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Tolle JJ, Jadhao S, Patel B, Sun H, Eastman S, Hartert T, Ku DN, Anderson LJ. Detection of pathogenic bacteria and biomarkers in lung specimens from cystic fibrosis patients. J Breath Res 2024; 18:046004. [PMID: 38861972 DOI: 10.1088/1752-7163/ad56bc] [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: 10/26/2023] [Accepted: 06/11/2024] [Indexed: 06/13/2024]
Abstract
Diagnosing lung infections is often challenging because of the lack of a high-quality specimen from the diseased lung. Since persons with cystic fibrosis are subject to chronic lung infection, there is frequently a need for a lung specimen. In this small, proof of principle study, we determined that PneumoniaCheckTM, a non-invasive device that captures coughed droplets from the lung on a filter, might help meet this need. We obtained 10 PneumoniaCheckTMcoughed specimens and 2 sputum specimens from adult CF patients hospitalized with an exacerbation of their illness. We detected amylase (upper respiratory tract) with an enzymatic assay, surfactant A (lower respiratory tract) with an immunoassay, pathogenic bacteria by PCR, and markers of inflammation by a Luminex multiplex immunoassay. The amylase and surfactant A levels suggested that 9/10 coughed specimens were from lower respiratory tract with minimal upper respiratory contamination. The PCR assays detected pathogenic bacteria in 7 of 9 specimens and multiplex Luminex assay detected a variety of cytokines or chemokines. These data indicate that the PneumoniaCheckTMcoughed specimens can capture good quality lower respiratory tract specimens that have the potential to help in diagnosis, management and understanding of CF exacerbations and other lung disease.
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Affiliation(s)
- James J Tolle
- Department of Medicine, Division of Allergy, Pulmonary & Critical Care Medicine, Nashville, TN, United States of America
| | - Samadhan Jadhao
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, United States of America
- Center for Childhood Infections and Vaccines, Children's Healthcare of Atlanta, Atlanta, GA, United States of America
| | - Brijesh Patel
- Department of Medicine, Division of Allergy, Pulmonary & Critical Care Medicine, Nashville, TN, United States of America
| | - Heying Sun
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, United States of America
- Center for Childhood Infections and Vaccines, Children's Healthcare of Atlanta, Atlanta, GA, United States of America
| | - Susan Eastman
- Department of Medicine, Division of Allergy, Pulmonary & Critical Care Medicine, Nashville, TN, United States of America
| | - Tina Hartert
- Department of Medicine, Division of Allergy, Pulmonary & Critical Care Medicine, Nashville, TN, United States of America
| | - David N Ku
- School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, United States of America
| | - Larry J Anderson
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, United States of America
- Center for Childhood Infections and Vaccines, Children's Healthcare of Atlanta, Atlanta, GA, United States of America
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Chiyaka TL, Nyawo GR, Naidoo C, Moodley S, Clemente JC, Malherbe ST, Warren R, Ku D, Segal LN, Theron G. A novel aerosol collection method shows the cough aeromicrobiome of people with tuberculosis is phylogenetically distinct from respiratory tract specimens. RESEARCH SQUARE 2024:rs.3.rs-4106141. [PMID: 38659922 PMCID: PMC11042404 DOI: 10.21203/rs.3.rs-4106141/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: 04/26/2024]
Abstract
Background Tuberculosis (TB), a major cause of disease and antimicrobial resistance, is spread via aerosols. Aerosols have diagnostic potential and airborne-microbes other than Mycobacterium tuberculosis complex (MTBC) may influence transmission. We evaluated whether PneumoniaCheck (PMC), a commercial aerosol collection device, captures MTBC and the aeromicrobiome of people with TB. Methods PMC was done in sputum culture-positive people (≥30 forced coughs each, n=16) pre-treatment and PMC air reservoir (bag, corresponding to upper airways) and filter (lower airways) washes underwent Xpert MTB/RIF Ultra (Ultra) and 16S rRNA gene sequencing (sequencing also done on sputum). In a subset (n=6), PMC microbiota (bag, filter) was compared to oral washes and bronchoalveolar lavage fluid (BALF). Findings 54% (7/13) bags and 46% (6/14) filters were Ultra-positive. Sequencing read counts and microbial diversity did not differ across bags, filters, and sputum. However, microbial composition in bags (Sphingobium-, Corynebacterium-, Novosphingobium-enriched) and filters (Mycobacterium-, Sphingobium-, Corynebacterium-enriched) each differed vs. sputum. Furthermore, sequencing only detected Mycobacterium in bags and filters but not sputum. In the subset, bag and filter microbial diversity did not differ vs. oral washes or BALF but microbial composition differed. Bags vs. BALF were Sphingobium-enriched and Mycobacterium-, Streptococcus-, and Anaerosinus-depleted (Anaerosinus also depleted in filters vs. BALF). Compared to BALF, none of the aerosol-enriched taxa were enriched in oral washes or sputum. Interpretation PMC captures aerosols with Ultra-detectable MTBC and MTBC is more detectable in aerosols than sputum by sequencing. The aeromicrobiome is distinct from sputum, oral washes and BALF and contains differentially-enriched lower respiratory tract microbes.
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Viral respiratory infections: a cause of community-acquired pneumonia or a predisposing factor? Curr Opin Pulm Med 2021; 26:208-214. [PMID: 32068577 DOI: 10.1097/mcp.0000000000000666] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
PURPOSE OF REVIEW A cause for community-acquired pneumonia (CAP) is only identified in ∼50% of cases. Nasopharyngeal PCR panels contain more viruses than previously. The problem then becomes determining the relevance of the organisms identified rather than figuring out which virus is present. This review addresses how to distinguish between viral CAP and bacterial CAP, how viral CAP predisposes to bacterial CAP and some novel antiviral treatment being conducted. RECENT FINDINGS The pneumonia severity index has been studied in patients with viral CAP. There are new studies using biomarkers to help determine when antimicrobial treatment is needed in CAP patients, and there is still no consensus. Newer devices are being invented in an effort to separate upper from lower respiratory organisms to make test results more relevant. Several outcome studies in patients with viral CAP are reviewed. SUMMARY In addition to clinical correlation, using biomarkers can be useful to distinguish viral from bacterial CAP. Outcomes in patients with a co-infection are generally worse as a viral infection may predispose someone to a bacterial pneumonia. Influenza CAP treatment may be initially accompanied with antimicrobials until a patient's diagnosis is clear (∼48-72 h). Future research is being conducted for antiviral treatment more than for influenza.
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Patrucco F, Gavelli F, Ravanini P, Daverio M, Statti G, Castello LM, Andreoni S, Balbo PE. Use of an innovative and non-invasive device for virologic sampling of cough aerosols in patients with community and hospital acquired pneumonia: a pilot study. J Breath Res 2019; 13:021001. [PMID: 30523983 PMCID: PMC7106764 DOI: 10.1088/1752-7163/aaf010] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 11/06/2018] [Accepted: 11/12/2018] [Indexed: 12/21/2022]
Abstract
BACKGROUND The aetiology of lower respiratory tract infections is challenging to investigate. Despite the wide array of diagnostic tools, invasive techniques, such as bronchoalveolar lavage (BAL), are often required to obtain adequate specimens. PneumoniaCheckTM is a new device that collects aerosol particles from cough, allowing microbiological analyses. Up to now it has been tested only for bacteria detection, but no study has investigated its usefulness for virus identification. METHODS In this pilot study we included 12 consecutive patients with pneumonia. After testing cough adequacy via a peak flow meter, a sampling with PneumoniaCheckTM was collected and a BAL was performed in each patient. Microbiological analyses for virus identification were performed on each sample and concordance between the two techniques was tested (sensitivity, specificity and positive/negative predictive values), taking BAL results as reference. RESULTS BAL was considered adequate in 10 patients. Among them, a viral pathogen was identified by PneumoniaCheckTM 6 times, each on different samples, whereas BAL allowed to detect the presence of a virus on 7 patients (14 positivities). Overall, the specificity for PneumoniaCheckTM to detect a virus was 100%, whereas the sensitivity was 66%. When considering only herpes viruses, PneumoniaCheckTM showed a lower sensitivity, detecting a virus in 1/4 of infected patients (25%). CONCLUSIONS In this pilot study PneumoniaCheckTM showed a good correlation with BAL for non-herpes virologic identification in pneumonia patients, providing excellent specificity. Further studies on larger population are needed to confirm these results and define its place in the panorama of rapid diagnostic tests for lower respiratory tract infections.
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Affiliation(s)
- Filippo Patrucco
- Medical Department, Division of Respiratory Diseases, University of Piemonte Orientale, Maggiore della Carità Hospital, Novara, Italy
| | - Francesco Gavelli
- Department of Translational Medicine, Emergency Medicine Unit, University of Piemonte Orientale, Maggiore della Carità Hospital, Novara, Italy
| | - Paolo Ravanini
- Laboratory Medicine Department, Microbiology and Virology Unit, University of Piemonte Orientale, Maggiore della Carità Hospital, Novara, Italy
| | - Matteo Daverio
- Medical Department, Division of Respiratory Diseases, University of Piemonte Orientale, Maggiore della Carità Hospital, Novara, Italy
| | - Giulia Statti
- Department of Translational Medicine, Emergency Medicine Unit, University of Piemonte Orientale, Maggiore della Carità Hospital, Novara, Italy
| | - Luigi Mario Castello
- Department of Translational Medicine, Emergency Medicine Unit, University of Piemonte Orientale, Maggiore della Carità Hospital, Novara, Italy
| | - Stefano Andreoni
- Laboratory Medicine Department, Microbiology and Virology Unit, University of Piemonte Orientale, Maggiore della Carità Hospital, Novara, Italy
| | - Piero Emilio Balbo
- Medical Department, Division of Respiratory Diseases, University of Piemonte Orientale, Maggiore della Carità Hospital, Novara, Italy
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Ku DN, Ku SK, Helfman B, McCarty NA, Wolff BJ, Winchell JM, Anderson LJ. Ability of device to collect bacteria from cough aerosols generated by adults with cystic fibrosis. F1000Res 2016; 5:1920. [PMID: 27781088 PMCID: PMC5054809 DOI: 10.12688/f1000research.9251.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/27/2016] [Indexed: 12/02/2022] Open
Abstract
Background: Identifying lung pathogens and acute spikes in lung counts remain a challenge in the treatment of patients with cystic fibrosis (CF). Bacteria from the deep lung may be sampled from aerosols produced during coughing. Methods: A new device was used to collect and measure bacteria levels from cough aerosols of patients with CF. Sputum and oral specimens were also collected and measured for comparison. Pseudomonas aeruginosa, Staphylococcus aureus, Klebsiella pneumoniae, and Streptococcus mitis were detected in specimens using Real-Time Polymerase Chain Reaction (RT-PCR) molecular assays. Results: Twenty adult patients with CF and 10 healthy controls participated. CF related bacteria (CFRB) were detected in 13/20 (65%) cough specimens versus 15/15 (100%) sputum specimens. Commensal S. mitis was present in 0/17 (0%, p=0.0002) cough specimens and 13/14 (93%) sputum samples. In normal controls, no bacteria were collected in cough specimens but 4/10 (40%) oral specimens were positive for CFRB. Conclusions: Non-invasive cough aerosol collection may detect lower respiratory pathogens in CF patients, with similar specificity and sensitivity to rates detected by BAL, without contamination by oral CFRB or commensal bacteria.
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Affiliation(s)
- David N. Ku
- Georgia Institute of Technology, Atlanta, GA, 30332, USA
- MD Innovate, Inc, Decatur, GA, 30030, USA
| | | | - Beth Helfman
- Emory Children’s Center for Cystic Fibrosis Research, Emory University, Atlanta, GA, 30322, USA
- Department of Pediatrics, Emory University, Atlanta, 30322, USA
| | - Nael A. McCarty
- Emory Children’s Center for Cystic Fibrosis Research, Emory University, Atlanta, GA, 30322, USA
- Department of Pediatrics, Emory University, Atlanta, 30322, USA
| | - Bernard J. Wolff
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA
| | - Jonas M. Winchell
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA
| | - Larry J. Anderson
- Division of Infectious Diseases, Department of Pediatrics, Emory University and Children’s Healthcare of Atlanta, Atlanta, GA, 30322, USA
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