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David SC, Schaub A, Terrettaz C, Motos G, Costa LJ, Nolan DS, Augugliaro M, Wynn HK, Glas I, Pohl MO, Klein LK, Luo B, Bluvshtein N, Violaki K, Hugentobler W, Krieger UK, Peter T, Stertz S, Nenes A, Kohn T. Stability of influenza A virus in droplets and aerosols is heightened by the presence of commensal respiratory bacteria. J Virol 2024:e0040924. [PMID: 38869284 DOI: 10.1128/jvi.00409-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 05/08/2024] [Indexed: 06/14/2024] Open
Abstract
Aerosol transmission remains a major challenge for control of respiratory viruses, particularly those causing recurrent epidemics, like influenza A virus (IAV). These viruses are rarely expelled alone, but instead are embedded in a consortium of microorganisms that populate the respiratory tract. The impact of microbial communities and inter-pathogen interactions upon stability of transmitted viruses is well-characterized for enteric pathogens, but is under-studied in the respiratory niche. Here, we assessed whether the presence of five different species of commensal respiratory bacteria could influence the persistence of IAV within phosphate-buffered saline and artificial saliva droplets deposited on surfaces at typical indoor air humidity, and within airborne aerosol particles. In droplets, presence of individual species or a mixed bacterial community resulted in 10- to 100-fold more infectious IAV remaining after 1 h, due to bacterial-mediated flattening of drying droplets and early efflorescence. Even when no efflorescence occurred at high humidity or the bacteria-induced changes in droplet morphology were abolished by aerosolization instead of deposition on a well plate, the bacteria remained protective. Staphylococcus aureus and Streptococcus pneumoniae were the most stabilizing compared to other commensals at equivalent density, indicating the composition of an individual's respiratory microbiota is a previously unconsidered factor influencing expelled virus persistence.IMPORTANCEIt is known that respiratory infections such as coronavirus disease 2019 and influenza are transmitted by release of virus-containing aerosols and larger droplets by an infected host. The survival time of viruses expelled into the environment can vary depending on temperature, room air humidity, UV exposure, air composition, and suspending fluid. However, few studies consider the fact that respiratory viruses are not alone in the respiratory tract-we are constantly colonized by a plethora of bacteria in our noses, mouth, and lower respiratory system. In the gut, enteric viruses are known to be stabilized against inactivation and environmental decay by gut bacteria. Despite the presence of a similarly complex bacterial microbiota in the respiratory tract, few studies have investigated whether viral stabilization could occur in this niche. Here, we address this question by investigating influenza A virus stabilization by a range of commensal bacteria in systems representing respiratory aerosols and droplets.
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Affiliation(s)
- Shannon C David
- Laboratory of Environmental Virology, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Aline Schaub
- Laboratory of Environmental Virology, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Céline Terrettaz
- Laboratory of Environmental Virology, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Laboratory of Atmospheric Processes and their Impacts, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Ghislain Motos
- Laboratory of Atmospheric Processes and their Impacts, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Laura J Costa
- Laboratory of Environmental Virology, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Laboratory of Atmospheric Processes and their Impacts, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Daniel S Nolan
- Laboratory of Environmental Virology, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Marta Augugliaro
- Institute for Atmospheric and Climate Science, ETH Zürich, Zürich, Switzerland
| | - Htet Kyi Wynn
- Laboratory of Environmental Virology, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Irina Glas
- Institute of Medical Virology, University of Zürich, Zürich, Switzerland
| | - Marie O Pohl
- Institute of Medical Virology, University of Zürich, Zürich, Switzerland
| | - Liviana K Klein
- Institute for Atmospheric and Climate Science, ETH Zürich, Zürich, Switzerland
| | - Beiping Luo
- Institute for Atmospheric and Climate Science, ETH Zürich, Zürich, Switzerland
| | - Nir Bluvshtein
- Institute for Atmospheric and Climate Science, ETH Zürich, Zürich, Switzerland
| | - Kalliopi Violaki
- Laboratory of Atmospheric Processes and their Impacts, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Walter Hugentobler
- Laboratory of Atmospheric Processes and their Impacts, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Ulrich K Krieger
- Institute for Atmospheric and Climate Science, ETH Zürich, Zürich, Switzerland
| | - Thomas Peter
- Institute for Atmospheric and Climate Science, ETH Zürich, Zürich, Switzerland
| | - Silke Stertz
- Institute of Medical Virology, University of Zürich, Zürich, Switzerland
| | - Athanasios Nenes
- Laboratory of Atmospheric Processes and their Impacts, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Institute of Chemical Engineering Sciences, Foundation for Research and Technology Hellas, Patras, Greece
| | - Tamar Kohn
- Laboratory of Environmental Virology, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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Matys J, Kensy J, Gedrange T, Zawiślak I, Grzech-Leśniak K, Dobrzyński M. A Molecular Approach for Detecting Bacteria and Fungi in Healthcare Environment Aerosols: A Systematic Review. Int J Mol Sci 2024; 25:4154. [PMID: 38673740 PMCID: PMC11050369 DOI: 10.3390/ijms25084154] [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: 02/25/2024] [Revised: 04/02/2024] [Accepted: 04/04/2024] [Indexed: 04/28/2024] Open
Abstract
Molecular methods have become integral to microbiological research for microbial identification. This literature review focuses on the application of molecular methods in examining airborne bacteria and fungi in healthcare facilities. In January 2024, a comprehensive electronic search was carried out in esteemed databases including PubMed, Web of Science, and Scopus, employing carefully selected keywords such as ((bacteria) OR (virus) OR (fungi)) AND (aerosol) AND ((hospital) OR (healthcare) OR (dental office)) AND ((molecular) OR (PCR) OR (NGS) OR (RNA) OR (DNA) OR (metagenomic) OR (microarray)), following the PRISMA protocol. The review specifically targets healthcare environments with elevated concentrations of pathogenic bacteria. A total of 487 articles were initially identified, but only 13 met the inclusion criteria and were included in the review. The study disclosed that the prevalent molecular methodology for appraising aerosol quality encompassed the utilization of the PCR method, incorporating either 16S rRNA (bacteria) or 18S rRNA (fungi) amplification techniques. Notably, five diverse molecular techniques, specifically PFGE, DGGE, SBT, LAMP, and DNA hybridization methods, were implemented in five distinct studies. These molecular tests exhibited superior capabilities compared to traditional bacterial and fungal cultures, providing precise strain identification. Additionally, the molecular methods allowed the detection of gene sequences associated with antibiotic resistance. In conclusion, molecular testing offers significant advantages over classical microbiological culture, providing more comprehensive information.
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Affiliation(s)
- Jacek Matys
- Oral Surgery Department, Medical University of Wroclaw, 50-425 Wroclaw, Poland; (T.G.); (K.G.-L.)
| | - Julia Kensy
- Faculty of Dentistry, Medical University of Wroclaw, 50-425 Wroclaw, Poland;
| | - Tomasz Gedrange
- Oral Surgery Department, Medical University of Wroclaw, 50-425 Wroclaw, Poland; (T.G.); (K.G.-L.)
| | - Ireneusz Zawiślak
- Faculty of Biotechnology and Food Sciences, Wrocław University of Environmental and Life Sciences, 37 Chełmońskiego Str., 51-630 Wrocław, Poland;
| | - Kinga Grzech-Leśniak
- Oral Surgery Department, Medical University of Wroclaw, 50-425 Wroclaw, Poland; (T.G.); (K.G.-L.)
- Department of Periodontics, School of Dentistry, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Maciej Dobrzyński
- Department of Pediatric Dentistry and Preclinical Dentistry, Wroclaw Medical University, Krakowska 26, 50-425 Wrocław, Poland;
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van Aerde KJ, Leegstraten A, van den Kieboom C, Merkus PJFM, Sintnicolaas C, Simons SO, van der Flier M, de Groot R, de Jonge M. Non-invasive diagnostics of pathogenic bacteria using a breath sampler in children with cystic fibrosis. J Breath Res 2022; 16. [PMID: 35868248 DOI: 10.1088/1752-7163/ac8369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 07/22/2022] [Indexed: 11/11/2022]
Abstract
Cystic fibrosis is a common autosomal recessive disease causing thick, viscous secretions leading to pulmonary infections with pathogenic bacteria. As part of routine patient care, colonization and infection with these bacteria is monitored with cough swab or sputum cultures and sometimes bronchoalveolar lavage. In this cross-sectional proof-of-concept study in a cohort of CF patients we collected swabs or sputa and exhaled breath samples with the Modular Breath Sampler (MBS), a newly developed two-way non-rebreathing sampling device. Pathogen specific polymerase chain reactions (PCRs) were performed on the MBS samples and compared with the results obtained with conventional diagnostics (i.e. culturing of swabs and sputa). A control group of stable asthma patients was used as negative control for the MBS measurements. The pathogens detected using MBS and conventional culturing differed: Staphylococcus aureus was found more often in swab or sputum samples whereas Pseudomonas aeruginosa and Streptococcus pneumoniae were found more often in MBS samples. We hypothesize that this is due to sampling of different compartments, MBS samples are derived from the lower respiratory tract while cultures from cough swabs and sputa are dominated by pathogens residing in the upper respiratory tract. Another important difference is the readout, i.e. culture versus PCR. The majority of CF patients in whom Pseudomonas aeruginosa was found did not have recent positive cultures suggesting higher sensitivity of MBS-based than conventional diagnostics. The majority of parents / patients found the MBS easy to use and less of a burden than respiratory sampling.
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Affiliation(s)
- Koen Jan van Aerde
- Pediatric Infectious Disease and Immunology, Amalia Children's Hospital, Radboudumc, Geert Grooteplein Zuid 10, Nijmegen, 6525 GA, NETHERLANDS
| | - Aniek Leegstraten
- Laboratory of Medical Immunology, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboudumc, Geert Grooteplein Zuid 10, Nijmegen, Gelderland, 6525 GA, NETHERLANDS
| | | | - Peter J F M Merkus
- Pediatric Pulmonology, Amalia Children's Hospital, Radboudumc, Geert Grooteplein Zuid 10, Nijmegen, Gelderland, 6525 GA, NETHERLANDS
| | - Coosje Sintnicolaas
- Pediatric Pulmonology, Amalia Children's Hospital, Radboudumc, Geert Grooteplein Zuid 10, Nijmegen, Gelderland, 6525 GA, NETHERLANDS
| | - Sami O Simons
- Respiratory Medicine, Maastricht University Medical Centre+, P. Debeyelaan 25, Maastricht, Limburg, 6229 HX, NETHERLANDS
| | - Michiel van der Flier
- Pediatric Infectious Disease and Immunology, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Lundlaan 6, Utrecht, Utrecht, 3584 EA, NETHERLANDS
| | - Ronald de Groot
- Laboratory of Medical Immunology, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboudumc, Geert Grooteplein Zuid 10, Nijmegen, Gelderland, 6525 GA, NETHERLANDS
| | - Marien de Jonge
- Laboratory of Medical Immunology, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboudumc, Geert Grooteplein Zuid 10, Nijmegen, Gelderland, 6525 GA, NETHERLANDS
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Fennelly KP, Acuna-Villaorduna C, Jones-Lopez E, Lindsley WG, Milton DK. Microbial Aerosols: New Diagnostic Specimens for Pulmonary Infections. Chest 2019; 157:540-546. [PMID: 31678308 DOI: 10.1016/j.chest.2019.10.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 10/04/2019] [Accepted: 10/09/2019] [Indexed: 01/20/2023] Open
Abstract
Pulmonary infections are important causes of global morbidity and mortality, but diagnostics are often limited by the ability to collect specimens easily, safely, and in a cost-effective manner. We review recent advances in the collection of infectious aerosols from patients with TB and with influenza. Although this research has been focused on assessing the infectious potential of such patients, we propose that these methods have the potential to lead to the use of patient-generated microbial aerosols as noninvasive diagnostic tests of disease and tests of infectiousness.
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Affiliation(s)
- Kevin P Fennelly
- National Institutes of Health, National Heart, Lung and Blood Institute, Bethesda, MD.
| | | | - Edward Jones-Lopez
- Boston Medical Center and Boston University School of Medicine, Boston, MA
| | - William G Lindsley
- National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV
| | - Donald K Milton
- Maryland Institute for Applied Environmental Health, School of Public Health, University of Maryland, College Park, MD
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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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