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Yang J, Li J, Zhang L, Shen Z, Xiao Y, Zhang G, Chen M, Chen F, Liu L, Wang Y, Chen L, Wang X, Zhang L, Wang L, Wang Z, Wang J, Li M, Ren L. Highly diverse sputum microbiota correlates with the disease severity in patients with community-acquired pneumonia: a longitudinal cohort study. Respir Res 2024; 25:223. [PMID: 38811936 DOI: 10.1186/s12931-024-02821-2] [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: 01/17/2024] [Accepted: 04/24/2024] [Indexed: 05/31/2024] Open
Abstract
BACKGROUND Community-acquired pneumonia (CAP) is a common and serious condition that can be caused by a variety of pathogens. However, much remains unknown about how these pathogens interact with the lower respiratory commensals, and whether any correlation exists between the dysbiosis of the lower respiratory microbiota and disease severity and prognosis. METHODS We conducted a retrospective cohort study to investigate the composition and dynamics of sputum microbiota in patients diagnosed with CAP. In total, 917 sputum specimens were collected consecutively from 350 CAP inpatients enrolled in six hospitals following admission. The V3-V4 region of the 16 S rRNA gene was then sequenced. RESULTS The sputum microbiota in 71% of the samples were predominately composed of respiratory commensals. Conversely, 15% of the samples demonstrated dominance by five opportunistic pathogens. Additionally, 5% of the samples exhibited sterility, resembling the composition of negative controls. Compared to non-severe CAP patients, severe cases exhibited a more disrupted sputum microbiota, characterized by the highly dominant presence of potential pathogens, greater deviation from a healthy state, more significant alterations during hospitalization, and sparser bacterial interactions. The sputum microbiota on admission demonstrated a moderate prediction of disease severity (AUC = 0.74). Furthermore, different pathogenic infections were associated with specific microbiota alterations. Acinetobacter and Pseudomonas were more abundant in influenza A infections, with Acinetobacter was also enriched in Klebsiella pneumoniae infections. CONCLUSION Collectively, our study demonstrated that pneumonia may not consistently correlate with severe dysbiosis of the respiratory microbiota. Instead, the degree of microbiota dysbiosis was correlated with disease severity in CAP patients.
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Affiliation(s)
- Jing Yang
- Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Changping Laboratory, Beijing, 102206, China
| | - Jinman Li
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Linfeng Zhang
- Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zijie Shen
- Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yan Xiao
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
- State Key Laboratory of Respiratory Health and Multimorbidity, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Guoliang Zhang
- Shenzhen Third People's Hospital, Shenzhen, 518112, China
| | - Mingwei Chen
- The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Fuhui Chen
- The Second Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Ling Liu
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, School of Medicine, Zhongda Hospital, Southeast University, Nanjing, 210009, China
| | - Ying Wang
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Lan Chen
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Xinming Wang
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Li Zhang
- Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing, 100101, China
| | - Lu Wang
- Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing, 100101, China
| | - Zhang Wang
- Institute of Ecological Sciences, South China Normal University, Guangzhou, 510631, China
| | - Jianwei Wang
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
| | - Mingkun Li
- Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Lili Ren
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
- State Key Laboratory of Respiratory Health and Multimorbidity, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
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Mink S, Reimann P, Fraunberger P. Prognostic value of anti-SARS-CoV-2 antibodies: a systematic review. Clin Chem Lab Med 2024; 62:1029-1043. [PMID: 38349073 DOI: 10.1515/cclm-2023-1487] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 02/02/2024] [Indexed: 04/30/2024]
Abstract
OBJECTIVES Globally, over 772 million cases of COVID-19 have been reported. New variants of interest with corresponding spikes in case numbers continue to be identified. Vulnerable patients, including older adults or patients with severe comorbidities, continue to be at risk. A large body of evidence has been accumulated regarding anti-SARS-CoV-2-antibodies and COVID-19 but the usefulness of antibody measurements remains unclear. This systematic review aims to assess the prognostic value of anti-SARS-CoV-2-antibodies and their usefulness for guiding booster vaccinations. METHODS Studies in English and published between January 2020 and October 2023 were included. Studies that relied on multiparameter-models or comprised fewer than 100 participants were excluded. PubMed and via the WHO COVID-19 research database, Embase and Medline databases were searched. Study selection and quality assessment was conducted independently by two researchers. RESULTS After screening 1,160 studies, 33 studies comprising >30 million individuals were included. Anti-SARS-CoV-2-antibodies were strongly associated with reduced risk of SARS-CoV-2-infection and better outcomes, including mortality. Risk of infection and COVID-19 severity decreased with increasing antibody levels. CONCLUSIONS Anti-SARS-CoV-2-antibodies are useful for early identification of high-risk patients and timely adjustment of therapy. Protective thresholds may be applied to advise booster vaccinations but verification in separate cohorts is required.
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Affiliation(s)
- Sylvia Mink
- Central Medical Laboratories, Feldkirch, Austria
- Private University in the Principality of Liechtenstein, Triesen, Principality of Liechtenstein
| | - Patrick Reimann
- Private University in the Principality of Liechtenstein, Triesen, Principality of Liechtenstein
- Department of Internal Medicine, Academic Teaching Hospital Feldkirch, Feldkirch, Austria
| | - Peter Fraunberger
- Central Medical Laboratories, Feldkirch, Austria
- Private University in the Principality of Liechtenstein, Triesen, Principality of Liechtenstein
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3
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Shi FS, Xie YH, Yang YL, Xu LD, Li JJ, Wang X, Zhu LY, Wang WW, Shen PL, Huang YW, Li XQ. Fucoidan from Ascophyllum nodosum and Undaria pinnatifida attenuate SARS-CoV-2 infection in vitro and in vivo by suppressing ACE2 and alleviating inflammation. Carbohydr Polym 2024; 332:121884. [PMID: 38431405 DOI: 10.1016/j.carbpol.2024.121884] [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: 09/11/2023] [Revised: 01/21/2024] [Accepted: 01/26/2024] [Indexed: 03/05/2024]
Abstract
The global healthcare challenge posed by COVID-19 necessitates the continuous exploration for novel antiviral agents. Fucoidans have demonstrated antiviral activity. However, the underlying structure-activity mechanism responsible for the inhibitory activity of fucoidans from Ascophyllum nodosum (FUCA) and Undaria pinnatifida (FUCU) against SARS-CoV-2 remains unclear. FUCA was characterized as a homopolymer with a backbone structure of repeating (1 → 3) and (1 → 4) linked α-l-fucopyranose residues, whereas FUCU was a heteropolysaccharide composed of Fuc1-3Gal1-6 repeats. Furthermore, FUCA demonstrated significantly higher anti-SARS-CoV-2 activity than FUCU (EC50: 48.66 vs 69.52 μg/mL), suggesting the degree of branching rather than sulfate content affected the antiviral activity. Additionally, FUCA exhibited a dose-dependent inhibitory effect on ACE2, surpassing the inhibitory activity of FUCU. In vitro, both FUCA and FUCU treatments downregulated the expression of pro-inflammatory cytokines (IL-6, IFN-α, IFN-γ, and TNF-α) and anti-inflammatory cytokines (IL-10 and IFN-β) induced by viral infection. In hamsters, FUCA demonstrated greater effectiveness in attenuating lung and gastrointestinal injury and reducing ACE2 expression, compared to FUCU. Analysis of the 16S rRNA gene sequencing revealed that only FUCU partially alleviated the gut microbiota dysbiosis caused by SARS-CoV-2. Consequently, our study provides a scientific basis for considering fucoidans as poteintial prophylactic food components against SARS-CoV-2.
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Affiliation(s)
- Fang-Shu Shi
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products and Institute of Food Sciences, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Department of Veterinary Medicine, Zhejiang University, Hangzhou 310028, China
| | - Yv-Hao Xie
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products and Institute of Food Sciences, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; College of Animal Science, Shanxi Agricultural University, Taigu 030801, China
| | - Yong-Le Yang
- Department of Veterinary Medicine, Zhejiang University, Hangzhou 310028, China
| | - Ling-Dong Xu
- Department of Veterinary Medicine, Zhejiang University, Hangzhou 310028, China
| | - Jin-Jun Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products and Institute of Food Sciences, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xin Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products and Institute of Food Sciences, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Li-Ying Zhu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products and Institute of Food Sciences, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Wei-Wei Wang
- College of Animal Science, Shanxi Agricultural University, Taigu 030801, China
| | - Pei-Li Shen
- State Key Laboratory of Marine Food Processing & Safety Control, Qingdao Bright Moon Seaweed Group Co., Ltd., Qingdao, Shandong, China
| | - Yao-Wei Huang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Department of Veterinary Medicine, Zhejiang University, Hangzhou 310028, China.
| | - Xiao-Qiong Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products and Institute of Food Sciences, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
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4
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Imbert S, Revers M, Enaud R, Orieux A, Camino A, Massri A, Villeneuve L, Carrié C, Petit L, Boyer A, Berger P, Gruson D, Delhaes L, Prével R. Lower airway microbiota compositions differ between influenza, COVID-19 and bacteria-related acute respiratory distress syndromes. Crit Care 2024; 28:133. [PMID: 38649970 PMCID: PMC11036773 DOI: 10.1186/s13054-024-04922-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 04/17/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND Acute respiratory distress syndrome (ARDS) is responsible for 400,000 deaths annually worldwide. Few improvements have been made despite five decades of research, partially because ARDS is a highly heterogeneous syndrome including various types of aetiologies. Lower airway microbiota is involved in chronic inflammatory diseases and recent data suggest that it could also play a role in ARDS. Nevertheless, whether the lower airway microbiota composition varies between the aetiologies of ARDS remain unknown. The aim of this study is to compare lower airway microbiota composition between ARDS aetiologies, i.e. pulmonary ARDS due to influenza, SARS-CoV-2 or bacterial infection. METHODS Consecutive ARDS patients according to Berlin's classification requiring invasive ventilation with PCR-confirmed influenza or SARS-CoV-2 infections and bacterial infections (> 105 CFU/mL on endotracheal aspirate) were included. Endotracheal aspirate was collected at admission, V3-V4 and ITS2 regions amplified by PCR, deep-sequencing performed on MiSeq sequencer (Illumina®) and data analysed using DADA2 pipeline. RESULTS Fifty-three patients were included, 24 COVID-19, 18 influenza, and 11 bacterial CAP-related ARDS. The lower airway bacteriobiota and mycobiota compositions (β-diversity) were dissimilar between the three groups (p = 0.05 and p = 0.01, respectively). The bacterial α-diversity was significantly lower in the bacterial CAP-related ARDS group compared to the COVID-19 ARDS group (p = 0.04). In contrast, influenza-related ARDS patients had higher lung mycobiota α-diversity than the COVID-19-related ARDS (p = 0 < 01). CONCLUSION Composition of lower airway microbiota (both microbiota and mycobiota) differs between influenza, COVID-19 and bacterial CAP-related ARDS. Future studies investigating the role of lung microbiota in ARDS pathophysiology should take aetiology into account.
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Affiliation(s)
- Sébastien Imbert
- HU Bordeaux, Mycology-Parasitology Department, CIC 1401, 33000, Bordeaux, France
- Centre de Recherche Cardio-Thoracique de Bordeaux, Inserm UMR 1045, Univ Bordeaux, 33000, Bordeaux, France
| | - Mathilde Revers
- HU Bordeaux, Mycology-Parasitology Department, CIC 1401, 33000, Bordeaux, France
- Centre de Recherche Cardio-Thoracique de Bordeaux, Inserm UMR 1045, Univ Bordeaux, 33000, Bordeaux, France
| | - Raphaël Enaud
- Centre de Recherche Cardio-Thoracique de Bordeaux, Inserm UMR 1045, Univ Bordeaux, 33000, Bordeaux, France
- CHU Bordeaux, CRCM Pédiatrique, CIC 1401, 33000, Bordeaux, France
| | - Arthur Orieux
- CHU Bordeaux, Medical Intensive Care Unit, 33000, Bordeaux, France
| | - Adrian Camino
- Centre de Recherche Cardio-Thoracique de Bordeaux, Inserm UMR 1045, Univ Bordeaux, 33000, Bordeaux, France
| | | | | | - Cédric Carrié
- d CHU Bordeaux, Surgical Intensive Care Unit, 33000, Bordeaux, France
| | - Laurent Petit
- d CHU Bordeaux, Surgical Intensive Care Unit, 33000, Bordeaux, France
| | - Alexandre Boyer
- Centre de Recherche Cardio-Thoracique de Bordeaux, Inserm UMR 1045, Univ Bordeaux, 33000, Bordeaux, France
- CHU Bordeaux, Medical Intensive Care Unit, 33000, Bordeaux, France
| | - Patrick Berger
- Centre de Recherche Cardio-Thoracique de Bordeaux, Inserm UMR 1045, Univ Bordeaux, 33000, Bordeaux, France
| | - Didier Gruson
- Centre de Recherche Cardio-Thoracique de Bordeaux, Inserm UMR 1045, Univ Bordeaux, 33000, Bordeaux, France
- CHU Bordeaux, Medical Intensive Care Unit, 33000, Bordeaux, France
| | - Laurence Delhaes
- HU Bordeaux, Mycology-Parasitology Department, CIC 1401, 33000, Bordeaux, France
- Centre de Recherche Cardio-Thoracique de Bordeaux, Inserm UMR 1045, Univ Bordeaux, 33000, Bordeaux, France
| | - Renaud Prével
- Centre de Recherche Cardio-Thoracique de Bordeaux, Inserm UMR 1045, Univ Bordeaux, 33000, Bordeaux, France.
- CHU Bordeaux, Medical Intensive Care Unit, 33000, Bordeaux, France.
- Medical Intensive Care Unit, Pellegrin Hospital, Place Amélie Raba-Léon, 33076, Bordeaux, France.
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5
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Phan HV, Tsitsiklis A, Maguire CP, Haddad EK, Becker PM, Kim-Schulze S, Lee B, Chen J, Hoch A, Pickering H, van Zalm P, Altman MC, Augustine AD, Calfee CS, Bosinger S, Cairns CB, Eckalbar W, Guan L, Jayavelu ND, Kleinstein SH, Krammer F, Maecker HT, Ozonoff A, Peters B, Rouphael N, Montgomery RR, Reed E, Schaenman J, Steen H, Levy O, Diray-Arce J, Langelier CR. Host-microbe multiomic profiling reveals age-dependent immune dysregulation associated with COVID-19 immunopathology. Sci Transl Med 2024; 16:eadj5154. [PMID: 38630846 DOI: 10.1126/scitranslmed.adj5154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 03/15/2024] [Indexed: 04/19/2024]
Abstract
Age is a major risk factor for severe coronavirus disease 2019 (COVID-19), yet the mechanisms behind this relationship have remained incompletely understood. To address this, we evaluated the impact of aging on host immune response in the blood and the upper airway, as well as the nasal microbiome in a prospective, multicenter cohort of 1031 vaccine-naïve patients hospitalized for COVID-19 between 18 and 96 years old. We performed mass cytometry, serum protein profiling, anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibody assays, and blood and nasal transcriptomics. We found that older age correlated with increased SARS-CoV-2 viral abundance upon hospital admission, delayed viral clearance, and increased type I interferon gene expression in both the blood and upper airway. We also observed age-dependent up-regulation of innate immune signaling pathways and down-regulation of adaptive immune signaling pathways. Older adults had lower naïve T and B cell populations and higher monocyte populations. Over time, older adults demonstrated a sustained induction of pro-inflammatory genes and serum chemokines compared with younger individuals, suggesting an age-dependent impairment in inflammation resolution. Transcriptional and protein biomarkers of disease severity differed with age, with the oldest adults exhibiting greater expression of pro-inflammatory genes and proteins in severe disease. Together, our study finds that aging is associated with impaired viral clearance, dysregulated immune signaling, and persistent and potentially pathologic activation of pro-inflammatory genes and proteins.
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Affiliation(s)
- Hoang Van Phan
- University of California San Francisco, San Francisco, CA 94115, USA
| | | | | | - Elias K Haddad
- Drexel University, Tower Health Hospital, Philadelphia, PA 19104, USA
| | - Patrice M Becker
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20814, USA
| | | | - Brian Lee
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jing Chen
- Precision Vaccines Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Research Computing, Department of Information Technology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Annmarie Hoch
- Precision Vaccines Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Harry Pickering
- David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Patrick van Zalm
- Precision Vaccines Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Matthew C Altman
- Benaroya Research Institute, University of Washington, Seattle, WA 98101, USA
| | - Alison D Augustine
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20814, USA
| | - Carolyn S Calfee
- University of California San Francisco, San Francisco, CA 94115, USA
| | | | - Charles B Cairns
- Drexel University, Tower Health Hospital, Philadelphia, PA 19104, USA
| | - Walter Eckalbar
- University of California San Francisco, San Francisco, CA 94115, USA
| | - Leying Guan
- Yale School of Public Health, New Haven, CT 06510, USA
| | | | | | - Florian Krammer
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Holden T Maecker
- Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | - Al Ozonoff
- Precision Vaccines Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Research Computing, Department of Information Technology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Bjoern Peters
- La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | | | | | - Elaine Reed
- David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Joanna Schaenman
- David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Hanno Steen
- Precision Vaccines Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ofer Levy
- Precision Vaccines Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Joann Diray-Arce
- Precision Vaccines Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Charles R Langelier
- University of California San Francisco, San Francisco, CA 94115, USA
- Chan Zuckerberg Biohub San Francisco, San Francisco, CA 94158, USA
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6
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Xie L, Luo G, Yang Z, Wu WC, Chen J, Ren Y, Zeng Z, Ye G, Pan Y, Zhao WJ, Chen YQ, Hou W, Sun Y, Guo D, Yang Z, Li J, Holmes EC, Li Y, Chen L, Shi M. The clinical outcome of COVID-19 is strongly associated with microbiome dynamics in the upper respiratory tract. J Infect 2024; 88:106118. [PMID: 38342382 DOI: 10.1016/j.jinf.2024.01.017] [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: 07/20/2023] [Revised: 01/24/2024] [Accepted: 01/30/2024] [Indexed: 02/13/2024]
Abstract
OBJECTIVES The respiratory tract is the portal of entry for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Although a variety of respiratory pathogens other than SARS-CoV-2 have been associated with severe cases of COVID-19 disease, the dynamics of the upper respiratory microbiota during disease the course of disease, and how they impact disease manifestation, remain uncertain. METHODS We collected 349 longitudinal upper respiratory samples from a cohort of 65 COVID-19 patients (cohort 1), 28 samples from 28 recovered COVID-19 patients (cohort 2), and 59 samples from 59 healthy controls (cohort 3). All COVID-19 patients originated from the earliest stage of the epidemic in Wuhan. Based on a modified clinical scale, the disease course was divided into five clinical disease phases (pseudotimes): "Healthy" (pseudotime 0), "Incremental" (pseudotime 1), "Critical" (pseudotime 2), "Complicated" (pseudotime 3), "Convalescent" (pseudotime 4), and "Long-term follow-up" (pseudotime 5). Using meta-transcriptomics, we investigated the features and dynamics of transcriptionally active microbes in the upper respiratory tract (URT) over the course of COVID-19 disease, as well as its association with disease progression and clinical outcomes. RESULTS Our results revealed that the URT microbiome exhibits substantial heterogeneity during disease course. Two clusters of microbial communities characterized by low alpha diversity and enrichment for multiple pathogens or potential pathobionts (including Acinetobacter and Candida) were associated with disease progression and a worse clinical outcome. We also identified a series of microbial indicators that classified disease progression into more severe stages. Longitudinal analysis revealed that although the microbiome exhibited complex and changing patterns during COVID-19, a restoration of URT microbiomes from early dysbiosis toward more diverse status in later disease stages was observed in most patients. In addition, a group of potential pathobionts were strongly associated with the concentration of inflammatory indicators and mortality. CONCLUSION This study revealed strong links between URT microbiome dynamics and disease progression and clinical outcomes in COVID-19, implying that the treatment of severe disease should consider the full spectrum of microbial pathogens present.
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Affiliation(s)
- Linlin Xie
- Wuhan Research Center for Infectious Diseases and Tumors of the Chinese Academy of Medical Sciences/Hubei Engineering Center for Infectious Disease Prevention, Control and Treatment/Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Gengyan Luo
- State key laboratory for biocontrol, Shenzhen Key Laboratory of Systems Medicine for inflammatory diseases, School of Medicine, Shenzhen campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Zhongzhou Yang
- State key laboratory for biocontrol, Shenzhen Key Laboratory of Systems Medicine for inflammatory diseases, School of Medicine, Shenzhen campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Wei-Chen Wu
- State key laboratory for biocontrol, Shenzhen Key Laboratory of Systems Medicine for inflammatory diseases, School of Medicine, Shenzhen campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Jintao Chen
- State Key Laboratory of Virology/Department of Laboratory Medicine/Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences/Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Yuting Ren
- State Key Laboratory of Virology/Department of Laboratory Medicine/Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences/Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Zhikun Zeng
- Wuhan Research Center for Infectious Diseases and Tumors of the Chinese Academy of Medical Sciences/Hubei Engineering Center for Infectious Disease Prevention, Control and Treatment/Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Guangming Ye
- Wuhan Research Center for Infectious Diseases and Tumors of the Chinese Academy of Medical Sciences/Hubei Engineering Center for Infectious Disease Prevention, Control and Treatment/Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yunbao Pan
- Wuhan Research Center for Infectious Diseases and Tumors of the Chinese Academy of Medical Sciences/Hubei Engineering Center for Infectious Disease Prevention, Control and Treatment/Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Wen-Jing Zhao
- State key laboratory for biocontrol, Shenzhen Key Laboratory of Systems Medicine for inflammatory diseases, School of Medicine, Shenzhen campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Yao-Qing Chen
- School of Public Health (Shenzhen), Shenzhen campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Wei Hou
- State Key Laboratory of Virology/Department of Laboratory Medicine/Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences/Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Yanni Sun
- Department of Electrical Engineering, City University of Hong Kong, Hong Kong, China
| | - Deying Guo
- State key laboratory for biocontrol, Shenzhen Key Laboratory of Systems Medicine for inflammatory diseases, School of Medicine, Shenzhen campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Zifeng Yang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jun Li
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, Australia
| | - Yirong Li
- Wuhan Research Center for Infectious Diseases and Tumors of the Chinese Academy of Medical Sciences/Hubei Engineering Center for Infectious Disease Prevention, Control and Treatment/Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China.
| | - Liangjun Chen
- Wuhan Research Center for Infectious Diseases and Tumors of the Chinese Academy of Medical Sciences/Hubei Engineering Center for Infectious Disease Prevention, Control and Treatment/Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China.
| | - Mang Shi
- State key laboratory for biocontrol, Shenzhen Key Laboratory of Systems Medicine for inflammatory diseases, School of Medicine, Shenzhen campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China.
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7
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González-Paz L, Lossada C, Hurtado-León ML, Vera-Villalobos J, Paz JL, Marrero-Ponce Y, Martinez-Rios F, Alvarado Y. Biophysical Analysis of Potential Inhibitors of SARS-CoV-2 Cell Recognition and Their Effect on Viral Dynamics in Different Cell Types: A Computational Prediction from In Vitro Experimental Data. ACS OMEGA 2024; 9:8923-8939. [PMID: 38434903 PMCID: PMC10905729 DOI: 10.1021/acsomega.3c06968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 01/20/2024] [Accepted: 02/05/2024] [Indexed: 03/05/2024]
Abstract
Recent reports have suggested that the susceptibility of cells to SARS-CoV-2 infection can be influenced by various proteins that potentially act as receptors for the virus. To investigate this further, we conducted simulations of viral dynamics using different cellular systems (Vero E6, HeLa, HEK293, and CaLu3) in the presence and absence of drugs (anthelmintic, ARBs, anticoagulant, serine protease inhibitor, antimalarials, and NSAID) that have been shown to impact cellular recognition by the spike protein based on experimental data. Our simulations revealed that the susceptibility of the simulated cell systems to SARS-CoV-2 infection was similar across all tested systems. Notably, CaLu3 cells exhibited the highest susceptibility to SARS-CoV-2 infection, potentially due to the presence of receptors other than ACE2, which may account for a significant portion of the observed susceptibility. Throughout the study, all tested compounds showed thermodynamically favorable and stable binding to the spike protein. Among the tested compounds, the anticoagulant nafamostat demonstrated the most favorable characteristics in terms of thermodynamics, kinetics, theoretical antiviral activity, and potential safety (toxicity) in relation to SARS-CoV-2 spike protein-mediated infections in the tested cell lines. This study provides mathematical and bioinformatic models that can aid in the identification of optimal cell lines for compound evaluation and detection, particularly in studies focused on repurposed drugs and their mechanisms of action. It is important to note that these observations should be experimentally validated, and this research is expected to inspire future quantitative experiments.
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Affiliation(s)
- Lenin González-Paz
- Centro
de Biomedicina Molecular (CBM). Laboratorio de Biocomputación
(LB),Instituto Venezolano de Investigaciones
Científicas (IVIC),Maracaibo, Zulia 4001, República Bolivariana de Venezuela
| | - Carla Lossada
- Centro
de Biomedicina Molecular (CBM). Laboratorio de Biocomputación
(LB),Instituto Venezolano de Investigaciones
Científicas (IVIC),Maracaibo, Zulia 4001, República Bolivariana de Venezuela
| | - María Laura Hurtado-León
- Facultad
Experimental de Ciencias (FEC). Departamento de Biología. Laboratorio
de Genética y Biología Molecular (LGBM),Universidad del Zulia (LUZ),Maracaibo 4001, República Bolivariana de Venezuela
| | - Joan Vera-Villalobos
- Facultad
de Ciencias Naturales y Matemáticas, Departamento de Química
y Ciencias Ambientales, Laboratorio de Análisis Químico
Instrumental (LAQUINS), Escuela Superior
Politécnica del Litoral, Guayaquil EC090112, Ecuador
| | - José L. Paz
- Departamento
Académico de Química Inorgánica, Facultad de
Química e Ingeniería Química, Universidad Nacional Mayor de San Marcos. Cercado de Lima, Lima 15081, Perú
| | - Yovani Marrero-Ponce
- Grupo
de Medicina Molecular y Traslacional (MeM&T), Colegio de Ciencias
de la Salud (COCSA), Escuela de Medicina, Edificio de Especialidades
Médicas; e Instituto de Simulación Computacional (ISC-USFQ),
Diego de Robles y vía Interoceánica, Universidad San Francisco de Quito (USFQ), Quito, Pichincha 170157, Ecuador
| | - Felix Martinez-Rios
- Universidad
Panamericana. Facultad de Ingeniería. Augusto Rodin 498, Ciudad de México 03920, México
| | - Ysaías.
J. Alvarado
- Centro
de Biomedicina Molecular (CBM). Laboratorio de Química Biofísica
Teórica y Experimental (LQBTE),Instituto
Venezolano de Investigaciones Científicas (IVIC),Maracaibo, Zulia 4001, República Bolivariana
de Venezuela
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8
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Liu Y, Fachrul M, Inouye M, Méric G. Harnessing human microbiomes for disease prediction. Trends Microbiol 2024:S0966-842X(23)00339-6. [PMID: 38246848 DOI: 10.1016/j.tim.2023.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 12/12/2023] [Accepted: 12/12/2023] [Indexed: 01/23/2024]
Abstract
The human microbiome has been increasingly recognized as having potential use for disease prediction. Predicting the risk, progression, and severity of diseases holds promise to transform clinical practice, empower patient decisions, and reduce the burden of various common diseases, as has been demonstrated for cardiovascular disease or breast cancer. Combining multiple modifiable and non-modifiable risk factors, including high-dimensional genomic data, has been traditionally favored, but few studies have incorporated the human microbiome into models for predicting the prospective risk of disease. Here, we review research into the use of the human microbiome for disease prediction with a particular focus on prospective studies as well as the modulation and engineering of the microbiome as a therapeutic strategy.
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Affiliation(s)
- Yang Liu
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK; Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia; Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Melbourne, Victoria, Australia; Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK; British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Muhamad Fachrul
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia; Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Melbourne, Victoria, Australia; Human Genomics and Evolution Unit, St Vincent's Institute of Medical Research, Victoria, Australia; Melbourne Integrative Genomics, University of Melbourne, Parkville, Victoria, Australia; School of BioSciences, University of Melbourne, Parkville, Victoria, Australia
| | - Michael Inouye
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK; Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia; Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK; British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK; Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK; British Heart Foundation Cambridge Centre of Research Excellence, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Guillaume Méric
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia; Department of Cardiometabolic Health, University of Melbourne, Melbourne, Victoria, Australia; Central Clinical School, Monash University, Melbourne, Victoria, Australia; Department of Medical Science, Molecular Epidemiology, Uppsala University, Uppsala, Sweden; Department of Cardiovascular Research, Translation, and Implementation, La Trobe University, Melbourne, Victoria, Australia.
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9
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Puray-Chavez M, LaPak KM, Jasuja R, Pan J, Xu J, Eschbach JE, Mohammed S, Lawson DQ, Wang Q, Brody SL, Major MB, Goldfarb D, Kutluay SB. A basally active cGAS-STING pathway limits SARS-CoV-2 replication in a subset of ACE2 positive airway cell models. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.07.574522. [PMID: 38260460 PMCID: PMC10802478 DOI: 10.1101/2024.01.07.574522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Host factors that define the cellular tropism of SARS-CoV-2 beyond the cognate ACE2 receptor are poorly defined. From a screen of human airway derived cell lines that express varying levels of ACE2/TMPRSS2, we found a subset that express comparably high endogenous levels of ACE2 but surprisingly did not support SARS-CoV-2 replication. Here we report that this resistance is mediated by a basally active cGAS-STING pathway culminating in interferon (IFN)-mediated restriction of SARS-CoV-2 replication at a post-entry step. Pharmacological inhibition of JAK1/2, depletion of the IFN-α receptor and cGAS-STING pathway effectors substantially increased SARS-CoV-2 replication in these cell models. While depletion of cGAS or STING was sufficient to reduce the preexisting levels of IFN-stimulated genes (ISGs), SARS-CoV-2 infection in STING knockout cells independently induced ISG expression. Remarkably, SARS-CoV-2-induced ISG expression in STING knockout cell as well as in primary human airway cultures was limited to uninfected bystander cells, demonstrating efficient antagonism of the type I/III IFN-pathway, but not viral sensing or IFN production, in productively infected cells. Of note, SARS-CoV-2-infected primary human airway cells also displayed markedly lower levels of STING expression, raising the possibility that SARS-CoV-2 can target STING expression or preferentially infect cells that express low levels of STING. Finally, ectopic ACE2 overexpression overcame the IFN-mediated blocks, suggesting the ability of SARS-CoV-2 to overcome these possibly saturable blocks to infection. Our study highlights that in addition to viral receptors, basal activation of the cGAS-STING pathway and innate immune defenses may contribute to defining SARS-CoV-2 cellular tropism.
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Affiliation(s)
- Maritza Puray-Chavez
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, MO, USA
| | - Kyle M LaPak
- Department of Cell Biology and Physiology, Washington University in St. Louis, St. Louis, MO, USA
| | - Ria Jasuja
- Department of Cell Biology and Physiology, Washington University in St. Louis, St. Louis, MO, USA
| | - Jiehong Pan
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Washington University in St. Louis, School of Medicine, St. Louis, MO, USA
| | - Jian Xu
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Washington University in St. Louis, School of Medicine, St. Louis, MO, USA
| | - Jenna E Eschbach
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, MO, USA
| | - Shawn Mohammed
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, MO, USA
| | - Dana Q Lawson
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, MO, USA
| | - Qibo Wang
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, MO, USA
| | - Steven L Brody
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Washington University in St. Louis, School of Medicine, St. Louis, MO, USA
| | - Michael B Major
- Department of Cell Biology and Physiology, Washington University in St. Louis, St. Louis, MO, USA
- Department of Otolaryngology, Washington University in St. Louis, St. Louis, MO, USA
| | - Dennis Goldfarb
- Department of Cell Biology and Physiology, Washington University in St. Louis, St. Louis, MO, USA
- Institute for Informatics, Data Science & Biostatistics, Washington University in St. Louis, St. Louis, MO, USA
| | - Sebla B Kutluay
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, MO, USA
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10
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Gu Z, Zhang Y, Zhao X, Liu T, Sheng S, Song R, Jin R. Comparing sputum microbiota characteristics between severe and critically ill influenza patients. Front Cell Infect Microbiol 2023; 13:1297946. [PMID: 38188635 PMCID: PMC10766813 DOI: 10.3389/fcimb.2023.1297946] [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: 09/20/2023] [Accepted: 11/27/2023] [Indexed: 01/09/2024] Open
Abstract
Background Currently, limited attention has been directed toward utilizing clinical cohorts as a starting point to elucidate alterations in the lower respiratory tract (LRT) microbiota following influenza A virus (IAV) infection. Objectives Our objective was to undertake a comparative analysis of the diversity and composition of sputum microbiota in individuals afflicted by severe and critically ill influenza patients. Methods Sputum specimens were procured from patients diagnosed with IAV infection for the purpose of profiling the microbiota using 16S-rDNA sequencing. To ascertain taxonomic differences between the severe and critically ill influenza cohorts, we leveraged Linear Discriminant Analysis Effect Size (LEfSe). Additionally, Spearman correlation analysis was employed to illuminate associations between sputum microbiota and influenza Ct values alongside laboratory indicators. Results Our study encompassed a total cohort of 64 patients, comprising 48 within the severe group and 16 within the critically ill group. Intriguingly, Bacteroidetes exhibited significant depletion in the critically ill cohort (p=0.031). The sputum microbiomes of the severe influenza group were hallmarked by an overrepresentation of Neisseria, Porphyromonas, Actinobacillus, Alloprevotella, TM7x, and Clostridia_UCG-014, yielding ROC-plot AUC values of 0.71, 0.68, 0.60, 0.70, 0.70, and 0.68, respectively. Notably, Alloprevotella exhibited an inverse correlation with influenza Ct values. Moreover, C-reactive protein (CRP) manifested a positive correlation with Haemophilus and Porphyromonas. Conclusion The outcomes of this investigation lay the groundwork for future studies delving into the connection between the LRT microbiome and respiratory disorders. Further exploration is warranted to elucidate the intricate mechanisms underlying the interaction between IAV and Alloprevotella, particularly in disease progression.
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Affiliation(s)
- Zhixia Gu
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- Beijing Institute of Infectious Diseases, Beijing, China
- National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing, China
| | - Yuanyuan Zhang
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- Beijing Institute of Infectious Diseases, Beijing, China
- National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing, China
| | - Xue Zhao
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Tingting Liu
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- Beijing Institute of Infectious Diseases, Beijing, China
- National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing, China
| | - Shugui Sheng
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- Beijing Institute of Infectious Diseases, Beijing, China
- National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing, China
| | - Rui Song
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing, China
| | - Ronghua Jin
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- Beijing Institute of Infectious Diseases, Beijing, China
- National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing, China
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11
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Sulaiman I, Wu BG, Chung M, Isaacs B, Tsay JCJ, Holub M, Barnett CR, Kwok B, Kugler MC, Natalini JG, Singh S, Li Y, Schluger R, Carpenito J, Collazo D, Perez L, Kyeremateng Y, Chang M, Campbell CD, Hansbro PM, Oppenheimer BW, Berger KI, Goldring RM, Koralov SB, Weiden MD, Xiao R, D’Armiento J, Clemente JC, Ghedin E, Segal LN. Lower Airway Dysbiosis Augments Lung Inflammatory Injury in Mild-to-Moderate Chronic Obstructive Pulmonary Disease. Am J Respir Crit Care Med 2023; 208:1101-1114. [PMID: 37677136 PMCID: PMC10867925 DOI: 10.1164/rccm.202210-1865oc] [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: 10/18/2022] [Accepted: 09/07/2023] [Indexed: 09/09/2023] Open
Abstract
Rationale: Chronic obstructive pulmonary disease (COPD) is associated with high morbidity, mortality, and healthcare costs. Cigarette smoke is a causative factor; however, not all heavy smokers develop COPD. Microbial colonization and infections are contributing factors to disease progression in advanced stages. Objectives: We investigated whether lower airway dysbiosis occurs in mild-to-moderate COPD and analyzed possible mechanistic contributions to COPD pathogenesis. Methods: We recruited 57 patients with a >10 pack-year smoking history: 26 had physiological evidence of COPD, and 31 had normal lung function (smoker control subjects). Bronchoscopy sampled the upper airways, lower airways, and environmental background. Samples were analyzed by 16S rRNA gene sequencing, whole genome, RNA metatranscriptome, and host RNA transcriptome. A preclinical mouse model was used to evaluate the contributions of cigarette smoke and dysbiosis on lower airway inflammatory injury. Measurements and Main Results: Compared with smoker control subjects, microbiome analyses showed that the lower airways of subjects with COPD were enriched with common oral commensals. The lower airway host transcriptomics demonstrated differences in markers of inflammation and tumorigenesis, such as upregulation of IL-17, IL-6, ERK/MAPK, PI3K, MUC1, and MUC4 in mild-to-moderate COPD. Finally, in a preclinical murine model exposed to cigarette smoke, lower airway dysbiosis with common oral commensals augments the inflammatory injury, revealing transcriptomic signatures similar to those observed in human subjects with COPD. Conclusions: Lower airway dysbiosis in the setting of smoke exposure contributes to inflammatory injury early in COPD. Targeting the lower airway microbiome in combination with smoking cessation may be of potential therapeutic relevance.
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Affiliation(s)
- Imran Sulaiman
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
- Department of Respiratory Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
- Department of Respiratory Medicine, Beaumont Hospital, Dublin, Ireland
| | - Benjamin G. Wu
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
- Division of Pulmonary and Critical Care Medicine, Veterans Affairs (VA) New York Harbor Healthcare System, New York, New York
| | - Matthew Chung
- Systems Genomics Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Bradley Isaacs
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
| | - Jun-Chieh J. Tsay
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
- Division of Pulmonary and Critical Care Medicine, Veterans Affairs (VA) New York Harbor Healthcare System, New York, New York
| | - Meredith Holub
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
- Division of Pulmonary and Critical Care Medicine, Hartford Health Care, Hartford, Connecticut
| | - Clea R. Barnett
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
| | - Benjamin Kwok
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
| | | | - Jake G. Natalini
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
| | - Shivani Singh
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
| | - Yonghua Li
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
| | - Rosemary Schluger
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
| | - Joseph Carpenito
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
| | - Destiny Collazo
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
| | - Luisanny Perez
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
| | - Yaa Kyeremateng
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
| | - Miao Chang
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
| | - Christina D. Campbell
- Department of Respiratory Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
- Department of Respiratory Medicine, Beaumont Hospital, Dublin, Ireland
| | - Philip M. Hansbro
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, School of Life Sciences, Sydney, New South Wales, Australia
| | | | - Kenneth I. Berger
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
| | | | | | - Michael D. Weiden
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
| | - Rui Xiao
- Department of Physiology and Cellular Biophysics, Columbia University School of Medicine, New York, New York; and
| | - Jeanine D’Armiento
- Department of Physiology and Cellular Biophysics, Columbia University School of Medicine, New York, New York; and
| | - Jose C. Clemente
- Department of Genetics and Genomic Sciences and Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Elodie Ghedin
- Systems Genomics Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Leopoldo N. Segal
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
- Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, New York University (NYU) Langone Health, New York, New York
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12
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Wang L, Cao JB, Xia BB, Li YJ, Zhang X, Mo GX, Wang RJ, Guo SQ, Zhang YQ, Xiao K, Zhu GF, Liu PF, Song LC, Ma XH, Xiang PC, Wang J, Liu YH, Xie F, Zhang XD, Li XX, Sun WL, Cao Y, Wang KF, Zhang WH, Zhao WC, Yan P, Chen JC, Yang YW, Yu ZK, Tang JS, Xiao L, Zhou JM, Xie LX, Wang J. Metatranscriptome of human lung microbial communities in a cohort of mechanically ventilated COVID-19 Omicron patients. Signal Transduct Target Ther 2023; 8:432. [PMID: 37949875 PMCID: PMC10638395 DOI: 10.1038/s41392-023-01684-1] [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: 05/14/2023] [Revised: 09/21/2023] [Accepted: 10/18/2023] [Indexed: 11/12/2023] Open
Abstract
The Omicron variant of the severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) infected a substantial proportion of Chinese population, and understanding the factors underlying the severity of the disease and fatality is valuable for future prevention and clinical treatment. We recruited 64 patients with invasive ventilation for COVID-19 and performed metatranscriptomic sequencing to profile host transcriptomic profiles, plus viral, bacterial, and fungal content, as well as virulence factors and examined their relationships to 28-day mortality were examined. In addition, the bronchoalveolar lavage fluid (BALF) samples from invasive ventilated hospital/community-acquired pneumonia patients (HAP/CAP) sampled in 2019 were included for comparison. Genomic analysis revealed that all Omicron strains belong to BA.5 and BF.7 sub-lineages, with no difference in 28-day mortality between them. Compared to HAP/CAP cohort, invasive ventilated COVID-19 patients have distinct host transcriptomic and microbial signatures in the lower respiratory tract; and in the COVID-19 non-survivors, we found significantly lower gene expressions in pathways related viral processes and positive regulation of protein localization to plasma membrane, higher abundance of opportunistic pathogens including bacterial Alloprevotella, Caulobacter, Escherichia-Shigella, Ralstonia and fungal Aspergillus sydowii and Penicillium rubens. Correlational analysis further revealed significant associations between host immune responses and microbial compositions, besides synergy within viral, bacterial, and fungal pathogens. Our study presents the relationships of lower respiratory tract microbiome and transcriptome in invasive ventilated COVID-19 patients, providing the basis for future clinical treatment and reduction of fatality.
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Affiliation(s)
- Lin Wang
- College of Pulmonary & Critical Care Medicine, 8th Medical Center of Chinese PLA General Hospital, Beijing, 100091, China
| | - Jia-Bao Cao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Bin-Bin Xia
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yue-Juan Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuan Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- Faculty of Biological Science and Technology, Baotou Teacher's College, Baotou, 014030, China
| | - Guo-Xin Mo
- College of Pulmonary & Critical Care Medicine, 8th Medical Center of Chinese PLA General Hospital, Beijing, 100091, China
| | - Rui-Juan Wang
- Department of Respiratory Medicine, PLA Strategic Support Force Medical Center, Beijing, 100101, China
| | - Si-Qi Guo
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yu-Qing Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kun Xiao
- College of Pulmonary & Critical Care Medicine, 8th Medical Center of Chinese PLA General Hospital, Beijing, 100091, China
| | - Guang-Fa Zhu
- Department of Respiratory and Critical Care Medicine, Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart, Lung and Blood Vessel Diseases, Beijing, 100029, China
| | - Peng-Fei Liu
- College of Pulmonary & Critical Care Medicine, 8th Medical Center of Chinese PLA General Hospital, Beijing, 100091, China
| | - Li-Cheng Song
- College of Pulmonary & Critical Care Medicine, 8th Medical Center of Chinese PLA General Hospital, Beijing, 100091, China
| | - Xi-Hui Ma
- Respiratory Research Institute, Department of Pulmonary & Critical Care Medicine, Beijing Key Laboratory of OTIR, the 8th Medical Center of Chinese PLA General Hospital, Beijing, 100091, China
| | - Ping-Chao Xiang
- Shougang hospital of Peking University, Beijing, 100144, China
| | - Jiang Wang
- College of Pulmonary & Critical Care Medicine, 8th Medical Center of Chinese PLA General Hospital, Beijing, 100091, China
| | - Yu-Hong Liu
- College of Pulmonary & Critical Care Medicine, 8th Medical Center of Chinese PLA General Hospital, Beijing, 100091, China
| | - Fei Xie
- College of Pulmonary & Critical Care Medicine, 8th Medical Center of Chinese PLA General Hospital, Beijing, 100091, China
| | - Xu-Dong Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiang-Xin Li
- Department of Respiratory Medicine, Beijing Changping Hospital, Beijing, 102200, China
| | - Wan-Lu Sun
- Department of Respiratory and Critical Care Medicine, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China
| | - Yan Cao
- Pulmonary research institute, Senior Department of Respiratory and Critical Care Medicine, the 8th medical center of Chinese PLA general hospital, Beijing, 100091, China
| | - Kai-Fei Wang
- College of Pulmonary & Critical Care Medicine, Chinese PLA General Hospital, Beijing, 100853, China
| | - Wen-Hui Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei-Chao Zhao
- Department of Respiratory Medicine, PLA Strategic Support Force Medical Center, Beijing, 100101, China
| | - Peng Yan
- China Aerospace Science & Industry Corporation 731 hospital, Beijing, 100074, China
| | - Ji-Chao Chen
- Department of Respiratory and Critical Care Medicine, Aerospace Center Hospital, Beijing, 100049, China
| | - Yu-Wei Yang
- Respiratory Research Institute, Department of Pulmonary & Critical Care Medicine, Beijing Key Laboratory of OTIR, the 8th Medical Center of Chinese PLA General Hospital, Beijing, 100091, China
| | - Zhong-Kuo Yu
- College of Pulmonary & Critical Care Medicine, 8th Medical Center of Chinese PLA General Hospital, Beijing, 100091, China
| | - Jing-Si Tang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Li Xiao
- Respiratory Research Institute, Department of Pulmonary & Critical Care Medicine, Beijing Key Laboratory of OTIR, the 8th Medical Center of Chinese PLA General Hospital, Beijing, 100091, China
| | - Jie-Min Zhou
- Vision Medicals Center for Infectious Diseases, Guangzhou, 510700, China
| | - Li-Xin Xie
- College of Pulmonary & Critical Care Medicine, 8th Medical Center of Chinese PLA General Hospital, Beijing, 100091, China.
| | - Jun Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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13
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Bondareva M, Budzinski L, Durek P, Witkowski M, Angermair S, Ninnemann J, Kreye J, Letz P, Ferreira-Gomes M, Semin I, Guerra GM, Momsen Reincke S, Sánchez-Sendin E, Yilmaz S, Sempert T, Heinz GA, Tizian C, Raftery M, Schönrich G, Matyushkina D, Smirnov IV, Govorun VM, Schrezenmeier E, Stefanski AL, Dörner T, Zocche S, Viviano E, Klement N, Sehmsdorf KJ, Lunin A, Chang HD, Drutskaya M, Kozlovskaya L, Treskatsch S, Radbruch A, Diefenbach A, Prüss H, Enghard P, Mashreghi MF, Kruglov AA. Cross-regulation of antibody responses against the SARS-CoV-2 Spike protein and commensal microbiota via molecular mimicry. Cell Host Microbe 2023; 31:1866-1881.e10. [PMID: 37944493 DOI: 10.1016/j.chom.2023.10.007] [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: 09/28/2022] [Revised: 07/11/2023] [Accepted: 10/06/2023] [Indexed: 11/12/2023]
Abstract
The commensal microflora provides a repertoire of antigens that illicit mucosal antibodies. In some cases, these antibodies can cross-react with host proteins, inducing autoimmunity, or with other microbial antigens. We demonstrate that the oral microbiota can induce salivary anti-SARS-CoV-2 Spike IgG antibodies via molecular mimicry. Anti-Spike IgG antibodies in the saliva correlated with enhanced abundance of Streptococcus salivarius 1 month after anti-SARS-CoV-2 vaccination. Several human commensal bacteria, including S. salivarius, were recognized by SARS-CoV-2-neutralizing monoclonal antibodies and induced cross-reactive anti-Spike antibodies in mice, facilitating SARS-CoV-2 clearance. A specific S. salivarius protein, RSSL-01370, contains regions with homology to the Spike receptor-binding domain, and immunization of mice with RSSL-01370 elicited anti-Spike IgG antibodies in the serum. Additionally, oral S. salivarius supplementation enhanced salivary anti-Spike antibodies in vaccinated individuals. Altogether, these data show that distinct species of the human microbiota can express molecular mimics of SARS-CoV-2 Spike protein, potentially enhancing protective immunity.
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Affiliation(s)
- Marina Bondareva
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117 Berlin, Germany; Belozersky Institute of Physico-Chemical Biology and Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Lisa Budzinski
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117 Berlin, Germany
| | - Pawel Durek
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117 Berlin, Germany
| | - Mario Witkowski
- Berlin Institute of Health (BIH), 10178 Berlin, Germany; Laboratory of Innate Immunity, Department of Microbiology and Infection Immunology, Charité-Universitätsmedizin Berlin, 12203 Berlin, Germany; Mucosal and Developmental Immunology, Deutsches Rheuma-Forschungszentrum, an Institute of the Leibniz Association, 10117 Berlin, Germany
| | - Stefan Angermair
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Department of Anesthesiology and Intensive Care Medicine, Charité Campus Benjamin Franklin, Berlin, Germany
| | - Justus Ninnemann
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117 Berlin, Germany
| | - Jakob Kreye
- Berlin Institute of Health (BIH), 10178 Berlin, Germany; German Center for Neurodegenerative Diseases (DZNE), 10117 Berlin, Germany; Helmholtz Innovation Lab BaoBab (Brain Antibody-omics and B-cell Lab), 10117 Berlin, Germany; Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität Berlin, and Berlin Institute of Health, 10117 Berlin, Germany; Department of Pediatric Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Philine Letz
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117 Berlin, Germany
| | - Marta Ferreira-Gomes
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117 Berlin, Germany
| | - Iaroslav Semin
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117 Berlin, Germany; Belozersky Institute of Physico-Chemical Biology and Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Gabriela Maria Guerra
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117 Berlin, Germany
| | - S Momsen Reincke
- Berlin Institute of Health (BIH), 10178 Berlin, Germany; German Center for Neurodegenerative Diseases (DZNE), 10117 Berlin, Germany; Helmholtz Innovation Lab BaoBab (Brain Antibody-omics and B-cell Lab), 10117 Berlin, Germany; Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Elisa Sánchez-Sendin
- German Center for Neurodegenerative Diseases (DZNE), 10117 Berlin, Germany; Helmholtz Innovation Lab BaoBab (Brain Antibody-omics and B-cell Lab), 10117 Berlin, Germany; Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Selin Yilmaz
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117 Berlin, Germany
| | - Toni Sempert
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117 Berlin, Germany
| | - Gitta Anne Heinz
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117 Berlin, Germany
| | - Caroline Tizian
- Berlin Institute of Health (BIH), 10178 Berlin, Germany; Laboratory of Innate Immunity, Department of Microbiology and Infection Immunology, Charité-Universitätsmedizin Berlin, 12203 Berlin, Germany; Mucosal and Developmental Immunology, Deutsches Rheuma-Forschungszentrum, an Institute of the Leibniz Association, 10117 Berlin, Germany
| | - Martin Raftery
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Günther Schönrich
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Daria Matyushkina
- Scientific Research Institute for Systems Biology and Medicine, Scientific Driveway, 18, 117246 Moscow, Russia
| | - Ivan V Smirnov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Vadim M Govorun
- Scientific Research Institute for Systems Biology and Medicine, Scientific Driveway, 18, 117246 Moscow, Russia
| | - Eva Schrezenmeier
- Berlin Institute of Health (BIH), 10178 Berlin, Germany; Department of Nephrology and Intensive Care Medicine, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Anna-Luisa Stefanski
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117 Berlin, Germany; Department of Rheumatology and Clinical Immunology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Thomas Dörner
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117 Berlin, Germany; Department of Rheumatology and Clinical Immunology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Silvia Zocche
- Departments of Pediatric Gastroenterology, Nephrology and Metabolic Diseases, Charité University Medicine, 10117 Berlin, Germany
| | - Edoardo Viviano
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin and Berlin Institute of Health, Institute of Physiology, Center for Space Medicine and Extreme Environments Berlin, 10117 Berlin, Germany
| | - Nele Klement
- Department of Nephrology and Intensive Care Medicine, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Katharina Johanna Sehmsdorf
- Department of Nephrology and Intensive Care Medicine, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Alexander Lunin
- Chumakov Scientific Center for Research and Development of Immune-and-Biological Products, Russian Academy of Sciences (Institute of Poliomyelitis), 108819 Moscow, Russia
| | - Hyun-Dong Chang
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117 Berlin, Germany; Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Marina Drutskaya
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Liubov Kozlovskaya
- Chumakov Scientific Center for Research and Development of Immune-and-Biological Products, Russian Academy of Sciences (Institute of Poliomyelitis), 108819 Moscow, Russia; Institute for Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Sascha Treskatsch
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Department of Anesthesiology and Intensive Care Medicine, Charité Campus Benjamin Franklin, Berlin, Germany
| | - Andreas Radbruch
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117 Berlin, Germany; Department of Rheumatology and Clinical Immunology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Andreas Diefenbach
- Berlin Institute of Health (BIH), 10178 Berlin, Germany; Laboratory of Innate Immunity, Department of Microbiology and Infection Immunology, Charité-Universitätsmedizin Berlin, 12203 Berlin, Germany; Mucosal and Developmental Immunology, Deutsches Rheuma-Forschungszentrum, an Institute of the Leibniz Association, 10117 Berlin, Germany
| | - Harald Prüss
- German Center for Neurodegenerative Diseases (DZNE), 10117 Berlin, Germany; Helmholtz Innovation Lab BaoBab (Brain Antibody-omics and B-cell Lab), 10117 Berlin, Germany; Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Philipp Enghard
- Department of Nephrology and Intensive Care Medicine, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Mir-Farzin Mashreghi
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117 Berlin, Germany
| | - Andrey A Kruglov
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117 Berlin, Germany; Belozersky Institute of Physico-Chemical Biology and Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, 119234 Moscow, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; Biological Faculty, M.V. Lomonosov Moscow State University, 119234 Moscow, Russia.
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14
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Kitsios GD, Sayed K, Fitch A, Yang H, Britton N, Shah F, Bain W, Evankovich JW, Qin S, Wang X, Li K, Patel A, Zhang Y, Radder J, Dela Cruz C, Okin DA, Huang CY, van Tyne D, Benos PV, Methé B, Lai P, Morris A, McVerry BJ. Prognostic Insights from Longitudinal Multicompartment Study of Host-Microbiota Interactions in Critically Ill Patients. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.25.23296086. [PMID: 37808745 PMCID: PMC10557814 DOI: 10.1101/2023.09.25.23296086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Critical illness can disrupt the composition and function of the microbiome, yet comprehensive longitudinal studies are lacking. We conducted a longitudinal analysis of oral, lung, and gut microbiota in a large cohort of 479 mechanically ventilated patients with acute respiratory failure. Progressive dysbiosis emerged in all three body compartments, characterized by reduced alpha diversity, depletion of obligate anaerobe bacteria, and pathogen enrichment. Clinical variables, including chronic obstructive pulmonary disease, immunosuppression, and antibiotic exposure, shaped dysbiosis. Notably, of the three body compartments, unsupervised clusters of lung microbiota diversity and composition independently predicted survival, transcending clinical predictors, organ dysfunction severity, and host-response sub-phenotypes. These independent associations of lung microbiota may serve as valuable biomarkers for prognostication and treatment decisions in critically ill patients. Insights into the dynamics of the microbiome during critical illness highlight the potential for microbiota-targeted interventions in precision medicine.
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Affiliation(s)
- Georgios D. Kitsios
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Khaled Sayed
- Department of Epidemiology, University of Florida, Gainesville, FL, USA
- Department of Electrical and Computer Engineering & Computer Science, University of New Haven, West Haven, CT, USA
| | - Adam Fitch
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Haopu Yang
- School of Medicine, Tsinghua University, Beijing, China
| | - Noel Britton
- Division of Pulmonary Critical Care Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Faraaz Shah
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Veteran’s Affairs Pittsburgh Healthcare System, Pittsburgh, PA, USA
| | - William Bain
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Veteran’s Affairs Pittsburgh Healthcare System, Pittsburgh, PA, USA
| | - John W. Evankovich
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Shulin Qin
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Xiaohong Wang
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kelvin Li
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Asha Patel
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yingze Zhang
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Josiah Radder
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Charles Dela Cruz
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Daniel A Okin
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Ching-Ying Huang
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Daria van Tyne
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Barbara Methé
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Peggy Lai
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Alison Morris
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Bryan J. McVerry
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
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15
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Kitsios GD, Sayed K, Fitch A, Yang H, Britton N, Shah F, Bain W, Evankovich JW, Qin S, Wang X, Li K, Patel A, Zhang Y, Radder J, Cruz CD, Okin DA, Huang CY, van Tyne D, Benos PV, Methé B, Lai P, Morris A, McVerry BJ. Prognostic Insights from Longitudinal Multicompartment Study of Host-Microbiota Interactions in Critically Ill Patients. RESEARCH SQUARE 2023:rs.3.rs-3338762. [PMID: 37841841 PMCID: PMC10571606 DOI: 10.21203/rs.3.rs-3338762/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
Critical illness can disrupt the composition and function of the microbiome, yet comprehensive longitudinal studies are lacking. We conducted a longitudinal analysis of oral, lung, and gut microbiota in a large cohort of 479 mechanically ventilated patients with acute respiratory failure. Progressive dysbiosis emerged in all three body compartments, characterized by reduced alpha diversity, depletion of obligate anaerobe bacteria, and pathogen enrichment. Clinical variables, including chronic obstructive pulmonary disease, immunosuppression, and antibiotic exposure, shaped dysbiosis. Notably, of the three body compartments, unsupervised clusters of lung microbiota diversity and composition independently predicted survival, transcending clinical predictors, organ dysfunction severity, and host-response sub-phenotypes. These independent associations of lung microbiota may serve as valuable biomarkers for prognostication and treatment decisions in critically ill patients. Insights into the dynamics of the microbiome during critical illness highlight the potential for microbiota-targeted interventions in precision medicine.
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Affiliation(s)
- Georgios D. Kitsios
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Khaled Sayed
- Department of Epidemiology, University of Florida, Gainesville, FL, USA
- Department of Electrical and Computer Engineering & Computer Science, University of New Haven, West Haven, CT, USA
| | - Adam Fitch
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Haopu Yang
- School of Medicine, Tsinghua University, Beijing, China
| | - Noel Britton
- Division of Pulmonary Critical Care Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Faraaz Shah
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Veteran’s Affairs Pittsburgh Healthcare System, Pittsburgh, PA, USA
| | - William Bain
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Veteran’s Affairs Pittsburgh Healthcare System, Pittsburgh, PA, USA
| | - John W. Evankovich
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Shulin Qin
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Xiaohong Wang
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kelvin Li
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Asha Patel
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yingze Zhang
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Josiah Radder
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Charles Dela Cruz
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Daniel A Okin
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Ching-Ying Huang
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Daria van Tyne
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Barbara Methé
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Peggy Lai
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Alison Morris
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Bryan J. McVerry
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
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16
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Zuo T, Liang G, Huang Z, Cao Z, Bai F, Zhou Y, Wu X, Wu X, Chen YQ, Balati M, Maimaitiyiming M, Lan P. Baseline gut microbiome features prior to SARS-CoV-2 infection are associated with host symptoms in and post COVID-19. J Med Virol 2023; 95:e29083. [PMID: 37698033 DOI: 10.1002/jmv.29083] [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: 05/23/2023] [Revised: 07/21/2023] [Accepted: 08/29/2023] [Indexed: 09/13/2023]
Abstract
The human gut microbiome varies substantially across individuals and populations and differentially tames our immunity at steady-state. Hence, we hypothesize that the large heterogeneity of gut microbiomes at steady-state may shape our baseline immunity differentially, and then mediate discrepant immune responses and symptoms when one encounters a viral infection, such as SARS-CoV-2 infection. To validate this hypothesis, we conducted an exploratory, longitudinal microbiome-COVID-19 study involving homogenous young participants from two geographically different regions in China. Subjects were recruited and sampled of fecal specimens before the 3-week surge window of COVID-19 (between December 11 and December 31, 2022) in China, and then were followed up for assessment of COVID-19 and post-COVID-19 manifestations. Our data showed that the baseline gut microbiome composition was intricately associated with different COVID-19 manifestations, particularly gastrointestinal involvement and post-COVID-19 lingering symptoms, in both an individual- and population-dependent manner. Our study intriguingly for the first time highlight that the gut microbiome at steady-state may prepare us differentially for weathering a respiratory viral infection.
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Affiliation(s)
- Tao Zuo
- Key Laboratory of Human Microbiome and Chronic Diseases, Ministry of Education, Sun Yat-sen University, Guangzhou, China
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Fecal Microbiota Transplantation Research, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Guanzhan Liang
- Key Laboratory of Human Microbiome and Chronic Diseases, Ministry of Education, Sun Yat-sen University, Guangzhou, China
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Ziyu Huang
- Key Laboratory of Human Microbiome and Chronic Diseases, Ministry of Education, Sun Yat-sen University, Guangzhou, China
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Fecal Microbiota Transplantation Research, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Zhirui Cao
- Key Laboratory of Human Microbiome and Chronic Diseases, Ministry of Education, Sun Yat-sen University, Guangzhou, China
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Fecal Microbiota Transplantation Research, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Feiyu Bai
- Key Laboratory of Human Microbiome and Chronic Diseases, Ministry of Education, Sun Yat-sen University, Guangzhou, China
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yingqian Zhou
- Key Laboratory of Human Microbiome and Chronic Diseases, Ministry of Education, Sun Yat-sen University, Guangzhou, China
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xianrui Wu
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xiaojian Wu
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yao-Qing Chen
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Maimaitituerxun Balati
- Department of Gastroenterology, The First People's Hospital of Kashi Prefecture, Kashgar, China
| | - Muyessar Maimaitiyiming
- Department of Gastroenterology, The First People's Hospital of Kashi Prefecture, Kashgar, China
| | - Ping Lan
- Key Laboratory of Human Microbiome and Chronic Diseases, Ministry of Education, Sun Yat-sen University, Guangzhou, China
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Fecal Microbiota Transplantation Research, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China
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17
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Zhou Y, Li J, Huang F, Ai H, Gao J, Chen C, Huang L. Characterization of the pig lower respiratory tract antibiotic resistome. Nat Commun 2023; 14:4868. [PMID: 37573429 PMCID: PMC10423206 DOI: 10.1038/s41467-023-40587-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 07/31/2023] [Indexed: 08/14/2023] Open
Abstract
Respiratory diseases and its treatments are highly concerned in both the pig industry and human health. However, the composition and distribution of antibiotic resistance genes (ARGs) in swine lower respiratory tract microbiome remain unknown. The relationships of ARGs with mobile genetic elements (MGEs) and lung health are unclear. Here, we characterize antibiotic resistomes of the swine lower respiratory tract microbiome containing 1228 open reading frames belonging to 372 ARGs using 745 metagenomes from 675 experimental pigs. Twelve ARGs conferring resistance to tetracycline are related to an MGE Tn916 family, and multiple types of ARGs are related to a transposase gene tnpA. Most of the linkage complexes between ARGs and MGEs (the Tn916 family and tnpA) are also observed in pig gut microbiomes and human lung microbiomes, suggesting the high risk of these MGEs mediating ARG transfer to both human and pig health. Gammaproteobacteria are the major ARG carriers, within which Escherichia coli harbored >50 ARGs and >10 MGEs. Although the microbial compositions structure the compositions of ARGs, we identify 73 ARGs whose relative abundances are significantly associated with the severity of lung lesions. Our results provide the first overview of ARG profiles in the swine lower respiratory tract microbiome.
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Affiliation(s)
- Yunyan Zhou
- National Key Laboratory of Swine Genetic Improvement and Germplasm Innovation, Jiangxi Agricultural University, Nanchang, 330045, China
- Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Jingquan Li
- National Key Laboratory of Swine Genetic Improvement and Germplasm Innovation, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Fei Huang
- National Key Laboratory of Swine Genetic Improvement and Germplasm Innovation, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Huashui Ai
- National Key Laboratory of Swine Genetic Improvement and Germplasm Innovation, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Jun Gao
- National Key Laboratory of Swine Genetic Improvement and Germplasm Innovation, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Congying Chen
- National Key Laboratory of Swine Genetic Improvement and Germplasm Innovation, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Lusheng Huang
- National Key Laboratory of Swine Genetic Improvement and Germplasm Innovation, Jiangxi Agricultural University, Nanchang, 330045, China.
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18
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Belizário J, Garay-Malpartida M, Faintuch J. Lung microbiome and origins of the respiratory diseases. CURRENT RESEARCH IN IMMUNOLOGY 2023; 4:100065. [PMID: 37456520 PMCID: PMC10339129 DOI: 10.1016/j.crimmu.2023.100065] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 05/08/2023] [Accepted: 06/13/2023] [Indexed: 07/18/2023] Open
Abstract
The studies on the composition of the human microbiomes in healthy individuals, its variability in the course of inflammation, infection, antibiotic therapy, diets and different pathological conditions have revealed their intra and inter-kingdom relationships. The lung microbiome comprises of major species members of the phylum Bacteroidetes, Firmicutes, Actinobacteria, Fusobacteria and Proteobacteria, which are distributed in ecological niches along nasal cavity, nasopharynx, oropharynx, trachea and in the lungs. Commensal and pathogenic species are maintained in equilibrium as they have strong relationships. Bacterial overgrowth after dysbiosis and/or imbalanced of CD4+ helper T cells, CD8+ cytotoxic T cells and regulatory T cells (Treg) populations can promote lung inflammatory reactions and distress, and consequently acute and chronic respiratory diseases. This review is aimed to summarize the latest advances in resident lung microbiome and its participation in most common pulmonary infections and pneumonia, community-acquired pneumonia (CAP), ventilator-associated pneumonia (VAP), immunodeficiency associated pneumonia, SARS-CoV-2-associated pneumonia, acute respiratory distress syndrome (ARDS) and chronic obstructive pulmonary disease (COPD). We briefly describe physiological and immunological mechanisms that selectively create advantages or disadvantages for relative growth of pathogenic bacterial species in the respiratory tract. At the end, we propose some directions and analytical methods that may facilitate the identification of key genera and species of resident and transient microbes involved in the respiratory diseases' initiation and progression.
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Affiliation(s)
- José Belizário
- School of Arts, Sciences and Humanities of the University of Sao Paulo, Rua Arlindo Bettio, 1000, São Paulo, CEP 03828-000, Brazil
| | - Miguel Garay-Malpartida
- School of Arts, Sciences and Humanities of the University of Sao Paulo, Rua Arlindo Bettio, 1000, São Paulo, CEP 03828-000, Brazil
| | - Joel Faintuch
- Department of Gastroenterology of the Clinics Hospital of the University of São Paulo, Av. Dr. Enéas de Carvalho Aguiar, 255, São Paulo, CEP 05403-000, Brazil
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19
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Calabrese F, Lunardi F, Baldasso E, Pezzuto F, Kilitci A, Olteanu GE, Del Vecchio C, Fortarezza F, Boscolo A, Schiavon M, Vedovelli L, Cattelan A, Gregori D, Rea F, Navalesi P. Comprehensive bronchoalveolar lavage characterization in COVID-19 associated acute respiratory distress syndrome patients: a prospective cohort study. Respir Res 2023; 24:152. [PMID: 37296478 DOI: 10.1186/s12931-023-02464-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
COVID-19-related acute respiratory distress syndrome (CARDS) is associated with high mortality rates. We still have limited knowledge of the complex alterations developing in the lung microenvironment. The goal of the present study was to comprehensively analyze the cellular components, inflammatory signature, and respiratory pathogens in bronchoalveolar lavage (BAL) of CARDS patients (16) in comparison to those of other invasively mechanically ventilated patients (24). In CARDS patients, BAL analysis revealed: SARS-CoV-2 infection frequently associated with other respiratory pathogens, significantly higher neutrophil granulocyte percentage, remarkably low interferon-gamma expression, and high levels of interleukins (IL)-1β and IL-9. The most important predictive variables for worse outcomes were age, IL-18 expression, and BAL neutrophilia. To the best of our knowledge, this is the first study that was able to identify, through a comprehensive analysis of BAL, several aspects relevant to the complex pathophysiology of CARDS.
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Affiliation(s)
- Fiorella Calabrese
- Department of Cardiac, Thoracic, Vascular Sciences, and Public Health, University of Padova Medical School, Padova, Italy.
- Pathological Anatomy Unit, Padova University Hospital, Padova, Italy.
| | - Francesca Lunardi
- Department of Cardiac, Thoracic, Vascular Sciences, and Public Health, University of Padova Medical School, Padova, Italy
- Pathological Anatomy Unit, Padova University Hospital, Padova, Italy
| | - Elisa Baldasso
- Department of Medicine, University of Padova Medical School, Padova, Italy
- Microbiology and Virology Unit, Padova University Hospital, Padova, Italy
| | - Federica Pezzuto
- Department of Cardiac, Thoracic, Vascular Sciences, and Public Health, University of Padova Medical School, Padova, Italy
- Pathological Anatomy Unit, Padova University Hospital, Padova, Italy
| | - Asuman Kilitci
- Department of Medical Pathology, Faculty of Medicine, Düzce University, Düzce, Turkey
| | - Gheorghe-Emilian Olteanu
- Department of Infectious Diseases, Discipline of Pulmonology, Center for Research and Innovation in Personalized Medicine of Respiratory Diseases, "Victor Babes" University of Medicine and Pharmacy, Timisoara, Romania
- Center of Expertise for Rare Lung Diseases, Clinical Hospital of Infectious Diseases and Pneumophisiology "Dr. Victor Babes", Timisoara, Romania
| | - Claudia Del Vecchio
- Department of Medicine, University of Padova Medical School, Padova, Italy
- Microbiology and Virology Unit, Padova University Hospital, Padova, Italy
| | | | - Annalisa Boscolo
- Department of Cardiac, Thoracic, Vascular Sciences, and Public Health, University of Padova Medical School, Padova, Italy
- Department of Medicine, University of Padova Medical School, Padova, Italy
- Institute of Anaesthesia and Intensive Care, Padova University Hospital, Padova, Italy
| | - Marco Schiavon
- Department of Cardiac, Thoracic, Vascular Sciences, and Public Health, University of Padova Medical School, Padova, Italy
- Thoracic Surgery Unit, Padova University Hospital, Padova, Italy
| | - Luca Vedovelli
- Department of Cardiac, Thoracic, Vascular Sciences, and Public Health, University of Padova Medical School, Padova, Italy
| | - Annamaria Cattelan
- Infectious Diseases Unit, Department of Medicine, Padova University Hospital, Padova, Italy
| | - Dario Gregori
- Department of Cardiac, Thoracic, Vascular Sciences, and Public Health, University of Padova Medical School, Padova, Italy
| | - Federico Rea
- Department of Cardiac, Thoracic, Vascular Sciences, and Public Health, University of Padova Medical School, Padova, Italy
- Thoracic Surgery Unit, Padova University Hospital, Padova, Italy
| | - Paolo Navalesi
- Department of Medicine, University of Padova Medical School, Padova, Italy
- Institute of Anaesthesia and Intensive Care, Padova University Hospital, Padova, Italy
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20
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Lu S, Zhou Y, Hu Y, Wang J, Li H, Lin Y, Wang D, Xian J, Zhao S, Ma J, Zhu Z, Yang S, Meng Q, Kang Y, Chen B, Li W. Metatranscriptomic analysis revealed Prevotella as a potential biomarker of oropharyngeal microbiomes in SARS-CoV-2 infection. Front Cell Infect Microbiol 2023; 13:1161763. [PMID: 37333851 PMCID: PMC10272425 DOI: 10.3389/fcimb.2023.1161763] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 05/09/2023] [Indexed: 06/20/2023] Open
Abstract
Background and objectives Disease severity and prognosis of coronavirus disease 2019 (COVID-19) disease with other viral infections can be affected by the oropharyngeal microbiome. However, limited research had been carried out to uncover how these diseases are differentially affected by the oropharyngeal microbiome of the patient. Here, we aimed to explore the characteristics of the oropharyngeal microbiota of COVID-19 patients and compare them with those of patients with similar symptoms. Methods COVID-19 was diagnosed in patients through the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by quantitative reverse transcription polymerase chain reaction (RT-qPCR). Characterization of the oropharyngeal microbiome was performed by metatranscriptomic sequencing analyses of oropharyngeal swab specimens from 144 COVID-19 patients, 100 patients infected with other viruses, and 40 healthy volunteers. Results The oropharyngeal microbiome diversity in patients with SARS-CoV-2 infection was different from that of patients with other infections. Prevotella and Aspergillus could play a role in the differentiation between patients with SARS-CoV-2 infection and patients with other infections. Prevotella could also influence the prognosis of COVID-19 through a mechanism that potentially involved the sphingolipid metabolism regulation pathway. Conclusion The oropharyngeal microbiome characterization was different between SARS-CoV-2 infection and infections caused by other viruses. Prevotella could act as a biomarker for COVID-19 diagnosis and of host immune response evaluation in SARS-CoV-2 infection. In addition, the cross-talk among Prevotella, SARS-CoV-2, and sphingolipid metabolism pathways could provide a basis for the precise diagnosis, prevention, control, and treatment of COVID-19.
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Affiliation(s)
- Sifen Lu
- Precision Medicine Key Laboratory of Sichuan Province and Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yongzhao Zhou
- Department of Integrated Care Management Center, Frontier Science Center of Disease Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Ya Hu
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Jing Wang
- Precision Medicine Key Laboratory of Sichuan Province and Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Honghao Li
- Department of Hospital Management, West China Hospital, Sichuan University, Chengdu, China
| | - Yifei Lin
- Precision Medicine Key Laboratory of Sichuan Province and Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Denian Wang
- Precision Medicine Key Laboratory of Sichuan Province and Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jinghong Xian
- Department of Clinical Research Management, West China Hospital, Sichuan University, Chengdu, China
| | - Shengmei Zhao
- Department of Clinical Research Management, West China Hospital, Sichuan University, Chengdu, China
| | - Jinmin Ma
- Beijing Genomics Institution (BGI)-PathoGenesis Pharmaceutical Technology, Beijing Genomics Institution (BGI)-Shenzhen, Shenzhen, China
| | - Zhongyi Zhu
- Beijing Genomics Institution (BGI)-PathoGenesis Pharmaceutical Technology, Beijing Genomics Institution (BGI)-Shenzhen, Shenzhen, China
| | - Shengying Yang
- Department of Computer and Software, Jincheng College of Chengdu, Chengdu, China
| | - Qinghui Meng
- Beijing Milu Ecological Research Center, Beijing Research Institute of Science and Technology, Beijing, China
| | - Yulin Kang
- Institute of Environmental Information, Chinese Research academy of Environmental Sciences, Beijing, China
| | - Bojiang Chen
- Precision Medicine Key Laboratory of Sichuan Province and Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Weimin Li
- Precision Medicine Key Laboratory of Sichuan Province and Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Integrated Care Management Center, Frontier Science Center of Disease Molecular Network, West China Hospital, Sichuan University, Chengdu, China
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21
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Forst CV, Zeng L, Wang Q, Zhou X, Vatansever S, Xu P, Song W, Tu Z, Zhang B. Multiscale network analysis identifies potential receptors for SARS-CoV-2 and reveals their tissue-specific and age-dependent expression. FEBS Lett 2023; 597:1384-1402. [PMID: 36951513 PMCID: PMC10294276 DOI: 10.1002/1873-3468.14613] [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: 07/11/2022] [Revised: 02/13/2023] [Accepted: 02/27/2023] [Indexed: 03/24/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has affected tens of millions of individuals and caused hundreds of thousands of deaths worldwide. Here, we present a comprehensive, multiscale network analysis of the transcriptional response to the virus. In particular, we focused on key regulators, cell receptors, and host processes that were hijacked by the virus for its advantage. ACE2-controlled processes involved CD300e (a TYROBP receptor) as a key regulator and the activation of IL-2 pro-inflammatory cytokine signaling. We further investigated the age dependency of such receptors in different tissues. In summary, this study provides novel insights into the gene regulatory organization during the SARS-CoV-2 infection and the tissue-specific, age-dependent expression of the cell receptors involved in COVID-19.
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Affiliation(s)
- Christian V. Forst
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNYUSA
- Mount Sinai Center for Transformative Disease ModelingIcahn School of Medicine at Mount SinaiNew YorkNYUSA
- Icahn Institute for Data Science and Genomic TechnologyIcahn School of Medicine at Mount SinaiNew YorkNYUSA
- Department of MicrobiologyIcahn School of Medicine at Mount SinaiNew YorkNYUSA
| | - Lu Zeng
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNYUSA
| | - Qian Wang
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNYUSA
- Mount Sinai Center for Transformative Disease ModelingIcahn School of Medicine at Mount SinaiNew YorkNYUSA
- Icahn Institute for Data Science and Genomic TechnologyIcahn School of Medicine at Mount SinaiNew YorkNYUSA
| | - Xianxiao Zhou
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNYUSA
- Mount Sinai Center for Transformative Disease ModelingIcahn School of Medicine at Mount SinaiNew YorkNYUSA
- Icahn Institute for Data Science and Genomic TechnologyIcahn School of Medicine at Mount SinaiNew YorkNYUSA
| | - Sezen Vatansever
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNYUSA
- Mount Sinai Center for Transformative Disease ModelingIcahn School of Medicine at Mount SinaiNew YorkNYUSA
- Icahn Institute for Data Science and Genomic TechnologyIcahn School of Medicine at Mount SinaiNew YorkNYUSA
| | - Peng Xu
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNYUSA
- Mount Sinai Center for Transformative Disease ModelingIcahn School of Medicine at Mount SinaiNew YorkNYUSA
- Icahn Institute for Data Science and Genomic TechnologyIcahn School of Medicine at Mount SinaiNew YorkNYUSA
| | - Won‐Min Song
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNYUSA
- Mount Sinai Center for Transformative Disease ModelingIcahn School of Medicine at Mount SinaiNew YorkNYUSA
- Icahn Institute for Data Science and Genomic TechnologyIcahn School of Medicine at Mount SinaiNew YorkNYUSA
| | - Zhidong Tu
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNYUSA
- Icahn Institute for Data Science and Genomic TechnologyIcahn School of Medicine at Mount SinaiNew YorkNYUSA
| | - Bin Zhang
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNYUSA
- Mount Sinai Center for Transformative Disease ModelingIcahn School of Medicine at Mount SinaiNew YorkNYUSA
- Icahn Institute for Data Science and Genomic TechnologyIcahn School of Medicine at Mount SinaiNew YorkNYUSA
- Department of Pharmacological SciencesIcahn School of Medicine at Mount SinaiNew YorkNYUSA
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22
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Bermejo-Martin JF, García-Mateo N, Motos A, Resino S, Tamayo L, Ryan Murua P, Bustamante-Munguira E, Gallego Curto E, Úbeda-Iglesias A, de la Torre MDC, Estella Á, Campos-Fernández S, Martínez Varela I, Pérez-García F, Socias L, López Messa J, Vidal-Cortés P, Sagredo Meneses V, González-Rivera M, Carbonell N, de Gonzalo-Calvo D, Martín Delgado MC, Valdivia LJ, Martín-López C, Jorge García RN, Maseda E, Loza-Vázquez A, Kelvin DJ, Barbé F, Torres A. Effect of viral storm in patients admitted to intensive care units with severe COVID-19 in Spain: a multicentre, prospective, cohort study. THE LANCET. MICROBE 2023:S2666-5247(23)00041-1. [PMID: 37116517 PMCID: PMC10129133 DOI: 10.1016/s2666-5247(23)00041-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 01/09/2023] [Accepted: 02/08/2023] [Indexed: 04/30/2023]
Abstract
BACKGROUND The contribution of the virus to the pathogenesis of severe COVID-19 is still unclear. We aimed to evaluate associations between viral RNA load in plasma and host response, complications, and deaths in critically ill patients with COVID-19. METHODS We did a prospective cohort study across 23 hospitals in Spain. We included patients aged 18 years or older with laboratory-confirmed SARS-CoV-2 infection who were admitted to an intensive care unit between March 16, 2020, and Feb 27, 2021. RNA of the SARS-CoV-2 nucleocapsid region 1 (N1) was quantified in plasma samples collected from patients in the first 48 h following admission, using digital PCR. Patients were grouped on the basis of N1 quantity: VIR-N1-Zero (<1 N1 copies per mL), VIR-N1-Low (1-2747 N1 copies per mL), and VIR-N1-Storm (>2747 N1 copies per mL). The primary outcome was all-cause death within 90 days after admission. We evaluated odds ratios (ORs) for the primary outcome between groups using a logistic regression analysis. FINDINGS 1068 patients met the inclusion criteria, of whom 117 had insufficient plasma samples and 115 had key information missing. 836 patients were included in the analysis, of whom 403 (48%) were in the VIR-N1-Low group, 283 (34%) were in the VIR-N1-Storm group, and 150 (18%) were in the VIR-N1-Zero group. Overall, patients in the VIR-N1-Storm group had the most severe disease: 266 (94%) of 283 patients received invasive mechanical ventilation (IMV), 116 (41%) developed acute kidney injury, 180 (65%) had secondary infections, and 148 (52%) died within 90 days. Patients in the VIR-N1-Zero group had the least severe disease: 81 (54%) of 150 received IMV, 34 (23%) developed acute kidney injury, 47 (32%) had secondary infections, and 26 (17%) died within 90 days (OR for death 0·30, 95% CI 0·16-0·55; p<0·0001, compared with the VIR-N1-Storm group). 106 (26%) of 403 patients in the VIR-N1-Low group died within 90 days (OR for death 0·39, 95% CI 0·26-0·57; p<0·0001, compared with the VIR-N1-Storm group). INTERPRETATION The presence of a so-called viral storm is associated with increased all-cause death in patients admitted to the intensive care unit with severe COVID-19. Preventing this viral storm could help to reduce poor outcomes. Viral storm could be an enrichment marker for treatment with antivirals or purification devices to remove viral components from the blood. FUNDING Instituto de Salud Carlos III, Canadian Institutes of Health Research, Li Ka-Shing Foundation, Research Nova Scotia, and European Society of Clinical Microbiology and Infectious Diseases. TRANSLATION For the Spanish translation of the abstract see Supplementary Materials section.
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Affiliation(s)
- Jesús F Bermejo-Martin
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, Gerencia Regional de Salud de Castilla y León, Salamanca, Spain; Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain; Research Unit, Hospital Universitario Rio Hortega, Gerencia Regional de Salud de Castilla y León, Valladolid, Spain; School of Medicine, Universidad de Salamanca, Salamanca, Spain.
| | - Nadia García-Mateo
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, Gerencia Regional de Salud de Castilla y León, Salamanca, Spain
| | - Anna Motos
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain; Department of Pulmonology, Hospital Clinic de Barcelona, Institut D Investigacions August Pi I Sunyer (IDIBAPS), Universidad de Barcelona, Barcelona, Spain
| | - Salvador Resino
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain; Viral Infection and Immunity Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain
| | - Luis Tamayo
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain; Critical Care Medicine Service, Hospital Universitario Rio Hortega, Gerencia Regional de Salud de Castilla y León, Valladolid, Spain
| | - Pablo Ryan Murua
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain; Internal Medicine Service, Hospital Infanta Leonor, Madrid, Spain
| | - Elena Bustamante-Munguira
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain; Critical Care Medicine Service, Hospital Clínico Universitario de Valladolid, Gerencia Regional de Salud de Castilla y León, Valladolid, Spain
| | - Elena Gallego Curto
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain; Critical Care Medicine Service, Hospital San Pedro de Alcántara, Cáceres, Spain
| | | | | | - Ángel Estella
- Intensive Care Unit, Hospital Universitario de Jerez, Departamento de Medicina Universidad de Cádiz, INiBICA, Cádiz, Spain
| | - Sandra Campos-Fernández
- Critical Care Medicine Service, Hospital Universitario Marqués de Valdecilla, Santander, Spain
| | | | - Felipe Pérez-García
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain; Clinical Microbiology Service, Hospital Universitario Príncipe de Asturias, Alcalá de Henares, Spain; Biomedicine and Biotechnology Department, Faculty of Medicine, Universidad de Alcalá, Alcalá de Henares, Spain
| | | | - Juan López Messa
- Critical Care Medicine Service, Complejo Asistencial Universitario de Palencia, Palencia, Spain
| | - Pablo Vidal-Cortés
- Intensive Care Unit, Complejo Hospitalario Universitario de Ourense, Ourense, Spain
| | | | | | - Nieves Carbonell
- Intensive Care Unit, Hospital Clínico Universitario de Valencia, Valencia, Spain
| | - David de Gonzalo-Calvo
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain; Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, Lleida, Spain
| | | | | | | | | | - Emilio Maseda
- Anesthesiology and Reanimation Service, Hospital Universitario de la Paz, Madrid, Spain
| | - Ana Loza-Vázquez
- Critical Care Medicine Service, Hospital Universitario Nuestra Señora de Valme, Sevilla, Spain
| | - David J Kelvin
- Department of Microbiology and Immunology, Faculty of Medicine, Canadian Center for Vaccinology, Dalhousie University, Halifax, NS, Canada; Laboratory of Immunity, Shantou University Medical College, Shantou, Guangdong, China
| | - Ferrán Barbé
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain; Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, Lleida, Spain
| | - Antoni Torres
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain; Department of Pulmonology, Hospital Clinic de Barcelona, Institut D Investigacions August Pi I Sunyer (IDIBAPS), Universidad de Barcelona, Barcelona, Spain
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23
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Zafar H, Saier MH. Understanding the Relationship of the Human Bacteriome with COVID-19 Severity and Recovery. Cells 2023; 12:cells12091213. [PMID: 37174613 PMCID: PMC10177376 DOI: 10.3390/cells12091213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/05/2023] [Accepted: 04/11/2023] [Indexed: 05/15/2023] Open
Abstract
The Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) first emerged in 2019 in China and has resulted in millions of human morbidities and mortalities across the globe. Evidence has been provided that this novel virus originated in animals, mutated, and made the cross-species jump to humans. At the time of this communication, the Coronavirus disease (COVID-19) may be on its way to an endemic form; however, the threat of the virus is more for susceptible (older and immunocompromised) people. The human body has millions of bacterial cells that influence health and disease. As a consequence, the bacteriomes in the human body substantially influence human health and disease. The bacteriomes in the body and the immune system seem to be in constant association during bacterial and viral infections. In this review, we identify various bacterial spp. In major bacteriomes (oral, nasal, lung, and gut) of the body in healthy humans and compare them with dysbiotic bacteriomes of COVID-19 patients. We try to identify key bacterial spp. That have a positive effect on the functionality of the immune system and human health. These select bacterial spp. Could be used as potential probiotics to counter or prevent COVID-19 infections. In addition, we try to identify key metabolites produced by probiotic bacterial spp. That could have potential anti-viral effects against SARS-CoV-2. These metabolites could be subject to future therapeutic trials to determine their anti-viral efficacies.
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Affiliation(s)
- Hassan Zafar
- Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, CA 92093-0116, USA
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | - Milton H Saier
- Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, CA 92093-0116, USA
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24
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Wu J, Liu W, Zhu L, Li N, Luo G, Gu M, Peng M, Zeng S, Wu S, Zhang S, Chen Q, Cai M, Cao W, Jiang Y, Luo C, Tian D, Shi M, Shu Y, Chang G, Luo H. Dysbiosis of oropharyngeal microbiome and antibiotic resistance in hospitalized COVID-19 patients. J Med Virol 2023; 95:e28727. [PMID: 37185870 DOI: 10.1002/jmv.28727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/28/2023] [Accepted: 04/04/2023] [Indexed: 05/17/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic is ongoing and multiple studies have elucidated its pathogenesis, however, the related- microbiome imbalance caused by SARS-CoV-2 is still not clear. In this study, we have comprehensively compared the microbiome composition and associated function alterations in the oropharyngeal swabs of healthy controls and coronavirus disease 2019 (COVID-19) patients with moderate or severe symptoms by metatranscriptomic sequencing. We did observe a reduced microbiome alpha-diversity but significant enrichment of opportunistic microorganisms in patients with COVID-19 compared with healthy controls, and the microbial homeostasis was rebuilt following the recovery of COVID-19 patients. Correspondingly, less functional genes in multiple biological processes and weakened metabolic pathways such as carbohydrate metabolism, energy metabolism were also observed in COVID-19 patients. We only found higher relative abundance of limited genera such as Lachnoanaerobaculum between severe patients and moderate patients while no worthy-noting microbiome diversity and function alteration were observed. Finally, we noticed that the co-occurrence of antibiotic resistance and virulence was closely related to the microbiome alteration caused by SRAS-CoV-2. Overall, our findings demonstrate that microbial dysbiosis may enhance the pathogenesis of SARS-CoV-2 and the antibiotics treatment should be critically considered.
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Affiliation(s)
- Jiani Wu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
- Department of AIDS and STD Control and Prevention, Shaoxing Center for Disease Control and Prevention, Shaoxing, China
| | - Wei Liu
- Department of Immunology, Center for Disease Prevention and Control of PLA, Beijing, China
| | - Lin Zhu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Nina Li
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Gengyan Luo
- The Centre for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Ming Gu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Minwu Peng
- The Centre for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Shike Zeng
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Shu Wu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Shengze Zhang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Qiqi Chen
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Meiqi Cai
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Wei Cao
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Ying Jiang
- Environment Health Department, Shenzhen Nanshan Center for Disease Control and Prevention, Shenzhen, China
| | - Chuming Luo
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Dechao Tian
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Mang Shi
- The Centre for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Yuelong Shu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Guohui Chang
- Department of Immunology, Center for Disease Prevention and Control of PLA, Beijing, China
| | - Huanle Luo
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Shenzhen, China
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25
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Anesi GL, Andrews A, Bai HJ, Bhatraju PK, Brett-Major DM, Broadhurst MJ, Campbell ES, Cobb JP, Gonzalez M, Homami S, Hypes CD, Irwin A, Kratochvil CJ, Krolikowski K, Kumar VK, Landsittel DP, Lee RA, Liebler JM, Lutrick K, Marts LT, Mosier JM, Mukherjee V, Postelnicu R, Rodina V, Segal LN, Sevransky JE, Spainhour C, Srivastava A, Uyeki TM, Wurfel MM, Wyles D, Evans L. Perceived Hospital Stress, Severe Acute Respiratory Syndrome Coronavirus 2 Activity, and Care Process Temporal Variance During the COVID-19 Pandemic. Crit Care Med 2023; 51:445-459. [PMID: 36790189 PMCID: PMC10012837 DOI: 10.1097/ccm.0000000000005802] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
OBJECTIVES The COVID-19 pandemic threatened standard hospital operations. We sought to understand how this stress was perceived and manifested within individual hospitals and in relation to local viral activity. DESIGN Prospective weekly hospital stress survey, November 2020-June 2022. SETTING Society of Critical Care Medicine's Discovery Severe Acute Respiratory Infection-Preparedness multicenter cohort study. SUBJECTS Thirteen hospitals across seven U.S. health systems. INTERVENTIONS None. MEASUREMENTS AND MAIN RESULTS We analyzed 839 hospital-weeks of data over 85 pandemic weeks and five viral surges. Perceived overall hospital, ICU, and emergency department (ED) stress due to severe acute respiratory infection patients during the pandemic were reported by a mean of 43% ( sd , 36%), 32% (30%), and 14% (22%) of hospitals per week, respectively, and perceived care deviations in a mean of 36% (33%). Overall hospital stress was highly correlated with ICU stress (ρ = 0.82; p < 0.0001) but only moderately correlated with ED stress (ρ = 0.52; p < 0.0001). A county increase in 10 severe acute respiratory syndrome coronavirus 2 cases per 100,000 residents was associated with an increase in the odds of overall hospital, ICU, and ED stress by 9% (95% CI, 5-12%), 7% (3-10%), and 4% (2-6%), respectively. During the Delta variant surge, overall hospital stress persisted for a median of 11.5 weeks (interquartile range, 9-14 wk) after local case peak. ICU stress had a similar pattern of resolution (median 11 wk [6-14 wk] after local case peak; p = 0.59) while the resolution of ED stress (median 6 wk [5-6 wk] after local case peak; p = 0.003) was earlier. There was a similar but attenuated pattern during the Omicron BA.1 subvariant surge. CONCLUSIONS During the COVID-19 pandemic, perceived care deviations were common and potentially avoidable patient harm was rare. Perceived hospital stress persisted for weeks after surges peaked.
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Affiliation(s)
- George L Anesi
- Division of Pulmonary, Allergy, and Critical Care, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Adair Andrews
- Society of Critical Care Medicine, Mount Prospect, IL
| | - He Julia Bai
- Department of Epidemiology, College of Public Health, University of Nebraska Medical Center, Omaha, NE
| | - Pavan K Bhatraju
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington School of Medicine, Seattle, WA
| | - David M Brett-Major
- Department of Epidemiology, College of Public Health, University of Nebraska Medical Center, Omaha, NE
- Global Center for Health Security, University of Nebraska Medical Center, Omaha, NE
| | - M Jana Broadhurst
- Global Center for Health Security, University of Nebraska Medical Center, Omaha, NE
- Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, Omaha, NE
| | | | - J Perren Cobb
- Departments of Surgery and Anesthesiology, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | | | - Sonya Homami
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington School of Medicine, Seattle, WA
| | - Cameron D Hypes
- Department of Emergency Medicine, College of Medicine, University of Arizona, Tucson, AZ
- Division of Pulmonary, Allergy, Critical Care and Sleep, Department of Medicine, College of Medicine, University of Arizona, Tucson, AZ
| | - Amy Irwin
- Division of Infectious Diseases, Denver Health Medical Center, Denver, CO
| | | | - Kelsey Krolikowski
- Division of Pulmonary, Critical Care, and Sleep Medicine, NYU Grossman School of Medicine, NYU Langone Health, New York, NY
| | | | - Douglas P Landsittel
- Department of Epidemiology and Biostatistics, School of Public Health, Indiana University, Bloomington, IN
| | - Richard A Lee
- Division of Pulmonary Diseases and Critical Care Medicine, University of California, Irvine, School of Medicine, Irvine, CA
| | - Janice M Liebler
- Division of Pulmonary, Critical Care and Sleep Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Karen Lutrick
- Department of Family and Community Medicine, College of Medicine, University of Arizona, Tucson, AZ
| | - Lucian T Marts
- Division of Pulmonary, Allergy, Critical Care and Sleep, School of Medicine, Emory University, Atlanta, GA
| | - Jarrod M Mosier
- Department of Emergency Medicine, College of Medicine, University of Arizona, Tucson, AZ
- Division of Pulmonary, Allergy, Critical Care and Sleep, Department of Medicine, College of Medicine, University of Arizona, Tucson, AZ
| | - Vikramjit Mukherjee
- Division of Pulmonary, Critical Care, and Sleep Medicine, NYU Grossman School of Medicine, NYU Langone Health, New York, NY
| | - Radu Postelnicu
- Division of Pulmonary, Critical Care, and Sleep Medicine, NYU Grossman School of Medicine, NYU Langone Health, New York, NY
| | - Valentina Rodina
- Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Leopoldo N Segal
- Division of Pulmonary, Critical Care, and Sleep Medicine, NYU Grossman School of Medicine, NYU Langone Health, New York, NY
| | - Jonathan E Sevransky
- Division of Pulmonary, Allergy, Critical Care and Sleep, School of Medicine, Emory University, Atlanta, GA
- Emory Critical Care Center, Emory Healthcare, Atlanta, GA
| | | | - Avantika Srivastava
- Department of Biomedical Informatics, School of Medicine, University of Pittsburgh, Pittsburgh, PA
| | - Timothy M Uyeki
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention (CDC), Atlanta, GA
| | - Mark M Wurfel
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington School of Medicine, Seattle, WA
| | - David Wyles
- Division of Infectious Diseases, Denver Health Medical Center, Denver, CO
| | - Laura Evans
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington School of Medicine, Seattle, WA
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26
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Abstract
New methods and technologies within the field of lung biology are beginning to shed new light into the microbial world of the respiratory tract. Long considered to be a sterile environment, it is now clear that the human lungs are frequently exposed to live microbes and their by-products. The nature of the lung microbiome is quite distinct from other microbial communities inhabiting our bodies such as those in the gut. Notably, the microbiome of the lung exhibits a low biomass and is dominated by dynamic fluxes of microbial immigration and clearance, resulting in a bacterial burden and microbiome composition that is fluid in nature rather than fixed. As our understanding of the microbial ecology of the lung improves, it is becoming increasingly apparent that certain disease states can disrupt the microbial-host interface and ultimately affect disease pathogenesis. In this Review, we provide an overview of lower airway microbial dynamics in health and disease and discuss future work that is required to uncover novel therapeutic targets to improve lung health.
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27
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Tsounis EP, Triantos C, Konstantakis C, Marangos M, Assimakopoulos SF. Intestinal barrier dysfunction as a key driver of severe COVID-19. World J Virol 2023; 12:68-90. [PMID: 37033148 PMCID: PMC10075050 DOI: 10.5501/wjv.v12.i2.68] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/08/2022] [Accepted: 01/16/2023] [Indexed: 03/21/2023] Open
Abstract
The intestinal lumen harbors a diverse consortium of microorganisms that participate in reciprocal crosstalk with intestinal immune cells and with epithelial and endothelial cells, forming a multi-layered barrier that enables the efficient absorption of nutrients without an excessive influx of pathogens. Despite being a lung-centered disease, severe coronavirus disease 2019 (COVID-19) affects multiple systems, including the gastrointestinal tract and the pertinent gut barrier function. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can inflict either direct cytopathic injury to intestinal epithelial and endothelial cells or indirect immune-mediated damage. Alternatively, SARS-CoV-2 undermines the structural integrity of the barrier by modifying the expression of tight junction proteins. In addition, SARS-CoV-2 induces profound alterations to the intestinal microflora at phylogenetic and metabolomic levels (dysbiosis) that are accompanied by disruption of local immune responses. The ensuing dysregulation of the gut-lung axis impairs the ability of the respiratory immune system to elicit robust and timely responses to restrict viral infection. The intestinal vasculature is vulnerable to SARS-CoV-2-induced endothelial injury, which simultaneously triggers the activation of the innate immune and coagulation systems, a condition referred to as “immunothrombosis” that drives severe thrombotic complications. Finally, increased intestinal permeability allows an aberrant dissemination of bacteria, fungi, and endotoxin into the systemic circulation and contributes, to a certain degree, to the over-exuberant immune responses and hyper-inflammation that dictate the severe form of COVID-19. In this review, we aim to elucidate SARS-CoV-2-mediated effects on gut barrier homeostasis and their implications on the progression of the disease.
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Affiliation(s)
- Efthymios P Tsounis
- Division of Gastroenterology, Department of Internal Medicine, Medical School, University Hospital of Patras, Patras 26504, Greece
| | - Christos Triantos
- Division of Gastroenterology, Department of Internal Medicine, Medical School, University Hospital of Patras, Patras 26504, Greece
| | - Christos Konstantakis
- Division of Gastroenterology, Department of Internal Medicine, Medical School, University Hospital of Patras, Patras 26504, Greece
| | - Markos Marangos
- Division of Infectious Diseases, Department of Internal Medicine, Medical School, University of Patras, University Hospital of Patras, Patras 26504, Greece
| | - Stelios F Assimakopoulos
- Division of Infectious Diseases, Department of Internal Medicine, Medical School, University of Patras, University Hospital of Patras, Patras 26504, Greece
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28
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D'Alessandro VF, D'Alessandro-Gabazza CN, Yasuma T, Toda M, Takeshita A, Tomaru A, Tharavecharak S, Lasisi IO, Hess RY, Nishihama K, Fujimoto H, Kobayashi T, Cann I, Gabazza EC. Inhibition of a Microbiota-derived Peptide Ameliorates Established Acute Lung Injury. THE AMERICAN JOURNAL OF PATHOLOGY 2023:S0002-9440(23)00113-X. [PMID: 36965776 PMCID: PMC10035802 DOI: 10.1016/j.ajpath.2023.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 02/20/2023] [Accepted: 03/07/2023] [Indexed: 03/25/2023]
Abstract
Acute lung injury is a clinical syndrome characterized by a diffuse lung inflammation that commonly evolves into acute respiratory distress syndrome and respiratory failure. The lung microbiota is involved in the pathogenesis of acute lung injury. Corisin, a proapoptotic peptide derived from the lung microbiota, plays a role in acute lung injury and acute exacerbation of pulmonary fibrosis. Preventive therapeutic intervention with a monoclonal anticorisin antibody inhibits acute lung injury in mice. However, whether inhibition of corisin with the antibody ameliorates established acute lung injury is unknown. Here, the therapeutic effectiveness of the anticorisin antibody in already established acute lung injury in mice was assessed. Lipopolysaccharide was used to induce acute lung injury in mice. After causing acute lung injury, the mice were treated with a neutralizing anticorisin antibody. Mice treated with the antibody showed significant improvement in lung radiological and histopathological findings, decreased lung infiltration of inflammatory cells, reduced markers of lung tissue damage, and inflammatory cytokines in bronchoalveolar lavage fluid compared to untreated mice. In addition, the mice treated with anticorisin antibody showed significantly increased expression of antiapoptotic proteins with decreased caspase-3 activation in the lungs compared to control mice treated with an irrelevant antibody. In conclusion, these observations suggest that the inhibition of corisin is a novel and promising approach for treating established acute lung injury.
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Affiliation(s)
- Valeria Fridman D'Alessandro
- Department of Immunology, Mie University Faculty and Graduate School of Medicine, Edobashi 2-174, Tsu, Mie 514-8507, Japan
| | - Corina N D'Alessandro-Gabazza
- Department of Immunology, Mie University Faculty and Graduate School of Medicine, Edobashi 2-174, Tsu, Mie 514-8507, Japan;; Center for Intractable Diseases, Mie University, Edobashi 2-174, Tsu, Mie 514-8507, Japan; Carl R. Woese Institute for Genomic Biology (Microbiome Metabolic Engineering), University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Taro Yasuma
- Department of Immunology, Mie University Faculty and Graduate School of Medicine, Edobashi 2-174, Tsu, Mie 514-8507, Japan;; Department of Diabetes and Endocrinology, Mie University Faculty and Graduate School of Medicine, Edobashi 2-174, Tsu, Mie 514-8507, Japan
| | - Masaaki Toda
- Department of Immunology, Mie University Faculty and Graduate School of Medicine, Edobashi 2-174, Tsu, Mie 514-8507, Japan
| | - Atsuro Takeshita
- Department of Immunology, Mie University Faculty and Graduate School of Medicine, Edobashi 2-174, Tsu, Mie 514-8507, Japan;; Department of Diabetes and Endocrinology, Mie University Faculty and Graduate School of Medicine, Edobashi 2-174, Tsu, Mie 514-8507, Japan
| | - Atsushi Tomaru
- Department of Pulmonary and Critical care Medicine, Mie University Faculty and Graduate School of Medicine, Edobashi 2-174, Tsu, Mie 514-8507, Japan
| | - Suphachai Tharavecharak
- Department of Immunology, Mie University Faculty and Graduate School of Medicine, Edobashi 2-174, Tsu, Mie 514-8507, Japan
| | - Isaiah O Lasisi
- School of Molecular and Cellular Biology, the University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Rebecca Y Hess
- School of Molecular and Cellular Biology, the University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Kota Nishihama
- Department of Diabetes and Endocrinology, Mie University Faculty and Graduate School of Medicine, Edobashi 2-174, Tsu, Mie 514-8507, Japan
| | - Hajime Fujimoto
- Department of Pulmonary and Critical care Medicine, Mie University Faculty and Graduate School of Medicine, Edobashi 2-174, Tsu, Mie 514-8507, Japan
| | - Tetsu Kobayashi
- Department of Pulmonary and Critical care Medicine, Mie University Faculty and Graduate School of Medicine, Edobashi 2-174, Tsu, Mie 514-8507, Japan
| | - Isaac Cann
- School of Molecular and Cellular Biology, the University of Illinois at Urbana-Champaign, Urbana, IL, United States; Department of Animal Science, the University of Illinois at Urbana-Champaign, Urbana, IL, United States; Department of Microbiology, the University of Illinois at Urbana-Champaign, Urbana, IL, United States; Division of Nutritional Sciences, the University of Illinois at Urbana-Champaign, Urbana, IL, United States; Center for East Asian & Pacific Studies, the University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Esteban C Gabazza
- Department of Immunology, Mie University Faculty and Graduate School of Medicine, Edobashi 2-174, Tsu, Mie 514-8507, Japan;; Center for Intractable Diseases, Mie University, Edobashi 2-174, Tsu, Mie 514-8507, Japan; Carl R. Woese Institute for Genomic Biology (Microbiome Metabolic Engineering), University of Illinois at Urbana-Champaign, Urbana, IL, United States.
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29
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Langford BJ, So M, Simeonova M, Leung V, Lo J, Kan T, Raybardhan S, Sapin ME, Mponponsuo K, Farrell A, Leung E, Soucy JPR, Cassini A, MacFadden D, Daneman N, Bertagnolio S. Antimicrobial resistance in patients with COVID-19: a systematic review and meta-analysis. THE LANCET. MICROBE 2023; 4:e179-e191. [PMID: 36736332 PMCID: PMC9889096 DOI: 10.1016/s2666-5247(22)00355-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 10/08/2022] [Accepted: 11/24/2022] [Indexed: 02/03/2023]
Abstract
BACKGROUND Frequent use of antibiotics in patients with COVID-19 threatens to exacerbate antimicrobial resistance. We aimed to establish the prevalence and predictors of bacterial infections and antimicrobial resistance in patients with COVID-19. METHODS We did a systematic review and meta-analysis of studies of bacterial co-infections (identified within ≤48 h of presentation) and secondary infections (>48 h after presentation) in outpatients or hospitalised patients with COVID-19. We searched the WHO COVID-19 Research Database to identify cohort studies, case series, case-control trials, and randomised controlled trials with populations of at least 50 patients published in any language between Jan 1, 2019, and Dec 1, 2021. Reviews, editorials, letters, pre-prints, and conference proceedings were excluded, as were studies in which bacterial infection was not microbiologically confirmed (or confirmed via nasopharyngeal swab only). We screened titles and abstracts of papers identified by our search, and then assessed the full text of potentially relevant articles. We reported the pooled prevalence of bacterial infections and antimicrobial resistance by doing a random-effects meta-analysis and meta-regression. Our primary outcomes were the prevalence of bacterial co-infection and secondary infection, and the prevalence of antibiotic-resistant pathogens among patients with laboratory-confirmed COVID-19 and bacterial infections. The study protocol was registered with PROSPERO (CRD42021297344). FINDINGS We included 148 studies of 362 976 patients, which were done between December, 2019, and May, 2021. The prevalence of bacterial co-infection was 5·3% (95% CI 3·8-7·4), whereas the prevalence of secondary bacterial infection was 18·4% (14·0-23·7). 42 (28%) studies included comprehensive data for the prevalence of antimicrobial resistance among bacterial infections. Among people with bacterial infections, the proportion of infections that were resistant to antimicrobials was 60·8% (95% CI 38·6-79·3), and the proportion of isolates that were resistant was 37·5% (26·9-49·5). Heterogeneity in the reported prevalence of antimicrobial resistance in organisms was substantial (I2=95%). INTERPRETATION Although infrequently assessed, antimicrobial resistance is highly prevalent in patients with COVID-19 and bacterial infections. Future research and surveillance assessing the effect of COVID-19 on antimicrobial resistance at the patient and population level are urgently needed. FUNDING WHO.
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Affiliation(s)
- Bradley J Langford
- Public Health Ontario, Toronto, ON, Canada; Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada.
| | - Miranda So
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada; University Health Network, Toronto, ON, Canada
| | | | - Valerie Leung
- Public Health Ontario, Toronto, ON, Canada; Toronto East Health Network, Toronto, ON, Canada
| | - Jennifer Lo
- Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Tiffany Kan
- North York General Hospital, Toronto, ON, Canada
| | | | - Mia E Sapin
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, ON, Canada
| | - Kwadwo Mponponsuo
- University of Calgary, Calgary, AB, Canada; Alberta Health Services, Calgary, AB, Canada
| | | | - Elizabeth Leung
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada; Unity Health Toronto, Toronto, ON, UK
| | - Jean-Paul R Soucy
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | | | - Derek MacFadden
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, ON, Canada; Ottawa Hospital, Ottawa, ON, Canada
| | - Nick Daneman
- Public Health Ontario, Toronto, ON, Canada; Sunnybrook Health Sciences Centre, Toronto, ON, Canada
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30
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Ojala T, Kankuri E, Kankainen M. Understanding human health through metatranscriptomics. Trends Mol Med 2023; 29:376-389. [PMID: 36842848 DOI: 10.1016/j.molmed.2023.02.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 02/02/2023] [Accepted: 02/08/2023] [Indexed: 02/27/2023]
Abstract
Metatranscriptomics has revolutionized our ability to explore and understand transcriptional programs in microbial communities. Moreover, it has enabled us to gain deeper and more specific insight into the microbial activities in human gut, respiratory, oral, and vaginal communities. Perhaps the most important contribution of metatranscriptomics arises, however, from the analyses of disease-associated communities. We review the advantages and disadvantages of metatranscriptomics analyses in understanding human health and disease. We focus on human tissues low in microbial biomass and conditions associated with dysbiotic microbiota. We conclude that a more widespread use of metatranscriptomics and increased knowledge on microbe activities will uncover critical interactions between microbes and host in human health and provide diagnostic basis for culturing-independent, direct functional pathogen identification.
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Affiliation(s)
- Teija Ojala
- Department of Pharmacology, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Laboratory of Genetics, HUS Diagnostic Center, Hospital District of Helsinki and Uusimaa (HUS), Helsinki, Finland
| | - Esko Kankuri
- Department of Pharmacology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Matti Kankainen
- Laboratory of Genetics, HUS Diagnostic Center, Hospital District of Helsinki and Uusimaa (HUS), Helsinki, Finland; Hematology Research Unit Helsinki, University of Helsinki, Helsinki, Finland.
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31
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Lavrinenko A, Kolesnichenko S, Kadyrova I, Turmukhambetova A, Akhmaltdinova L, Klyuyev D. Bacterial Co-Infections and Antimicrobial Resistance in Patients Hospitalized with Suspected or Confirmed COVID-19 Pneumonia in Kazakhstan. Pathogens 2023; 12:pathogens12030370. [PMID: 36986292 PMCID: PMC10052929 DOI: 10.3390/pathogens12030370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 02/26/2023] Open
Abstract
Our study was carried out to characterize respiratory tract microbiota in patients with “COVID-like pneumonia” in Kazakhstan and analyze differences between COVID-19 positive and negative groups. Sputum samples were collected from hospitalized patients, ≥18 years old, in the three cities in Kazakhstan with the highest COVID-19 burden in July 2020. Isolates were identified by MALDI-TOF MS. Susceptibility testing was performed by disk diffusion. We used SPSS 26 and MedCalc 19 for statistical analysis. Among 209 patients with pneumonia, the median age was 62 years and 55% were male. RT-PCR-confirmed SARS-CoV-2 cases were found in 40% of patients, and 46% had a bacterial co-infection. Co-infection was not associated with SARS-CoV-2 RT-PCR test results, but antibiotic use was. The most frequent bacteria were Klebsiella pneumoniae (23%), Escherichia coli (12%), and Acinetobacter baumannii (11%). Notably, 68% of Klebsiella pneumoniae had phenotypic evidence of extended-spectrum beta-lactamases in disk diffusion assays, 87% of Acinetobacter baumannii exhibited resistance to beta-lactams, and >50% of E. coli strains had evidence of ESBL production and 64% were resistant to fluoroquinolones. Patients with a bacterial co-infection had a higher proportion of severe disease than those without a co-infection. The results reinforce the importance of using appropriate targeted antibiotics and effective infection control practices to prevent the spread of resistant nosocomial infections.
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Affiliation(s)
- Alyona Lavrinenko
- Research Laboratory, Karaganda Medical University, Karaganda 100008, Kazakhstan
| | - Svetlana Kolesnichenko
- Research Laboratory, Karaganda Medical University, Karaganda 100008, Kazakhstan
- Correspondence: ; Tel.: +7-702-599-0225
| | - Irina Kadyrova
- Research Laboratory, Karaganda Medical University, Karaganda 100008, Kazakhstan
| | - Anar Turmukhambetova
- Management Department, Karaganda Medical University, Karaganda 100008, Kazakhstan
| | | | - Dmitriy Klyuyev
- Research Laboratory, Karaganda Medical University, Karaganda 100008, Kazakhstan
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Kwok B, Wu BG, Kocak IF, Sulaiman I, Schluger R, Li Y, Anwer R, Goparaju C, Ryan DJ, Sagatelian M, Dreier MS, Murthy V, Rafeq S, Michaud GC, Sterman DH, Bessich JL, Pass HI, Segal LN, Tsay JCJ. Pleural fluid microbiota as a biomarker for malignancy and prognosis. Sci Rep 2023; 13:2229. [PMID: 36755121 PMCID: PMC9908925 DOI: 10.1038/s41598-023-29001-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 01/27/2023] [Indexed: 02/10/2023] Open
Abstract
Malignant pleural effusions (MPE) complicate malignancies and portend worse outcomes. MPE is comprised of various components, including immune cells, cancer cells, and cell-free DNA/RNA. There have been investigations into using these components to diagnose and prognosticate MPE. We hypothesize that the microbiome of MPE is unique and may be associated with diagnosis and prognosis. We compared the microbiota of MPE against microbiota of pleural effusions from non-malignant and paramalignant states. We collected a total of 165 pleural fluid samples from 165 subjects; Benign (n = 16), Paramalignant (n = 21), MPE-Lung (n = 57), MPE-Other (n = 22), and Mesothelioma (n = 49). We performed high throughput 16S rRNA gene sequencing on pleural fluid samples and controls. We showed that there are compositional differences among pleural effusions related to non-malignant, paramalignant, and malignant disease. Furthermore, we showed differential enrichment of bacterial taxa within MPE depending on the site of primary malignancy. Pleural fluid of MPE-Lung and Mesothelioma were associated with enrichment with oral and gut bacteria that are commonly thought to be commensals, including Rickettsiella, Ruminococcus, Enterococcus, and Lactobacillales. Mortality in MPE-Lung is associated with enrichment in Methylobacterium, Blattabacterium, and Deinococcus. These observations lay the groundwork for future studies that explore host-microbiome interactions and their influence on carcinogenesis.
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Affiliation(s)
- Benjamin Kwok
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University Grossman School of Medicine, 462 First Avenue 7N21, New York, NY, 10016, USA
| | - Benjamin G Wu
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University Grossman School of Medicine, 462 First Avenue 7N21, New York, NY, 10016, USA
- Division of Pulmonary and Critical Care Medicine, Veterans Affairs New York Harbor Healthcare System, New York, NY, USA
| | - Ibrahim F Kocak
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University Grossman School of Medicine, 462 First Avenue 7N21, New York, NY, 10016, USA
| | - Imran Sulaiman
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University Grossman School of Medicine, 462 First Avenue 7N21, New York, NY, 10016, USA
- Department of Respiratory Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
- Department of Respiratory Medicine, Beaumont Hospital, Dublin, Ireland
| | - Rosemary Schluger
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University Grossman School of Medicine, 462 First Avenue 7N21, New York, NY, 10016, USA
| | - Yonghua Li
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University Grossman School of Medicine, 462 First Avenue 7N21, New York, NY, 10016, USA
| | - Raheel Anwer
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University Grossman School of Medicine, 462 First Avenue 7N21, New York, NY, 10016, USA
| | - Chandra Goparaju
- Department of Cardiothoracic Surgery, New York University Grossman School of Medicine, New York, NY, USA
| | - Daniel J Ryan
- Department of Respiratory Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
- Department of Respiratory Medicine, Beaumont Hospital, Dublin, Ireland
| | - Marla Sagatelian
- School of Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Matthew S Dreier
- New York University Grossman School of Medicine, New York, NY, USA
| | - Vivek Murthy
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University Grossman School of Medicine, 462 First Avenue 7N21, New York, NY, 10016, USA
- Department of Cardiothoracic Surgery, New York University Grossman School of Medicine, New York, NY, USA
| | - Samaan Rafeq
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University Grossman School of Medicine, 462 First Avenue 7N21, New York, NY, 10016, USA
- Department of Cardiothoracic Surgery, New York University Grossman School of Medicine, New York, NY, USA
| | - Gaetane C Michaud
- Division of Pulmonary, Critical Care, and Sleep Medicine, University of South Florida Health, Tampa, FL, USA
| | - Daniel H Sterman
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University Grossman School of Medicine, 462 First Avenue 7N21, New York, NY, 10016, USA
- Department of Cardiothoracic Surgery, New York University Grossman School of Medicine, New York, NY, USA
| | - Jamie L Bessich
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University Grossman School of Medicine, 462 First Avenue 7N21, New York, NY, 10016, USA
- Department of Cardiothoracic Surgery, New York University Grossman School of Medicine, New York, NY, USA
| | - Harvey I Pass
- Department of Cardiothoracic Surgery, New York University Grossman School of Medicine, New York, NY, USA
| | - Leopoldo N Segal
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University Grossman School of Medicine, 462 First Avenue 7N21, New York, NY, 10016, USA
| | - Jun-Chieh J Tsay
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University Grossman School of Medicine, 462 First Avenue 7N21, New York, NY, 10016, USA.
- Division of Pulmonary and Critical Care Medicine, Veterans Affairs New York Harbor Healthcare System, New York, NY, USA.
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Rosas-Salazar C, Kimura KS, Shilts MH, Strickland BA, Freeman MH, Wessinger BC, Gupta V, Brown HM, Boone HH, Rajagopala SV, Turner JH, Das SR. Upper respiratory tract microbiota dynamics following COVID-19 in adults. Microb Genom 2023; 9:mgen000957. [PMID: 36820832 PMCID: PMC9997743 DOI: 10.1099/mgen.0.000957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
To date, little is known about the effect of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for the coronavirus disease 2019 (COVID-19) pandemic, on the upper respiratory tract (URT) microbiota over time. To fill this knowledge gap, we used 16S ribosomal RNA gene sequencing to characterize the URT microbiota in 48 adults, including (1) 24 participants with mild-to-moderate COVID-19 who had serial mid-turbinate swabs collected up to 21 days after enrolment and (2) 24 asymptomatic, uninfected controls who had mid-turbinate swabs collected at enrolment only. To compare the URT microbiota between groups in a comprehensive manner, different types of statistical analyses that are frequently employed in microbial ecology were used, including ⍺-diversity, β-diversity and differential abundance analyses. Final statistical models included age, sex and the presence of at least one comorbidity as covariates. The median age of all participants was 34.00 (interquartile range=28.75-46.50) years. In comparison to samples from controls, those from participants with COVID-19 had a lower observed species index at day 21 (linear regression coefficient=-13.30; 95 % CI=-21.72 to -4.88; q=0.02). In addition, the Jaccard index was significantly different between samples from participants with COVID-19 and those from controls at all study time points (PERMANOVA q<0.05 for all comparisons). The abundance of three amplicon sequence variants (ASVs) (one Corynebacterium ASV, Frederiksenia canicola, and one Lactobacillus ASV) were decreased in samples from participants with COVID-19 at all seven study time points, whereas the abundance of one ASV (from the family Neisseriaceae) was increased in samples from participants with COVID-19 at five (71.43 %) of the seven study time points. Our results suggest that mild-to-moderate COVID-19 can lead to alterations of the URT microbiota that persist for several weeks after the initial infection.
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Affiliation(s)
- Christian Rosas-Salazar
- Division of Allergy, Immunology, and Pulmonary Medicine, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Kyle S Kimura
- Department of Otolaryngology - Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Meghan H Shilts
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Britton A Strickland
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Michael H Freeman
- Department of Otolaryngology - Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | | | - Veerain Gupta
- Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Hunter M Brown
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Helen H Boone
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Seesandra V Rajagopala
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Justin H Turner
- Department of Otolaryngology - Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Suman Ranjan Das
- Department of Otolaryngology - Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, Tennessee, USA.,Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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Zsichla L, Müller V. Risk Factors of Severe COVID-19: A Review of Host, Viral and Environmental Factors. Viruses 2023; 15:175. [PMID: 36680215 PMCID: PMC9863423 DOI: 10.3390/v15010175] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/04/2023] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
The clinical course and outcome of COVID-19 are highly variable, ranging from asymptomatic infections to severe disease and death. Understanding the risk factors of severe COVID-19 is relevant both in the clinical setting and at the epidemiological level. Here, we provide an overview of host, viral and environmental factors that have been shown or (in some cases) hypothesized to be associated with severe clinical outcomes. The factors considered in detail include the age and frailty, genetic polymorphisms, biological sex (and pregnancy), co- and superinfections, non-communicable comorbidities, immunological history, microbiota, and lifestyle of the patient; viral genetic variation and infecting dose; socioeconomic factors; and air pollution. For each category, we compile (sometimes conflicting) evidence for the association of the factor with COVID-19 outcomes (including the strength of the effect) and outline possible action mechanisms. We also discuss the complex interactions between the various risk factors.
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Affiliation(s)
- Levente Zsichla
- Institute of Biology, Eötvös Loránd University, 1117 Budapest, Hungary
- National Laboratory for Health Security, Eötvös Loránd University, 1117 Budapest, Hungary
| | - Viktor Müller
- Institute of Biology, Eötvös Loránd University, 1117 Budapest, Hungary
- National Laboratory for Health Security, Eötvös Loránd University, 1117 Budapest, Hungary
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Bhatraju PK, Morrell ED, Stanaway IB, Sathe NA, Srivastava A, Postelnicu R, Green R, Andrews A, Gonzalez M, Kratochvil CJ, Kumar VK, Hsiang TY, Gale M, Anesi GL, Wyles D, Broadhurst MJ, Brett-Major D, Mukherjee V, Sevransky JE, Landsittel D, Hung C, Altemeier WA, Gharib SA, Uyeki TM, Cobb JP, Liebler JM, Crosslin DR, Jarvik GP, Segal LN, Evans L, Mikacenic C, Wurfel MM. Angiopoietin-Like4 Is a Novel Marker of COVID-19 Severity. Crit Care Explor 2023; 5:e0827. [PMID: 36600780 PMCID: PMC9803343 DOI: 10.1097/cce.0000000000000827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Vascular dysfunction and capillary leak are common in critically ill COVID-19 patients, but identification of endothelial pathways involved in COVID-19 pathogenesis has been limited. Angiopoietin-like 4 (ANGPTL4) is a protein secreted in response to hypoxic and nutrient-poor conditions that has a variety of biological effects including vascular injury and capillary leak. OBJECTIVES To assess the role of ANGPTL4 in COVID-19-related outcomes. DESIGN SETTING AND PARTICIPANTS Two hundred twenty-five COVID-19 ICU patients were enrolled from April 2020 to May 2021 in a prospective, multicenter cohort study from three different medical centers, University of Washington, University of Southern California and New York University. MAIN OUTCOMES AND MEASURES Plasma ANGPTL4 was measured on days 1, 7, and 14 after ICU admission. We used previously published tissue proteomic data and lung single nucleus RNA (snRNA) sequencing data from specimens collected from COVID-19 patients to determine the tissues and cells that produce ANGPTL4. RESULTS Higher plasma ANGPTL4 concentrations were significantly associated with worse hospital mortality (adjusted odds ratio per log2 increase, 1.53; 95% CI, 1.17-2.00; p = 0.002). Higher ANGPTL4 concentrations were also associated with higher proportions of venous thromboembolism and acute respiratory distress syndrome. Longitudinal ANGPTL4 concentrations were significantly different during the first 2 weeks of hospitalization in patients who subsequently died compared with survivors (p for interaction = 8.1 × 10-5). Proteomics analysis demonstrated abundance of ANGPTL4 in lung tissue compared with other organs in COVID-19. ANGPTL4 single-nuclear RNA gene expression was significantly increased in pulmonary alveolar type 2 epithelial cells and fibroblasts in COVID-19 lung tissue compared with controls. CONCLUSIONS AND RELEVANCE ANGPTL4 is expressed in pulmonary epithelial cells and fibroblasts and is associated with clinical prognosis in critically ill COVID-19 patients.
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Affiliation(s)
- Pavan K Bhatraju
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington Medical Center, Seattle, WA
- School of Medicine, University of Washington, Sepsis Center of Research Excellence-University of Washington (SCORE-UW), Seattle, WA
- Kidney Research Institute, Division of Nephrology, Department of Medicine, University of Washington Medical Center, Seattle, WA
| | - Eric D Morrell
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington Medical Center, Seattle, WA
| | - Ian B Stanaway
- Kidney Research Institute, Division of Nephrology, Department of Medicine, University of Washington Medical Center, Seattle, WA
| | - Neha A Sathe
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington Medical Center, Seattle, WA
| | - Avantika Srivastava
- Department of Biomedical Informatics, School of Medicine, University of Pittsburgh, Pittsburgh, PA
| | - Radu Postelnicu
- Division of Pulmonary, Critical Care, and Sleep Medicine, NYU Grossman School of Medicine, NYU Langone Health, New York, NY
| | - Richard Green
- Departments of Medicine (Division of Medical Genetics) and Genome Sciences, University of Washington Medical Center, Seattle, WA
| | - Adair Andrews
- Society of Critical Care Medicine, Mount Prospect, IL
| | | | | | | | | | - Michael Gale
- Department of Immunology, University of Washington, Seattle, WA
| | - George L Anesi
- Division of Pulmonary, Allergy, and Critical Care, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - David Wyles
- Division of Infectious Diseases, Denver Health Medical Center, Denver, CO
| | - M Jana Broadhurst
- Global Center for Health Security, University of Nebraska Medical Center, Omaha, NE
| | - David Brett-Major
- Global Center for Health Security, University of Nebraska Medical Center, Omaha, NE
| | - Vikramjit Mukherjee
- Division of Pulmonary, Critical Care, and Sleep Medicine, NYU Grossman School of Medicine, NYU Langone Health, New York, NY
| | - Jonathan E Sevransky
- Division of Pulmonary, Allergy, Critical Care and Sleep, School of Medicine, Emory University, Atlanta, GA
- Emory Critical Care Center, Emory Healthcare, Atlanta, GA
| | - Douglas Landsittel
- Department of Epidemiology and Biostatistics, School of Public Health, Indiana University, Bloomington, IN
| | - Chi Hung
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington Medical Center, Seattle, WA
| | - William A Altemeier
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington Medical Center, Seattle, WA
| | - Sina A Gharib
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington Medical Center, Seattle, WA
| | - Timothy M Uyeki
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA
| | - J Perren Cobb
- Departments of Surgery and Anesthesiology, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA
| | - Janice M Liebler
- Division of Pulmonary, Critical Care and Sleep Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - David R Crosslin
- Division of Biomedical Informatics and Genomics, John W. Deming Department of Medicine, Tulane University, School of Medicine, New Orleans, LA
| | - Gail P Jarvik
- Departments of Medicine (Division of Medical Genetics) and Genome Sciences, University of Washington Medical Center, Seattle, WA
| | - Leopoldo N Segal
- Division of Pulmonary, Critical Care, and Sleep Medicine, NYU Grossman School of Medicine, NYU Langone Health, New York, NY
| | - Laura Evans
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington Medical Center, Seattle, WA
| | - Carmen Mikacenic
- Translational Research, Benaroya Research Institute, Seattle, WA
| | - Mark M Wurfel
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington Medical Center, Seattle, WA
- School of Medicine, University of Washington, Sepsis Center of Research Excellence-University of Washington (SCORE-UW), Seattle, WA
- Kidney Research Institute, Division of Nephrology, Department of Medicine, University of Washington Medical Center, Seattle, WA
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Mancabelli L, Ciociola T, Lugli GA, Tarracchini C, Fontanta F, Viappiani A, Turroni F, Ticinesi A, Meschi T, Conti S, Ventura M, Milani C. Guideline for the analysis of the microbial communities of the human upper airways. J Oral Microbiol 2022; 14:2103282. [PMID: 35923899 PMCID: PMC9341376 DOI: 10.1080/20002297.2022.2103282] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Affiliation(s)
- Leonardo Mancabelli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Tecla Ciociola
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Chiara Tarracchini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Federico Fontanta
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | | | - Francesca Turroni
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
| | - Andrea Ticinesi
- Department of Medicine and Surgery, University of Parma, Parma, Italy
- Geriatric-Rehabilitation Department, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Tiziana Meschi
- Department of Medicine and Surgery, University of Parma, Parma, Italy
- Geriatric-Rehabilitation Department, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Stefania Conti
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Marco Ventura
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
| | - Christian Milani
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
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Metatranscriptomic Analysis Reveals Disordered Alterations in Oropharyngeal Microbiome during the Infection and Clearance Processes of SARS-CoV-2: A Warning for Secondary Infections. Biomolecules 2022; 13:biom13010006. [PMID: 36671391 PMCID: PMC9856197 DOI: 10.3390/biom13010006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/07/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022] Open
Abstract
This study was conducted to investigate oropharyngeal microbiota alterations during the progression of coronavirus disease 2019 (COVID-19) by analyzing these alterations during the infection and clearance processes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The diagnosis of COVID-19 was confirmed by using positive SARS-CoV-2 quantitative reverse transcription polymerase chain reaction (RT-qPCR). The alterations in abundance, diversity, and potential function of the oropharyngeal microbiome were identified using metatranscriptomic sequencing analyses of oropharyngeal swab specimens from 47 patients with COVID-19 (within a week after diagnosis and within two months after recovery from COVID-19) and 40 healthy individuals. As a result, in the infection process of SARS-CoV-2, compared to the healthy individuals, the relative abundances of Prevotella, Aspergillus, and Epstein-Barr virus were elevated; the alpha diversity was decreased; the beta diversity was disordered; the relative abundance of Gram-negative bacteria was increased; and the relative abundance of Gram-positive bacteria was decreased. After the clearance of SARS-CoV-2, compared to the healthy individuals and patients with COVID-19, the above disordered alterations persisted in the patients who had recovered from COVID-19 and did not return to the normal level observed in the healthy individuals. Additionally, the expressions of several antibiotic resistance genes (especially multi-drug resistance, glycopeptide, and tetracycline) in the patients with COVID-19 were higher than those in the healthy individuals. After SARS-CoV-2 was cleared, the expressions of these genes in the patients who had recovered from COVID-19 were lower than those in the patients with COVID-19, and they were different from those in the healthy individuals. In conclusion, our findings provide evidence that potential secondary infections with oropharyngeal bacteria, fungi, and viruses in patients who have recovered from COVID-19 should not be ignored; this evidence also highlights the clinical significance of the oropharyngeal microbiome in the early prevention of potential secondary infections of COVID-19 and suggests that it is imperative to choose appropriate antibiotics for subsequent bacterial secondary infection in patients with COVID-19.
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Cuenca S, Soler Z, Serrano-Gómez G, Xie Z, Barquinero J, Roca J, Sirvent JM, Manichanh C. Dysbiosis: An Indicator of COVID-19 Severity in Critically Ill Patients. Int J Mol Sci 2022; 23:ijms232415808. [PMID: 36555453 PMCID: PMC9779860 DOI: 10.3390/ijms232415808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 11/29/2022] [Accepted: 12/10/2022] [Indexed: 12/15/2022] Open
Abstract
Here, we examined the dynamics of the gut and respiratory microbiomes in severe COVID-19 patients in need of mechanical ventilation in the intensive care unit (ICU). We recruited 85 critically ill patients (53 with COVID-19 and 32 without COVID-19) and 17 healthy controls (HCs) and monitored them for up to 4 weeks. We analyzed the bacterial and fungal taxonomic profiles and loads of 232 gut and respiratory samples and we measured the blood levels of Interleukin 6, IgG, and IgM in COVID-19 patients. Upon ICU admission, the bacterial composition and load in the gut and respiratory samples were altered in critically ill patients compared with HCs. During their ICU stay, the patients experienced increased bacterial and fungal loads, drastic decreased bacterial richness, and progressive changes in bacterial and fungal taxonomic profiles. In the gut samples, six bacterial taxa could discriminate ICU-COV(+) from ICU-COV(-) cases upon ICU admission and the bacterial taxa were associated according to age, PaO2/FiO2, and CRP levels. In the respiratory samples of the ICU-COV(+) patients, bacterial signatures including Pseudomonas and Streptococcus were found to be correlated with the length of ICU stay. Our findings demonstrated that the gut and respiratory microbiome dysbiosis and bacterial signatures associated with critical illness emerged as biomarkers of COVID-19 severity and could be a potential predictor of ICU length of stay. We propose using a high-throughput sequencing approach as an alternative to traditional isolation techniques to monitor ICU patient infection.
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Affiliation(s)
- Silvia Cuenca
- Intensive Care Department (ICU), University Hospital of Girona Dr. Josep Trueta, Avda. França s/n, 17007 Girona, Spain
- Medicine Department, Autonomous University of Barcelona (UAB), 08193 Cerdanyola del Vallès, Spain
| | - Zaida Soler
- Medicine Department, Autonomous University of Barcelona (UAB), 08193 Cerdanyola del Vallès, Spain
- Gut Microbiome Group, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
| | - Gerard Serrano-Gómez
- Medicine Department, Autonomous University of Barcelona (UAB), 08193 Cerdanyola del Vallès, Spain
| | - Zixuan Xie
- Medicine Department, Autonomous University of Barcelona (UAB), 08193 Cerdanyola del Vallès, Spain
- Gut Microbiome Group, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
| | - Jordi Barquinero
- Gene and Cell Therapy, VHIR, Vall d’Hebron Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
| | - Joaquim Roca
- Molecular Biology Institute of Barcelona (IBMB), Spanish National Research Council (CSIC), 08028 Barcelona, Spain
| | - Jose-Maria Sirvent
- Intensive Care Department (ICU), University Hospital of Girona Dr. Josep Trueta, Avda. França s/n, 17007 Girona, Spain
- Institute of Biomedical Research of Girona Dr. Josep Trueta (IDIBGI), 17190 Salt, Spain
| | - Chaysavanh Manichanh
- Medicine Department, Autonomous University of Barcelona (UAB), 08193 Cerdanyola del Vallès, Spain
- Gut Microbiome Group, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
- Correspondence: ; Tel.:+34-934894036
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Floridia M, Giuliano M, Monaco M, Palmieri L, Lo Noce C, Palamara AT, Pantosti A, Brusaferro S, Onder G, Palmieri L, Agazio E, Barbariol P, Bella A, Benelli E, Bertinato L, Bocci M, Boros S, Bressi M, Calcagnini G, Canevelli M, Censi F, Ciervo A, Colaizzo E, Da Cas R, Del Manso M, Di Benedetto C, Donfrancesco C, Fabiani M, Facchiano F, Floridia M, Galati F, Giuliano M, Grisetti T, Guastadisegni C, Lega I, Lo Noce C, Maiozzi P, Manno V, Martini M, Massari M, Urdiales AM, Mattei E, Meduri C, Meli P, Menniti Ippolito F, Minelli G, Onder G, Petrone D, Pezzotti P, Pricci F, Punzo O, Quarata F, Raparelli V, Riccardo F, Rocchetto S, Sacco C, Salerno P, Sarti G, Serra D, Spila Alegiani S, Spuri M, Tallon M, Tamburo De Bella M, Tiple D, Toccaceli Blasi M, Trentin F, Unim B, Vaianella L, Vanacore N, Vescio MF, Villani ER, Weimer LE, Brusaferro S. Microbiologically confirmed infections and antibiotic-resistance in a national surveillance study of hospitalised patients who died with COVID-19, Italy 2020–2021. Antimicrob Resist Infect Control 2022; 11:74. [PMID: 35598032 PMCID: PMC9123740 DOI: 10.1186/s13756-022-01113-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 05/07/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Patients hospitalised for COVID-19 may present with or acquire bacterial or fungal infections that can affect the course of the disease. The aim of this study was to describe the microbiological characteristics of laboratory-confirmed infections in hospitalised patients with severe COVID-19.
Methods
We reviewed the hospital charts of a sample of patients deceased with COVID-19 from the Italian National COVID-19 Surveillance, who had laboratory-confirmed bacterial or fungal bloodstream infections (BSI) or lower respiratory tract infections (LRTI), evaluating the pathogens responsible for the infections and their antimicrobial susceptibility.
Results
Among 157 patients with infections hospitalised from February 2020 to April 2021, 28 (17.8%) had co-infections (≤ 48 h from admission) and 138 (87.9%) had secondary infections (> 48 h). Most infections were bacterial; LRTI were more frequent than BSI. The most common co-infection was pneumococcal LRTI. In secondary infections, Enterococci were the most frequently recovered pathogens in BSI (21.7% of patients), followed by Enterobacterales, mainly K. pneumoniae, while LRTI were mostly associated with Gram-negative bacteria, firstly Enterobacterales (27.4% of patients, K. pneumoniae 15.3%), followed by A. baumannii (19.1%). Fungal infections, both BSI and LRTI, were mostly due to C. albicans. Antibiotic resistance rates were extremely high in Gram-negative bacteria, with almost all A. baumannii isolates resistant to carbapenems (95.5%), and K. pneumoniae and P. aeruginosa showing carbapenem resistance rates of 59.5% and 34.6%, respectively.
Conclusions
In hospitalised patients with severe COVID-19, secondary infections are considerably more common than co-infections, and are mostly due to Gram-negative bacterial pathogens showing a very high rate of antibiotic resistance.
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van Charante F, Wieme A, Rigole P, De Canck E, Ostyn L, Grassi L, Deforce D, Crabbé A, Vandamme P, Joossens M, Van Nieuwerburgh F, Depuydt P, Coenye T. Microbial diversity and antimicrobial susceptibility in endotracheal tube biofilms recovered from mechanically ventilated COVID-19 patients. Biofilm 2022; 4:100079. [PMID: 35720435 PMCID: PMC9192360 DOI: 10.1016/j.bioflm.2022.100079] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 06/02/2022] [Accepted: 06/02/2022] [Indexed: 11/17/2022] Open
Abstract
In patients with acute respiratory failure, mechanical ventilation through an endotracheal tube (ET) may be required to correct hypoxemia and hypercarbia. However, biofilm formation on these ETs is a risk factor for infections in intubated patients, as the ET can act as a reservoir of microorganisms that can cause infections in the lungs. As severely ill COVID-19 patients often need to be intubated, a better knowledge of the composition of ET biofilms in this population is important. In Spring 2020, during the first wave of the COVID-19 pandemic in Europe, 31 ETs were obtained from COVID-19 patients at Ghent University Hospital (Ghent, Belgium). Biofilms were collected from the ET and the biofilm composition was determined using culture-dependent (MALDI-TOF mass spectrometry and biochemical tests) and culture-independent (16S and ITS1 rRNA amplicon sequencing) approaches. In addition, antimicrobial resistance was assessed for isolates collected via the culture-dependent approach using disc diffusion for 11 antimicrobials commonly used to treat lower respiratory tract infections. The most common microorganisms identified by the culture-dependent approach were those typically found during lung infections and included both presumed commensal and potentially pathogenic microorganisms like Staphylococcus epidermidis, Enterococcus faecalis, Pseudomonas aeruginosa and Candida albicans. More unusual organisms, such as Paracoccus yeei, were also identified, but each only in a few patients. The culture-independent approach revealed a wide variety of microbes present in the ET biofilms and showed large variation in biofilm composition between patients. Some biofilms contained a diverse set of bacteria of which many are generally considered as non-pathogenic commensals, whereas others were dominated by a single or a few pathogens. Antimicrobial resistance was widespread in the isolates, e.g. 68% and 53% of all isolates tested were resistant against meropenem and gentamicin, respectively. Different isolates from the same species recovered from the same ET biofilm often showed differences in antibiotic susceptibility. Our data suggest that ET biofilms are a potential risk factor for secondary infections in intubated COVID-19 patients, as is the case in mechanically-ventilated non-COVID-19 patients.
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Affiliation(s)
- Frits van Charante
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Anneleen Wieme
- Laboratory of Microbiology, Ghent University, Ghent, Belgium
- BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Ghent University, Ghent, Belgium
| | - Petra Rigole
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | | | - Lisa Ostyn
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Lucia Grassi
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | - Aurélie Crabbé
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology, Ghent University, Ghent, Belgium
- BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Ghent University, Ghent, Belgium
| | - Marie Joossens
- Laboratory of Microbiology, Ghent University, Ghent, Belgium
| | | | - Pieter Depuydt
- Department of Intensive Care, Ghent University Hospital, Ghent, Belgium
| | - Tom Coenye
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
- Corresponding author.
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Muacevic A, Adler JR. Efficacy and Safety of Inhalation of Nebulized Ethanol in COVID-19 Treatment: A Randomized Clinical Trial. Cureus 2022; 14:e32218. [PMID: 36505954 PMCID: PMC9728981 DOI: 10.7759/cureus.32218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/04/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Coronavirus disease 2019 (COVID-19) is a pandemic caused by the SARS-CoV-2 virus. Many efforts have been made and are currently being made to prevent and treat this global disease. OBJECTIVES This study was designed to evaluate the efficacy and safety of nebulized ethanol (EtOH) in treating COVID-19. METHODS A randomized clinical trial (RCT) of 99 symptomatic and real-time polymerase chain reaction (RT-PCR)-positive patients admitted to a hospital receiving remdesivir-dexamethasone was conducted. They were randomly assigned to receive distilled water spray (control group (CG)) or 35% EtOH spray (intervention group (IG)). Both groups inhaled three puffs of spray (nebulizer) every six hours for a week. The primary outcome included Global Symptomatic Score (GSS) between the two groups at the first visit and on days three, seven, and 14. Secondary outcomes included the Clinical Status Scale (CSS; a seven-point ordinal scale ranging from death to complete recovery) and readmission rate. RESULTS A total of 44 and 55 patients were enrolled in the IG and CG, respectively. Although there was no difference at admission, the GSS and CSS improved significantly in the IG (p = 0.016 and p = 0.001, respectively). The IG readmission rate was considerably lower (0% vs. 10.9%; p = 0.02). CONCLUSIONS Inhaled-nebulized EtOH is effective in rapidly improving the clinical status and reducing further treatment. Due to its low cost, availability, and absent/tolerable adverse events, it could be recommended as an adjunctive treatment for moderate COVID-19. Further research on curative effects in more serious cases and in prevention is advisable.
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Kullberg RFJ, de Brabander J, Boers LS, Bos LDJ, Wiersinga WJ. Reply to: Microbial Burden-associated Cytokine Storm May Explain Non-Resolving ARDS in COVID-19 Patients. Am J Respir Crit Care Med 2022; 206:1183-1184. [PMID: 35867884 PMCID: PMC9704841 DOI: 10.1164/rccm.202207-1346le] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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Postelnicu R, Srivastava A, Bhatraju PK, Wurfelc MM, Anesi GL, Gonzalez M, Andrews A, Lutrick K, Kumar VK, Uyeki TM, Cobb PJ, Segal LN, Brett-Major D, Liebler JM, Kratochvil CJ, Mukherjee V, Broadhurst MJ, Lee R, Wyles D, Sevransky JE, Evans L, Landsittel D. Severe Acute Respiratory Infection-Preparedness: Protocol for a Multicenter Prospective Cohort Study of Viral Respiratory Infections. Crit Care Explor 2022; 4:e0773. [PMID: 36284548 PMCID: PMC9586923 DOI: 10.1097/cce.0000000000000773] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Respiratory virus infections cause significant morbidity and mortality ranging from mild uncomplicated acute respiratory illness to severe complications, such as acute respiratory distress syndrome, multiple organ failure, and death during epidemics and pandemics. We present a protocol to systematically study patients with severe acute respiratory infection (SARI), including severe acute respiratory syndrome coronavirus 2, due to respiratory viral pathogens to evaluate the natural history, prognostic biomarkers, and characteristics, including hospital stress, associated with clinical outcomes and severity. DESIGN Prospective cohort study. SETTING Multicenter cohort of patients admitted to an acute care ward or ICU from at least 15 hospitals representing diverse geographic regions across the United States. PATIENTS Patients with SARI caused by infection with respiratory viruses that can cause outbreaks, epidemics, and pandemics. INTERVENTIONS None. MEASUREMENTS AND MAIN RESULTS Measurements include patient demographics, signs, symptoms, and medications; microbiology, imaging, and associated tests; mechanical ventilation, hospital procedures, and other interventions; and clinical outcomes and hospital stress, with specimens collected on days 0, 3, and 7-14 after enrollment and at discharge. The primary outcome measure is the number of consecutive days alive and free of mechanical ventilation (VFD) in the first 30 days after hospital admission. Important secondary outcomes include organ failure-free days before acute kidney injury, shock, hepatic failure, disseminated intravascular coagulation, 28-day mortality, adaptive immunity, as well as immunologic and microbiologic outcomes. CONCLUSIONS SARI-Preparedness is a multicenter study under the collaboration of the Society of Critical Care Medicine Discovery, Resilience Intelligence Network, and National Emerging Special Pathogen Training and Education Center, which seeks to improve understanding of prognostic factors associated with worse outcomes and increased resource utilization. This can lead to interventions to mitigate the clinical impact of respiratory virus infections associated with SARI.
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Affiliation(s)
- Radu Postelnicu
- Division of Pulmonary, Critical Care, and Sleep Medicine, NYU Grossman School of Medicine, NYU Langone Health, New York, NY
| | - Avantika Srivastava
- Department of Biomedical Informatics, School of Medicine, University of Pittsburgh, Pittsburgh, PA
| | - Pavan K. Bhatraju
- Division of Pulmonary, Critical Care and Sleep Medicine, School of Medicine, Seattle, WA
| | - Mark M. Wurfelc
- Division of Pulmonary, Critical Care and Sleep Medicine, School of Medicine, Seattle, WA
| | - George L. Anesi
- Division of Pulmonary, Allergy, and Critical Care, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | | | - Adair Andrews
- Society of Critical Care Medicine, Mount Prospect, IL
| | - Karen Lutrick
- Department of Family and Community Medicine, College of Medicine, University of Arizona, Tucson, AZ
| | | | - Timothy M. Uyeki
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA
| | - Perren J. Cobb
- Departments of Surgery and Anesthesiology, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA
| | - Leopoldo N. Segal
- Division of Pulmonary, Critical Care, and Sleep Medicine, NYU Grossman School of Medicine, NYU Langone Health, New York, NY
| | - David Brett-Major
- Department of Epidemiology, College of Public Health, University of Nebraska Medical Center, Omaha, NE., Global Center for Health Security, University of Nebraska Medical Center, Omaha, NE
| | - Janice M. Liebler
- Division of Pulmonary, Critical Care and Sleep Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | | | - Vikramjit Mukherjee
- Division of Pulmonary, Critical Care, and Sleep Medicine, NYU Grossman School of Medicine, NYU Langone Health, New York, NY
| | - M. Jana Broadhurst
- Global Center for Health Security, University of Nebraska Medical Center, Omaha, NE., Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, Omaha, NE
| | - Richard Lee
- Division of Pulmonary Diseases and Critical Care Medicine, University of California, Irvine, CA
| | - David Wyles
- Division of Infectious Diseases, Denver Health Medical Center, Denver, CO
| | - Jonathan E. Sevransky
- Division of Pulmonary, Allergy, Critical Care and Sleep, School of Medicine, Emory University, Atlanta, GA., Emory Critical Care Center, Emory Healthcare, Atlanta, GA
| | - Laura Evans
- Division of Pulmonary, Critical Care and Sleep Medicine, School of Medicine, Seattle, WA
| | - Douglas Landsittel
- Department of Epidemiology and Biostatistics, School of Public Health, Indiana University, Bloomington, IN
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Merenstein C, Bushman FD, Collman RG. Alterations in the respiratory tract microbiome in COVID-19: current observations and potential significance. MICROBIOME 2022; 10:165. [PMID: 36195943 PMCID: PMC9532226 DOI: 10.1186/s40168-022-01342-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 08/02/2022] [Indexed: 06/16/2023]
Abstract
SARS-CoV-2 infection causes COVID-19 disease, which can result in consequences ranging from undetectable to fatal, focusing attention on the modulators of outcomes. The respiratory tract microbiome is thought to modulate the outcomes of infections such as influenza as well as acute lung injury, raising the question to what degree does the airway microbiome influence COVID-19? Here, we review the results of 56 studies examining COVID-19 and the respiratory tract microbiome, summarize the main generalizations, and point to useful avenues for further research. Although the results vary among studies, a few consistent findings stand out. The diversity of bacterial communities in the oropharynx typically declined with increasing disease severity. The relative abundance of Haemophilus and Neisseria also declined with severity. Multiple microbiome measures tracked with measures of systemic immune responses and COVID outcomes. For many of the conclusions drawn in these studies, the direction of causality is unknown-did an alteration in the microbiome result in increased COVID severity, did COVID severity alter the microbiome, or was some third factor the primary driver, such as medication use. Follow-up mechanistic studies can help answer these questions. Video Abstract.
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Affiliation(s)
- Carter Merenstein
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Frederic D. Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Ronald G. Collman
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104 USA
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Seibert B, Cáceres CJ, Carnaccini S, Cardenas-Garcia S, Gay LC, Ortiz L, Geiger G, Rajao DS, Ottesen E, Perez DR. Pathobiology and dysbiosis of the respiratory and intestinal microbiota in 14 months old Golden Syrian hamsters infected with SARS-CoV-2. PLoS Pathog 2022; 18:e1010734. [PMID: 36279276 PMCID: PMC9632924 DOI: 10.1371/journal.ppat.1010734] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 11/03/2022] [Accepted: 10/05/2022] [Indexed: 11/06/2022] Open
Abstract
The pandemic of severe acute respiratory syndrome coronavirus 2 (SARS2) affected the geriatric population. Among research models, Golden Syrian hamsters (GSH) are one of the most representative to study SARS2 pathogenesis and host responses. However, animal studies that recapitulate the effects of SARS2 in the human geriatric population are lacking. To address this gap, we inoculated 14 months old GSH with a prototypic ancestral strain of SARS2 and studied the effects on virus pathogenesis, virus shedding, and respiratory and gastrointestinal microbiome changes. SARS2 infection led to high vRNA loads in the nasal turbinates (NT), lungs, and trachea as well as higher pulmonary lesions scores later in infection. Dysbiosis throughout SARS2 disease progression was observed in the pulmonary microbial dynamics with the enrichment of opportunistic pathogens (Haemophilus, Fusobacterium, Streptococcus, Campylobacter, and Johnsonella) and microbes associated with inflammation (Prevotella). Changes in the gut microbial community also reflected an increase in multiple genera previously associated with intestinal inflammation and disease (Helicobacter, Mucispirillum, Streptococcus, unclassified Erysipelotrichaceae, and Spirochaetaceae). Influenza A virus (FLUAV) pre-exposure resulted in slightly more pronounced pathology in the NT and lungs early on (3 dpc), and more notable changes in lungs compared to the gut microbiome dynamics. Similarities among aged GSH and the microbiome in critically ill COVID-19 patients, particularly in the lower respiratory tract, suggest that GSHs are a representative model to investigate microbial changes during SARS2 infection. The relationship between the residential microbiome and other confounding factors, such as SARS2 infection, in a widely used animal model, contributes to a better understanding of the complexities associated with the host responses during viral infections.
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Affiliation(s)
- Brittany Seibert
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - C. Joaquín Cáceres
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Silvia Carnaccini
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Stivalis Cardenas-Garcia
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - L. Claire Gay
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Lucia Ortiz
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Ginger Geiger
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Daniela S. Rajao
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Elizabeth Ottesen
- Department of Microbiology, University of Georgia, Athens, Georgia, United States of America
| | - Daniel R. Perez
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
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Barnett CR, Segal LN. Untangling Lower Airway Dysbiosis in Critically Ill Patients with COVID-19. Am J Respir Crit Care Med 2022; 206:806-808. [PMID: 35696343 PMCID: PMC9799272 DOI: 10.1164/rccm.202206-1074ed] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Affiliation(s)
- Clea R Barnett
- Division of Pulmonary and Critical Care Medicine New York University Grossman School of Medicine New York, New York
| | - Leopoldo N Segal
- Division of Pulmonary and Critical Care Medicine New York University Grossman School of Medicine New York, New York
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Kullberg RFJ, de Brabander J, Boers LS, Biemond JJ, Nossent EJ, Heunks LMA, Vlaar APJ, Bonta PI, van der Poll T, Duitman J, Bos LDJ, Wiersinga WJ. Lung Microbiota of Critically Ill Patients with COVID-19 Are Associated with Nonresolving Acute Respiratory Distress Syndrome. Am J Respir Crit Care Med 2022; 206:846-856. [PMID: 35616585 PMCID: PMC9799265 DOI: 10.1164/rccm.202202-0274oc] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Rationale: Bacterial lung microbiota are correlated with lung inflammation and acute respiratory distress syndrome (ARDS) and altered in severe coronavirus disease (COVID-19). However, the association between lung microbiota (including fungi) and resolution of ARDS in COVID-19 remains unclear. We hypothesized that increased lung bacterial and fungal burdens are related to nonresolving ARDS and mortality in COVID-19. Objectives: To determine the relation between lung microbiota and clinical outcomes of COVID-19-related ARDS. Methods: This observational cohort study enrolled mechanically ventilated patients with COVID-19. All patients had ARDS and underwent bronchoscopy with BAL. Lung microbiota were profiled using 16S rRNA gene sequencing and quantitative PCR targeting the 16S and 18S rRNA genes. Key features of lung microbiota (bacterial and fungal burden, α-diversity, and community composition) served as predictors. Our primary outcome was successful extubation adjudicated 60 days after intubation, analyzed using a competing risk regression model with mortality as competing risk. Measurements and Main Results: BAL samples of 114 unique patients with COVID-19 were analyzed. Patients with increased lung bacterial and fungal burden were less likely to be extubated (subdistribution hazard ratio, 0.64 [95% confidence interval, 0.42-0.97]; P = 0.034 and 0.59 [95% confidence interval, 0.42-0.83]; P = 0.0027 per log10 increase in bacterial and fungal burden, respectively) and had higher mortality (bacterial burden, P = 0.012; fungal burden, P = 0.0498). Lung microbiota composition was associated with successful extubation (P = 0.0045). Proinflammatory cytokines (e.g., tumor necrosis factor-α) were associated with the microbial burdens. Conclusions: Bacterial and fungal lung microbiota are related to nonresolving ARDS in COVID-19 and represent an important contributor to heterogeneity in COVID-19-related ARDS.
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Affiliation(s)
| | | | - Leonoor S. Boers
- Department of Intensive Care Medicine,,Laboratory of Experimental Intensive Care and Anesthesiology
| | | | | | | | - Alexander P. J. Vlaar
- Department of Intensive Care Medicine,,Laboratory of Experimental Intensive Care and Anesthesiology
| | | | - Tom van der Poll
- Center for Experimental and Molecular Medicine,,Division of Infectious Diseases, and
| | - JanWillem Duitman
- Department of Pulmonary Medicine,,Department of Experimental Immunology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands
| | - Lieuwe D. J. Bos
- Department of Intensive Care Medicine,,Laboratory of Experimental Intensive Care and Anesthesiology,,Department of Pulmonary Medicine
| | - W. Joost Wiersinga
- Center for Experimental and Molecular Medicine,,Division of Infectious Diseases, and
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ACE2-containing defensosomes serve as decoys to inhibit SARS-CoV-2 infection. PLoS Biol 2022; 20:e3001754. [PMID: 36099266 PMCID: PMC9469972 DOI: 10.1371/journal.pbio.3001754] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 07/12/2022] [Indexed: 12/24/2022] Open
Abstract
Extracellular vesicles of endosomal origin, exosomes, mediate intercellular communication by transporting substrates with a variety of functions related to tissue homeostasis and disease. Their diagnostic and therapeutic potential has been recognized for diseases such as cancer in which signaling defects are prominent. However, it is unclear to what extent exosomes and their cargo inform the progression of infectious diseases. We recently defined a subset of exosomes termed defensosomes that are mobilized during bacterial infection in a manner dependent on autophagy proteins. Through incorporating protein receptors on their surface, defensosomes mediated host defense by binding and inhibiting pore-forming toxins secreted by bacterial pathogens. Given this capacity to serve as decoys that interfere with surface protein interactions, we investigated the role of defensosomes during infection by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the etiological agent of Coronavirus Disease 2019 (COVID-19). Consistent with a protective function, exosomes containing high levels of the viral receptor ACE2 in bronchoalveolar lavage fluid (BALF) from critically ill COVID-19 patients was associated with reduced intensive care unit (ICU) and hospitalization times. We found ACE2+ exosomes were induced by SARS-CoV-2 infection and activation of viral sensors in cell culture, which required the autophagy protein ATG16L1, defining these as defensosomes. We further demonstrate that ACE2+ defensosomes directly bind and block viral entry. These findings suggest that defensosomes may contribute to the antiviral response against SARS-CoV-2 and expand our knowledge on the regulation and effects of extracellular vesicles during infection. Autophagy proteins mediate the production of extracellular vesicles termed defensosomes in response to innate immune ligands. This study reveals that ACE2-containing defensosomes bind and inhibit SARS-CoV-2 infection, and are associated with reduced length of hospital stay for patients with COVID-19.
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Microbiological and Clinical Findings of SARS-CoV-2 Infection after 2 Years of Pandemic: From Lung to Gut Microbiota. Diagnostics (Basel) 2022; 12:diagnostics12092143. [PMID: 36140544 PMCID: PMC9498253 DOI: 10.3390/diagnostics12092143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/29/2022] [Accepted: 09/02/2022] [Indexed: 01/08/2023] Open
Abstract
Early recognition and prompt management are crucial for improving survival in COVID-19 patients, and after 2 years of the pandemic, many efforts have been made to obtain an early diagnosis. A key factor is the use of fast microbiological techniques, considering also that COVID-19 patients may show no peculiar signs and symptoms that may differentiate COVID-19 from other infective or non-infective diseases. These techniques were developed to promptly identify SARS-CoV-2 infection and to prevent viral spread and transmission. However, recent data about clinical, radiological and laboratory features of COVID-19 at time of hospitalization could help physicians in early suspicion of SARS-CoV-2 infection and distinguishing it from other etiologies. The knowledge of clinical features and microbiological techniques will be crucial in the next years when the endemic circulation of SARS-CoV-2 will be probably associated with clusters of infection. In this review we provide a state of the art about new advances in microbiological and clinical findings of SARS-CoV-2 infection in hospitalized patients with a focus on pulmonary and extrapulmonary characteristics, including the role of gut microbiota.
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50
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Multi-omics analyses of airway host-microbe interactions in chronic obstructive pulmonary disease identify potential therapeutic interventions. Nat Microbiol 2022; 7:1361-1375. [PMID: 35995842 DOI: 10.1038/s41564-022-01196-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 07/05/2022] [Indexed: 11/08/2022]
Abstract
The mechanistic role of the airway microbiome in chronic obstructive pulmonary disease (COPD) remains largely unexplored. We present a landscape of airway microbe-host interactions in COPD through an in-depth profiling of the sputum metagenome, metabolome, host transcriptome and proteome from 99 patients with COPD and 36 healthy individuals in China. Multi-omics data were integrated using sequential mediation analysis, to assess in silico associations of the microbiome with two primary COPD inflammatory endotypes, neutrophilic or eosinophilic inflammation, mediated through microbial metabolic interaction with host gene expression. Hypotheses of microbiome-metabolite-host interaction were identified by leveraging microbial genetic information and established metabolite-human gene pairs. A prominent hypothesis for neutrophil-predominant COPD was altered tryptophan metabolism in airway lactobacilli associated with reduced indole-3-acetic acid (IAA), which was in turn linked to perturbed host interleukin-22 signalling and epithelial cell apoptosis pathways. In vivo and in vitro studies showed that airway microbiome-derived IAA mitigates neutrophilic inflammation, apoptosis, emphysema and lung function decline, via macrophage-epithelial cell cross-talk mediated by interleukin-22. Intranasal inoculation of two airway lactobacilli restored IAA and recapitulated its protective effects in mice. These findings provide the rationale for therapeutically targeting microbe-host interaction in COPD.
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