomical site from where the specimen was collected. Self collection of the upper respiratory swabs will not only increase the testing rate but also preserve the scarce PPE and reduces health care worker’s COVID 19 infection rate in South Africa.
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Affiliation(s)
- Adeloye A Adeniji
- Division of Family Medicine and Primary Care, Faculty of Health Sciences, Stellenbosch University, Cape Town, South Africa; and, Ceres Hospital, Cape Winelands Health District, Department of Health, Ceres.
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12
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Oropharyngeal microbiome of a college population following a meningococcal disease outbreak. Sci Rep 2020; 10:632. [PMID: 31959912 PMCID: PMC6971049 DOI: 10.1038/s41598-020-57450-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 12/16/2019] [Indexed: 11/19/2022] Open
Abstract
Asymptomatic oropharyngeal carriage of Neisseria meningitidis peaks in adolescence and young adulthood. Following a meningococcal disease outbreak at a U.S. college, we profiled the oropharyngeal microbiomes of 158 students to identify associations between bacterial community composition and meningococcal carriage or risk factors for carriage, including male gender, smoking, and frequent social mixing. Metagenomic shotgun sequencing identified 268 bacterial taxa at the genus or species level, with Streptococcus, Veillonella, and Rothia species being most abundant. Microbiome composition showed weak associations with meningococcal carriage and risk factors for carriage. N. meningitidis abundance was positively correlated with that of Fusobacterium nucleatum, consistent with hypothesized propionic acid cross-feeding. Additional species had positive abundance correlations with N. meningitidis, including Aggregatibacter aphrophilus, Campylobacter rectus, Catonella morbi, Haemophilus haemolyticus, and Parvimonas micra. N. meningitidis abundance was negatively correlated with unidentified Veillonella species. Several of these species are commonly found in dental plaque, while N. meningitidis is primarily found in the pharynx, suggesting that ecological interactions extend throughout the oral cavity. Although risk factors for meningococcal carriage do not strongly impact most bacterial species in the oropharynx, variation in the upper respiratory tract microbiome may create conditions that are more or less favorable for N. meningitidis carriage.
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Ahmed N, Daniel B, Varghese J, Evangeline R, Jose T. Oropharyngeal microbiome of an HIV-positive patient. Microb Pathog 2019; 139:103805. [PMID: 31790791 DOI: 10.1016/j.micpath.2019.103805] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Revised: 07/07/2019] [Accepted: 10/14/2019] [Indexed: 12/12/2022]
Abstract
Studies on understanding the human microbiome continue to grow rapidly; nonetheless, reports on alterations in the microbiome post HIV infection are limited. Human microbiome is an aggregate of bacteria, fungi, viruses and archaea that have co-evolved with humans. These microbes have important roles in immune modulation, vitamin synthesis, metabolism etc. The human pharyngeal microbiome, which resides in the junction between digestive and respiratory tracts, might have a key role in the prevention of respiratory tract infections, akin to the actions of the intestinal microbiome against enteric infections. The respiratory tract is constantly exposed to various environmental and endogenous microbes; however, unlike other similar mucosal surfaces, there has been limited investigation of the microbiome of the respiratory tract. HIV infection is associated with alterations in the respiratory microbiome. The aim of this study was to use next-generation sequencing to determine the composition of the oropharyngeal microbiome in a HIV-positive individual. The bacterial composition was determined by illumina sequencing using MiSeq of partial 16S rRNA genes (V3-V4). A total of 3, 57,926 reads were analyzed. Overall, the genera Proteus, Enterococcus, Bacteroides, Prevotella and Clostridium were most prevalent bacterial populations in the oropharynx of an HIV positive patient.
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Affiliation(s)
- Nihal Ahmed
- St. Joseph's College of Post graduate and Research Studies, Bangalore, 560027, India
| | - Betty Daniel
- St. Joseph's College of Post graduate and Research Studies, Bangalore, 560027, India.
| | - Jancy Varghese
- Bharathiar University, Coimbatore, Tamil Nadu, 641046, India
| | | | - Tony Jose
- St. Joseph's College of Post graduate and Research Studies, Bangalore, 560027, India
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Escapa IF, Chen T, Huang Y, Gajare P, Dewhirst FE, Lemon KP. New Insights into Human Nostril Microbiome from the Expanded Human Oral Microbiome Database (eHOMD): a Resource for the Microbiome of the Human Aerodigestive Tract. mSystems 2018; 3:e00187-18. [PMID: 30534599 PMCID: PMC6280432 DOI: 10.1128/msystems.00187-18] [Citation(s) in RCA: 310] [Impact Index Per Article: 51.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 11/02/2018] [Indexed: 12/22/2022] Open
Abstract
The expanded Human Oral Microbiome Database (eHOMD) is a comprehensive microbiome database for sites along the human aerodigestive tract that revealed new insights into the nostril microbiome. The eHOMD provides well-curated 16S rRNA gene reference sequences linked to available genomes and enables assignment of species-level taxonomy to most next-generation sequences derived from diverse aerodigestive tract sites, including the nasal passages, sinuses, throat, esophagus, and mouth. Using minimum entropy decomposition coupled with the RDP Classifier and our eHOMD V1-V3 training set, we reanalyzed 16S rRNA V1-V3 sequences from the nostrils of 210 Human Microbiome Project participants at the species level, revealing four key insights. First, we discovered that Lawsonella clevelandensis, a recently named bacterium, and Neisseriaceae [G-1] HMT-174, a previously unrecognized bacterium, are common in adult nostrils. Second, just 19 species accounted for 90% of the total sequences from all participants. Third, 1 of these 19 species belonged to a currently uncultivated genus. Fourth, for 94% of the participants, 2 to 10 species constituted 90% of their sequences, indicating that the nostril microbiome may be represented by limited consortia. These insights highlight the strengths of the nostril microbiome as a model system for studying interspecies interactions and microbiome function. Also, in this cohort, three common nasal species (Dolosigranulum pigrum and two Corynebacterium species) showed positive differential abundance when the pathobiont Staphylococcus aureus was absent, generating hypotheses regarding colonization resistance. By facilitating species-level taxonomic assignment to microbes from the human aerodigestive tract, the eHOMD is a vital resource enhancing clinical relevance of microbiome studies. IMPORTANCE The eHOMD (http://www.ehomd.org) is a valuable resource for researchers, from basic to clinical, who study the microbiomes and the individual microbes in body sites in the human aerodigestive tract, which includes the nasal passages, sinuses, throat, esophagus, and mouth, and the lower respiratory tract, in health and disease. The eHOMD is an actively curated, web-based, open-access resource. eHOMD provides the following: (i) species-level taxonomy based on grouping 16S rRNA gene sequences at 98.5% identity, (ii) a systematic naming scheme for unnamed and/or uncultivated microbial taxa, (iii) reference genomes to facilitate metagenomic, metatranscriptomic, and proteomic studies and (iv) convenient cross-links to other databases (e.g., PubMed and Entrez). By facilitating the assignment of species names to sequences, the eHOMD is a vital resource for enhancing the clinical relevance of 16S rRNA gene-based microbiome studies, as well as metagenomic studies.
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Affiliation(s)
- Isabel F. Escapa
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
- Department of Oral Medicine, Infection & Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, USA
| | - Tsute Chen
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
- Department of Oral Medicine, Infection & Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, USA
| | - Yanmei Huang
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
- Department of Oral Medicine, Infection & Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, USA
| | - Prasad Gajare
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
| | - Floyd E. Dewhirst
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
- Department of Oral Medicine, Infection & Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, USA
| | - Katherine P. Lemon
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
- Division of Infectious Diseases, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
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Ta LDH, Yap GC, Tay CJX, Lim ASM, Huang CH, Chu CW, De Sessions PF, Shek LP, Goh A, Van Bever HPS, Teoh OH, Soh JY, Thomas B, Ramamurthy MB, Goh DYT, Lay C, Soh SE, Chan YH, Saw SM, Kwek K, Chong YS, Godfrey KM, Hibberd ML, Lee BW. Establishment of the nasal microbiota in the first 18 months of life: Correlation with early-onset rhinitis and wheezing. J Allergy Clin Immunol 2018; 142:86-95. [PMID: 29452199 DOI: 10.1016/j.jaci.2018.01.032] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 12/19/2017] [Accepted: 01/24/2018] [Indexed: 12/18/2022]
Abstract
BACKGROUND Dynamic establishment of the nasal microbiota in early life influences local mucosal immune responses and susceptibility to childhood respiratory disorders. OBJECTIVE The aim of this case-control study was to monitor, evaluate, and compare development of the nasal microbiota of infants with rhinitis and wheeze in the first 18 months of life with those of healthy control subjects. METHODS Anterior nasal swabs of 122 subjects belonging to the Growing Up in Singapore Towards Healthy Outcomes (GUSTO) birth cohort were collected longitudinally over 7 time points in the first 18 months of life. Nasal microbiota signatures were analyzed by using 16S rRNA multiplexed pair-end sequencing from 3 clinical groups: (1) patients with rhinitis alone (n = 28), (2) patients with rhinitis with concomitant wheeze (n = 34), and (3) healthy control subjects (n = 60). RESULTS Maturation of the nasal microbiome followed distinctive patterns in infants from both rhinitis groups compared with control subjects. Bacterial diversity increased over the period of 18 months of life in control infants, whereas infants with rhinitis showed a decreasing trend (P < .05). An increase in abundance of the Oxalobacteraceae family (Proteobacteria phylum) and Aerococcaceae family (Firmicutes phylum) was associated with rhinitis and concomitant wheeze (adjusted P < .01), whereas the Corynebacteriaceae family (Actinobacteria phylum) and early colonization with the Staphylococcaceae family (Firmicutes phylum; 3 weeks until 9 months) were associated with control subjects (adjusted P < .05). The only difference between the rhinitis and control groups was a reduced abundance of the Corynebacteriaceae family (adjusted P < .05). Determinants of nasal microbiota succession included sex, mode of delivery, presence of siblings, and infant care attendance. CONCLUSION Our results support the hypothesis that the nasal microbiome is involved in development of early-onset rhinitis and wheeze in infants.
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Affiliation(s)
- Le Duc Huy Ta
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Gaik Chin Yap
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Carina Jing Xuan Tay
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Alicia Shi Min Lim
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Chiung-Hui Huang
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Collins Wenhan Chu
- Genome Institute of Singapore, Agency for Science, Technology and Research Singapore, Singapore
| | | | - Lynette P Shek
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore
| | - Anne Goh
- Department of Paediatrics, KK Women's and Children's Hospital, Singapore
| | - Hugo P S Van Bever
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore
| | - Oon Hoe Teoh
- Department of Paediatrics, KK Women's and Children's Hospital, Singapore
| | - Jian Yi Soh
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore
| | - Biju Thomas
- Department of Paediatrics, KK Women's and Children's Hospital, Singapore
| | - Mahesh Babu Ramamurthy
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore
| | - Daniel Y T Goh
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore
| | - Christophe Lay
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Danone Nutricia Research, Singapore
| | - Shu-E Soh
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Yiong Huak Chan
- Biostatistics Unit, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Seang-Mei Saw
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Kenneth Kwek
- Department of Maternal Fetal Medicine, KK Women's and Children's Hospital, Singapore
| | - Yap-Seng Chong
- Department of Obstetrics & Gynaecology, National University of Singapore, Singapore; Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research Singapore, Singapore
| | - Keith M Godfrey
- MRC Lifecourse Epidemiology Unit and NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Martin Lloyd Hibberd
- Genome Institute of Singapore, Agency for Science, Technology and Research Singapore, Singapore
| | - Bee Wah Lee
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
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