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Barbieri F, Carlen V, Martina MG, Sannio F, Cancade S, Perini C, Restori M, Crespan E, Maga G, Docquier JD, Cagno V, Radi M. 4-Trifluoromethyl bithiazoles as broad-spectrum antimicrobial agents for virus-related bacterial infections or co-infections. RSC Med Chem 2024; 15:1589-1600. [PMID: 38784463 PMCID: PMC11110737 DOI: 10.1039/d3md00686g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 03/07/2024] [Indexed: 05/25/2024] Open
Abstract
Respiratory tract infections involving a variety of microorganisms such as viruses, bacteria, and fungi are a prominent cause of morbidity and mortality globally, exacerbating various pre-existing respiratory and non-respiratory conditions. Moreover, the ability of bacteria and viruses to coexist might impact the development and severity of lung infections, promoting bacterial colonization and subsequent disease exacerbation. Secondary bacterial infections following viral infections represent a complex challenge to be overcome from a therapeutic point of view. We report herein our efforts in the development of new bithiazole derivatives showing broad-spectrum antimicrobial activity against both viruses and bacteria. A series of 4-trifluoromethyl bithiazole analogues was synthesized and screened against selected viruses (hRVA16, EVD68, and ZIKV) and a panel of Gram-positive and Gram-negative bacteria. Among them, two promising broad-spectrum antimicrobial compounds (8a and 8j) have been identified: both compounds showed low micromolar activity against all tested viruses, 8a showed synergistic activity against E. coli and A. baumannii in the presence of a subinhibitory concentration of colistin, while 8j showed a broader spectrum of activity against Gram-positive and Gram-negative bacteria. Activity against antibiotic-resistant clinical isolates is also reported. Given the ever-increasing need to adequately address viral and bacterial infections or co-infections, this study paves the way for the development of new agents with broad antimicrobial properties and synergistic activity with common antivirals and antibacterials.
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Affiliation(s)
- Francesca Barbieri
- Dipartimento di Scienze degli Alimenti e del Farmaco (DipALIFAR), Università degli Studi di Parma Viale delle Scienze, 27/A 43124 Parma Italy
| | - Vincent Carlen
- Institute of Microbiology, University Hospital of Lausanne, University of Lausanne 1011 Lausanne Switzerland
| | - Maria Grazia Martina
- Dipartimento di Scienze degli Alimenti e del Farmaco (DipALIFAR), Università degli Studi di Parma Viale delle Scienze, 27/A 43124 Parma Italy
| | - Filomena Sannio
- Dipartimento di Biotecnologie Mediche, Università degli Studi di Siena Viale Bracci 16 53100 Siena Italy
| | - Sacha Cancade
- Dipartimento di Biotecnologie Mediche, Università degli Studi di Siena Viale Bracci 16 53100 Siena Italy
| | - Cecilia Perini
- Institute of Molecular Genetics IGM-CNR "Luigi Luca Cavalli-Sforza" Via Abbiategrasso 207 I-27100 Pavia Italy
| | - Margherita Restori
- Dipartimento di Scienze degli Alimenti e del Farmaco (DipALIFAR), Università degli Studi di Parma Viale delle Scienze, 27/A 43124 Parma Italy
| | - Emmanuele Crespan
- Institute of Molecular Genetics IGM-CNR "Luigi Luca Cavalli-Sforza" Via Abbiategrasso 207 I-27100 Pavia Italy
| | - Giovanni Maga
- Institute of Molecular Genetics IGM-CNR "Luigi Luca Cavalli-Sforza" Via Abbiategrasso 207 I-27100 Pavia Italy
| | - Jean-Denis Docquier
- Dipartimento di Biotecnologie Mediche, Università degli Studi di Siena Viale Bracci 16 53100 Siena Italy
| | - Valeria Cagno
- Institute of Microbiology, University Hospital of Lausanne, University of Lausanne 1011 Lausanne Switzerland
| | - Marco Radi
- Dipartimento di Scienze degli Alimenti e del Farmaco (DipALIFAR), Università degli Studi di Parma Viale delle Scienze, 27/A 43124 Parma Italy
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Risk Factors for Influenza-Induced Exacerbations and Mortality in Non-Cystic Fibrosis Bronchiectasis. Viruses 2023; 15:v15020537. [PMID: 36851751 PMCID: PMC9961441 DOI: 10.3390/v15020537] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/09/2023] [Accepted: 02/13/2023] [Indexed: 02/17/2023] Open
Abstract
Influenza infection is a cause of exacerbations in patients with chronic pulmonary diseases. The aim of this study was to investigate the clinical outcomes and identify risk factors associated with hospitalization and mortality following influenza infection in adult patients with bronchiectasis. Using the Chang Gung Research Database, we identified patients with bronchiectasis and influenza-related infection (ICD-9-CM 487 and anti-viral medicine) between 2008 and 2017. The main outcomes were influenza-related hospitalization and in-hospital mortality rate. Eight hundred sixty-five patients with bronchiectasis and influenza infection were identified. Five hundred thirty-six (62%) patients with bronchiectasis were hospitalized for influenza-related infection and 118 (22%) patients had respiratory failure. Compared to the group only seen in clinic, the hospitalization group was older, with more male patients, a lower FEV1, higher bronchiectasis aetiology comorbidity index (BACI), and more acute exacerbations in the previous year. Co-infections were evident in 55.6% of hospitalized patients, mainly caused by Pseudomonas aeruginosa (15%), fungus (7%), and Klebsiella pneumoniae (6%). The respiratory failure group developed acute kidney injury (36% vs. 16%; p < 0.001), and shock (47% vs. 6%; p < 0.001) more often than influenza patients without respiratory failure. The overall mortality rate was 10.8% and the respiratory failure group exhibited significantly higher in-hospital mortality rates (27.1% vs. 6.2%; p < 0.001). Age, BACI, and previous exacerbations were independently associated with influenza-related hospitalization. Age, presence of shock, and low platelet counts were associated with increased hospital mortality. Influenza virus caused severe exacerbation in bronchiectasis, especially in those who were older and who had high BACI scores and previous exacerbations. A high risk of respiratory failure and mortality were observed in influenza-related hospitalization in bronchiectasis. We highlight the importance of preventing or treating influenza infection in bronchiectasis.
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Erdmann N, Schilling T, Hentschel J, Lehmann T, von Bismarck P, Ankermann T, Duckstein F, Baier M, Zagoya C, Mainz JG. Divergent dynamics of inflammatory mediators and multiplex PCRs during airway infection in cystic fibrosis patients and healthy controls: Serial upper airway sampling by nasal lavage. Front Immunol 2022; 13:947359. [PMID: 36466839 PMCID: PMC9716083 DOI: 10.3389/fimmu.2022.947359] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 10/27/2022] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND In cystic fibrosis (CF), acute respiratory exacerbations critically enhance pulmonary destruction. Since these mainly occur outside regular appointments, they remain unexplored. We previously elaborated a protocol for home-based upper airway (UAW) sampling obtaining nasal-lavage fluid (NLF), which, in contrast to sputum, does not require immediate processing. The aim of this study was to compare UAW inflammation and pathogen colonization during stable phases and exacerbations in CF patients and healthy controls. METHODS Initially, we obtained NLF by rinsing 10 ml of isotonic saline/nostril during stable phases. During exacerbations, subjects regularly collected NLF at home. CF patients directly submitted one aliquot for microbiological cultures. The remaining samples were immediately frozen until transfer on ice to our clinic, where PCR analyses were performed and interleukin (IL)-1β/IL-6/IL-8, neutrophil elastase (NE), matrix metalloproteinase (MMP)-9, and tissue inhibitor of metalloproteinase (TIMP)-1 were assessed. RESULTS Altogether, 49 CF patients and 38 healthy controls (HCs) completed the study, and 214 NLF samples were analyzed. Of the 49 CF patients, 20 were at least intermittently colonized with P. aeruginosa and received azithromycin and/or inhaled antibiotics as standard therapy. At baseline, IL-6 and IL-8 tended to be elevated in CF compared to controls. During infection, inflammatory mediators increased in both cohorts, reaching significance only for IL-6 in controls (p=0.047). Inflammatory responses tended to be higher in controls [1.6-fold (NE) to 4.4-fold (MMP-9)], while in CF, mediators increased only moderately [1.2-1.5-fold (IL-6/IL-8/NE/TIMP-1/MMP-9)]. Patients receiving inhalative antibiotics or azithromycin (n=20 and n=15, respectively) revealed lower levels of IL-1β/IL-6/IL-8 and NE during exacerbation compared to CF patients not receiving those antibiotics. In addition, CF patients receiving azithromycin showed MMP-9 levels significantly lower than CF patients not receiving azithromycin at stable phase and exacerbation. Altogether, rhinoviruses were the most frequently detected virus, detected at least once in n=24 (49.0%) of the 49 included pwCF and in n=26 (68.4%) of the 38 healthy controls over the 13-month duration of the study. Remarkably, during exacerbation, rhinovirus detection rates were significantly higher in the HC group compared to those in CF patients (65.8% vs. 22.4%; p<0.0001). CONCLUSION Non-invasive and partially home-based UAW sampling opens new windows for the assessment of inflammation and pathogen colonization in the unified airway system.
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Affiliation(s)
- Nina Erdmann
- Cystic Fibrosis Centre, Brandenburg Medical School (MHB) University, Klinikum Westbrandenburg, Brandenburg an der Havel, Germany
| | | | - Julia Hentschel
- Institute of Human Genetics, Leipzig University Hospital, Leipzig, Germany
| | - Thomas Lehmann
- Jena University Hospital, Center for Clinical Studies (Biometrics), Jena, Germany
| | - Philipp von Bismarck
- Klinik für Kinder- und Jugendmedizin I, Universitätsklinikum Schleswig-Holstein (UKSH), Kiel, Germany
| | - Tobias Ankermann
- Klinik für Kinder- und Jugendmedizin I, Universitätsklinikum Schleswig-Holstein (UKSH), Kiel, Germany
| | - Franziska Duckstein
- Cystic Fibrosis Centre, Brandenburg Medical School (MHB) University, Klinikum Westbrandenburg, Brandenburg an der Havel, Germany
| | - Michael Baier
- Jena University Hospital, Department of Medical Microbiology, Jena, Germany
| | - Carlos Zagoya
- Cystic Fibrosis Centre, Brandenburg Medical School (MHB) University, Klinikum Westbrandenburg, Brandenburg an der Havel, Germany
| | - Jochen G. Mainz
- Cystic Fibrosis Centre, Brandenburg Medical School (MHB) University, Klinikum Westbrandenburg, Brandenburg an der Havel, Germany
- Jena University Hospital, CF-Center, Jena, Germany
- Faculty of Health Sciences, joint Faculty of the Brandenburg University of Technology Cottbus-Senftenberg, the Brandenburg Medical School Theodor Fontane and the University of Potsdam, Cottbus, Brandenburg an der Havel and Potsdam, Germany
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Sanders DB, Deschamp AR, Hatch JE, Slaven JE, Gebregziabher N, Corput MKVD, Tiddens HAWM, Rosenow T, Storch GA, Hall GL, Stick SM, Ranganathan S, Ferkol TW, Davis SD. Association between early respiratory viral infections and structural lung disease in infants with cystic fibrosis. J Cyst Fibros 2022; 21:1020-1026. [PMID: 35523715 PMCID: PMC10564322 DOI: 10.1016/j.jcf.2022.04.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 04/15/2022] [Accepted: 04/17/2022] [Indexed: 11/18/2022]
Abstract
BACKGROUND Infants with cystic fibrosis (CF) develop structural lung disease early in life, and viral infections are associated with progressive lung disease. We hypothesized that the presence of respiratory viruses would be associated with structural lung disease on computed tomography (CT) of the chest in infants with CF. METHODS Infants with CF were enrolled before 4 months of age. Multiplex PCR assays were performed on nasal swabs to detect respiratory viruses during routine visits and when symptomatic. Participants underwent CT imaging at approximately 12 months of age. Associations between Perth-Rotterdam Annotated Grid Morphometric Analysis for CF (PRAGMA-CF) CT scores and respiratory viruses and symptoms were assessed with Spearman correlation coefficients. RESULTS Sixty infants were included for analysis. Human rhinovirus was the most common virus detected, on 28% of tested nasal swabs and in 85% of participants. The median (IQR) extent of lung fields that was healthy based on PRAGMA-CF was 98.7 (0.8)%. There were no associations between PRAGMA-CF and age at first virus, or detection of any virus, including rhinovirus, respiratory syncytial virus, or parainfluenza. The extent of airway wall thickening was associated with ever having wheezed (ρ = 0.31, p = 0.02) and number of encounters with cough (ρ = 0.25, p = 0.0495). CONCLUSIONS Infants with CF had minimal structural lung disease. We did not find an association between respiratory viruses and CT abnormalities. Wheezing and frequency of cough were associated with early structural changes.
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Affiliation(s)
- Don B Sanders
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA.
| | - Ashley R Deschamp
- Department of Pediatrics, University of Nebraska Medical Center, Children's Hospital and Medical Center, Omaha, NE, USA
| | - Joseph E Hatch
- Department of Pediatrics, UNC Children's, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - James E Slaven
- Department of Biostatistics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Netsanet Gebregziabher
- Department of Biostatistics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Mariette Kemner-van de Corput
- Department of Paediatrics, Erasmus MC - Sophia Children's Hospital, University Medial Center Rotterdam, Netherlands; Department of Radiology and Nuclear Medicine, Erasmus MC - Sophia Children's Hospital, University Medial Center Rotterdam, Netherlands
| | - Harm A W M Tiddens
- Department of Paediatrics, Erasmus MC - Sophia Children's Hospital, University Medial Center Rotterdam, Netherlands; Department of Radiology and Nuclear Medicine, Erasmus MC - Sophia Children's Hospital, University Medial Center Rotterdam, Netherlands
| | - Tim Rosenow
- The Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, Nedlands, Western Australia; Children's Lung Health, Wal-yan Respiratory Research Centre, Telethon Kids Institute and School of Physiotherapy and Exercise Science, Curtin University, Perth, Australia
| | - Gregory A Storch
- Department of Pediatrics, Washington University, St. Louis Children's Hospital, St. Louis, MO, USA
| | - Graham L Hall
- Children's Lung Health, Wal-yan Respiratory Research Centre, Telethon Kids Institute and School of Physiotherapy and Exercise Science, Curtin University, Perth, Australia
| | - Stephen M Stick
- Department of Pediatrics, University of Western Australia, Telethon Kids Institute, Perth, Australia
| | - Sarath Ranganathan
- Department of Respiratory and Sleep Medicine, Royal Children's Hospital, Parkville, Australia; Infection and Immunity, Murdoch Children's Research Institute, Parkville, Australia; Department of Paediatrics, University of Melbourne, Parkville, Australia
| | - Thomas W Ferkol
- Department of Pediatrics, Washington University, St. Louis Children's Hospital, St. Louis, MO, USA
| | - Stephanie D Davis
- Department of Pediatrics, UNC Children's, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
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5
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Unravelling the molecular mechanisms underlying chronic respiratory diseases for the development of novel therapeutics via in vitro experimental models. Eur J Pharmacol 2022; 919:174821. [DOI: 10.1016/j.ejphar.2022.174821] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 02/01/2022] [Accepted: 02/09/2022] [Indexed: 12/11/2022]
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Viral and Bacterial Co-Infections in the Lungs: Dangerous Liaisons. Viruses 2021; 13:v13091725. [PMID: 34578306 PMCID: PMC8472850 DOI: 10.3390/v13091725] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 08/26/2021] [Accepted: 08/27/2021] [Indexed: 12/23/2022] Open
Abstract
Respiratory tract infections constitute a significant public health problem, with a therapeutic arsenal that remains relatively limited and that is threatened by the emergence of antiviral and/or antibiotic resistance. Viral–bacterial co-infections are very often associated with the severity of these respiratory infections and have been explored mainly in the context of bacterial superinfections following primary influenza infection. This review summarizes our current knowledge of the mechanisms underlying these co-infections between respiratory viruses (influenza viruses, RSV, and SARS-CoV-2) and bacteria, at both the physiological and immunological levels. This review also explores the importance of the microbiome and the pathological context in the evolution of these respiratory tract co-infections and presents the different in vitro and in vivo experimental models available. A better understanding of the complex functional interactions between viruses/bacteria and host cells will allow the development of new, specific, and more effective diagnostic and therapeutic approaches.
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Corvol H, de Miranda S, Lemonnier L, Kemgang A, Reynaud Gaubert M, Chiron R, Dalphin ML, Durieu I, Dubus JC, Houdouin V, Prevotat A, Ramel S, Revillion M, Weiss L, Guillot L, Boelle PY, Burgel PR. First Wave of COVID-19 in French Patients with Cystic Fibrosis. J Clin Med 2020; 9:E3624. [PMID: 33182847 PMCID: PMC7697588 DOI: 10.3390/jcm9113624] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 10/27/2020] [Accepted: 11/09/2020] [Indexed: 12/13/2022] Open
Abstract
Viral infections are known to lead to serious respiratory complications in cystic fibrosis (CF) patients. Hypothesizing that CF patients were a population at high risk for severe respiratory complications from SARS-CoV-2 infection, we conducted a national study to describe the clinical expression of COVID-19 in French CF patients. This prospective observational study involves all 47 French CF centers caring for approximately 7500 CF patients. Between March 1st and June 30th 2020, 31 patients were diagnosed with COVID-19: 19 had positive SARS-CoV-2 RT-PCR in nasopharyngeal swabs; 1 had negative RT-PCR but typical COVID-19 signs on a CT scan; and 11 had positive SARS-CoV-2 serology. Fifteen were males, median (range) age was 31 (9-60) years, and 12 patients were living with a lung transplant. The majority of the patients had CF-related diabetes (n = 19, 61.3%), and a mild lung disease (n = 19, 65%, with percent-predicted forced expiratory volume in 1 s (ppFEV1) > 70). Three (10%) patients remained asymptomatic. For the 28 (90%) patients who displayed symptoms, most common symptoms at admission were fever (n = 22, 78.6%), fatigue (n = 14, 50%), and increased cough (n = 14, 50%). Nineteen were hospitalized (including 11 out of the 12 post-lung transplant patients), seven required oxygen therapy, and four (3 post-lung transplant patients) were admitted to an Intensive Care Unit (ICU). Ten developed complications (including acute respiratory distress syndrome in two post-lung transplant patients), but all recovered and were discharged home without noticeable short-term sequelae. Overall, French CF patients were rarely diagnosed with COVID-19. Further research should establish whether they were not infected or remained asymptomatic upon infection. In diagnosed cases, the short-term evolution was favorable with rare acute respiratory distress syndrome and no death. Post-lung transplant patients had more severe outcomes and should be monitored more closely.
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Affiliation(s)
- Harriet Corvol
- Pediatric Pulmonology Department and Pediatric CF Center, Assistance Publique Hôpitaux de Paris (APHP) Hôpital Trousseau, 75012 Paris, France
- Centre de Recherche Saint‑Antoine (CRSA), INSERM UMR_S938, Sorbonne Université, 75012 Paris, France; (A.K.); (L.G.)
| | - Sandra de Miranda
- Pulmonology Department and CF Center, Hôpital Foch, 92151 Suresnes, France;
| | | | - Astrid Kemgang
- Centre de Recherche Saint‑Antoine (CRSA), INSERM UMR_S938, Sorbonne Université, 75012 Paris, France; (A.K.); (L.G.)
| | - Martine Reynaud Gaubert
- Pulmonology Department and CF Adult Center, Hôpital Nord, Assistance Publique Hôpitaux de Marseille (APHM), 13915 Marseille, France;
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), IHU Méditerranée Infection, MEPHI, 13005 Marseille, France
| | - Raphael Chiron
- CF Center, Hôpital Arnaud de Villeneuve, CHU de Montpellier, 34295 Montpellier, France;
| | - Marie-Laure Dalphin
- Pediatric CF Center, Hôpital Jean-Minjoz, CHU de Besançon, 25030 Besançon, France;
| | - Isabelle Durieu
- Internal Medicine Department and Adult CF Center, Hospices Civils de Lyon, EA 7425 HESPER, Université de Lyon, 69495 Lyon, France;
| | - Jean-Christophe Dubus
- Pediatric Pulmonology Department and Pediatric CF Center, APHM, 13385 Marseille, France;
| | | | - Anne Prevotat
- Adult CF Center, Hôpital Calmette and University Lille, 59037 Lille, France;
| | - Sophie Ramel
- Pediatric and Adult CF Center, 29680 Roscoff, France;
| | - Marine Revillion
- Pediatric CF Center, Hôpital Jeanne de Flandres, CHU Lille, 59037 Lille, France;
| | - Laurence Weiss
- Pediatric CF Center, Hôpitaux Universitaires de Strasbourg, 67098 Strasbourg, France;
| | - Loic Guillot
- Centre de Recherche Saint‑Antoine (CRSA), INSERM UMR_S938, Sorbonne Université, 75012 Paris, France; (A.K.); (L.G.)
| | - Pierre-Yves Boelle
- Institut Pierre Louis d’Epidémiologie et de Santé Publique, INSERM, APHP, Sorbonne Université, 75012 Paris, France;
| | - Pierre-Régis Burgel
- Respiratory Medicine and National Reference CF Center, AP-HP Hôpital Cochin, 75014 Paris, France;
- Institut Cochin, Inserm U-1016, Université de Paris, 75014 Paris, France
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Stanton BA, Hampton TH, Ashare A. SARS-CoV-2 (COVID-19) and cystic fibrosis. Am J Physiol Lung Cell Mol Physiol 2020; 319:L408-L415. [PMID: 32668165 PMCID: PMC7518058 DOI: 10.1152/ajplung.00225.2020] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/06/2020] [Accepted: 07/06/2020] [Indexed: 12/16/2022] Open
Abstract
Cystic fibrosis (CF) is a genetic disease caused by mutations in the CFTR gene. Although viral respiratory tract infections are, in general, more severe in patients with CF compared with the general population, a small number of studies indicate that SARS-CoV-2 does not cause a worse infection in CF. This is surprising since comorbidities including preexisting lung disease have been reported to be associated with worse outcomes in SARS-CoV-2 infections. Several recent studies provide insight into why SARS-CoV-2 may not produce more severe outcomes in CF. First, ACE and ACE2, genes that play key roles in SARS-CoV-2 infection, have some variants that are predicted to reduce the severity of SARS-CoV-2 infection. Second, mRNA for ACE2 is elevated and mRNA for TMPRSS2, a serine protease, is decreased in CF airway epithelial cells. Increased ACE2 is predicted to enhance SARS-CoV-2 binding to cells but would increase conversion of angiotensin II, which is proinflammatory, to angiotensin-1-7, which is anti-inflammatory. Thus, increased ACE2 would reduce inflammation and lung damage due to SARS-CoV-2. Moreover, decreased TMPRSS2 would reduce SARS-CoV-2 entry into airway epithelial cells. Second, many CF patients are treated with azithromycin, which suppresses viral infection and lung inflammation and inhibits the activity of furin, a serine protease. Finally, the CF lung contains high levels of serine protease inhibitors including ecotin and SERPINB1, which are predicted to reduce the ability of TMPRSS2 to facilitate SARS-CoV-2 entry into airway epithelial cells. Thus, a variety of factors may mitigate the severity of SARS-CoV-2 in CF.
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Affiliation(s)
- Bruce A Stanton
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Thomas H Hampton
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Alix Ashare
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
- Section of Pulmonology, Department of Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire
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9
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Cornforth DM, Diggle FL, Melvin JA, Bomberger JM, Whiteley M. Quantitative Framework for Model Evaluation in Microbiology Research Using Pseudomonas aeruginosa and Cystic Fibrosis Infection as a Test Case. mBio 2020; 11:e03042-19. [PMID: 31937646 PMCID: PMC6960289 DOI: 10.1128/mbio.03042-19] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 11/27/2019] [Indexed: 01/14/2023] Open
Abstract
Laboratory models are a cornerstone of modern microbiology, but the accuracy of these models has not been systematically evaluated. As a result, researchers often choose models based on intuition or incomplete data. We propose a general quantitative framework to assess model accuracy from RNA sequencing data and use this framework to evaluate models of Pseudomonas aeruginosa cystic fibrosis (CF) lung infection. We found that an in vitro synthetic CF sputum medium model and a CF airway epithelial cell model had the highest genome-wide accuracy but underperformed on distinct functional categories, including porins and polyamine biosynthesis for the synthetic sputum medium and protein synthesis for the epithelial cell model. We identified 211 "elusive" genes that were not mimicked in a reference strain grown in any laboratory model but found that many were captured by using a clinical isolate. These methods provide researchers with an evidence-based foundation to select and improve laboratory models.IMPORTANCE Laboratory models have become a cornerstone of modern microbiology. However, the accuracy of even the most commonly used models has never been evaluated. Here, we propose a quantitative framework based on gene expression data to evaluate model performance and apply it to models of Pseudomonas aeruginosa cystic fibrosis lung infection. We discovered that these models captured different aspects of P. aeruginosa infection physiology, and we identify which functional categories are and are not captured by each model. These methods will provide researchers with a solid basis to choose among laboratory models depending on the scientific question of interest and will help improve existing experimental models.
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Affiliation(s)
- Daniel M Cornforth
- School of Biological Sciences, Georgia Institute of Technology, Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, USA
- Emory-Children's Cystic Fibrosis Center, Atlanta, Georgia, USA
| | - Frances L Diggle
- School of Biological Sciences, Georgia Institute of Technology, Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, USA
- Emory-Children's Cystic Fibrosis Center, Atlanta, Georgia, USA
| | - Jeffrey A Melvin
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Jennifer M Bomberger
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Marvin Whiteley
- School of Biological Sciences, Georgia Institute of Technology, Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, USA
- Emory-Children's Cystic Fibrosis Center, Atlanta, Georgia, USA
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10
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Characterization of cellular transcriptomic signatures induced by different respiratory viruses in human reconstituted airway epithelia. Sci Rep 2019; 9:11493. [PMID: 31391513 PMCID: PMC6685967 DOI: 10.1038/s41598-019-48013-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 07/29/2019] [Indexed: 11/17/2022] Open
Abstract
Acute respiratory infections, a large part being of viral origin, constitute a major public health issue. To propose alternative and/or new therapeutic approaches, it is necessary to increase our knowledge about the interactions between respiratory viruses and their primary cellular targets using the most biologically relevant experimental models. In this study, we used RNAseq to characterize and compare the transcriptomic signature of infection induced by different major respiratory viruses (Influenza viruses, hRSV and hMPV) in a model of reconstituted human airway epithelia. Our results confirm the importance of several cellular pathways commonly or specifically induced by these respiratory viruses, such as the innate immune response or antiviral defense. A very interesting common feature revealed by the global virogenomic signature shared between hRSV, hMPV and influenza viruses is the global downregulation of cilium-related gene expression, in good agreement with experimental evaluation of mucociliary clearance. Beyond providing new information about respiratory virus/host interactions, our study also underlines the interest of using biologically relevant experimental models to study human respiratory viruses.
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Polineni D, Dang H, Gallins PJ, Jones LC, Pace RG, Stonebraker JR, Commander LA, Krenicky JE, Zhou YH, Corvol H, Cutting GR, Drumm ML, Strug LJ, Boyle MP, Durie PR, Chmiel JF, Zou F, Wright FA, O'Neal WK, Knowles MR. Airway Mucosal Host Defense Is Key to Genomic Regulation of Cystic Fibrosis Lung Disease Severity. Am J Respir Crit Care Med 2019; 197:79-93. [PMID: 28853905 DOI: 10.1164/rccm.201701-0134oc] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
RATIONALE The severity of cystic fibrosis (CF) lung disease varies widely, even for Phe508del homozygotes. Heritability studies show that more than 50% of the variability reflects non-cystic fibrosis transmembrane conductance regulator (CFTR) genetic variation; however, the full extent of the pertinent genetic variation is not known. OBJECTIVES We sought to identify novel CF disease-modifying mechanisms using an integrated approach based on analyzing "in vivo" CF airway epithelial gene expression complemented with genome-wide association study (GWAS) data. METHODS Nasal mucosal RNA from 134 patients with CF was used for RNA sequencing. We tested for associations of transcriptomic (gene expression) data with a quantitative phenotype of CF lung disease severity. Pathway analysis of CF GWAS data (n = 5,659 patients) was performed to identify novel pathways and assess the concordance of genomic and transcriptomic data. Association of gene expression with previously identified CF GWAS risk alleles was also tested. MEASUREMENTS AND MAIN RESULTS Significant evidence of heritable gene expression was identified. Gene expression pathways relevant to airway mucosal host defense were significantly associated with CF lung disease severity, including viral infection, inflammation/inflammatory signaling, lipid metabolism, apoptosis, ion transport, Phe508del CFTR processing, and innate immune responses, including HLA (human leukocyte antigen) genes. Ion transport and CFTR processing pathways, as well as HLA genes, were identified across differential gene expression and GWAS signals. CONCLUSIONS Transcriptomic analyses of CF airway epithelia, coupled to genomic (GWAS) analyses, highlight the role of heritable host defense variation in determining the pathophysiology of CF lung disease. The identification of these pathways provides opportunities to pursue targeted interventions to improve CF lung health.
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Affiliation(s)
- Deepika Polineni
- 1 Department of Internal Medicine, University of Kansas Medical Center, Kansas City, Kansas.,2 Cystic Fibrosis/Pulmonary Research and Treatment Center, Marsico Lung Institute, School of Medicine, and
| | - Hong Dang
- 2 Cystic Fibrosis/Pulmonary Research and Treatment Center, Marsico Lung Institute, School of Medicine, and
| | - Paul J Gallins
- 3 Bioinformatics Research Center, Department of Biological Sciences
| | - Lisa C Jones
- 2 Cystic Fibrosis/Pulmonary Research and Treatment Center, Marsico Lung Institute, School of Medicine, and
| | - Rhonda G Pace
- 2 Cystic Fibrosis/Pulmonary Research and Treatment Center, Marsico Lung Institute, School of Medicine, and
| | - Jaclyn R Stonebraker
- 2 Cystic Fibrosis/Pulmonary Research and Treatment Center, Marsico Lung Institute, School of Medicine, and
| | - Leah A Commander
- 2 Cystic Fibrosis/Pulmonary Research and Treatment Center, Marsico Lung Institute, School of Medicine, and
| | - Jeanne E Krenicky
- 4 Department of Pediatrics, Rainbow Babies and Children's Hospital, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Yi-Hui Zhou
- 3 Bioinformatics Research Center, Department of Biological Sciences
| | - Harriet Corvol
- 5 Pediatric Pulmonary Department, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Trousseau, Institut National de la Santé et la Recherche Médicale (INSERM) U938, Paris, France.,6 Sorbonne Universités, Université Pierre et Marie Curie (UPMC), Paris 6, Paris, France
| | - Garry R Cutting
- 7 McKusick-Nathans Institute of Genetic Medicine.,8 Department of Pediatrics, and
| | - Mitchell L Drumm
- 4 Department of Pediatrics, Rainbow Babies and Children's Hospital, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Lisa J Strug
- 9 Program in Genetics and Genome Biology.,10 Division of Biostatistics, Dalla Lana School of Public Health, and
| | - Michael P Boyle
- 11 Division of Pulmonary and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Peter R Durie
- 12 Physiology and Experimental Medicine Research Program, and.,13 Division of Gastroenterology, Hepatology and Nutrition, The Hospital for Sick Children, Toronto, Ontario, Canada; and.,14 Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada
| | - James F Chmiel
- 4 Department of Pediatrics, Rainbow Babies and Children's Hospital, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Fei Zou
- 15 Department of Biostatistics, School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Fred A Wright
- 16 Department of Statistics, and.,17 Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina
| | - Wanda K O'Neal
- 2 Cystic Fibrosis/Pulmonary Research and Treatment Center, Marsico Lung Institute, School of Medicine, and
| | - Michael R Knowles
- 2 Cystic Fibrosis/Pulmonary Research and Treatment Center, Marsico Lung Institute, School of Medicine, and
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12
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Crane MJ, Lee KM, FitzGerald ES, Jamieson AM. Surviving Deadly Lung Infections: Innate Host Tolerance Mechanisms in the Pulmonary System. Front Immunol 2018; 9:1421. [PMID: 29988424 PMCID: PMC6024012 DOI: 10.3389/fimmu.2018.01421] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 06/07/2018] [Indexed: 12/16/2022] Open
Abstract
Much research on infectious diseases focuses on clearing the pathogen through the use of antimicrobial drugs, the immune response, or a combination of both. Rapid clearance of pathogens allows for a quick return to a healthy state and increased survival. Pathogen-targeted approaches to combating infection have inherent limitations, including their pathogen-specific nature, the potential for antimicrobial resistance, and poor vaccine efficacy, among others. Another way to survive an infection is to tolerate the alterations to homeostasis that occur during a disease state through a process called host tolerance or resilience, which is independent from pathogen burden. Alterations in homeostasis during infection are numerous and include tissue damage, increased inflammation, metabolic changes, temperature changes, and changes in respiration. Given its importance and sensitivity, the lung is a good system for understanding host tolerance to infectious disease. Pneumonia is the leading cause of death for children under five worldwide. One reason for this is because when the pulmonary system is altered dramatically it greatly impacts the overall health and survival of a patient. Targeting host pathways involved in maintenance of pulmonary host tolerance during infection could provide an alternative therapeutic avenue that may be broadly applicable across a variety of pathologies. In this review, we will summarize recent findings on tolerance to host lung infection. We will focus on the involvement of innate immune responses in tolerance and how an initial viral lung infection may alter tolerance mechanisms in leukocytic, epithelial, and endothelial compartments to a subsequent bacterial infection. By understanding tolerance mechanisms in the lung we can better address treatment options for deadly pulmonary infections.
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Affiliation(s)
| | | | | | - Amanda M. Jamieson
- Division of Biology and Medicine, Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, United States
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13
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Novel protective mechanism for interleukin-33 at the mucosal barrier during influenza-associated bacterial superinfection. Mucosal Immunol 2018; 11:199-208. [PMID: 28401938 PMCID: PMC5638662 DOI: 10.1038/mi.2017.32] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 03/01/2017] [Indexed: 02/04/2023]
Abstract
Influenza A is a highly contagious respiratory virus that causes seasonal epidemics and occasional worldwide pandemics. The primary cause of influenza-related mortality is bacterial superinfection. There are numerous mechanisms by which preceding influenza infection attenuates host defense, allowing for increased susceptibility to bacterial pneumonia. Herein, we demonstrate that influenza inhibits Staphylococcus aureus-induced production of interleukin-33 (IL-33). Restoration of IL-33 during influenza A and methicillin-resistant S. aureus superinfection enhanced bacterial clearance and improved mortality. Innate lymphoid Type 2 cells and alternatively activated macrophages are not required for IL-33-mediated protection during superinfection. We show that IL-33 treatment resulted in neutrophil recruitment to the lung, associated with improved bacterial clearance. These findings identify a novel role for IL-33 in antibacterial host defense at the mucosal barrier.
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14
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De Luna X, Hartshorn KL. Influenza Casts a Lung Shadow. THE AMERICAN JOURNAL OF PATHOLOGY 2017; 187:697-699. [PMID: 28222276 DOI: 10.1016/j.ajpath.2017.01.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 01/26/2017] [Indexed: 10/20/2022]
Abstract
This commentary highlights the article by Pociask et al that provides new insights into the lingering effects of influenza infection.
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Affiliation(s)
- Xavier De Luna
- Department of Medicine, Section of Hematology and Oncology, Boston University School of Medicine, Boston, Massachusetts
| | - Kevan L Hartshorn
- Department of Medicine, Section of Hematology and Oncology, Boston University School of Medicine, Boston, Massachusetts.
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15
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16
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Melvin JA, Bomberger JM. Compromised Defenses: Exploitation of Epithelial Responses During Viral-Bacterial Co-Infection of the Respiratory Tract. PLoS Pathog 2016; 12:e1005797. [PMID: 27631788 PMCID: PMC5025022 DOI: 10.1371/journal.ppat.1005797] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Affiliation(s)
- Jeffrey A. Melvin
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Jennifer M. Bomberger
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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