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Liu Z, Chen H, Chen D, Wu X, Xu H, Chen P, Wang R, Chen Y. Metagenomic next-generation sequencing for the diagnosis of invasive pulmonary aspergillosis in type 2 diabetes mellitus patients. Sci Rep 2024; 14:16618. [PMID: 39025875 PMCID: PMC11258266 DOI: 10.1038/s41598-024-67174-8] [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: 03/18/2024] [Accepted: 07/09/2024] [Indexed: 07/20/2024] Open
Abstract
Invasive pulmonary aspergillosis (IPA) in patients with diabetes mellitus has high incidence, especially in Type 2 diabetes mellitus (T2DM). The aim of this study was to evaluate the diagnostic efficacy of metagenomic next-generation sequencing (mNGS) for IPA in patients with T2DM. A total of 66 patients with T2DM were included, including 21 IPA and 45 non-IPA patients, from January 2022 to December 2022. The demographic characteristics, comorbidities, laboratory test results, antibiotic treatment response, and 30-day mortality rate of patients were analyzed. The diagnostic accuracy of mNGS and conventional methods was compared, including sensitivity, specificity, positive predictive value and negative predictive value. The sensitivity and specificity of mNGS were 66.7% and 100.0%, respectively, which were significantly higher than those of fluorescence staining (42.1% and 100%), serum 1,3-β-D-glucan detection (38.1% and 90.9%), serum galactomannan detection (14.3% and 94.9%) and BALF galactomannan detection (47.3% and 70.7%). Although the sensitivity of BALF culture (75.0%) was higher than that of mNGS (66.7%), the turnover time of mNGS was significantly shorter than that of traditional culture (1.6 days vs. 5.0 days). The sensitivity of mNGS combined with BALF culture reached 100.0%. In addition, mNGS has a stronger ability to detect co-pathogens with IPA. 47.6% of T2DM patients with IPA were adjusted the initial antimicrobial therapy according to the mNGS results. This is the first study to focus on the diagnostic performance of mNGS in IPA infection in T2DM patients. MNGS can be used as a supplement to conventional methods for the diagnosis of IPA in patients with T2DM.
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Affiliation(s)
- Zhiyun Liu
- Department of Clinical Laboratory, Huizhou Central People's Hospital, Huizhou, 516001, Guangdong, China
| | - Hengxin Chen
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China
| | - Dubo Chen
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China
| | - Xianjin Wu
- Department of Clinical Laboratory, Huizhou Central People's Hospital, Huizhou, 516001, Guangdong, China
| | - Hongxu Xu
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China
| | - Peisong Chen
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China
| | - Ruizhi Wang
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China.
| | - Yili Chen
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China.
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Conradie T, Caparros-Martin JA, Egan S, Kicic A, Koks S, Stick SM, Agudelo-Romero P. Exploring the Complexity of the Human Respiratory Virome through an In Silico Analysis of Shotgun Metagenomic Data Retrieved from Public Repositories. Viruses 2024; 16:953. [PMID: 38932245 PMCID: PMC11209621 DOI: 10.3390/v16060953] [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: 03/21/2024] [Revised: 05/31/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND Respiratory viruses significantly impact global morbidity and mortality, causing more disease in humans than any other infectious agent. Beyond pathogens, various viruses and bacteria colonize the respiratory tract without causing disease, potentially influencing respiratory diseases' pathogenesis. Nevertheless, our understanding of respiratory microbiota is limited by technical constraints, predominantly focusing on bacteria and neglecting crucial populations like viruses. Despite recent efforts to improve our understanding of viral diversity in the human body, our knowledge of viral diversity associated with the human respiratory tract remains limited. METHODS Following a comprehensive search in bibliographic and sequencing data repositories using keyword terms, we retrieved shotgun metagenomic data from public repositories (n = 85). After manual curation, sequencing data files from 43 studies were analyzed using EVEREST (pipEline for Viral assEmbly and chaRactEriSaTion). Complete and high-quality contigs were further assessed for genomic and taxonomic characterization. RESULTS Viral contigs were obtained from 194 out of the 868 FASTQ files processed through EVEREST. Of the 1842 contigs that were quality assessed, 8% (n = 146) were classified as complete/high-quality genomes. Most of the identified viral contigs were taxonomically classified as bacteriophages, with taxonomic resolution ranging from the superkingdom level down to the species level. Captured contigs were spread across 25 putative families and varied between RNA and DNA viruses, including previously uncharacterized viral genomes. Of note, airway samples also contained virus(es) characteristic of the human gastrointestinal tract, which have not been previously described as part of the lung virome. Additionally, by performing a meta-analysis of the integrated datasets, ecological trends within viral populations linked to human disease states and their biogeographical distribution along the respiratory tract were observed. CONCLUSION By leveraging publicly available repositories of shotgun metagenomic data, the present study provides new insights into viral genomes associated with specimens from the human respiratory tract across different disease spectra. Further studies are required to validate our findings and evaluate the potential impact of these viral communities on respiratory tract physiology.
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Affiliation(s)
- Talya Conradie
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, Perth, WA 6009, Australia
- Medical, Molecular and Forensic Sciences, Murdoch University, Perth, WA 6150, Australia
| | | | - Siobhon Egan
- Medical, Molecular and Forensic Sciences, Murdoch University, Perth, WA 6150, Australia
- Centre for Computational and Systems Medicine, Health Future Institute, Murdoch University, Perth, WA 6150, Australia
| | - Anthony Kicic
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, Perth, WA 6009, Australia
- Department of Respiratory and Sleep Medicine, Perth Children’s Hospital for Children, Perth, WA 6009, Australia
- Centre for Cell Therapy and Regenerative Medicine, School of Medicine and Pharmacology, Perth, WA 6009, Australia
- School of Population Health, Curtin University, Perth, WA 6102, Australia
| | - Sulev Koks
- Perron Institute for Neurological and Translational Science, Perth, WA 6009, Australia
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA 6150, Australia
| | - Stephen M. Stick
- Department of Respiratory and Sleep Medicine, Perth Children’s Hospital for Children, Perth, WA 6009, Australia
- Centre for Cell Therapy and Regenerative Medicine, School of Medicine and Pharmacology, Perth, WA 6009, Australia
| | - Patricia Agudelo-Romero
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, Perth, WA 6009, Australia
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
- European Virus Bioinformatics Centre, Friedrich-Schiller-Universitat Jena, 07737 Jena, Germany
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Robert M, Yatim N, Sacré K, Duffy D. Sarcoidosis immunopathogenesis - a new concept of maladaptive trained immunity. Trends Immunol 2024; 45:406-418. [PMID: 38796404 DOI: 10.1016/j.it.2024.04.013] [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: 03/26/2024] [Revised: 04/30/2024] [Accepted: 04/30/2024] [Indexed: 05/28/2024]
Abstract
Sarcoidosis is a chronic immune disease of unknown origin for which we still lack an immunological framework unifying causal agents, host factors, and natural history of disease. Here, we discuss the initial triggers of disease, and how myeloid cells drive granuloma formation and contribute to immunopathogenesis. We highlight recent advances in our understanding of innate immune memory and propose the hypothesis that maladaptive innate immune training connects previous environmental exposure to granuloma maintenance and expansion. Lastly, we consider how this hypothesis may open novel therapeutic avenues, while corticosteroids remain the front-line treatment.
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Affiliation(s)
- Marie Robert
- Translational Immunology Unit, Institut Pasteur, Université Paris-Cité, Paris, France; Department of Internal Medicine, Hôpital Bichat, Paris, France; Université Paris-Cité, Centre de Recherche sur l'Inflammation, INSERM UMR1149, CNRS ERL8252, Faculté de Médecine site Bichat, Laboratoire d'Excellence Inflamex, Paris, France
| | - Nader Yatim
- Translational Immunology Unit, Institut Pasteur, Université Paris-Cité, Paris, France; Department of Internal Medicine, Hôpital Bichat, Paris, France
| | - Karim Sacré
- Department of Internal Medicine, Hôpital Bichat, Paris, France; Université Paris-Cité, Centre de Recherche sur l'Inflammation, INSERM UMR1149, CNRS ERL8252, Faculté de Médecine site Bichat, Laboratoire d'Excellence Inflamex, Paris, France
| | - Darragh Duffy
- Translational Immunology Unit, Institut Pasteur, Université Paris-Cité, Paris, France; CBUtechS, Institut Pasteur, Université Paris-Cité, Paris, France.
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Chioma OS, Wiggins Z, Rea S, Drake WP. Infectious and non-infectious precipitants of sarcoidosis. J Autoimmun 2024:103239. [PMID: 38821769 DOI: 10.1016/j.jaut.2024.103239] [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: 08/01/2023] [Revised: 04/04/2024] [Accepted: 05/02/2024] [Indexed: 06/02/2024]
Abstract
Sarcoidosis is a chronic inflammatory disease that can affect any organ in the body. Its exact cause remains unknown, but it is believed to result from a combination of genetic and environmental factors. Some potential causes of sarcoidosis include genetics, environmental triggers, immune system dysfunction, the gut microbiome, sex, and race/ethnicity. Genetic mutations are associated with protection against disease progression or an increased susceptibility to more severe disease, while exposure to certain chemicals, bacteria, viruses, or allergens can trigger the formation of immune cell congregations (granulomas) in different organs. Dysfunction of the immune system, including autoimmune reactions, may also contribute. The gut microbiome and factors such as being female or having African American, Scandinavian, Irish, or Puerto Rican heritage are additional contributors to disease outcome. Recent research has suggested that certain drugs, such as anti-Programmed Death-1 (PD-1) and antibiotics such as tuberculosis (TB) drugs, may raise the risk of developing sarcoidosis. Hormone levels, particularly higher levels of estrogen and progesterone in women, have also been linked to an increased likelihood of sarcoidosis. The diagnosis of sarcoidosis involves a comprehensive assessment that includes medical history, physical examination, laboratory tests, and imaging studies. While there is no cure for sarcoidosis, the symptoms can often be effectively managed through various treatment options. Treatment may involve the use of medications, surgical interventions, or lifestyle changes. These disparate factors suggests that sarcoidosis has multiple positive and negative exacerbants on disease severity, some of which can be ameliorated and others which cannot.
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Affiliation(s)
- Ozioma S Chioma
- Division of Infectious Disease, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - ZaDarreyal Wiggins
- Division of Infectious Disease, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Samantha Rea
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Wonder P Drake
- Division of Infectious Disease, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA; Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA.
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Chaudhary PP, Kaur M, Myles IA. Does "all disease begin in the gut"? The gut-organ cross talk in the microbiome. Appl Microbiol Biotechnol 2024; 108:339. [PMID: 38771520 PMCID: PMC11108886 DOI: 10.1007/s00253-024-13180-9] [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: 04/03/2024] [Revised: 05/06/2024] [Accepted: 05/10/2024] [Indexed: 05/22/2024]
Abstract
The human microbiome, a diverse ecosystem of microorganisms within the body, plays pivotal roles in health and disease. This review explores site-specific microbiomes, their role in maintaining health, and strategies for their upkeep, focusing on oral, lung, vaginal, skin, and gut microbiota, and their systemic connections. Understanding the intricate relationships between these microbial communities is crucial for unraveling mechanisms underlying human health. Recent research highlights bidirectional communication between the gut and distant microbiome sites, influencing immune function, metabolism, and disease susceptibility. Alterations in one microbiome can impact others, emphasizing their interconnectedness and collective influence on human physiology. The therapeutic potential of gut microbiota in modulating distant microbiomes offers promising avenues for interventions targeting various disorders. Through interdisciplinary collaboration and technological advancements, we can harness the power of the microbiome to revolutionize healthcare, emphasizing microbiome-centric approaches to promote holistic well-being while identifying areas for future research.
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Affiliation(s)
- Prem Prashant Chaudhary
- Laboratory of Clinical Immunology and Microbiology, Epithelial Therapeutics Unit, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Mahaldeep Kaur
- Laboratory of Clinical Immunology and Microbiology, Epithelial Therapeutics Unit, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Ian A Myles
- Laboratory of Clinical Immunology and Microbiology, Epithelial Therapeutics Unit, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, 20892, USA
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Puiu R, Motoc NS, Lucaciu S, Ruta MV, Rajnoveanu RM, Todea DA, Man MA. The Role of Lung Microbiome in Fibrotic Interstitial Lung Disease-A Systematic Review. Biomolecules 2024; 14:247. [PMID: 38540667 PMCID: PMC10968628 DOI: 10.3390/biom14030247] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 02/11/2024] [Accepted: 02/13/2024] [Indexed: 07/23/2024] Open
Abstract
Interstitial Lung Disease (ILD) involves lung disorders marked by chronic inflammation and fibrosis. ILDs include pathologies like idiopathic pulmonary fibrosis (IPF), connective tissue disease-associated ILD (CTD-ILD), hypersensitivity pneumonitis (HP) or sarcoidosis. Existing data covers pathogenesis, diagnosis (especially using high-resolution computed tomography), and treatments like antifibrotic agents. Despite progress, ILD diagnosis and management remains challenging with significant morbidity and mortality. Recent focus is on Progressive Fibrosing ILD (PF-ILD), characterized by worsening symptoms and fibrosis on HRCT. Prevalence is around 30%, excluding IPF, with a poor prognosis. Early diagnosis is crucial for optimizing outcomes in PF-ILD individuals. The lung microbiome comprises all the microorganisms that are in the respiratory tract. Relatively recent research try to evaluate its role in respiratory disease. Healthy lungs have a diverse microbial community. An imbalance in bacterial composition, changes in bacterial metabolic activities, or changes in bacterial distribution within the lung termed dysbiosis is linked to conditions like COPD, asthma and ILDs. We conducted a systematic review of three important scientific data base using a focused search strategy to see how the lung microbiome is involved in the progression of ILDs. Results showed that some differences in the composition and quality of the lung microbiome exist in ILDs that show progressive fibrosing phenotype. The results seem to suggest that the lung microbiota could be involved in ILD progression, but more studies showing its exact pathophysiological mechanisms are needed.
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Affiliation(s)
- Ruxandra Puiu
- Department of Medical Sciences, Pulmonology, Faculty of Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania or (R.P.); (S.L.); (D.A.T.); (M.A.M.)
| | - Nicoleta Stefania Motoc
- Department of Medical Sciences, Pulmonology, Faculty of Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania or (R.P.); (S.L.); (D.A.T.); (M.A.M.)
| | - Sergiu Lucaciu
- Department of Medical Sciences, Pulmonology, Faculty of Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania or (R.P.); (S.L.); (D.A.T.); (M.A.M.)
| | - Maria Victoria Ruta
- I Department of Pulmonology, “Leon Daniello” Clinical Hospital of Pulmonology, 400371 Cluj-Napoca, Romania;
| | - Ruxandra-Mioara Rajnoveanu
- Department of Palliative Medicine, Faculty of Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania;
| | - Doina Adina Todea
- Department of Medical Sciences, Pulmonology, Faculty of Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania or (R.P.); (S.L.); (D.A.T.); (M.A.M.)
| | - Milena Adina Man
- Department of Medical Sciences, Pulmonology, Faculty of Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania or (R.P.); (S.L.); (D.A.T.); (M.A.M.)
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Liu RT, Zhang D, Li S, Chen Y, Wan XX, Diao ST, Weng L, Peng JM, Du B. Comparison of different criteria of metagenomic next-generation sequencing for the diagnosis of invasive pulmonary aspergillosis in critically ill patients. Diagn Microbiol Infect Dis 2024; 108:116135. [PMID: 38065016 DOI: 10.1016/j.diagmicrobio.2023.116135] [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: 08/04/2023] [Revised: 11/09/2023] [Accepted: 11/11/2023] [Indexed: 01/22/2024]
Abstract
OBJECTIVE To compare different criteria of Metagenomic Next-Generation Sequencing (mNGS) in bronchoalveolar lavage fluid (BALF) for diagnosing invasive pulmonary aspergillosis (IPA). METHODS We compared the diagnostic agreement and performances of six BALF mNGS-derived criteria (SDSMRN>1, SDSMRN≥3, SMRN≥10, SMRN≥50, RPM ratio≥10, and relative abundance of genus>30 %) in pneumonia patients. RESULTS A total of 115 patients were analyzed, with 28 identified with IPA. Diagnostic agreement among the six mNGS-derived criteria was moderate, with a Cohen's kappa of 0.577(P < 0.001). mNGS-derived criteria had low sensitivity ranging from 21.4 % to 57.1 % and high specificity from 88 % to 92 %. The optimal threshold of SDSMRN, SMRN, RPM ratio, and relative abundance of genus for diagnosing IPA were 5, 0.25, 8, and 20 %, respectively. Although using the optimal threshold, the sensitivity of mNGS is lower than 50 %. CONCLUSIONS All mNGS-derived criteria had low sensitivity for diagnosing IPA. A combination of mNGS and conventional mycological tests may be the best diagnostic strategy.
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Affiliation(s)
- Rui-Ting Liu
- Medical ICU, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Peking, China; Department of Critical Care Medicine, The Second Affiliated Hospital of Air Force Medical University, Shaanxi, China
| | - Dong Zhang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Peking, China
| | - Shan Li
- Medical ICU, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Peking, China
| | - Yan Chen
- Medical ICU, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Peking, China
| | - Xi-Xi Wan
- Medical ICU, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Peking, China
| | - Shi-Tong Diao
- Medical ICU, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Peking, China
| | - Li Weng
- Medical ICU, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Peking, China
| | - Jin-Min Peng
- Medical ICU, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Peking, China.
| | - Bin Du
- Medical ICU, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Peking, China
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Akata K, Yamasaki K, Nemoto K, Ikegami H, Kawaguchi T, Noguchi S, Kawanami T, Fukuda K, Mukae H, Yatera K. Sarcoidosis Associated with Enlarged Mediastinal Lymph Nodes with the Detection of Streptococcus gordonii and Cutibacterium acnes Using a Clone Library Method. Intern Med 2024; 63:299-304. [PMID: 37258161 PMCID: PMC10864086 DOI: 10.2169/internalmedicine.1887-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 04/25/2023] [Indexed: 06/02/2023] Open
Abstract
A 77-year-old Japanese woman with mediastinal lymphadenopathy and uveitis was diagnosed with sarcoidosis. The bacterial flora in biopsied samples from mediastinal lymph nodes was analyzed using a clone library method with Sanger sequencing of the 16S rRNA gene, and Streptococcus gordonii (52 of 71 clones) and Cutibacterium acnes (19 of 71 clones) were detected. No previous study has conducted a bacterial floral analysis using the Sanger method for the mediastinal lymph node in sarcoidosis, making this case report the first to document the presence of S. gordonii and C. acnes in the mediastinal lymph node of a patient with sarcoidosis.
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Affiliation(s)
- Kentaro Akata
- Division of Infection Control and Prevention, University of Occupational and Environmental Health, Japan
- Department of Respiratory Medicine, University of Occupational and Environmental Health, Japan
| | - Kei Yamasaki
- Department of Respiratory Medicine, University of Occupational and Environmental Health, Japan
| | - Kazuki Nemoto
- Department of Respiratory Medicine, University of Occupational and Environmental Health, Japan
| | - Hiroaki Ikegami
- Department of Respiratory Medicine, University of Occupational and Environmental Health, Japan
| | - Takako Kawaguchi
- Department of Respiratory Medicine, University of Occupational and Environmental Health, Japan
| | - Shingo Noguchi
- Department of Respiratory Medicine, University of Occupational and Environmental Health, Japan
| | - Toshinori Kawanami
- Department of Respiratory Medicine, University of Occupational and Environmental Health, Japan
| | - Kazumasa Fukuda
- Department of Microbiology, University of Occupational and Environmental Health, Japan
| | - Hiroshi Mukae
- Department of Respiratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Japan
| | - Kazuhiro Yatera
- Department of Respiratory Medicine, University of Occupational and Environmental Health, Japan
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Shi Y, Peng JM, Hu XY, Yang QW, Wang Y. Metagenomic next-generation sequencing for detecting Aspergillosis pneumonia in immunocompromised patients: a retrospective study. Front Cell Infect Microbiol 2023; 13:1209724. [PMID: 38188627 PMCID: PMC10770824 DOI: 10.3389/fcimb.2023.1209724] [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] [Received: 04/21/2023] [Accepted: 12/07/2023] [Indexed: 01/09/2024] Open
Abstract
Purpose The identification of Aspergillus by metagenomic next-generation sequencing (mNGS) remains a challenging task due to the difficulty of nucleic acid extraction. The objective of this study was to determine whether mNGS could provide an accurate and efficient method for detecting invasive pulmonary aspergillosis (IPA) in immunocompromised patients (ICP). Methods A total of 133 ICP admitted to the ICU between January 2020 and September 2022 were enrolled in the study, of which 46 were diagnosed with IPA and 87 were non-IPA cases. The bronchoalveolar lavage fluid (BALF) was analyzed for the presence of Aspergillosis and other co-pathogens using mNGS, and its diagnostic performance was compared to conventional microbial tests (CMTs) that included smear, cultures, serum and BALF galactomannan (GM) test. Clinical composite diagnosis was used as the reference standard. Results mNGS had a sensitivity, specificity, and accuracy of 82.6%, 97.7%, and 92.5%, respectively, in diagnosing IPA. These findings were comparable to those of the combination of multiple CMTs. Interestingly, the sensitivity of mNGS was superior to that of any single CMT method, as demonstrated by comparisons with smears (8.7%, P < 0.001), culture (39.1%, P < 0.001), serum GM (23.9%, P < 0.001) and BALF GM (69.6%, P = 0.031). mNGS was capable of accurately distinguish strains of Aspergillus genus, with a consistency of 77.8% with culture. Furthermore, mNGS also identified A. fumigatus, A. flavus, A. terrestris, A. oryzae and Mucor spp. in culture-negative cases. The sequencing reads of Aspergillus by mNGS exhibited extensive variation, ranging from 11 to1702. A positive correlation was observed between the optical density index of BALF GM and unique reads by mNGS (r = 0.607, P = 0.001) in BALF-GM positive patients. Notably, mNGS was able to diagnose 35 out of 37 cases with mixed infection, with P. jirovecii and cytomegalovirus being the most common co-pathogens. Conclusions mNGS presents a feasible and remarkably sensitive approach for detecting Aspergillus in ICP, thereby serving as a valuable adjunctive tool to CMT. Furthermore, mNGS's ability to accurately identify fungal species and co-pathogens can assist in guiding appropriate antimicrobial therapy.
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Affiliation(s)
- Yan Shi
- Department of Medical ICU, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Jin-Min Peng
- Department of Medical ICU, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Xiao-Yun Hu
- Department of Medical ICU, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Qi-Wen Yang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Yao Wang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
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Kim J, Lee S, Moodley Y, Yagnik L, Birnie D, Dwivedi G. The role of the host-microbiome and metabolomics in sarcoidosis. Am J Physiol Cell Physiol 2023; 325:C1336-C1353. [PMID: 37746695 DOI: 10.1152/ajpcell.00316.2023] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/19/2023] [Accepted: 09/19/2023] [Indexed: 09/26/2023]
Abstract
Sarcoidosis is a complex inflammatory fibrotic disease that affects multiple organ systems. It is characterized by the infiltration of lymphocytes and mononuclear phagocytes, which form non-caseating granulomas in affected organs. The lungs and intrathoracic lymph nodes are the most commonly affected organs. The underlying cause of sarcoidosis is unknown, but it is believed to occur in genetically predisposed individuals who are exposed to pathogenic organisms, environmental contaminants, or self and non-self-antigens. Recent research has suggested that the microbiome may play a role in the development of respiratory conditions, including sarcoidosis. Additionally, metabolomic studies have identified potential biomarkers for monitoring sarcoidosis progression. This review will focus on recent microbiome and metabolomic findings in sarcoidosis, with the goal of shedding light on the pathogenesis and possible diagnostic and therapeutic approaches.
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Affiliation(s)
- Junwoo Kim
- Department of Advanced Clinical and Translational Cardiovascular Imaging, Harry Perkins Institute of Medical Research, Murdoch, Western Australia, Australia
- School of Medicine, The University of Western Australia, Crawley, Western Australia, Australia
| | - Silvia Lee
- Department of Advanced Clinical and Translational Cardiovascular Imaging, Harry Perkins Institute of Medical Research, Murdoch, Western Australia, Australia
- School of Medicine, The University of Western Australia, Crawley, Western Australia, Australia
| | - Yuben Moodley
- Department of Advanced Clinical and Translational Cardiovascular Imaging, Harry Perkins Institute of Medical Research, Murdoch, Western Australia, Australia
- School of Medicine, The University of Western Australia, Crawley, Western Australia, Australia
- Department of Respiratory Internal Medicine, Fiona Stanley Hospital, Murdoch, Western Australia, Australia
| | - Lokesh Yagnik
- Department of Advanced Clinical and Translational Cardiovascular Imaging, Harry Perkins Institute of Medical Research, Murdoch, Western Australia, Australia
- School of Medicine, The University of Western Australia, Crawley, Western Australia, Australia
- Department of Respiratory Internal Medicine, Fiona Stanley Hospital, Murdoch, Western Australia, Australia
| | - David Birnie
- Department of Advanced Clinical and Translational Cardiovascular Imaging, Harry Perkins Institute of Medical Research, Murdoch, Western Australia, Australia
- School of Medicine, The University of Western Australia, Crawley, Western Australia, Australia
- Division of Cardiology, Department of Medicine, University of Ottawa, University of Ottawa Heart Institute, Ottawa, Ontario, Canada
| | - Girish Dwivedi
- Department of Advanced Clinical and Translational Cardiovascular Imaging, Harry Perkins Institute of Medical Research, Murdoch, Western Australia, Australia
- School of Medicine, The University of Western Australia, Crawley, Western Australia, Australia
- Division of Cardiology, Department of Medicine, University of Ottawa, University of Ottawa Heart Institute, Ottawa, Ontario, Canada
- Department of Cardiology, Fiona Stanley Hospital, Murdoch, Western Australia, Australia
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11
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Hodzhev Y, Tsafarova B, Tolchkov V, Youroukova V, Ivanova S, Kostadinov D, Yanev N, Zhelyazkova M, Tsonev S, Kalfin R, Panaiotov S. Visualization of the individual blood microbiome to study the etiology of sarcoidosis. Comput Struct Biotechnol J 2023; 22:50-57. [PMID: 37928975 PMCID: PMC10624578 DOI: 10.1016/j.csbj.2023.10.027] [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] [Received: 06/19/2023] [Revised: 10/14/2023] [Accepted: 10/16/2023] [Indexed: 11/07/2023] Open
Abstract
Introduction Single microbial pathogens or host-microbiome dysbiosis are the causes of lung diseases with suspected infectious etiology. Metagenome sequencing provides an overview of the microbiome content. Due to the rarity of most granulomatous lung diseases collecting large systematic datasets is challenging. Thus, single-patient data often can only be summarized visually. Objective To increase the information gain from a single-case metagenome analysis we suggest a quantitative and qualitative approach. Results The 16S metagenomic results of 7 patients with pulmonary sarcoidosis were compared with those of 22 healthy individuals. From lysed blood, total microbial DNA was extracted and sequenced. Cleaned data reads were identified taxonomically using Kraken 2 software. Individual metagenomic data were visualized with a Sankey diagram, Krona chart, and a heat-map. We identified five genera that were exclusively present or significantly enhanced in patients with sarcoidosis - Veillonella, Prevotella, Cutibacterium, Corynebacterium, and Streptococcus. Conclusions Our approach can characterize the blood microbiome composition and diversity in rare diseases at an individual level. Investigation of the blood microbiome in patients with granulomatous lung diseases of unknown etiology, such as sarcoidosis could enhance our comprehension of their origin and pathogenesis and potentially uncover novel personalized therapeutics.
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Affiliation(s)
- Yordan Hodzhev
- Microbiology Department, National Center of Infectious and Parasitic Diseases, Yanko Sakazov 26 Blvd., Sofia 1504, Bulgaria
| | - Borislava Tsafarova
- Microbiology Department, National Center of Infectious and Parasitic Diseases, Yanko Sakazov 26 Blvd., Sofia 1504, Bulgaria
| | - Vladimir Tolchkov
- Microbiology Department, National Center of Infectious and Parasitic Diseases, Yanko Sakazov 26 Blvd., Sofia 1504, Bulgaria
| | - Vania Youroukova
- Department of Pulmonary Diseases, University Hospital for Pulmonary Diseases “St. Sofia”, Medical University of Sofia, Akad. Ivan Evstratiev Geshov 17 Blvd., Sofia 1431, Bulgaria
| | - Silvia Ivanova
- Department of Pulmonary Diseases, University Hospital for Pulmonary Diseases “St. Sofia”, Medical University of Sofia, Akad. Ivan Evstratiev Geshov 17 Blvd., Sofia 1431, Bulgaria
| | - Dimitar Kostadinov
- Department of Pulmonary Diseases, University Hospital for Pulmonary Diseases “St. Sofia”, Medical University of Sofia, Akad. Ivan Evstratiev Geshov 17 Blvd., Sofia 1431, Bulgaria
| | - Nikolay Yanev
- Department of Pulmonary Diseases, University Hospital for Pulmonary Diseases “St. Sofia”, Medical University of Sofia, Akad. Ivan Evstratiev Geshov 17 Blvd., Sofia 1431, Bulgaria
| | - Maya Zhelyazkova
- Faculti of Mathematics and Informatics, Sofia University St. Kliment Ohridski, 5 James Bourchier Blvd., 1164 Sofia, Bulgaria
| | - Stefan Tsonev
- Agrobioinstitute (ABI), 8 Dragan Tsankov, Blvd, Sofia 1164, Bulgaria
| | - Reni Kalfin
- Institute of Neurobiology, Bulgarian Academy of Sciences, Sofia 1113, Bulgaria
- Department of Health Care, South-West University “Neofit Rilski”, Blagoevgrad 2700, Bulgaria
| | - Stefan Panaiotov
- Microbiology Department, National Center of Infectious and Parasitic Diseases, Yanko Sakazov 26 Blvd., Sofia 1504, Bulgaria
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12
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Britton N, Villabona-Rueda A, Whiteside SA, Mathew J, Kelley M, Agbor-Enoh S, McDyer JF, Christie JD, Collman RG, Cox AL, Shah P, D'Alessio F. Pseudomonas-dominant microbiome elicits sustained IL-1β upregulation in alveolar macrophages from lung transplant recipients. J Heart Lung Transplant 2023; 42:1166-1174. [PMID: 37088343 PMCID: PMC10538944 DOI: 10.1016/j.healun.2023.04.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 02/22/2023] [Accepted: 04/09/2023] [Indexed: 04/25/2023] Open
Abstract
BACKGROUND Isolation of Pseudomonas aeruginosa (PsA) is associated with increased BAL (bronchoalveolar lavage) inflammation and lung allograft injury in lung transplant recipients (LTR). However, the effect of PsA on macrophage responses in this population is incompletely understood. We examined human alveolar macrophage (AMΦ) responses to PsA and Pseudomonas dominant microbiome in healthy LTR. METHODS We stimulated THP-1 derived macrophages (THP-1MΦ) and human AMΦ from LTR with different bacteria and LTR BAL derived microbiome characterized as Pseudomonas-dominant. Macrophage responses were assessed by high dimensional flow cytometry, including their intracellular production of cytokines (TNF-α, IL-6, IL-8, IL-1β, IL-10, IL-1RA, and TGF-β). Pharmacological inhibitors were utilized to evaluate the role of the inflammasome in PsA-macrophage interaction. RESULTS We observed upregulation of pro-inflammatory cytokines (TNF-α, IL-6, IL-8, IL-1β) following stimulation by PsA compared to other bacteria (Staphylococcus aureus (S.Aur), Prevotella melaninogenica, Streptococcus pneumoniae) in both THP-1MΦ and LTR AMΦ, predominated by IL-1β. IL-1β production from THP-1MΦ was sustained after PsA stimulation for up to 96 hours and 48 hours in LTR AMΦ. Treatment with the inflammasome inhibitor BAY11-7082 abrogated THP-1MΦ IL-1β production after PsA exposure. BAL Pseudomonas-dominant microbiota elicited an increased IL-1β, similar to PsA, an effect abrogated by the addition of antibiotics. CONCLUSION PsA and PsA-dominant lung microbiota induce sustained IL-1β production in LTR AMΦ. Pharmacological targeting of the inflammasome reduces PsA-macrophage-IL-1β responses, underscoring their use in lung transplant recipients.
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Affiliation(s)
- Noel Britton
- Division of Pulmonary and Critical Care, School of Medicine, Johns Hopkins University, Baltimore, Maryland.
| | - Andres Villabona-Rueda
- Division of Pulmonary and Critical Care, School of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Samantha A Whiteside
- Division of Pulmonary, Allergy, and Critical Care, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Joby Mathew
- Division of Pulmonary and Critical Care, School of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Matthew Kelley
- Division of Pulmonary and Critical Care, School of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Sean Agbor-Enoh
- Division of Pulmonary and Critical Care, School of Medicine, Johns Hopkins University, Baltimore, Maryland; Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute, Bethesda, Maryland
| | - John F McDyer
- Division of Pulmonary, Allergy, and Critical Care, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Jason D Christie
- Division of Pulmonary, Allergy, and Critical Care, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ronald G Collman
- Division of Pulmonary, Allergy, and Critical Care, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Andrea L Cox
- Department of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Pali Shah
- Division of Pulmonary and Critical Care, School of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Franco D'Alessio
- Division of Pulmonary and Critical Care, School of Medicine, Johns Hopkins University, Baltimore, Maryland
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Farahat RA, Nazir A, Ochani S, Khan SH, Mahjabin A, Mohammed S, Jahan I, Kubra K, Swed S, Dhama K. Hidden relationship between sarcoidosis and gut microbiota: recent evidence and future implications. THE EGYPTIAN JOURNAL OF INTERNAL MEDICINE 2023. [DOI: 10.1186/s43162-023-00199-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023] Open
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14
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Keeler EL, Vukmirovic M, Yan X, Gulino K, Ghedin E, Kaminski N, Sullivan KE, Bushman FD, Collman RG, Rosenbach M. Metagenomic sequencing of the bronchoalveolar lavage extracellular virome and cellular transcriptome of sarcoidosis patients does not detect rubella virus. SARCOIDOSIS, VASCULITIS, AND DIFFUSE LUNG DISEASES : OFFICIAL JOURNAL OF WASOG 2022; 39:e2022040. [PMID: 36533601 PMCID: PMC9798337 DOI: 10.36141/svdld.v39i4.13407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 11/16/2022] [Indexed: 01/09/2023]
Abstract
BACKGROUND Sarcoidosis is a multisystem granulomatous inflammatory disease of unclear etiology that involves the lung, skin and other organs, with an unknown antigenic trigger. Recently, evidence has been found in both immune deficient and immune competent patients for rubella virus in cutaneous granulomas. These granulomatous lesions share overlapping features with cutaneous sarcoidosis, raising the question of rubella virus in sarcoidosis. OBJECTIVE To investigate the presence of rubella virus in sarcoidosis lung samples. METHODS We employed metagenomic sequencing to interrogate extracellular virome preparations and cellular transcriptomes from bronchoalveolar lavage (BAL) of 209 sarcoidosis patients for rubella virus sequences. RESULTS We found no evidence for rubella virus genomes in acellular fluid or rubella virus gene expression in BAL cells of sarcoidosis patients. CONCLUSIONS These findings argue against rubella virus infection or persistence within the lung at time of sampling as a sarcoidosis trigger.
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Affiliation(s)
- Emma L Keeler
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA.
| | - Milica Vukmirovic
- Department of Medicine, Yale University School of Medicine, New Haven, CT, USA.
| | - Xiting Yan
- Department of Medicine, Yale University School of Medicine, New Haven, CT, USA.
| | - Kristin Gulino
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA.
| | - Elodie Ghedin
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA and Laboratory of Parasitic Diseases, NIAID, NIH, Washington, DC, USA.
| | - Naftali Kaminski
- Department of Medicine, Yale University School of Medicine, New Haven, CT, USA.
| | - Kathleen E Sullivan
- Department of Pediatrics, University of Pennsylvania School of Medicine, and Children's Hospital of Philadelphia, Philadelphia, PA, USA.
| | - Frederic D Bushman
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA.
| | - Ronald G Collman
- Departments of Medicine and Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA.
| | - Misha Rosenbach
- Department of Dermatology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA.
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15
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McGinniss JE, Whiteside SA, Deek RA, Simon-Soro A, Graham-Wooten J, Oyster M, Brown MD, Cantu E, Diamond JM, Li H, Christie JD, Bushman FD, Collman RG. The Lung Allograft Microbiome Associates with Pepsin, Inflammation, and Primary Graft Dysfunction. Am J Respir Crit Care Med 2022; 206:1508-1521. [PMID: 36103583 PMCID: PMC9757091 DOI: 10.1164/rccm.202112-2786oc] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 09/14/2022] [Indexed: 12/24/2022] Open
Abstract
Rationale: Primary graft dysfunction (PGD) is the principal cause of early morbidity and mortality after lung transplantation. The lung microbiome has been implicated in later transplantation outcomes but has not been investigated in PGD. Objectives: To define the peritransplant bacterial lung microbiome and relationship to host response and PGD. Methods: This was a single-center prospective cohort study. Airway lavage samples from donor lungs before organ procurement and recipient allografts immediately after implantation underwent bacterial 16S ribosomal ribonucleic acid gene sequencing. Recipient allograft samples were analyzed for cytokines by multiplex array and pepsin by ELISA. Measurements and Main Results: We enrolled 139 transplant subjects and obtained donor lung (n = 109) and recipient allograft (n = 136) samples. Severe PGD (persistent grade 3) developed in 15 subjects over the first 72 hours, and 40 remained without PGD (persistent grade 0). The microbiome of donor lungs differed from healthy lungs, and recipient allograft microbiomes differed from donor lungs. Development of severe PGD was associated with enrichment in the immediate postimplantation lung of oropharyngeal anaerobic taxa, particularly Prevotella. Elevated pepsin, a gastric biomarker, and a hyperinflammatory cytokine profile were present in recipient allografts in severe PGD and strongly correlated with microbiome composition. Together, immediate postimplantation allograft Prevotella/Streptococcus ratio, pepsin, and indicator cytokines were associated with development of severe PGD during the 72-hour post-transplantation period (area under the curve = 0.81). Conclusions: Lung allografts that develop PGD have a microbiome enriched in anaerobic oropharyngeal taxa, elevated gastric pepsin, and hyperinflammatory phenotype. These findings suggest a possible role for peritransplant aspiration in PGD, a potentially actionable mechanism that warrants further investigation.
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Affiliation(s)
- John E. McGinniss
- Division of Pulmonary, Allergy, and Critical Care, Department of Medicine
| | | | | | - Aurea Simon-Soro
- Division of Pulmonary, Allergy, and Critical Care, Department of Medicine
| | | | - Michelle Oyster
- Division of Pulmonary, Allergy, and Critical Care, Department of Medicine
| | - Melanie D. Brown
- Division of Pulmonary, Allergy, and Critical Care, Department of Medicine
| | | | - Joshua M. Diamond
- Division of Pulmonary, Allergy, and Critical Care, Department of Medicine
| | - Hongzhe Li
- Department of Epidemiology, Biostatistics, and Informatics
| | - Jason D. Christie
- Division of Pulmonary, Allergy, and Critical Care, Department of Medicine
| | - Frederic D. Bushman
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ronald G. Collman
- Division of Pulmonary, Allergy, and Critical Care, Department of Medicine
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
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16
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Knudsen KS, Lehmann S, Nielsen R, Tangedal S, Paytuvi-Gallart A, Sanseverino W, Martinsen EMH, Hiemstra PS, Eagan TM. The lower airways microbiota and antimicrobial peptides indicate dysbiosis in sarcoidosis. MICROBIOME 2022; 10:175. [PMID: 36258251 PMCID: PMC9580159 DOI: 10.1186/s40168-022-01362-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 08/30/2022] [Indexed: 05/14/2023]
Abstract
BACKGROUND The role of the pulmonary microbiome in sarcoidosis is unknown. The objectives of this study were the following: (1) examine whether the pulmonary fungal and bacterial microbiota differed in patients with sarcoidosis compared with controls; (2) examine whether there was an association between the microbiota and levels of the antimicrobial peptides (AMPs) in protected bronchoalveolar lavage (PBAL). METHODS Thirty-five sarcoidosis patients and 35 healthy controls underwent bronchoscopy and were sampled with oral wash (OW), protected BAL (PBAL), and left protected sterile brushes (LPSB). The fungal ITS1 region and the V3V4 region of the bacterial 16S rRNA gene were sequenced. Bioinformatic analyses were performed with QIIME 2. The AMPs secretory leucocyte protease inhibitor (SLPI) and human beta defensins 1 and 2 (hBD-1 and hBD-2), were measured in PBAL by enzyme-linked immunosorbent assay (ELISA). RESULTS Aspergillus dominated the PBAL samples in sarcoidosis. Differences in bacterial taxonomy were minor. There was no significant difference in fungal alpha diversity between sarcoidosis and controls, but the bacterial alpha diversity in sarcoidosis was significantly lower in OW (p = 0.047) and PBAL (p = 0.03) compared with controls. The beta diversity for sarcoidosis compared with controls differed for both fungi and bacteria. AMP levels were significantly lower in sarcoidosis compared to controls (SLPI and hBD-1: p < 0.01). No significant correlations were found between alpha diversity and AMPs. CONCLUSIONS The pulmonary fungal and bacterial microbiota in sarcoidosis differed from in controls. Lower antimicrobial peptides levels were seen in sarcoidosis, indicating an interaction between the microbiota and the innate immune system. Whether this dysbiosis represents a pathogenic mechanism in sarcoidosis needs to be confirmed in experimental studies. Video Abstract.
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Affiliation(s)
| | - Sverre Lehmann
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway
| | - Rune Nielsen
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway
| | - Solveig Tangedal
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | | | | | | | - Pieter S. Hiemstra
- Department of Pulmonology, Leiden University Medical Center, Leiden, Netherlands
| | - Tomas M. Eagan
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway
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Kraaijvanger R, Veltkamp M. The Role of Cutibacterium acnes in Sarcoidosis: From Antigen to Treatable Trait? Microorganisms 2022; 10:microorganisms10081649. [PMID: 36014067 PMCID: PMC9415339 DOI: 10.3390/microorganisms10081649] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/04/2022] [Accepted: 08/08/2022] [Indexed: 11/19/2022] Open
Abstract
Cutibacterium acnes (C. acnes, formerly Propionibacterium acnes) is considered to be a non-pathogenic resident of the human skin, as well as mucosal surfaces. However, it also has been demonstrated that C. acnes plays a pathogenic role in diseases such as acne vulgaris or implant infections after orthopedic surgery. Besides a role in infectious disease, this bacterium also seems to harbor immunomodulatory effects demonstrated by studies using C. acnes to enhance anti-tumor activity in various cancers or vaccination response. Sarcoidosis is a systemic inflammatory disorder of unknown causes. Cultures of C. acnes in biopsy samples of sarcoidosis patients, its presence in BAL fluid, tissue samples as well as antibodies against this bacterium found in serum of patients with sarcoidosis suggest an etiological role in this disease. In this review we address the antigenic as well as immunomodulatory potential of C. acnes with a focus on sarcoidosis. Furthermore, a potential role for antibiotic treatment in patients with sarcoidosis will be explored.
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Affiliation(s)
- Raisa Kraaijvanger
- Interstitial Lung Diseases Centre of Excellence, Department of Pulmonology, St. Antonius Hospital, 3435 CM Nieuwegein, The Netherlands
| | - Marcel Veltkamp
- Interstitial Lung Diseases Centre of Excellence, Department of Pulmonology, St. Antonius Hospital, 3435 CM Nieuwegein, The Netherlands
- Division of Hearth and Lungs, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
- Correspondence:
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18
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Shi Y, Peng JM, Qin HY, Du B. Metagenomic next-generation sequencing: A promising tool for diagnosis and treatment of suspected pneumonia in rheumatic patients with acute respiratory failure: Retrospective cohort study. Front Cell Infect Microbiol 2022; 12:941930. [PMID: 35992169 PMCID: PMC9381725 DOI: 10.3389/fcimb.2022.941930] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/12/2022] [Indexed: 11/17/2022] Open
Abstract
Background The effectiveness of metagenomic next-generation sequencing (mNGS) in respiratory pathogen detection and clinical decision-making in critically rheumatic patients remains largely unexplored. Methods A single-center retrospective study of 58 rheumatic patients who were admitted to ICU due to suspected pneumonia with acute respiratory failure if they underwent both bronchoalveolar lavage fluid specimen mNGS and combined microbiological tests (CMTs) was conducted to compare their diagnostic performance, using clinical composite diagnosis as the gold standard. Treatment modifications based on mNGS results were also reviewed. Results Forty-three patients were diagnosed with microbiologically confirmed pneumonia and 15 were considered as a non-infectious disease. mNGS outperformed CMTs in the accurate diagnosis of infectious and non-infectious lung infiltration (98.1% [57/58] vs. 87.9% [51/58], P = 0.031). A total of 94 causative pathogens were defined by the gold standard and 27 patients had polymicrobial pneumonia. The sensitivity of pathogen detection and complete concordance with the gold standard by mNGS exceeded those by CMTs (92.6% [87/94] vs. 76.6% [72/94], P < 0.001 and 72.1% [31/43] vs. 51.2% [22/43], P = 0.004, respectively). Moreover, 22 pathogens were detected only by mNGS and confirmed by orthogonal test. Accordingly, the etiological diagnosis changed in 19 cases, and the empirical treatment improved in 14 cases, including 8 cases of rescue treatment and 11 of antibiotics de-escalation. At the pathogen-type level, both methods were comparable for bacteria, but mNGS was advantageous to identify viruses (accuracy: 100% vs. 81%, P = 0.004). For Pneumocystis jirovecii detection, mNGS improved the sensitivity compared with Gomori’s methenamine silver stain (91.7% vs. 4.2%, P < 0.001) and was higher than polymerase chain reaction (79.2%), but the difference was not significant (P = 0.289). In terms of Aspergillus, the better sensitivity with a combination of culture and galactomannan test than that with mNGS was found (100% vs. 66.7%, P = 0.033). Conclusions mNGS has an excellent accuracy in etiological diagnosis and pathogen detection of suspected pneumonia in critically rheumatic patients, which has potential significance for clinical decision-making. Its superiority to different types of pathogens depends on the comprehensiveness of CMTs.
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Schmidt A, Schneider C, Decker P, Hohberg K, Römbke J, Lehmitz R, Bálint M. Shotgun metagenomics of soil invertebrate communities reflects taxonomy, biomass, and reference genome properties. Ecol Evol 2022; 12:e8991. [PMID: 35784064 PMCID: PMC9170594 DOI: 10.1002/ece3.8991] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 05/11/2022] [Accepted: 05/17/2022] [Indexed: 12/03/2022] Open
Abstract
Metagenomics - shotgun sequencing of all DNA fragments from a community DNA extract - is routinely used to describe the composition, structure, and function of microorganism communities. Advances in DNA sequencing and the availability of genome databases increasingly allow the use of shotgun metagenomics on eukaryotic communities. Metagenomics offers major advances in the recovery of biomass relationships in a sample, in comparison to taxonomic marker gene-based approaches (metabarcoding). However, little is known about the factors which influence metagenomics data from eukaryotic communities, such as differences among organism groups, the properties of reference genomes, and genome assemblies.We evaluated how shotgun metagenomics records composition and biomass in artificial soil invertebrate communities at different sequencing efforts. We generated mock communities of controlled biomass ratios from 28 species from all major soil mesofauna groups: mites, springtails, nematodes, tardigrades, and potworms. We shotgun sequenced these communities and taxonomically assigned them with a database of over 270 soil invertebrate genomes.We recovered over 95% of the species, and observed relatively high false-positive detection rates. We found strong differences in reads assigned to different taxa, with some groups (e.g., springtails) consistently attracting more hits than others (e.g., enchytraeids). Original biomass could be predicted from read counts after considering these taxon-specific differences. Species with larger genomes, and with more complete assemblies, consistently attracted more reads than species with smaller genomes. The GC content of the genome assemblies had no effect on the biomass-read relationships. Results were similar among different sequencing efforts.The results show considerable differences in taxon recovery and taxon specificity of biomass recovery from metagenomic sequence data. The properties of reference genomes and genome assemblies also influence biomass recovery, and they should be considered in metagenomic studies of eukaryotes. We show that low- and high-sequencing efforts yield similar results, suggesting high cost-efficiency of metagenomics for eukaryotic communities. We provide a brief roadmap for investigating factors which influence metagenomics-based eukaryotic community reconstructions. Understanding these factors is timely as accessibility of DNA sequencing and momentum for reference genomes projects show a future where the taxonomic assignment of DNA from any community sample becomes a reality.
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Affiliation(s)
- Alexandra Schmidt
- Senckenberg Biodiversity Climate Research CenterFrankfurt am MainGermany
- Biology DepartmentJ.W. Goethe UniversityFrankfurt am MainGermany
- Loewe Center for Translational Biodiversity Genomics (LOEWE‐TBG)Frankfurt am MainGermany
- Limnological Institute (Environmental Genomics)University of KonstanzKonstanzGermany
| | - Clément Schneider
- Loewe Center for Translational Biodiversity Genomics (LOEWE‐TBG)Frankfurt am MainGermany
- Soil Zoology DepartmentSenckenberg Museum of Natural History GörlitzGörlitzGermany
| | - Peter Decker
- Loewe Center for Translational Biodiversity Genomics (LOEWE‐TBG)Frankfurt am MainGermany
- Blumenstr. 5GörlitzGermany
| | - Karin Hohberg
- Loewe Center for Translational Biodiversity Genomics (LOEWE‐TBG)Frankfurt am MainGermany
- Soil Zoology DepartmentSenckenberg Museum of Natural History GörlitzGörlitzGermany
| | - Jörg Römbke
- ECT Oekotoxikologie GmbHFlörsheim am MainGermany
| | - Ricarda Lehmitz
- Loewe Center for Translational Biodiversity Genomics (LOEWE‐TBG)Frankfurt am MainGermany
- Soil Zoology DepartmentSenckenberg Museum of Natural History GörlitzGörlitzGermany
| | - Miklós Bálint
- Senckenberg Biodiversity Climate Research CenterFrankfurt am MainGermany
- Loewe Center for Translational Biodiversity Genomics (LOEWE‐TBG)Frankfurt am MainGermany
- Institute for Insect BiotechnologyJustus Liebig UniversityGießenGermany
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Singh S, Natalini JG, Segal LN. Lung microbial-host interface through the lens of multi-omics. Mucosal Immunol 2022; 15:837-845. [PMID: 35794200 PMCID: PMC9391302 DOI: 10.1038/s41385-022-00541-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/23/2022] [Accepted: 06/19/2022] [Indexed: 02/04/2023]
Abstract
In recent years, our understanding of the microbial world within us has been revolutionized by the use of culture-independent techniques. The use of multi-omic approaches can now not only comprehensively characterize the microbial environment but also evaluate its functional aspects and its relationship with the host immune response. Advances in bioinformatics have enabled high throughput and in-depth analyses of transcripts, proteins and metabolites and enormously expanded our understanding of the role of the human microbiome in different conditions. Such investigations of the lower airways have specific challenges but as the field develops, new approaches will be facilitated. In this review, we focus on how integrative multi-omics can advance our understanding of the microbial environment and its effects on the host immune tone in the lungs.
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Affiliation(s)
- Shivani Singh
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY
| | - Jake G. Natalini
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY,NYU Langone Lung Transplant Institute, New York University Grossman School of Medicine, NYU Langone Health, New York, NY
| | - Leopoldo N. Segal
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY
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21
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Diagnostic value of metagenomic next-generation sequencing of bronchoalveolar lavage fluid for the diagnosis of suspected pneumonia in immunocompromised patients. BMC Infect Dis 2022; 22:416. [PMID: 35488253 PMCID: PMC9052728 DOI: 10.1186/s12879-022-07381-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 04/13/2022] [Indexed: 12/14/2022] Open
Abstract
Background To evaluate the diagnostic value of metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) in immunocompromised patients for the diagnosis of suspected pneumonia in comparison with that of conventional microbiological tests (CMTs). Methods Sixty-nine immunocompromised patients with suspected pneumonia received both CMTs and mNGS of BALF were analyzed retrospectively. The diagnostic value was compared between CMTs and mNGS, using the clinical composite diagnosis as the reference standard. Results Sixty patients were diagnosed of pneumonia including fifty-two patients with identified pathogens and eight patients with probable pathogens. Taking the composite reference standard as a gold standard, 42 pathogens were identified by CMTs including nine bacteria, 17 fungi, 8 virus, 6 Mycobacterium Tuberculosis, and two Legionella and 19(45%) of which were detected by BALF culture. As for mNGS, it identified 76 pathogens including 20 bacteria, 31 fungi, 14 virus, 5 Mycobacterium Tuberculosis, four Legionella and two Chlamydia psittaci. The overall detection rate of mNGS for pathogens were higher than that of CMTs. However, a comparable diagnostic accuracy of mNGS and CMTs were found for bacterial and viral infections. mNGS exhibited a higher diagnostic accuracy for fungal detection than CMTs (78% vs. 57%, P < 0.05), which mainly because of the high sensitivity of mNGS in patients with Pneumocystis jirovecii pneumonia (PJP) (100% vs. 28%, P < 0.05). Nineteen patients were identified as pulmonary co-infection, mNGS test showed a higher detection rate and broader spectrum for pathogen detection than that of CMTs in co-infection. Moreover, Pneumocystis jirovecii was the most common pathogen in co-infection and mNGS have identified much more co-pathogens of PJP than CMTs. Conclusions mNGS of BALF improved the microbial detection rate of pathogens and exhibited remarkable advantages in detecting PJP and identifying co-infection in immunocompromised patients. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-022-07381-8.
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22
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Bagavant H, Cizio K, Araszkiewicz AM, Papinska JA, Garman L, Li C, Pezant N, Drake WP, Montgomery CG, Deshmukh US. Systemic immune response to vimentin and granuloma formation in a model of pulmonary sarcoidosis. J Transl Autoimmun 2022; 5:100153. [PMID: 35434591 PMCID: PMC9006845 DOI: 10.1016/j.jtauto.2022.100153] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 03/10/2022] [Accepted: 03/30/2022] [Indexed: 11/16/2022] Open
Abstract
A characteristic feature of sarcoidosis is a dysregulated immune response to persistent stimuli, often leading to the formation of non-necrotizing granulomas in various organs. Although genetic susceptibility is an essential factor in disease development, the etiology of sarcoidosis is not fully understood. Specifically, whether autoimmunity contributes to the initiation or progression of the disease is uncertain. In this study, we investigated systemic autoimmunity to vimentin in sarcoidosis. IgG antibodies to human vimentin were measured in sera from sarcoidosis patients and healthy controls. Mice immunized with recombinant murine vimentin were challenged intravenously with vimentin-coated beads to mimic pulmonary sarcoidosis. Lungs from treated mice were studied for cellular infiltration, granuloma formation, and gene expression. Immune cells in the bronchoalveolar lavage fluid were evaluated by flow cytometry. Compared to healthy controls, sarcoidosis patients had a higher frequency and levels of circulating anti-vimentin IgG. Vimentin-immunized mice developed lung granulomas following intravenous challenge with vimentin-coated beads. These sarcoidosis-like granulomas showed the presence of Langhans and foreign body multinucleated giant cells, CD4 T cells, and a heterogeneous collection of MHC II positive and arginase 1-expressing macrophages. The lungs showed upregulated pro-inflammatory gene expression, including Ifng, Il17, and Tnfa, reflecting TH1/TH17 responses typical of sarcoidosis. In addition, genes in the TH2 canonical pathway were also upregulated, congruent with increased numbers of ILC2 in the bronchoalveolar lavage. Overall, these results further validate vimentin as an autoantigen in sarcoidosis and provide evidence for an anti-vimentin immune response in disease pathogenesis. Our study also highlights the possible role of ILC2-driven TH2-like responses in the formation of lung granulomas in sarcoidosis.
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Affiliation(s)
- Harini Bagavant
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Katarzyna Cizio
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Antonina M. Araszkiewicz
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Joanna A. Papinska
- Department of Microbiology and Immunology, University of Oklahoma, Health Sciences Center, Oklahoma City, OK, USA
| | - Lori Garman
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Chuang Li
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Nathan Pezant
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Wonder P. Drake
- Division of Infectious Diseases, Department of Medicine, Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Courtney G. Montgomery
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Umesh S. Deshmukh
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
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23
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Amati F, Stainer A, Mantero M, Gramegna A, Simonetta E, Suigo G, Voza A, Nambiar AM, Cariboni U, Oldham J, Molyneaux PL, Spagnolo P, Blasi F, Aliberti S. Lung Microbiome in Idiopathic Pulmonary Fibrosis and Other Interstitial Lung Diseases. Int J Mol Sci 2022; 23:ijms23020977. [PMID: 35055163 PMCID: PMC8779068 DOI: 10.3390/ijms23020977] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 01/07/2022] [Accepted: 01/12/2022] [Indexed: 02/01/2023] Open
Abstract
Interstitial lung diseases represent a heterogeneous and wide group of diseases in which factors leading to disease initiation and progression are not fully understood. Recent evidence suggests that the lung microbiome might influence the pathogenesis and progression of interstitial lung diseases. In recent years, the utilization of culture-independent methodologies has allowed the identification of complex and dynamic communities of microbes, in patients with interstitial lung diseases. However, the potential mechanisms by which these changes may drive disease pathogenesis and progression are largely unknown. The aim of this review is to discuss the role of the altered lung microbiome in several interstitial lung diseases. Untangling the host–microbiome interaction in the lung and airway of interstitial lung disease patients is a research priority. Thus, lung dysbiosis is a potentially treatable trait across several interstitial lung diseases, and its proper characterization and treatment might be crucial to change the natural history of these diseases and improve outcomes.
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Affiliation(s)
- Francesco Amati
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (A.S.); (G.S.); (A.V.); (S.A.)
- Respiratory Unit, IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, Italy
- Correspondence:
| | - Anna Stainer
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (A.S.); (G.S.); (A.V.); (S.A.)
- Respiratory Unit, IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, Italy
| | - Marco Mantero
- Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy; (M.M.); (A.G.); (E.S.); (F.B.)
- Internal Medicine Department, Respiratory Unit and Cystic Fibrosis Adult Center, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Andrea Gramegna
- Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy; (M.M.); (A.G.); (E.S.); (F.B.)
- Internal Medicine Department, Respiratory Unit and Cystic Fibrosis Adult Center, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Edoardo Simonetta
- Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy; (M.M.); (A.G.); (E.S.); (F.B.)
- Internal Medicine Department, Respiratory Unit and Cystic Fibrosis Adult Center, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Giulia Suigo
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (A.S.); (G.S.); (A.V.); (S.A.)
- Respiratory Unit, IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, Italy
| | - Antonio Voza
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (A.S.); (G.S.); (A.V.); (S.A.)
- Emergency Medicine Unit, IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, Italy
| | - Anoop M. Nambiar
- Division of Pulmonary and Critical Care, Department of Medicine, University of Texas Health San Antonio, South Texas Health Care System, San Antonio, TX 78229, USA;
| | - Umberto Cariboni
- Department of General and Thoracic Surgery, Humanitas Research Hospital, 20089 Rozzano, Italy;
| | - Justin Oldham
- Division of Pulmonary, Critical Care and Sleep Medicine, University of California Davis, Sacramento, CA 95616, USA;
| | - Philip L. Molyneaux
- National Heart and Lung Institute, Imperial College London, London SW7 2AZ, UK;
| | - Paolo Spagnolo
- Respiratory Disease Unit, Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, 35128 Padova, Italy;
| | - Francesco Blasi
- Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy; (M.M.); (A.G.); (E.S.); (F.B.)
- Internal Medicine Department, Respiratory Unit and Cystic Fibrosis Adult Center, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Stefano Aliberti
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (A.S.); (G.S.); (A.V.); (S.A.)
- Respiratory Unit, IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, Italy
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24
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Casto AM, Fredricks DN, Hill JA. Diagnosis of infectious diseases in immunocompromised hosts using metagenomic next generation sequencing-based diagnostics. Blood Rev 2021; 53:100906. [PMID: 34802773 DOI: 10.1016/j.blre.2021.100906] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 10/28/2021] [Accepted: 11/01/2021] [Indexed: 02/07/2023]
Abstract
The diagnosis of infectious diseases in immunocompromised hosts presents unique challenges for the clinician. Metagenomic next generation sequencing (mNGS) based diagnostics that identify microbial nucleic acids in clinical samples (mNGS for pathogen identification or mNGSpi) may be a useful tool in addressing some of these challenges. Studies of mNGSpi in immunocompromised hosts have demonstrated that these diagnostics are capable of identifying causative organisms in a subset of patients for whom conventional testing has been negative. While these studies provide proof of concept for mNGSpi utility, they have a number of limitations, which make it difficult to confidently assess test performance and clinical impact based on current data. Future studies will likely feature larger cohort sizes and controlled interventional study designs that assess the impact of mNGSpi on clinical endpoints. They will also likely include assessments of the clinical value of data generated by mNGS beyond pathogen identification.
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Affiliation(s)
- Amanda M Casto
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA, United States of America; Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America.
| | - David N Fredricks
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA, United States of America; Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America.
| | - Joshua A Hill
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA, United States of America; Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America.
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25
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Greaves SA, Ravindran A, Santos RG, Chen L, Falta MT, Wang Y, Mitchell AM, Atif SM, Mack DG, Tinega AN, Maier LA, Dai S, Pinilla C, Grunewald J, Fontenot AP. CD4+ T cells in the lungs of acute sarcoidosis patients recognize an Aspergillus nidulans epitope. J Exp Med 2021; 218:212583. [PMID: 34410304 PMCID: PMC8383815 DOI: 10.1084/jem.20210785] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 06/18/2021] [Accepted: 07/22/2021] [Indexed: 11/05/2022] Open
Abstract
Löfgren’s syndrome (LS) is an acute form of sarcoidosis characterized by a genetic association with HLA-DRB1*03 (HLA-DR3) and an accumulation of CD4+ T cells of unknown specificity in the bronchoalveolar lavage (BAL). Here, we screened related LS-specific TCRs for antigen specificity and identified a peptide derived from NAD-dependent histone deacetylase hst4 (NDPD) of Aspergillus nidulans that stimulated these CD4+ T cells in an HLA-DR3–restricted manner. Using ELISPOT analysis, a greater number of IFN-γ– and IL-2–secreting T cells in the BAL of DR3+ LS subjects compared with DR3+ control subjects was observed in response to the NDPD peptide. Finally, increased IgG antibody responses to A. nidulans NDPD were detected in the serum of DR3+ LS subjects. Thus, our findings identify a ligand for CD4+ T cells derived from the lungs of LS patients and suggest a role of A. nidulans in the etiology of LS.
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Affiliation(s)
- Sarah A Greaves
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Avinash Ravindran
- Department of Medicine, Solna, Karolinska University Hospital, Stockholm, Sweden.,Centre for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Radleigh G Santos
- Department of Mathematics, Nova Southeastern University, Ft. Lauderdale, FL
| | - Lan Chen
- Department of Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Michael T Falta
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Yang Wang
- Department of Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Angela M Mitchell
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Shaikh M Atif
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Douglas G Mack
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Alex N Tinega
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Lisa A Maier
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO.,Department of Medicine, National Jewish Health, Denver, CO
| | - Shaodong Dai
- Department of Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Clemencia Pinilla
- Center for Translational Science, Florida International University, Port St. Lucie, FL
| | - Johan Grunewald
- Department of Medicine, Solna, Karolinska University Hospital, Stockholm, Sweden
| | - Andrew P Fontenot
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO.,Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO
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26
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Merenstein C, Liang G, Whiteside SA, Cobián-Güemes AG, Merlino MS, Taylor LJ, Glascock A, Bittinger K, Tanes C, Graham-Wooten J, Khatib LA, Fitzgerald AS, Reddy S, Baxter AE, Giles JR, Oldridge DA, Meyer NJ, Wherry EJ, McGinniss JE, Bushman FD, Collman RG. Signatures of COVID-19 Severity and Immune Response in the Respiratory Tract Microbiome. mBio 2021; 12:e0177721. [PMID: 34399607 PMCID: PMC8406335 DOI: 10.1128/mbio.01777-21] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 07/14/2021] [Indexed: 01/12/2023] Open
Abstract
Viral infection of the respiratory tract can be associated with propagating effects on the airway microbiome, and microbiome dysbiosis may influence viral disease. Here, we investigated the respiratory tract microbiome in coronavirus disease 2019 (COVID-19) and its relationship to disease severity, systemic immunologic features, and outcomes. We examined 507 oropharyngeal, nasopharyngeal, and endotracheal samples from 83 hospitalized COVID-19 patients as well as non-COVID patients and healthy controls. Bacterial communities were interrogated using 16S rRNA gene sequencing, and the commensal DNA viruses Anelloviridae and Redondoviridae were quantified by qPCR. We found that COVID-19 patients had upper respiratory microbiome dysbiosis and greater change over time than critically ill patients without COVID-19. Oropharyngeal microbiome diversity at the first time point correlated inversely with disease severity during hospitalization. Microbiome composition was also associated with systemic immune parameters in blood, as measured by lymphocyte/neutrophil ratios and immune profiling of peripheral blood mononuclear cells. Intubated patients showed patient-specific lung microbiome communities that were frequently highly dynamic, with prominence of Staphylococcus. Anelloviridae and Redondoviridae showed more frequent colonization and higher titers in severe disease. Machine learning analysis demonstrated that integrated features of the microbiome at early sampling points had high power to discriminate ultimate level of COVID-19 severity. Thus, the respiratory tract microbiome and commensal viruses are disturbed in COVID-19 and correlate with systemic immune parameters, and early microbiome features discriminate disease severity. Future studies should address clinical consequences of airway dysbiosis in COVID-19, its possible use as biomarkers, and the role of bacterial and viral taxa identified here in COVID-19 pathogenesis. IMPORTANCE COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection of the respiratory tract, results in highly variable outcomes ranging from minimal illness to death, but the reasons for this are not well understood. We investigated the respiratory tract bacterial microbiome and small commensal DNA viruses in hospitalized COVID-19 patients and found that each was markedly abnormal compared to that in healthy people and differed from that in critically ill patients without COVID-19. Early airway samples tracked with the level of COVID-19 illness reached during hospitalization, and the airway microbiome also correlated with immune parameters in blood. These findings raise questions about the mechanisms linking SARS-CoV-2 infection and other microbial inhabitants of the airway, including whether the microbiome might regulate severity of COVID-19 disease and/or whether early microbiome features might serve as biomarkers to discriminate disease severity.
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Affiliation(s)
- Carter Merenstein
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Guanxiang Liang
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Samantha A. Whiteside
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Ana G. Cobián-Güemes
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Madeline S. Merlino
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Louis J. Taylor
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Abigail Glascock
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Ceylan Tanes
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Jevon Graham-Wooten
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Layla A. Khatib
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Ayannah S. Fitzgerald
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Shantan Reddy
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Amy E. Baxter
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Josephine R. Giles
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Derek A. Oldridge
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Nuala J. Meyer
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - E. John Wherry
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - John E. McGinniss
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Frederic D. Bushman
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Ronald G. Collman
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
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27
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McGinniss JE, Whiteside SA, Simon-Soro A, Diamond JM, Christie JD, Bushman FD, Collman RG. The lung microbiome in lung transplantation. J Heart Lung Transplant 2021; 40:733-744. [PMID: 34120840 PMCID: PMC8335643 DOI: 10.1016/j.healun.2021.04.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 04/13/2021] [Accepted: 04/19/2021] [Indexed: 12/21/2022] Open
Abstract
Culture-independent study of the lower respiratory tract after lung transplantation has enabled an understanding of the microbiome - that is, the collection of bacteria, fungi, and viruses, and their respective gene complement - in this niche. The lung has unique features as a microbial environment, with balanced entry from the upper respiratory tract, clearance, and local replication. There are many pressures impacting the microbiome after transplantation, including donor allograft factors, recipient host factors such as underlying disease and ongoing exposure to the microbe-rich upper respiratory tract, and transplantation-related immunosuppression, antimicrobials, and postsurgical changes. To date, we understand that the lung microbiome after transplant is dysbiotic; that is, it has higher biomass and altered composition compared to a healthy lung. Emerging data suggest that specific microbiome features may be linked to host responses, both immune and non-immune, and clinical outcomes such as chronic lung allograft dysfunction (CLAD), but many questions remain. The goal of this review is to put into context our burgeoning understanding of the lung microbiome in the postlung transplant patient, the interactions between microbiome and host, the role the microbiome may play in post-transplant complications, and critical outstanding research questions.
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Affiliation(s)
- John E McGinniss
- Division of Pulmonary, Allergy and Critical Care Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Samantha A Whiteside
- Division of Pulmonary, Allergy and Critical Care Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Aurea Simon-Soro
- Department of Orthodontics and Divisions of Community Oral Health and Pediatric Dentistry, School of Dental Medicine at the University of Pennsylvania
| | - Joshua M Diamond
- Division of Pulmonary, Allergy and Critical Care Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jason D Christie
- Division of Pulmonary, Allergy and Critical Care Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania; Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Fredrick D Bushman
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ronald G Collman
- Division of Pulmonary, Allergy and Critical Care Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania; Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
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28
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Sulaiman I, Wu BG, Li Y, Tsay JC, Sauthoff M, Scott AS, Ji K, Koralov SB, Weiden M, Clemente JC, Jones D, Huang YJ, Stringer KA, Zhang L, Geber A, Banakis S, Tipton L, Ghedin E, Segal LN. Functional lower airways genomic profiling of the microbiome to capture active microbial metabolism. Eur Respir J 2021; 58:13993003.03434-2020. [PMID: 33446604 DOI: 10.1183/13993003.03434-2020] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/19/2020] [Indexed: 12/31/2022]
Abstract
BACKGROUND Microbiome studies of the lower airways based on bacterial 16S rRNA gene sequencing assess microbial community structure but can only infer functional characteristics. Microbial products, such as short-chain fatty acids (SCFAs), in the lower airways have significant impact on the host's immune tone. Thus, functional approaches to the analyses of the microbiome are necessary. METHODS Here we used upper and lower airway samples from a research bronchoscopy smoker cohort. In addition, we validated our results in an experimental mouse model. We extended our microbiota characterisation beyond 16S rRNA gene sequencing with the use of whole-genome shotgun (WGS) and RNA metatranscriptome sequencing. SCFAs were also measured in lower airway samples and correlated with each of the sequencing datasets. In the mouse model, 16S rRNA gene and RNA metatranscriptome sequencing were performed. RESULTS Functional evaluations of the lower airway microbiota using inferred metagenome, WGS and metatranscriptome data were dissimilar. Comparison with measured levels of SCFAs shows that the inferred metagenome from the 16S rRNA gene sequencing data was poorly correlated, while better correlations were noted when SCFA levels were compared with WGS and metatranscriptome data. Modelling lower airway aspiration with oral commensals in a mouse model showed that the metatranscriptome most efficiently captures transient active microbial metabolism, which was overestimated by 16S rRNA gene sequencing. CONCLUSIONS Functional characterisation of the lower airway microbiota through metatranscriptome data identifies metabolically active organisms capable of producing metabolites with immunomodulatory capacity, such as SCFAs.
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Affiliation(s)
- Imran Sulaiman
- Division of Pulmonary, Critical Care, and Sleep Medicine, Dept of Medicine, New York University School of Medicine, New York, NY, USA
| | - Benjamin G Wu
- Division of Pulmonary, Critical Care, and Sleep Medicine, Dept of Medicine, New York University School of Medicine, New York, NY, USA
| | - Yonghua Li
- Division of Pulmonary, Critical Care, and Sleep Medicine, Dept of Medicine, New York University School of Medicine, New York, NY, USA
| | - Jun-Chieh Tsay
- Division of Pulmonary, Critical Care, and Sleep Medicine, Dept of Medicine, New York University School of Medicine, New York, NY, USA
| | - Maya Sauthoff
- Division of Pulmonary, Critical Care, and Sleep Medicine, Dept of Medicine, New York University School of Medicine, New York, NY, USA
| | - Adrienne S Scott
- Division of Pulmonary, Critical Care, and Sleep Medicine, Dept of Medicine, New York University School of Medicine, New York, NY, USA
| | - Kun Ji
- Division of Pulmonary, Critical Care, and Sleep Medicine, Dept of Medicine, New York University School of Medicine, New York, NY, USA
| | - Sergei B Koralov
- Dept of Pathology, New York University School of Medicine, New York, NY, USA
| | - Michael Weiden
- Division of Pulmonary, Critical Care, and Sleep Medicine, Dept of Medicine, New York University School of Medicine, New York, NY, USA
| | - Jose C Clemente
- Dept of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Drew Jones
- Dept of Biochemistry and Molecular Pharmacology and Dept of Radiation Oncology, New York University School of Medicine, New York, NY, USA
| | - Yvonne J Huang
- Division of Pulmonary and Critical Care Medicine, Dept of Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Kathleen A Stringer
- Dept of Clinical Pharmacy, College of Pharmacy, and Division of Pulmonary and Critical Care Medicine, Dept of Medicine, School of Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Lingdi Zhang
- Center for Genomics and Systems Biology, Dept of Biology, New York University, New York, NY, USA
| | - Adam Geber
- Center for Genomics and Systems Biology, Dept of Biology, New York University, New York, NY, USA
| | - Stephanie Banakis
- Center for Genomics and Systems Biology, Dept of Biology, New York University, New York, NY, USA
| | - Laura Tipton
- Center for Genomics and Systems Biology, Dept of Biology, New York University, New York, NY, USA
| | - Elodie Ghedin
- Center for Genomics and Systems Biology, Dept of Biology, New York University, New York, NY, USA.,Dept of Epidemiology, School of Global Public Health, New York University, New York, NY, USA
| | - Leopoldo N Segal
- Division of Pulmonary, Critical Care, and Sleep Medicine, Dept of Medicine, New York University School of Medicine, New York, NY, USA
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29
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Merenstein C, Liang G, Whiteside SA, Cobián-Güemes AG, Merlino MS, Taylor LJ, Glascock A, Bittinger K, Tanes C, Graham-Wooten J, Khatib LA, Fitzgerald AS, Reddy S, Baxter AE, Giles JR, Oldridge DA, Meyer NJ, Wherry EJ, McGinniss JE, Bushman FD, Collman RG. Signatures of COVID-19 severity and immune response in the respiratory tract microbiome. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.04.02.21254514. [PMID: 33851179 PMCID: PMC8043476 DOI: 10.1101/2021.04.02.21254514] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Rationale Viral infection of the respiratory tract can be associated with propagating effects on the airway microbiome, and microbiome dysbiosis may influence viral disease. Objective To define the respiratory tract microbiome in COVID-19 and relationship disease severity, systemic immunologic features, and outcomes. Methods and Measurements We examined 507 oropharyngeal, nasopharyngeal and endotracheal samples from 83 hospitalized COVID-19 patients, along with non-COVID patients and healthy controls. Bacterial communities were interrogated using 16S rRNA gene sequencing, commensal DNA viruses Anelloviridae and Redondoviridae were quantified by qPCR, and immune features were characterized by lymphocyte/neutrophil (L/N) ratios and deep immune profiling of peripheral blood mononuclear cells (PBMC). Main Results COVID-19 patients had upper respiratory microbiome dysbiosis, and greater change over time than critically ill patients without COVID-19. Diversity at the first time point correlated inversely with disease severity during hospitalization, and microbiome composition was associated with L/N ratios and PBMC profiles in blood. Intubated patients showed patient-specific and dynamic lung microbiome communities, with prominence of Staphylococcus. Anelloviridae and Redondoviridae showed more frequent colonization and higher titers in severe disease. Machine learning analysis demonstrated that integrated features of the microbiome at early sampling points had high power to discriminate ultimate level of COVID-19 severity. Conclusions The respiratory tract microbiome and commensal virome are disturbed in COVID-19, correlate with systemic immune parameters, and early microbiome features discriminate disease severity. Future studies should address clinical consequences of airway dysbiosis in COVID-19, possible use as biomarkers, and role of bacterial and viral taxa identified here in COVID-19 pathogenesis.
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Affiliation(s)
- Carter Merenstein
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Guanxiang Liang
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Samantha A Whiteside
- Pulmonary, Allergy and Critical Care Division; Department of Medicine; University of Pennsylvania Perelman School of Medicine; Philadelphia, PA 19104
| | - Ana G Cobián-Güemes
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Madeline S Merlino
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Louis J Taylor
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Abigail Glascock
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA 19104
| | - Ceylan Tanes
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA 19104
| | - Jevon Graham-Wooten
- Pulmonary, Allergy and Critical Care Division; Department of Medicine; University of Pennsylvania Perelman School of Medicine; Philadelphia, PA 19104
| | - Layla A Khatib
- Pulmonary, Allergy and Critical Care Division; Department of Medicine; University of Pennsylvania Perelman School of Medicine; Philadelphia, PA 19104
| | - Ayannah S Fitzgerald
- Pulmonary, Allergy and Critical Care Division; Department of Medicine; University of Pennsylvania Perelman School of Medicine; Philadelphia, PA 19104
| | - Shantan Reddy
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Amy E Baxter
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Josephine R Giles
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Derek A Oldridge
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Nuala J Meyer
- Pulmonary, Allergy and Critical Care Division; Department of Medicine; University of Pennsylvania Perelman School of Medicine; Philadelphia, PA 19104
| | - E John Wherry
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - John E McGinniss
- Pulmonary, Allergy and Critical Care Division; Department of Medicine; University of Pennsylvania Perelman School of Medicine; Philadelphia, PA 19104
| | - Frederic D Bushman
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Ronald G Collman
- Pulmonary, Allergy and Critical Care Division; Department of Medicine; University of Pennsylvania Perelman School of Medicine; Philadelphia, PA 19104
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30
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Peng JM, Du B, Qin HY, Wang Q, Shi Y. Metagenomic next-generation sequencing for the diagnosis of suspected pneumonia in immunocompromised patients. J Infect 2021; 82:22-27. [PMID: 33609588 DOI: 10.1016/j.jinf.2021.01.029] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 12/18/2020] [Accepted: 01/12/2021] [Indexed: 12/17/2022]
Abstract
OBJECTIVES To evaluate the potential of metagenomic next-generation sequencing (mNGS), compared with that of comprehensive conventional microbiological tests (CMTs), of bronchoalveolar lavage fluid (BALF) as a front-line diagnostic for immunocompromised patients with suspected pneumonia. METHODS Sixty critically ill immunocompromised patients undergoing both mNGS of BALF and CMTs for suspected pneumonia were retrospectively analysed. The diagnostic performance was compared between mNGS and CMTs, using the composite diagnosis as the reference standard. RESULTS Forty-nine patients were diagnosed with microbiologically confirmed pneumonia, with 55% having polymicrobial infections. There was no significant difference in the overall diagnostic accuracy between mNGS and CMTs (61.7% vs 76.7%; P = 0.11). mNGS and CMTs had comparable diagnostic accuracy for bacterial and viral infections. Although mNGS identified more viral pneumonia, it had a much lower diagnostic accuracy for fungal infections (76.7% vs 99.2%; P < 0.001), mainly due to the low sensitivity for invasive pulmonary aspergillosis (45.5% vs 100%; P < 0.001). CONCLUSION The overall diagnostic performance of BALF mNGS as a first-line diagnostic was similar to that of comprehensive CMTs, except in the case of a lack of consideration of potential pathogens or limited CMTs. The combination of mNGS and CMTs may be the best diagnostic strategy.
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Affiliation(s)
- Jin-Min Peng
- Department of Medical Intensive Care Unit, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Bin Du
- Department of Medical Intensive Care Unit, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Han-Yu Qin
- Department of Medical Intensive Care Unit, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Qian Wang
- Department of Rheumatology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China; National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID) , Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing 100730, China
| | - Yan Shi
- Department of Medical Intensive Care Unit, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China
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31
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Chioma OS, Hesse LE, Chapman A, Drake WP. Role of the Microbiome in Interstitial Lung Diseases. Front Med (Lausanne) 2021; 8:595522. [PMID: 33604346 PMCID: PMC7885795 DOI: 10.3389/fmed.2021.595522] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Accepted: 01/06/2021] [Indexed: 12/14/2022] Open
Abstract
There are trillions of microorganisms in the human body, consisting of bacteria, viruses, fungi, and archaea; these collectively make up the microbiome. Recent studies suggest that the microbiome may serve as a biomarker for disease, a therapeutic target, or provide an explanation for pathophysiology in lung diseases. Studies describing the impact of the microorganisms found in the respiratory tract on lung health have been published and are discussed here in the context of interstitial lung diseases. Additionally, epidemiological and experimental evidence highlights the importance of cross-talk between the gut microbiota and the lungs, called the gut–lung axis. The gut-lung axis postulates that alterations in gut microbial communities may have a profound effect on lung disease. Dysbiosis in the microbial community of the gut is linked with changes in immune responses, homeostasis in the airways, and inflammatory conditions in the gastrointestinal tract itself. In this review, we summarize studies describing the role of the microbiome in interstitial lung disease and discuss the implications of these findings on the diagnosis and treatment of these diseases. This paper describes the impact of the microbial communities on the pathogenesis of lung diseases by assessing recent original research and identifying remaining gaps in knowledge.
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Affiliation(s)
- Ozioma S Chioma
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Laura E Hesse
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Austin Chapman
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Wonder P Drake
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, United States.,Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN, United States
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32
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Abstract
The human body hosts vast microbial communities, termed the microbiome. Less well known is the fact that the human body also hosts vast numbers of different viruses, collectively termed the 'virome'. Viruses are believed to be the most abundant and diverse biological entities on our planet, with an estimated 1031 particles on Earth. The human virome is similarly vast and complex, consisting of approximately 1013 particles per human individual, with great heterogeneity. In recent years, studies of the human virome using metagenomic sequencing and other methods have clarified aspects of human virome diversity at different body sites, the relationships to disease states and mechanisms of establishment of the human virome during early life. Despite increasing focus, it remains the case that the majority of sequence data in a typical virome study remain unidentified, highlighting the extent of unexplored viral 'dark matter'. Nevertheless, it is now clear that viral community states can be associated with adverse outcomes for the human host, whereas other states are characteristic of health. In this Review, we provide an overview of research on the human virome and highlight outstanding recent studies that explore the assembly, composition and dynamics of the human virome as well as host-virome interactions in health and disease.
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33
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Abbas A, Taylor LJ, Collman RG, Bushman FD, Ictv Report Consortium. ICTV Virus Taxonomy Profile: Redondoviridae. J Gen Virol 2020; 102. [PMID: 33258767 PMCID: PMC8116785 DOI: 10.1099/jgv.0.001526] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Viruses in the family Redondoviridae have a circular genome of 3.0 kb with three open reading frames. The packaged genome is inferred to be single-stranded DNA by analogy to related viruses. Redondoviruses were discovered through metagenomic sequencing methods in samples from human subjects and are inferred to replicate in humans. Evidence of redondovirus infection is associated with periodontitis and critical illness, but redondoviruses have not been shown to be the causative agent of any diseases. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Redondoviridae, which is available at ictv.global/report/redondoviridae.
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Affiliation(s)
- Arwa Abbas
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Louis J Taylor
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Ronald G Collman
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Frederic D Bushman
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
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34
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Current perspectives on the immunopathogenesis of sarcoidosis. Respir Med 2020; 173:106161. [PMID: 32992264 DOI: 10.1016/j.rmed.2020.106161] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 08/28/2020] [Accepted: 09/16/2020] [Indexed: 12/25/2022]
Abstract
Sarcoidosis is an inflammatory systemic disease that commonly affects the lungs or lymph nodes but can manifest in other organs. Herein, we review the latest evidence establishing how innate and adaptive immune responses contribute to the pathogenesis and clinical course of sarcoidosis. We discuss the possible role of microbial organisms as etiologic agents in sarcoidosis and the evidence supporting sarcoidosis as an autoimmune disease. We also discuss how animal and in vitro human models have advanced our understanding of the immunopathogenesis of sarcoidosis. Finally, we discuss therapeutics for sarcoidosis and the effects on the immune system.
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35
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Abstract
PURPOSE OF REVIEW Sarcoidosis is a systemic disease characterized by granulomatous inflammation of unknown cause. There is extensive heterogeneity between patients with respect to the number and types of organs involved, disease course, and response to therapy. Recent research in the field has leveraged 'omics' techniques such as transcriptomics to identify important 'molecular profiles' in the disease. These tools may help in identifying clinically useful biomarkers and targets for therapy. RECENT FINDINGS Several studies have used gene expression profiling of predesignated lists or the entire genome to find genes and markers that differentiate sarcoidosis from healthy controls, but only a few have compared sarcoidosis patients based on disease phenotypes and organ involvement. The common gene pathways that have been repeatedly identified include those related to the interferon response, T-cell receptor signaling, and the major histocompatibility complex. SUMMARY While the molecular profiling studies to date offer the ability to compare sarcoidosis and health as well as across tissues, further longitudinal studies that include sarcoidosis patients with varying outcomes with respect to organ involvement and response to treatment are needed to identify clinically important phenotypes in the disease that can then be differentiated based on molecular features.
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Affiliation(s)
- Nicholas K. Arger
- University of California, San Francisco, Division of Pulmonary and Critical Care, 505 Parnassus Ave, San Francisco, CA 94143, USA
| | - Brian O’Connor
- National Jewish Health, Center for Genes, Environment, & Health, 1400 Jackson St, Denver, CO 80206, USA
| | - Laura L. Koth
- University of California, San Francisco, Division of Pulmonary and Critical Care, 505 Parnassus Ave, San Francisco, CA 94143, USA
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36
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Zinter MS, Dvorak CC, Mayday MY, Iwanaga K, Ly NP, McGarry ME, Church GD, Faricy LE, Rowan CM, Hume JR, Steiner ME, Crawford ED, Langelier C, Kalantar K, Chow ED, Miller S, Shimano K, Melton A, Yanik GA, Sapru A, DeRisi JL. Pulmonary Metagenomic Sequencing Suggests Missed Infections in Immunocompromised Children. Clin Infect Dis 2020; 68:1847-1855. [PMID: 30239621 PMCID: PMC6784263 DOI: 10.1093/cid/ciy802] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 09/13/2018] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Despite improved diagnostics, pulmonary pathogens in immunocompromised children frequently evade detection, leading to significant mortality. Therefore, we aimed to develop a highly sensitive metagenomic next-generation sequencing (mNGS) assay capable of evaluating the pulmonary microbiome and identifying diverse pathogens in the lungs of immunocompromised children. METHODS We collected 41 lower respiratory specimens from 34 immunocompromised children undergoing evaluation for pulmonary disease at 3 children's hospitals from 2014-2016. Samples underwent mechanical homogenization, parallel RNA/DNA extraction, and metagenomic sequencing. Sequencing reads were aligned to the National Center for Biotechnology Information nucleotide reference database to determine taxonomic identities. Statistical outliers were determined based on abundance within each sample and relative to other samples in the cohort. RESULTS We identified a rich cross-domain pulmonary microbiome that contained bacteria, fungi, RNA viruses, and DNA viruses in each patient. Potentially pathogenic bacteria were ubiquitous among samples but could be distinguished as possible causes of disease by parsing for outlier organisms. Samples with bacterial outliers had significantly depressed alpha-diversity (median, 0.61; interquartile range [IQR], 0.33-0.72 vs median, 0.96; IQR, 0.94-0.96; P < .001). Potential pathogens were detected in half of samples previously negative by clinical diagnostics, demonstrating increased sensitivity for missed pulmonary pathogens (P < .001). CONCLUSIONS An optimized mNGS assay for pulmonary microbes demonstrates significant inoculation of the lower airways of immunocompromised children with diverse bacteria, fungi, and viruses. Potential pathogens can be identified based on absolute and relative abundance. Ongoing investigation is needed to determine the pathogenic significance of outlier microbes in the lungs of immunocompromised children with pulmonary disease.
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Affiliation(s)
- Matt S Zinter
- Division of Critical Care, University of California, San Francisco School of Medicine
| | - Christopher C Dvorak
- Division of Allergy, Immunology, and Blood & Marrow Transplantation, University of California, San Francisco School of Medicine
| | - Madeline Y Mayday
- Division of Critical Care, University of California, San Francisco School of Medicine
| | - Kensho Iwanaga
- Division of Pulmonology, Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco School of Medicine
| | - Ngoc P Ly
- Division of Pulmonology, Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco School of Medicine
| | - Meghan E McGarry
- Division of Pulmonology, Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco School of Medicine
| | - Gwynne D Church
- Division of Pulmonology, Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco School of Medicine
| | - Lauren E Faricy
- Division of Pulmonology, Department of Pediatrics, University of Vermont School of Medicine, Burlington
| | - Courtney M Rowan
- Division of Critical Care, Department of Pediatrics, Riley Hospital for Children, Indiana University School of Medicine, Indianapolis
| | - Janet R Hume
- Division of Critical Care, University of Minnesota School of Medicine, Minneapolis
| | - Marie E Steiner
- Division of Critical Care, University of Minnesota School of Medicine, Minneapolis.,Hematology/Oncology, Department of Pediatrics, Masonic Children's Hospital, University of Minnesota School of Medicine, Minneapolis
| | - Emily D Crawford
- Chan Zuckerberg Biohub, University of California-San Francisco School of Medicine.,Department of Biochemistry & Biophysics, University of California-San Francisco School of Medicine
| | - Charles Langelier
- Division of Infectious Diseases, Department of Internal Medicine, University of California-San Francisco School of Medicine
| | - Katrina Kalantar
- Department of Biochemistry & Biophysics, University of California-San Francisco School of Medicine
| | - Eric D Chow
- Department of Biochemistry & Biophysics, University of California-San Francisco School of Medicine
| | - Steve Miller
- Department of Laboratory Medicine, University of California-San Francisco School of Medicine
| | - Kristen Shimano
- Division of Allergy, Immunology, and Blood & Marrow Transplantation, University of California, San Francisco School of Medicine
| | - Alexis Melton
- Division of Allergy, Immunology, and Blood & Marrow Transplantation, University of California, San Francisco School of Medicine
| | - Gregory A Yanik
- Division of Oncology, Department of Pediatrics, Motts Children's Hospital, University of Michigan School of Medicine, Ann Arbor
| | - Anil Sapru
- Division of Critical Care, University of California, San Francisco School of Medicine.,Division of Critical Care, Department of Pediatrics, Mattel Children's Hospital, University of California-Los Angeles, Geffen School of Medicine
| | - Joseph L DeRisi
- Chan Zuckerberg Biohub, University of California-San Francisco School of Medicine.,Department of Biochemistry & Biophysics, University of California-San Francisco School of Medicine
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37
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Sulaiman I, Schuster S, Segal LN. Perspectives in lung microbiome research. Curr Opin Microbiol 2020; 56:24-29. [PMID: 32623064 DOI: 10.1016/j.mib.2020.06.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 05/05/2020] [Accepted: 06/01/2020] [Indexed: 12/18/2022]
Abstract
Our understanding of the existence and role of the lung microbiome has grown at a slower pace than other microbiome research areas. This is likely a consequence of the original dogma that the lung was a sterile environment although there are other barriers that are worth discussing. Here we will not be conducting an exhaustive review of the current literature on the lung microbiome, but rather we will focus on what we see as some important challenges that the field needs to face in order to improve our mechanistic understanding of the lung microbiome and its role on human health.
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Affiliation(s)
- Imran Sulaiman
- Division of Pulmonary, Critical Care, & Sleep Medicine, Department of Medicine, New York University School of Medicine, NY, United States
| | - Sheeja Schuster
- Division of Pulmonary, Critical Care, & Sleep Medicine, Department of Medicine, New York University School of Medicine, NY, United States
| | - Leopoldo N Segal
- Division of Pulmonary, Critical Care, & Sleep Medicine, Department of Medicine, New York University School of Medicine, NY, United States.
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38
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Abstract
Sarcoidosis is a multisystem granulomatous disease that may affect any body organ. Sarcoidosis is associated with many environmental and occupational exposures. Because the exact immunopathogenesis of sarcoidosis is unknown, it is not known whether these exposures are truly causing sarcoidosis, rendering the immune system more susceptible to the development of sarcoidosis, exacerbating subclinical cases of sarcoidosis, or causing a granulomatous condition distinct from sarcoidosis. This manuscript outlines what is known about the immunopathogenesis of sarcoidosis and postulates mechanisms whereby these exposures could cause or exacerbate the disease. We also describe the varied environmental and occupational exposures that have been associated with sarcoidosis. This includes potential infectious exposures such as mycobacteria and Propionibacterium acnes, a skin commensal bacterium, as well as non-infectious environmental exposures including inhaled bioaerosols, metal dusts and products of combustion. Further insights concerning the relationship of environmental exposures to the development of sarcoidosis may have a major impact on the prevention and treatment of this enigmatic disease.
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39
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Fukui S, Morimoto S, Ichinose K, Nakashima S, Ishimoto H, Hara A, Kakugawa T, Sakamoto N, Tsuji Y, Aramaki T, Koga T, Kawashiri SY, Iwamoto N, Tamai M, Nakamura H, Origuchi T, Ueki Y, Suzuki S, Mukae H, Kawakami A. Comparison of lung microbiota between antineutrophil cytoplasmic antibody-associated vasculitis and sarcoidosis. Sci Rep 2020; 10:9466. [PMID: 32528054 PMCID: PMC7289840 DOI: 10.1038/s41598-020-66178-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Accepted: 05/14/2020] [Indexed: 12/13/2022] Open
Abstract
Microbial involvement in the pathogenesis have been suggested in both antineutrophil cytoplasmic antibody-associated vasculitis (AAV) and sarcoidosis, both of which have lung involvement. However, exhaustive research to assess the bacteria in the lung in AAV and in sarcoidosis have not been performed. We sought to elucidate the distinct dysbiotic lung microbiota between AAV and sarcoidosis. We used 16S rRNA gene high-throughput sequencing to obtain the bacterial community composition of bronchoalveolar lavage fluid (BALF) in patients with AAV (n = 16) compared to patients with sarcoidosis (n = 21). The patients had not undergone therapy with immunosuppressive medication when their BALF was acquired. No difference was observed in α-diversity between patients with AAV and patients with sarcoidosis when using all the detected taxa. We defined the taxa of the oral cavity by using the data of oral microbiota of healthy individuals from the Human Microbiome Project (HMP). The analysis using only oral taxa made the difference in α-diversity between AAV and sarcoidosis clearer compared with those using all the detected taxa. Besides, the analysis using detected taxa except for oral taxa also made the difference in α-diversity between AAV and sarcoidosis clearer compared with those using all the detected taxa. A linear negative relationship between the α-diversity and Birmingham vasculitis activity score (BVAS) was detected in the AAV group. The observed p-value for the effect of the disease groups on the ß-diversity was small while the effect of other factors including sex and smoking status did not have small p-values. By excluding oral taxa from all the detected taxa, we found a cluster mainly consisted of sarcoidosis patients which was characterized with microbial community monopolized by Erythrobacteraceae family. Our results suggested the importance of considering the influence of oral microbiota in evaluating lung microbiota.
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Affiliation(s)
- Shoichi Fukui
- Department of Immunology and Rheumatology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
- Department of Community Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Shimpei Morimoto
- Innovation Platform & Office for Precision Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Kunihiro Ichinose
- Department of Immunology and Rheumatology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan.
| | - Shota Nakashima
- Department of Respiratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Hiroshi Ishimoto
- Department of Respiratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Atsuko Hara
- Department of Respiratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Tomoyuki Kakugawa
- Department of Respiratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Noriho Sakamoto
- Department of Respiratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Yoshika Tsuji
- Rheumatic and Collagen Disease Center, Sasebo Chuo Hospital, Sasebo, Japan
| | - Toshiyuki Aramaki
- Rheumatic and Collagen Disease Center, Sasebo Chuo Hospital, Sasebo, Japan
| | - Tomohiro Koga
- Department of Immunology and Rheumatology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
- Center for Bioinformatics and Molecular Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Shin-Ya Kawashiri
- Department of Immunology and Rheumatology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
- Department of Community Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Naoki Iwamoto
- Department of Immunology and Rheumatology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Mami Tamai
- Department of Immunology and Rheumatology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Hideki Nakamura
- Department of Immunology and Rheumatology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Tomoki Origuchi
- Department of Immunology and Rheumatology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
- Department of Rehabilitation Sciences, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Yukitaka Ueki
- Rheumatic and Collagen Disease Center, Sasebo Chuo Hospital, Sasebo, Japan
| | - Shino Suzuki
- Kochi Institute for Core Sample Research, X-star, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Japan
| | - Hiroshi Mukae
- Department of Respiratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Atsushi Kawakami
- Department of Immunology and Rheumatology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
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40
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Sgalla G, Kulkarni T, Antin-Ozerkis D, Thannickal VJ, Richeldi L. Update in Pulmonary Fibrosis 2018. Am J Respir Crit Care Med 2020; 200:292-300. [PMID: 31022351 DOI: 10.1164/rccm.201903-0542up] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Affiliation(s)
- Giacomo Sgalla
- 1Fondazione Policlinico Universitario A. Gemelli IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Tejaswini Kulkarni
- 2Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama; and
| | - Danielle Antin-Ozerkis
- 3Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, Connecticut
| | - Victor J Thannickal
- 2Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama; and
| | - Luca Richeldi
- 1Fondazione Policlinico Universitario A. Gemelli IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy
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Redondoviridae, a Family of Small, Circular DNA Viruses of the Human Oro-Respiratory Tract Associated with Periodontitis and Critical Illness. Cell Host Microbe 2019; 25:719-729.e4. [PMID: 31071295 DOI: 10.1016/j.chom.2019.04.001] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 01/24/2019] [Accepted: 04/01/2019] [Indexed: 12/21/2022]
Abstract
The global virome is largely uncharacterized but is now being unveiled by metagenomic DNA sequencing. Exploring the human respiratory virome, in particular, can provide insights into oro-respiratory diseases. Here, we use metagenomics to identify a family of small circular DNA viruses-named Redondoviridae-associated with human diseases. We first identified two redondovirus genomes from bronchoalveolar lavage samples from human lung donors. We then queried thousands of metagenomic samples and recovered 17 additional complete redondovirus genomes. Detections were exclusively in human samples and mostly from respiratory tract and oro-pharyngeal sites, where Redondoviridae was the second most prevalent eukaryotic DNA virus family. Redondovirus sequences were associated with periodontal disease, and abundances decreased with treatment. Some critically ill patients in a medical intensive care unit were found to harbor high levels of redondoviruses in respiratory samples. These results suggest that redondoviruses colonize human oro-respiratory sites and can bloom in several human disorders.
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Inaoka PT, Shono M, Kamada M, Espinoza JL. Host-microbe interactions in the pathogenesis and clinical course of sarcoidosis. J Biomed Sci 2019; 26:45. [PMID: 31182092 PMCID: PMC6558716 DOI: 10.1186/s12929-019-0537-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 05/22/2019] [Indexed: 12/27/2022] Open
Abstract
Sarcoidosis is a rare inflammatory disease characterized by the development of granulomas in various organs, especially in the lungs and lymph nodes. Clinics of the disease largely depends on the organ involved and may range from mild symptoms to life threatening manifestations. Over the last two decades, significant advances in the diagnosis, clinical assessment and treatment of sarcoidosis have been achieved, however, the precise etiology of this disease remains unknown. Current evidence suggests that, in genetically predisposed individuals, an excessive immune response to unknown antigen/s is crucial for the development of sarcoidosis. Epidemiological and microbiological studies suggest that, at least in a fraction of patients, microbes or their products may trigger the immune response leading to sarcoid granuloma formation. In this article, we discuss the scientific evidence on the interaction of microbes with immune cells that may be implicated in the immunopathogenesis of sarcoidosis, and highlight recent studies exploring potential implications of human microbiota in the pathogenesis and the clinical course of sarcoidosis.
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Affiliation(s)
- Pleiades T Inaoka
- Department of Physical Therapy, School of Health Sciences, Kanazawa University, Kodatsuno, Kanazawa, 577-8502, Japan
| | - Masato Shono
- Faculty of Medicine, Kindai University, 377-2, Ohno-Higashi, Osaka-Sayama, Osaka, 577-8502, Japan
| | - Mishio Kamada
- Faculty of Medicine, Kindai University, 377-2, Ohno-Higashi, Osaka-Sayama, Osaka, 577-8502, Japan
| | - J Luis Espinoza
- Department of Hematology and Rheumatology, Kindai University Faculty of Medicine, 377-2, Ohno-Higashi, Osaka-Sayama, Osaka, 577-8502, Japan.
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McGinniss JE, Imai I, Simon-Soro A, Brown MC, Knecht VR, Frye L, Ravindran PM, Dothard MI, Wadell DA, Sohn MB, Li H, Christie JD, Diamond JM, Haas AR, Lanfranco AR, DiBardino DM, Bushman FD, Collman RG. Molecular analysis of the endobronchial stent microbial biofilm reveals bacterial communities that associate with stent material and frequent fungal constituents. PLoS One 2019; 14:e0217306. [PMID: 31141557 PMCID: PMC6541290 DOI: 10.1371/journal.pone.0217306] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 05/08/2019] [Indexed: 12/19/2022] Open
Abstract
Endobronchial stents are increasingly used to treat airway complications in multiple conditions including lung transplantation but little is known about the biofilms that form on these devices. We applied deep sequencing to profile luminal biofilms of 46 endobronchial stents removed from 20 subjects primarily with lung transplantation-associated airway compromise. Microbial communities were analyzed by bacterial 16S rRNA and fungal ITS marker gene sequencing. Corynebacterium was the most common bacterial taxa across biofilm communities. Clustering analysis revealed three bacterial biofilm types: one low diversity and dominated by Corynebacterium; another was polymicrobial and characterized by Staphylococcus; and the third was polymicrobial and associated with Pseudomonas, Streptococcus, and Prevotella. Biofilm type was significantly correlated with stent material: covered metal with the Staphylococcus-type biofilm, silicone with the Corynebacterium-dominated biofilm, and uncovered metal with the polymicrobial biofilm. Subjects with sequential stents had frequent transitions between community types. Fungal analysis found Candida was most prevalent, Aspergillus was common and highly enriched in two of three stents associated with airway anastomotic dehiscence, and fungal taxa not typically considered pathogens were highly enriched in some stents. Thus, molecular analysis revealed a complex and dynamic endobronchial stent biofilm with three bacterial types that associate with stent material, a central role for Corynebacterium, and that both expected and unexpected fungi inhabit this unique niche. The current work provides a foundation for studies to investigate the relationship between stent biofilm composition and clinical outcomes, mechanisms of biofilm establishment, and strategies for improved stent technology and use in airway compromise.
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Affiliation(s)
- John E. McGinniss
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Ize Imai
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Aurea Simon-Soro
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Melanie C. Brown
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Vincent R. Knecht
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Laura Frye
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Priyanka M. Ravindran
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Marisol I. Dothard
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Dylan A. Wadell
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Michael B. Sohn
- Department of Epidemiology, Biostatistics and Informatics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Hongzhe Li
- Department of Epidemiology, Biostatistics and Informatics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Jason D. Christie
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Epidemiology, Biostatistics and Informatics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Joshua M. Diamond
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Andrew R. Haas
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Anthony R. Lanfranco
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - David M. DiBardino
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Frederic D. Bushman
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail: (RGC); (FDB)
| | - Ronald G. Collman
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail: (RGC); (FDB)
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Abbas AA, Young JC, Clarke EL, Diamond JM, Imai I, Haas AR, Cantu E, Lederer DJ, Meyer K, Milewski RK, Olthoff KM, Shaked A, Christie JD, Bushman FD, Collman RG. Bidirectional transfer of Anelloviridae lineages between graft and host during lung transplantation. Am J Transplant 2019; 19:1086-1097. [PMID: 30203917 PMCID: PMC6411461 DOI: 10.1111/ajt.15116] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 09/05/2018] [Accepted: 09/05/2018] [Indexed: 01/25/2023]
Abstract
Solid organ transplantation disrupts virus-host relationships, potentially resulting in viral transfer from donor to recipient, reactivation of latent viruses, and new viral infections. Viral transfer, colonization, and reactivation are typically monitored using assays for specific viruses, leaving the behavior of full viral populations (the "virome") understudied. Here we sought to investigate the temporal behavior of viruses from donor lungs and transplant recipients comprehensively. We interrogated the bronchoalveolar lavage and blood viromes during the peritransplant period and 6-16 months posttransplant in 13 donor-recipient pairs using shotgun metagenomic sequencing. Anelloviridae, ubiquitous human commensal viruses, were the most abundant human viruses identified. Herpesviruses, parvoviruses, polyomaviruses, and bacteriophages were also detected. Anelloviridae populations were complex, with some donor organs and hosts harboring multiple contemporaneous lineages. We identified transfer of Anelloviridae lineages from donor organ to recipient serum in 4 of 7 cases that could be queried, and immigration of lineages from recipient serum into the allograft in 6 of 10 such cases. Thus, metagenomic analyses revealed that viral populations move between graft and host in both directions, showing that organ transplantation involves implantation of both the allograft and commensal viral communities.
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Affiliation(s)
- A. A. Abbas
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - J. C. Young
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - E. L. Clarke
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - J. M. Diamond
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA,Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - I Imai
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - A. R. Haas
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - E. Cantu
- Department of Surgery, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - D. J. Lederer
- Departments of Medicine and Epidemiology, College of Physicians and Surgeons, Columbia University, New York, NY
| | - K. Meyer
- School of Medicine and Public Health, University of Wisconsin, Madison, WI
| | - R. K. Milewski
- Department of Surgery, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - K. M. Olthoff
- Department of Surgery, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - A. Shaked
- Department of Surgery, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - J. D. Christie
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA,Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - F. D. Bushman
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - R. G. Collman
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA,Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
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Clarke EL, Taylor LJ, Zhao C, Connell A, Lee JJ, Fett B, Bushman FD, Bittinger K. Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments. MICROBIOME 2019; 7:46. [PMID: 30902113 PMCID: PMC6429786 DOI: 10.1186/s40168-019-0658-x] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 03/11/2019] [Indexed: 05/25/2023]
Abstract
BACKGROUND Analysis of mixed microbial communities using metagenomic sequencing experiments requires multiple preprocessing and analytical steps to interpret the microbial and genetic composition of samples. Analytical steps include quality control, adapter trimming, host decontamination, metagenomic classification, read assembly, and alignment to reference genomes. RESULTS We present a modular and user-extensible pipeline called Sunbeam that performs these steps in a consistent and reproducible fashion. It can be installed in a single step, does not require administrative access to the host computer system, and can work with most cluster computing frameworks. We also introduce Komplexity, a software tool to eliminate potentially problematic, low-complexity nucleotide sequences from metagenomic data. A unique component of the Sunbeam pipeline is an easy-to-use extension framework that enables users to add custom processing or analysis steps directly to the workflow. The pipeline and its extension framework are well documented, in routine use, and regularly updated. CONCLUSIONS Sunbeam provides a foundation to build more in-depth analyses and to enable comparisons in metagenomic sequencing experiments by removing problematic, low-complexity reads and standardizing post-processing and analytical steps. Sunbeam is written in Python using the Snakemake workflow management software and is freely available at github.com/sunbeam-labs/sunbeam under the GPLv3.
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Affiliation(s)
- Erik L. Clarke
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Louis J. Taylor
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Chunyu Zhao
- Division of Gastroenterology, Hepatology and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Andrew Connell
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Jung-Jin Lee
- Division of Gastroenterology, Hepatology and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Bryton Fett
- Division of Gastroenterology, Hepatology and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Frederic D. Bushman
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
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46
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The composition of the pulmonary microbiota in sarcoidosis - an observational study. Respir Res 2019; 20:46. [PMID: 30819175 PMCID: PMC6396534 DOI: 10.1186/s12931-019-1013-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 02/20/2019] [Indexed: 12/27/2022] Open
Abstract
Background Sarcoidosis is a systemic disease of unknown etiology. The disease mechanisms are largely speculative and may include the role microbial patterns that initiate and drive an underlying immune process. The aim of this study was to characterize the microbiota of the lung of patients with sarcoidosis and compare its composition and diversity with the results from patients with other interstitial lung disease (ILD) and historic healthy controls. Methods Patients (sarcoidosis, n = 31; interstitial lung disease, n = 19) were recruited within the PULMOHOM study, a prospective cohort study to characterize inflammatory processes in pulmonary diseases. Bronchoscopy of the middle lobe or the lingula was performed and the recovered fluid was immediately sent for analysis of the pulmonary microbiota by 16sRNA gene sequencing. Subsequent bioinformatic analysis was performed to compare the groups. Results There were no significant differences between patients with sarcoidosis or other ILDs with regard to microbiome composition and diversity. In addition, the abundance of the genera Atopobium, Fusobacterium, Mycobacterium or Propionibacterium were not different between the two groups. There were no gross differences to historical healthy controls. Conclusion The analysis of the pulmonary microbiota based on 16sRNA gene sequencing did not show a significant dysbiosis in patients with sarcoidosis as compared to other ILD patients. These data do not exclude a microbiological component in the pathogenesis of sarcoidosis. Electronic supplementary material The online version of this article (10.1186/s12931-019-1013-2) contains supplementary material, which is available to authorized users.
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47
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Ramos-Casals M, Retamozo S, Sisó-Almirall A, Pérez-Alvarez R, Pallarés L, Brito-Zerón P. Clinically-useful serum biomarkers for diagnosis and prognosis of sarcoidosis. Expert Rev Clin Immunol 2019; 15:391-405. [DOI: 10.1080/1744666x.2019.1568240] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Manuel Ramos-Casals
- Laboratory of Autoimmune Diseases Josep Font, IDIBAPS-CELLEX, Department of Autoimmune Diseases, ICMiD, Hospital Clínic, Barcelona, Spain
- SarcoGEAS-SEMI Study Group, Study Group of Autoimmune Diseases (GEAS), Spanish Society of Internal Medicine (SEMI), Spain
| | - Soledad Retamozo
- Laboratory of Autoimmune Diseases Josep Font, IDIBAPS-CELLEX, Department of Autoimmune Diseases, ICMiD, Hospital Clínic, Barcelona, Spain
- Rheumatology Unit, Instituto Modelo de Cardiología Privado S.R.L, Córdoba, Argentina
- Rheumatology Unit, Instituto Universitario de Ciencias Biomédicas de Córdoba (IUCBC), Córdoba, Argentina
- Instituto De Investigaciones En Ciencias De La Salud (INICSA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba, Argentina
| | - Antoni Sisó-Almirall
- Centre d’Assistència Primària ABS Les Corts, CAPSBE, Barcelona, Spain
- Primary Healthcare Transversal Research Group, IDIBAPS, Barcelona, Spain
| | - Roberto Pérez-Alvarez
- SarcoGEAS-SEMI Study Group, Study Group of Autoimmune Diseases (GEAS), Spanish Society of Internal Medicine (SEMI), Spain
- Department of Internal Medicine, Hospital Alvaro Cunqueiro, Vigo, Spain
| | - Lucio Pallarés
- SarcoGEAS-SEMI Study Group, Study Group of Autoimmune Diseases (GEAS), Spanish Society of Internal Medicine (SEMI), Spain
- Systemic Autoimmune Diseases Uni, Department of Internal Medicine, Hospital de Son Espases, Palma de Mallorca, Spain
| | - Pilar Brito-Zerón
- Laboratory of Autoimmune Diseases Josep Font, IDIBAPS-CELLEX, Department of Autoimmune Diseases, ICMiD, Hospital Clínic, Barcelona, Spain
- SarcoGEAS-SEMI Study Group, Study Group of Autoimmune Diseases (GEAS), Spanish Society of Internal Medicine (SEMI), Spain
- Autoimmune Diseases Unit, Department of Medicine, Hospital CIMA, Sanitas, Spain
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48
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Clarke EL, Connell AJ, Six E, Kadry NA, Abbas AA, Hwang Y, Everett JK, Hofstaedter CE, Marsh R, Armant M, Kelsen J, Notarangelo LD, Collman RG, Hacein-Bey-Abina S, Kohn DB, Cavazzana M, Fischer A, Williams DA, Pai SY, Bushman FD. T cell dynamics and response of the microbiota after gene therapy to treat X-linked severe combined immunodeficiency. Genome Med 2018; 10:70. [PMID: 30261899 PMCID: PMC6161392 DOI: 10.1186/s13073-018-0580-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 09/04/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Mutation of the IL2RG gene results in a form of severe combined immune deficiency (SCID-X1), which has been treated successfully with hematopoietic stem cell gene therapy. SCID-X1 gene therapy results in reconstitution of the previously lacking T cell compartment, allowing analysis of the roles of T cell immunity in humans by comparing before and after gene correction. METHODS Here we interrogate T cell reconstitution using four forms of high throughput analysis. (1) Estimation of the numbers of transduced progenitor cells by monitoring unique positions of integration of the therapeutic gene transfer vector. (2) Estimation of T cell population structure by sequencing of the recombined T cell receptor (TCR) beta locus. (3) Metagenomic analysis of microbial populations in oropharyngeal, nasopharyngeal, and gut samples. (4) Metagenomic analysis of viral populations in gut samples. RESULTS Comparison of progenitor and mature T cell populations allowed estimation of a minimum number of cell divisions needed to generate the observed populations. Analysis of microbial populations showed the effects of immune reconstitution, including normalization of gut microbiota and clearance of viral infections. Metagenomic analysis revealed enrichment of genes for antibiotic resistance in gene-corrected subjects relative to healthy controls, likely a result of higher healthcare exposure. CONCLUSIONS This multi-omic approach enables the characterization of multiple effects of SCID-X1 gene therapy, including T cell repertoire reconstitution, estimation of numbers of cell divisions between progenitors and daughter T cells, normalization of the microbiome, clearance of microbial pathogens, and modulations in antibiotic resistance gene levels. Together, these results quantify several aspects of the long-term efficacy of gene therapy for SCID-X1. This study includes data from ClinicalTrials.gov numbers NCT01410019, NCT01175239, and NCT01129544.
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Affiliation(s)
- Erik L Clarke
- Department of Microbiology, University of Pennsylvania School of Medicine, 3610 Hamilton Walk, Philadelphia, PA, 19104-6076, USA
| | - A Jesse Connell
- Department of Microbiology, University of Pennsylvania School of Medicine, 3610 Hamilton Walk, Philadelphia, PA, 19104-6076, USA
| | - Emmanuelle Six
- Imagine Institute, Paris Descartes-Sorbonne Paris Cité University, Paris, France
- Laboratory of Human Lymphohematopoiesis, INSERM UMR 1163, Paris, France
| | - Nadia A Kadry
- Department of Microbiology, University of Pennsylvania School of Medicine, 3610 Hamilton Walk, Philadelphia, PA, 19104-6076, USA
| | - Arwa A Abbas
- Department of Microbiology, University of Pennsylvania School of Medicine, 3610 Hamilton Walk, Philadelphia, PA, 19104-6076, USA
| | - Young Hwang
- Department of Microbiology, University of Pennsylvania School of Medicine, 3610 Hamilton Walk, Philadelphia, PA, 19104-6076, USA
| | - John K Everett
- Department of Microbiology, University of Pennsylvania School of Medicine, 3610 Hamilton Walk, Philadelphia, PA, 19104-6076, USA
| | - Casey E Hofstaedter
- Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Rebecca Marsh
- Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229-3039, USA
| | - Myriam Armant
- Boston Children's Hospital, Karp 08125.3, 300 Longwood Avenue, Boston, MA, 02115, USA
| | - Judith Kelsen
- Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Luigi D Notarangelo
- Laboratory of Host Defenses, Laboratory of Clinical Infectious Diseases, Immune Deficiency Genetics Section, NIAID, NIH, Bethesda, MD, USA
| | - Ronald G Collman
- Department of Medicine, University of Pennsylvania School of Medicine, 3610 Hamilton Walk, Philadelphia, PA, 19104-6076, USA
| | - Salima Hacein-Bey-Abina
- Clinical Immunology Laboratory, Groupe Hospitalier Universitaire Paris-Sud, Hôpital Kremlin-Bicêtre, Assistance Publique-Hôpitaux de Paris, 78, r. du Général-Leclerc, 94270, Le-Kremlin-Bicêtre, France
- UTCBS CNRS UMR 8258, INSERM U1022, Faculté de Pharmacie de Paris, Université Paris Descartes, Sorbonne Paris Cité, Chimie Paris-Tech, 4 av. de l'observatoire, 75006, Paris, France
| | - Donald B Kohn
- Departments of Microbiology, Immunology & Molecular Genetics; and Pediatrics, University of California, Los Angeles, USA
| | - Marina Cavazzana
- Imagine Institute, Paris Descartes-Sorbonne Paris Cité University, Paris, France
- Laboratory of Human Lymphohematopoiesis, INSERM UMR 1163, Paris, France
- Biotherapy Department, Necker Children's Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
- Biotherapy Clinical Investigation Center, Groupe Hospitalier Universitaire Ouest, Assistance Publique-Hôpitaux de Paris, INSERM, Paris, France
| | - Alain Fischer
- Imagine Institute, Paris Descartes-Sorbonne Paris Cité University, Paris, France
- Laboratory of Human Lymphohematopoiesis, INSERM UMR 1163, Paris, France
- Pediatric Hemato-Immunology Department, Necker Children's Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
- Collège de France, Paris, France
| | - David A Williams
- Boston Children's Hospital, Karp 08125.3, 300 Longwood Avenue, Boston, MA, 02115, USA
- Havard Stem Cell Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Sung-Yun Pai
- Boston Children's Hospital, Karp 08125.3, 300 Longwood Avenue, Boston, MA, 02115, USA
| | - Frederic D Bushman
- Department of Microbiology, University of Pennsylvania School of Medicine, 3610 Hamilton Walk, Philadelphia, PA, 19104-6076, USA.
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49
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Dickson RP. Turning "Sarkoid" into "Dropsy". A Valiant, Next-Generation Attempt. Am J Respir Crit Care Med 2018; 197:154-155. [PMID: 28930643 PMCID: PMC5768908 DOI: 10.1164/rccm.201709-1843ed] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Robert P Dickson
- 1 Department of Internal Medicine and
- 2 Michigan Center for Integrative Research in Critical Care University of Michigan Ann Arbor, Michigan
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50
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van Moorsel CHM. To progress understanding of disease triggers and modifiers in sarcoidosis, stratification is the key. Eur Respir J 2017; 50:50/6/1702002. [PMID: 29242265 DOI: 10.1183/13993003.02002-2017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 11/03/2017] [Indexed: 12/26/2022]
Affiliation(s)
- Coline H M van Moorsel
- Interstitial Lung Diseases Center of Excellence, Dept of Pulmonology, St. Antonius Hospital, Nieuwegein, The Netherlands
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