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Naseem R, Howe N, Williams CJ, Pretorius S, Green K. What diagnostic tests are available for respiratory infections or pulmonary exacerbations in cystic fibrosis: A scoping literature review. Respir Investig 2024; 62:817-831. [PMID: 39024929 DOI: 10.1016/j.resinv.2024.07.005] [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: 05/03/2024] [Revised: 07/02/2024] [Accepted: 07/06/2024] [Indexed: 07/20/2024]
Abstract
A scoping review methodological framework formed the basis of this review. A search of two electronic databases captured relevant literature published from 2013. 1184 articles were screened, 200 of which met inclusion criteria. Included studies were categorised as tests for either respiratory infections OR pulmonary exacerbations. Data were extracted to ascertain test type, sample type, and indication of use for each test type. For infection, culture is the most common testing method, particularly for bacterial infections, whereas PCR is utilised more for the diagnosis of viral infections. Spirometry tests, indicating lung function, facilitate respiratory infection diagnoses. There is no clear definition of what an exacerbation is in persons with CF. A clinical checklist with risk criteria can determine if a patient is experiencing an exacerbation event, however the diagnosis is clinician-led and will vary between individuals. Fuchs criteria are one of the most frequently used tests to assess signs and symptoms of exacerbation in persons with CF. This scoping review highlights the development of home monitoring tests to facilitate earlier and easier diagnoses, and the identification of novel biomarkers for indication of infections/exacerbations as areas of current research and development. Research is particularly prevalent regarding exhaled breath condensate and volatile organic compounds as an alternative sampling/biomarker respectively for infection diagnosis. Whilst there are a wide range of tests available for diagnosing respiratory infections and/or exacerbations, these are typically used clinically in combination to ensure a rapid, accurate diagnosis which will ultimately benefit both the patient and clinician.
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Affiliation(s)
- Raasti Naseem
- NIHR Newcastle HealthTech Research Centre in Diagnostic and Technology Evaluation, Fourth floor William Leech Building, Newcastle University, Newcastle upon Tyne, NE2 4HH, United Kingdom
| | - Nicola Howe
- NIHR Newcastle HealthTech Research Centre in Diagnostic and Technology Evaluation, Fourth floor William Leech Building, Newcastle University, Newcastle upon Tyne, NE2 4HH, United Kingdom.
| | - Cameron J Williams
- NIHR Newcastle HealthTech Research Centre in Diagnostic and Technology Evaluation, Fourth floor William Leech Building, Newcastle University, Newcastle upon Tyne, NE2 4HH, United Kingdom
| | - Sara Pretorius
- NIHR Newcastle HealthTech Research Centre in Diagnostic and Technology Evaluation, Fourth floor William Leech Building, Newcastle University, Newcastle upon Tyne, NE2 4HH, United Kingdom
| | - Kile Green
- NIHR Newcastle HealthTech Research Centre in Diagnostic and Technology Evaluation, Fourth floor William Leech Building, Newcastle University, Newcastle upon Tyne, NE2 4HH, United Kingdom
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2
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Brackenborough K, Ellis H, Flight WG. Respiratory Viruses and Cystic Fibrosis. Semin Respir Crit Care Med 2023; 44:196-208. [PMID: 36535663 DOI: 10.1055/s-0042-1758728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The threat of respiratory virus infection to human health and well-being has been clearly highlighted by the coronavirus disease 2019 (COVID-19) pandemic. For people with cystic fibrosis (CF), the clinical significance of viral infections long predated the emergence of severe acute respiratory syndrome coronavirus 2. This article reviews the epidemiology, diagnosis, and treatment of respiratory virus infection in the context of CF as well as the current understanding of interactions between viruses and other microorganisms in the CF lung. The incidence of respiratory virus infection in CF varies by age with young children typically experiencing more frequent episodes than adolescents and adults. At all ages, respiratory viruses are very common in CF and are associated with pulmonary exacerbations. Respiratory viruses are identified at up to 69% of exacerbations, while viruses are also frequently detected during clinical stability. The full impact of COVID-19 in CF is yet to be established. Early studies found that rates of COVID-19 were lower in CF cohorts than in the general population. The reasons for this are unclear but may be related to the effects of shielding, infection control practices, maintenance CF therapies, or the inflammatory milieu in the CF lung. Observational studies have consistently identified that prior solid organ transplantation is a key risk factor for poor outcomes from COVID-19 in CF. Several key priorities for future research are highlighted. First, the impact of highly effective CFTR modulator therapy on the epidemiology and pathophysiology of viral infections in CF requires investigation. Second, the impact of respiratory viruses on the development and dynamics of the CF lung microbiota is poorly understood and viral infection may have important interactions with bacteria and fungi in the airway. Finally, bacteriophages represent a key focus of future investigation both for their role in transmission of antimicrobial resistance and as a promising treatment modality for multiresistant pathogens.
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Affiliation(s)
- Kate Brackenborough
- Oxford Centre for Respiratory Medicine, Oxford University Hospitals National Health Service Foundation Trust, Oxford, United Kingdom
| | - Huw Ellis
- Oxford Centre for Respiratory Medicine, Oxford University Hospitals National Health Service Foundation Trust, Oxford, United Kingdom
| | - William G Flight
- Oxford Centre for Respiratory Medicine, Oxford University Hospitals National Health Service Foundation Trust, Oxford, United Kingdom.,Research and Development, GlaxoSmithKline plc, Brentford, United Kingdom
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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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4
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Unexpected associations between respiratory viruses and bacteria with Pulmonary Function Testing in children suffering from Cystic Fibrosis (MUCOVIB study). J Cyst Fibros 2021; 21:e158-e164. [PMID: 34756681 DOI: 10.1016/j.jcf.2021.10.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 08/31/2021] [Accepted: 10/06/2021] [Indexed: 12/23/2022]
Abstract
BACKGROUND Various bacterial and viral assemblages composing Cystic Fibrosis (CF) lung microbiota contribute to long-term lung function decline over time. Yet, the impact of individual microorganisms on pulmonary functions remains uncertain in children with CF. METHODS As part of the 'Mucoviscidosis, respiratory VIruses, intracellular Bacteria and fastidious organisms'' project, children with CF were longitudinally followed in a Swiss multicentric study. Respiratory samples included mainly throat swabs and sputa samples for bacterial culture and 16S rRNA metagenomics and nasopharyngeal swabs for respiratory virus detection by molecular assays. Percentage of predicted Forced Expiratory Volume in one second (FEV1%) and Lung Clearance Index (LCI) were recorded. RESULTS Sixty-one children, of whom 20 (32.8%) presented with at least one pulmonary exacerbation, were included. Almost half of the 363 nasopharyngeal swabs tested by RT-PCR were positive for a respiratory virus, mainly rhinovirus (26.5%). From linear mixed-effects regression models, P. aeruginosa (-11.35, 95%CI [-17.90; -4.80], p = 0.001) was significantly associated with a decreased FEV1%, whereas rhinovirus was associated with a significantly higher FEV1% (+4.24 95%CI [1.67; 6.81], p = 0.001). Compared to conventional culture, 16S rRNA metagenomics showed a sensitivity and specificity of 80.0% and 85.4%, respectively for detection of typical CF pathogens. However, metagenomics detected a bacteria almost twice more often than culture. CONCLUSIONS As expected, P. aeruginosa impacted negatively on FEV1% while rhinovirus was surprisingly associated with better FEV1%. Culture-free assays identifies significantly more pathogens than standard culture, with disputable clinical correlation.
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Korten I, Oestreich MA, Frey U, Moeller A, Jung A, Spinas R, Mueller-Suter D, Trachsel D, Rochat I, Spycher B, Latzin P, Casaulta C, Ramsey K. Respiratory symptoms do not reflect functional impairment in early CF lung disease. J Cyst Fibros 2021; 20:957-964. [PMID: 34088612 DOI: 10.1016/j.jcf.2021.04.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 04/11/2021] [Accepted: 04/12/2021] [Indexed: 11/27/2022]
Abstract
BACKGROUND Lung disease can develop within the first year of life in infants with cystic fibrosis (CF). However, the frequency and severity of respiratory symptoms in infancy are not known. METHODS We assessed respiratory symptoms in 50 infants with CF and 50 healthy matched controls from two prospective birth cohort studies. Respiratory symptoms and respiratory rate were documented by standardized weekly interviews throughout the first year. Infants performed multiple breath washout in the first weeks of life. RESULTS We analyzed 4552 data points (2217 in CF). Respiratory symptoms (either mild or severe) were not more frequent in infants with CF (OR:1.1;95% CI:[0.76, 1.59]; p=0.6). Higher lung clearance index and higher respiratory rate in infants with CF were not associated with respiratory symptoms. CONCLUSIONS We found no difference in respiratory symptoms between healthy and CF infants. These data indicate that early CF lung disease may not be captured by clinical presentation alone.
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Affiliation(s)
- Insa Korten
- Division of Paediatric Respiratory Medicine and Allergology, Department of Paediatrics, Inselspital, Bern Unviersity Hospital, University of Bern, Switzerland
| | - Marc-Alexander Oestreich
- Division of Paediatric Respiratory Medicine and Allergology, Department of Paediatrics, Inselspital, Bern Unviersity Hospital, University of Bern, Switzerland; Graduate School for Health Sciences, University of Bern, Switzerland
| | - Urs Frey
- University of Basel Children's Hospital (UKBB), Basel, Switzerland
| | - Alexander Moeller
- Division of Respiratory Medicine, University Children's Hospital Zurich, Switzerland
| | - Andreas Jung
- Division of Respiratory Medicine, University Children's Hospital Zurich, Switzerland
| | - Renate Spinas
- Division of Respiratory Medicine, University Children's Hospital Zurich, Switzerland
| | | | - Daniel Trachsel
- University of Basel Children's Hospital (UKBB), Basel, Switzerland
| | - Isabelle Rochat
- Department of Paediatrics, Respiratory Unit, Lausanne University Hospital, Lausanne, Switzerland
| | - Ben Spycher
- Institute for Social and Preventive Medicine, University of Bern, Switzerland
| | - Philipp Latzin
- Division of Paediatric Respiratory Medicine and Allergology, Department of Paediatrics, Inselspital, Bern Unviersity Hospital, University of Bern, Switzerland
| | - Carmen Casaulta
- Division of Paediatric Respiratory Medicine and Allergology, Department of Paediatrics, Inselspital, Bern Unviersity Hospital, University of Bern, Switzerland
| | - Kathryn Ramsey
- Division of Paediatric Respiratory Medicine and Allergology, Department of Paediatrics, Inselspital, Bern Unviersity Hospital, University of Bern, Switzerland.
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6
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Meyer VMC, Siqueira MM, Costa PFBM, Caetano BC, Oliveira Lopes JC, Folescu TW, Motta FDC. Clinical impact of respiratory virus in pulmonary exacerbations of children with Cystic Fibrosis. PLoS One 2020; 15:e0240452. [PMID: 33112873 PMCID: PMC7592759 DOI: 10.1371/journal.pone.0240452] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 09/25/2020] [Indexed: 01/17/2023] Open
Abstract
Backgrounds Cystic Fibrosis (CF) is a genetic, multisystemic, progressive illness that causes chronic suppurative lung disease. A major cause of morbimortality in this condition are pulmonary exacerbations. Although classically attributed to bacterial infections, respiratory virus have been increasingly recognized in its ethiopathogeny. Methods Nasopharyngeal swab samples were collected from children < 18 years old with CF in Rio de Janeiro, Brazil, with pulmonary exacerbation criteria. Samples were submitted to RT-PCR for Adenovirus, Influenza A and B, Parainfluenza Virus, Respiratory Syncytial Virus (RSV), Metapneumovirus and Rhinovirus. Virus positive and virus negative groups were compared in regards to clinical presentation, severity of exacerbation and bacterial colonization. Results Out of 70 samples collected from 48 patients, 35.7% were positive for respiratory viruses. Rhinovirus were the most common (28% of all positive samples), followed by RSV. The virus positive group was associated with change in sinus discharge (p = 0.03). Considering only patients younger than five years old, positive virus detection was also associated with fever (p = 0.01). There was no significant difference in clinical severity or in bacterial colonization between virus positive and negative groups. Conclusions Prospective studies are still needed to assess the long term impact of viral infections in patients with CF, and their interaction with the bacterial microbiome in these patients.
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Affiliation(s)
- Viviane Mauro Correa Meyer
- Respiratory Virus and Measles Laboratory, Oswaldo Cruz Institute - IOC/FIOCRUZ, Rio de Janeiro, Brazil
- * E-mail:
| | - Marilda Mendonça Siqueira
- Respiratory Virus and Measles Laboratory, Oswaldo Cruz Institute - IOC/FIOCRUZ, Rio de Janeiro, Brazil
| | - Patricia Fernandes Barreto Machado Costa
- Pulmonology Department, National Institute of Women, Children and Adolescents Health Fernandes Figueira - IFF/FIOCRUZ, Rio de Janeiro, Brazil
- Pediatrics Department, Federal University of the State of Rio de Janeiro - UNIRIO, Rio de Janeiro, Brazil
| | - Braulia Costa Caetano
- Respiratory Virus and Measles Laboratory, Oswaldo Cruz Institute - IOC/FIOCRUZ, Rio de Janeiro, Brazil
| | | | - Tânia Wrobel Folescu
- Pulmonology Department, National Institute of Women, Children and Adolescents Health Fernandes Figueira - IFF/FIOCRUZ, Rio de Janeiro, Brazil
| | - Fernando do Couto Motta
- Respiratory Virus and Measles Laboratory, Oswaldo Cruz Institute - IOC/FIOCRUZ, Rio de Janeiro, Brazil
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7
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Margaroli C, Garratt LW, Horati H, Dittrich AS, Rosenow T, Montgomery ST, Frey DL, Brown MR, Schultz C, Guglani L, Kicic A, Peng L, Scholte BJ, Mall MA, Janssens HM, Stick SM, Tirouvanziam R. Elastase Exocytosis by Airway Neutrophils Is Associated with Early Lung Damage in Children with Cystic Fibrosis. Am J Respir Crit Care Med 2020; 199:873-881. [PMID: 30281324 DOI: 10.1164/rccm.201803-0442oc] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
RATIONALE Neutrophils are recruited to the airways of individuals with cystic fibrosis (CF). In adolescents and adults with CF, airway neutrophils actively exocytose the primary granule protease elastase (NE), whose extracellular activity correlates with lung damage. During childhood, free extracellular NE activity is measurable only in a subset of patients, and the exocytic function of airway neutrophils is unknown. OBJECTIVES To measure NE exocytosis by airway neutrophils in relation to free extracellular NE activity and lung damage in children with CF. METHODS We measured lung damage using chest computed tomography coupled with the Perth-Rotterdam Annotated Grid Morphometric Analysis for Cystic Fibrosis scoring system. Concomitantly, we phenotyped blood and BAL fluid leukocytes by flow and image cytometry, and measured free extracellular NE activity using spectrophotometric and Förster resonance energy transfer assays. Children with airway inflammation linked to aerodigestive disorder were enrolled as control subjects. MEASUREMENTS AND MAIN RESULTS Children with CF but not disease control children harbored BAL fluid neutrophils with high exocytosis of primary granules, before the detection of bronchiectasis. This measure of NE exocytosis correlated with lung damage (R = 0.55; P = 0.0008), whereas the molecular measure of free extracellular NE activity did not. This discrepancy may be caused by the inhibition of extracellular NE by BAL fluid antiproteases and its binding to leukocytes. CONCLUSIONS NE exocytosis by airway neutrophils occurs in all children with CF, and its cellular measure correlates with early lung damage. These findings implicate live airway neutrophils in early CF pathogenesis, which should instruct biomarker development and antiinflammatory therapy in children with CF.
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Affiliation(s)
- Camilla Margaroli
- 1 Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia.,2 Center for CF & Airways Disease Research, Children's Healthcare of Atlanta, Atlanta, Georgia
| | | | - Hamed Horati
- 4 Department of Pediatric Pulmonology, Erasmus University Medical Center/Sophia Children's Hospital, Rotterdam, the Netherlands
| | - A Susanne Dittrich
- 5 Department of Translational Pulmonology, Translational Lung Research Center, German Center for Lung Research, and.,6 Department of Pulmonology, and Critical Care Medicine, Thoraxklinik, University of Heidelberg, Heidelberg, Germany
| | | | | | - Dario L Frey
- 5 Department of Translational Pulmonology, Translational Lung Research Center, German Center for Lung Research, and
| | - Milton R Brown
- 1 Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia.,2 Center for CF & Airways Disease Research, Children's Healthcare of Atlanta, Atlanta, Georgia
| | - Carsten Schultz
- 7 Department of Physiology and Pharmacology, Oregon Health & Science University, Portland, Oregon
| | - Lokesh Guglani
- 1 Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia.,2 Center for CF & Airways Disease Research, Children's Healthcare of Atlanta, Atlanta, Georgia
| | - Anthony Kicic
- 3 Telethon Kids Institute, Perth, Australia.,8 Department of Respiratory Medicine, Perth Children's Hospital, Perth, Western Australia, Australia.,9 Faculty of Medicine, University of Western Australia, Perth, Western Australia, Australia
| | - Limin Peng
- 10 Department of Biostatistics, Emory University School of Public Health, Atlanta, Georgia
| | - Bob J Scholte
- 4 Department of Pediatric Pulmonology, Erasmus University Medical Center/Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Marcus A Mall
- 5 Department of Translational Pulmonology, Translational Lung Research Center, German Center for Lung Research, and.,11 Berlin Institute of Health, Berlin, Germany; and.,12 Department of Pediatric Pulmonology, Immunology and Intensive Care Medicine, Charité-Universitätmedizin Berlin, Berlin, Germany
| | - Hettie M Janssens
- 4 Department of Pediatric Pulmonology, Erasmus University Medical Center/Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Stephen M Stick
- 3 Telethon Kids Institute, Perth, Australia.,8 Department of Respiratory Medicine, Perth Children's Hospital, Perth, Western Australia, Australia.,9 Faculty of Medicine, University of Western Australia, Perth, Western Australia, Australia
| | - Rabindra Tirouvanziam
- 1 Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia.,2 Center for CF & Airways Disease Research, Children's Healthcare of Atlanta, Atlanta, Georgia
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8
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Eymery M, Morfin F, Doleans-Jordheim A, Perceval M, Ohlmann C, Mainguy C, Reix P. Viral respiratory tract infections in young children with cystic fibrosis: a prospective full-year seasonal study. Virol J 2019; 16:111. [PMID: 31481063 PMCID: PMC6724274 DOI: 10.1186/s12985-019-1208-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 07/25/2019] [Indexed: 12/24/2022] Open
Abstract
Background Viral respiratory tract infections are common during early childhood. How they impact cystic fibrosis lung disease history in young children is poorly known. The principal aim of our study was to determinate respiratory tract infections frequency in this cystic fibrosis young population. Secondary outcomes were nature of viral agents recovered and impact of such infections. Methods We conducted a prospective cohort study of 25 children affected by cystic fibrosis and aged less than 2 years. Nasal samplings were taken systematically monthly or bimonthly with additional samples taken during respiratory tract infections episodes. Ten pathogens were tested by a combination of five duplex RT-PCRs or PCRs: influenza A and B, respiratory syncytial virus (RSV), metapneumovirus (MPV), rhinovirus/enterovirus (RV/EV)), coronavirus (HKU1, NL63, 229E and OC43), parainfluenza virus (1–4), adenovirus and bocavirus (Respiratory Multi-Well System MWS r-gene®, BioMérieux, Marcy l’Étoile, France). Cycle thresholds (CTs) were reported for all positive samples and considered positive for values below 40. Quantitative variables were compared using a nonparametric statistical test (Wilcoxon signed rank for paired comparisons). Pearson’s correlation coefficient (r) was used to assess relationships between two variables. Statistical analyses were performed using SAS v9.4 (SAS Institute, Cary, NC, USA) or GraphPad Prism V6.00 (GraphPad Software, La Jolla, CA, USA). The significance level was set at 0.05. Results
The mean age at inclusion was 9.6 ± 6.7 months. The patients had 3.4 ± 1.7 respiratory tract infections episodes per child per year. Forty-four respiratory tract infections (69%) were associated with virus: rhinovirus and enterovirus (RV/EV) were implied in 61% of them and respiratory syncytial virus (RSV) in 14%. Only one patient required hospitalization for lower respiratory tract infections. 86% of the patients were treated by antibiotics for a mean of 13.8 ± 6.2 days. RSV infections (n = 6) were usually of mild severity. Conclusions Respiratory tract infections in young children with cystic fibrosis were of mild severity, rarely requiring hospitalization. Unsurprisingly, RV/EV were the most frequent agents. RSV-related morbidity seems low in this population. This raises the question of the usefulness of RSV preventive medication in this young population.
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Affiliation(s)
- Mathilde Eymery
- Service de pneumologie pédiatrique et CRCM enfant, Hôpital Femme Mère Enfant, Hospices civils de Lyon, Bron, France. .,Centre de ressources et de compétence pour la Mucoviscidose, 59 boulevard Pinel, 69677, BRON CEDEX, France.
| | - Florence Morfin
- Laboratory of Virology, Institut des Agents Infectieux, Groupement Hospitalier Nord, F69317, Lyon, France.,Centre National de Référence des virus respiratoires France Sud, Hospices Civils de Lyon, Lyon, France.,Faculté de Pharmacie, CIRI, Inserm U1111 CNRS UMR5308, Virpath, Univ Lyon, Université Lyon 1, Lyon, France
| | - Anne Doleans-Jordheim
- Equipe de Recherche, Bactéries Pathogènes Opportunistes et Environnement, UMR CNRS 5557 Ecologie Microbienne, Université Lyon 1 & VetAgro Sup, Villeurbanne, France.,Laboratory of Bacteriology, Institut des Agents Infectieux, Groupement Hospitalier Nord, Hospices Civils de Lyon, F69317, Lyon, France
| | - Marie Perceval
- Service de pneumologie pédiatrique et CRCM enfant, Hôpital Femme Mère Enfant, Hospices civils de Lyon, Bron, France
| | - Camille Ohlmann
- Service de pneumologie pédiatrique et CRCM enfant, Hôpital Femme Mère Enfant, Hospices civils de Lyon, Bron, France
| | - Catherine Mainguy
- Service de pneumologie pédiatrique et CRCM enfant, Hôpital Femme Mère Enfant, Hospices civils de Lyon, Bron, France
| | - Philippe Reix
- Service de pneumologie pédiatrique et CRCM enfant, Hôpital Femme Mère Enfant, Hospices civils de Lyon, Bron, France.,UMR 5558 (EMET). CNRS, LBBE, Université de Lyon, Villeurbanne, France
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9
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Early respiratory viral infections in infants with cystic fibrosis. J Cyst Fibros 2019; 18:844-850. [PMID: 30826285 PMCID: PMC6711838 DOI: 10.1016/j.jcf.2019.02.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Revised: 02/08/2019] [Accepted: 02/09/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND Viral infections contribute to morbidity in cystic fibrosis (CF), but the impact of respiratory viruses on the development of airway disease is poorly understood. METHODS Infants with CF identified by newborn screening were enrolled prior to 4 months of age to participate in a prospective observational study at 4 centers. Clinical data were collected at clinic visits and weekly phone calls. Multiplex PCR assays were performed on nasopharyngeal swabs to detect respiratory viruses during routine visits and when symptomatic. Participants underwent bronchoscopy with bronchoalveolar lavage (BAL) and a subset underwent pulmonary function testing. We present findings through 8.5 months of life. RESULTS Seventy infants were enrolled, mean age 3.1 ± 0.8 months. Rhinovirus was the most prevalent virus (66%), followed by parainfluenza (19%), and coronavirus (16%). Participants had a median of 1.5 viral positive swabs (range 0-10). Past viral infection was associated with elevated neutrophil concentrations and bacterial isolates in BAL fluid, including recovery of classic CF bacterial pathogens. When antibiotics were prescribed for respiratory-related indications, viruses were identified in 52% of those instances. CONCLUSIONS Early viral infections were associated with greater neutrophilic inflammation and bacterial pathogens. Early viral infections appear to contribute to initiation of lower airway inflammation in infants with CF. Antibiotics were commonly prescribed in the setting of a viral infection. Future investigations examining longitudinal relationships between viral infections, airway microbiome, and antibiotic use will allow us to elucidate the interplay between these factors in young children with CF.
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10
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Allemann A, Kraemer JG, Korten I, Ramsey K, Casaulta C, Wüthrich D, Ramette A, Endimiani A, Latzin P, Hilty M. Nasal Resistome Development in Infants With Cystic Fibrosis in the First Year of Life. Front Microbiol 2019; 10:212. [PMID: 30863369 PMCID: PMC6399209 DOI: 10.3389/fmicb.2019.00212] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 01/24/2019] [Indexed: 12/20/2022] Open
Abstract
Polymicrobial infections of the respiratory tract due to antibiotic resistant bacteria are a great concern in patients with cystic fibrosis (CF). We therefore aimed at establishing a functional metagenomic method to analyze the nasal resistome in infants with CF within the first year of life. We included samples from patients before antibiotic treatment, which allowed obtaining information regarding natural status of the resistome. In total, we analyzed 130 nasal swabs from 26 infants with CF and screened for β-lactams (ampicillin, amoxicillin-clavulanic acid, and cefuroxime) and other classes of antibiotic resistances (tetracycline, chloramphenicol and trimethoprim-sulfamethoxazole). For 69 swabs (53% of total), we found at least one non-susceptible phenotype. Analyses of the inserts recovered from non-susceptible clones by nanopore MinION sequencing revealed a large reservoir of resistance genes including mobile elements within the antibiotic naïve samples. Comparing the data of the resistome with the microbiota composition showed that the bacterial phyla and operational taxonomic units (OTUs) of the microbiota rather than the antibiotic treatment were associated with the majority of non-susceptible phenotypes in the resistome. Future studies will reveal if characterization of the resistome can help in clinical decision-making in patients with CF.
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Affiliation(s)
- Aurélie Allemann
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Julia G Kraemer
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland.,Institute for Work and Health (IST), University of Lausanne and University of Geneva, Epalinges, Switzerland
| | - Insa Korten
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland.,Division of Respiratory Medicine, Department of Paediatrics, Inselspital, University of Bern, Bern, Switzerland
| | - Kathryn Ramsey
- Division of Respiratory Medicine, Department of Paediatrics, Inselspital, University of Bern, Bern, Switzerland
| | - Carmen Casaulta
- Division of Respiratory Medicine, Department of Paediatrics, Inselspital, University of Bern, Bern, Switzerland
| | | | - Daniel Wüthrich
- Applied Microbiology Research Unit, Department of Biomedicine, University of Basel, Basel, Switzerland.,Division of Clinical Microbiology, University Hospital Basel, Basel, Switzerland
| | - Alban Ramette
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Philipp Latzin
- Division of Respiratory Medicine, Department of Paediatrics, Inselspital, University of Bern, Bern, Switzerland
| | - Markus Hilty
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
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Abstract
PURPOSE OF REVIEW To compile data from the past 10 years regarding the role of modifying genes in cystic fibrosis (CF). RECENT FINDINGS CF is a model disease for understanding of the action of modifying genes. Although it is a monogenic (CFTR) autosomal recessive disease, CF presents with wide phenotypic variability. In CF, variability occurs with different intensity among patients by each organ, being organ-specific, resulting from the mutual interaction of environmental and genetic factors, including CFTR mutations and various other genes, most of which are associated with inflammatory processes. In individuals, using precision medicine, gene modification studies have revealed individualized responses to drugs depending on particular CFTR mutations and modifying genes, most of which are alternative ion channels. SUMMARY Studies of modifying genes in CF allow: understanding of clinical variability among patients with the same CFTR genotype; evaluation of precision medicine; understanding of environmental and genetic effects at the organ level; understanding the involvement of genetic variants in inflammatory responses; improvements in genetic counseling; understanding the involvement of genetic variants in inflammatory responses in lung diseases, such as asthma; and understanding the individuality of the person with the disease.
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Nasher F, Heller M, Hathaway LJ. Streptococcus pneumoniae Proteins AmiA, AliA, and AliB Bind Peptides Found in Ribosomal Proteins of Other Bacterial Species. Front Microbiol 2018; 8:2688. [PMID: 29379482 PMCID: PMC5775242 DOI: 10.3389/fmicb.2017.02688] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 12/26/2017] [Indexed: 11/13/2022] Open
Abstract
The nasopharynx is frequently colonized by both commensal and pathogenic bacteria including Streptococcus pneumoniae (pneumococcus). Pneumococcus is an important pathogen responsible for bacterial meningitis and community acquired pneumonia but is also commonly an asymptomatic colonizer of the nasopharynx. Understanding interactions between microbes may provide insights into pathogenesis. Here, we investigated the ability of the three oligopeptide-binding proteins AmiA, AliA, and AliB of an ATP-binding cassette transporter of pneumococcus to detect short peptides found in other bacterial species. We found three possible peptide ligands for AmiA and four each for AliA and AliB of which two for each protein matched ribosomal proteins of other bacterial species. Using synthetic peptides we confirmed the following binding: AmiA binds peptide AKTIKITQTR, matching 50S ribosomal subunit protein L30, AliA binds peptide FNEMQPIVDRQ, matching 30S ribosomal protein S20, and AliB binds peptide AIQSEKARKHN, matching 30S ribosomal protein S20, without excluding the possibility of binding of the other peptides. These Ami-AliA/AliB peptide ligands are found in multiple species in the class of Gammaproteobacteria which includes common colonizers of the nostrils and nasopharynx. Binding such peptides may enable pneumococcus to detect and respond to neighboring species in its environment and is a potential mechanism for interspecies communication and environmental surveillance.
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Affiliation(s)
- Fauzy Nasher
- Institute for Infectious Diseases, Faculty of Medicine, University of Bern, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Manfred Heller
- Department of Clinical Research, Proteomics and Mass Spectrometry Core Facility, University of Bern, Bern, Switzerland
| | - Lucy J Hathaway
- Institute for Infectious Diseases, Faculty of Medicine, University of Bern, Bern, Switzerland
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