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Markussen DL, Kommedal Ø, Knoop ST, Ebbesen MH, Bjørneklett RO, Ritz C, Heggelund L, Ulvestad E, Serigstad S, Grewal HMS. Microbial aetiology of community-acquired pneumonia in hospitalised adults: A prospective study utilising comprehensive molecular testing. Int J Infect Dis 2024; 143:107019. [PMID: 38582145 DOI: 10.1016/j.ijid.2024.107019] [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: 02/16/2024] [Revised: 03/20/2024] [Accepted: 03/21/2024] [Indexed: 04/08/2024] Open
Abstract
OBJECTIVES This study aimed to describe the microbial aetiology of community-acquired pneumonia (CAP) in adults admitted to a tertiary care hospital and assess the impact of syndromic polymerase chain reaction (PCR) panels on pathogen detection. METHODS Conducted at Haukeland University Hospital, Norway, from September 2020 to April 2023, this prospective study enrolled adults with suspected CAP. We analysed lower respiratory tract samples using both standard-of-care tests and the BIOFIRE® FILMARRAY® Pneumonia Plus Panel (FAP plus). The added value of FAP Plus in enhancing the detection of clinically relevant pathogens, alongside standard-of-care diagnostics, was assessed. RESULTS Of the 3238 patients screened, 640 met the inclusion criteria, with 384 confirmed to have CAP at discharge. In these patients, pathogens with proven or probable clinical significance were identified in 312 (81.3%) patients. Haemophilus influenzae was the most prevalent pathogen, found in 118 patients (30.7%), followed by SARS-CoV-2 in 74 (19.3%), and Streptococcus pneumoniae in 64 (16.7%). Respiratory viruses were detected in 186 (48.4%) patients. The use of FAP plus improved the pathogen detection rate from 62.8% with standard-of-care methods to 81.3%. CONCLUSIONS Pathogens were identified in 81% of CAP patients, with Haemophilus influenzae and respiratory viruses being the most frequently detected pathogens. The addition of the FAP plus panel, markedly improved pathogen detection rates compared to standard-of-care diagnostics alone.
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Affiliation(s)
- Dagfinn Lunde Markussen
- Department of Clinical Science, Bergen Integrated Diagnostic Stewardship Cluster, Faculty of Medicine, University of Bergen, Bergen, Norway; Department of Emergency Medicine, Haukeland University Hospital, Bergen, Norway.
| | - Øyvind Kommedal
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | | | | | - Rune Oskar Bjørneklett
- Department of Emergency Medicine, Haukeland University Hospital, Bergen, Norway; Department of Clinical Medicine, Faculty of Medicine, University of Bergen, Bergen, Norway
| | - Christian Ritz
- National Institute of Public Health, University of Southern Denmark, Copenhagen, Denmark
| | - Lars Heggelund
- Department of Clinical Science, Bergen Integrated Diagnostic Stewardship Cluster, Faculty of Medicine, University of Bergen, Bergen, Norway; Department of Internal Medicine, Drammen Hospital, Vestre Viken Hospital Trust, Drammen, Norway
| | - Elling Ulvestad
- Department of Clinical Science, Bergen Integrated Diagnostic Stewardship Cluster, Faculty of Medicine, University of Bergen, Bergen, Norway; Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Sondre Serigstad
- Department of Clinical Science, Bergen Integrated Diagnostic Stewardship Cluster, Faculty of Medicine, University of Bergen, Bergen, Norway; Department of Emergency Medicine, Haukeland University Hospital, Bergen, Norway
| | - Harleen M S Grewal
- Department of Clinical Science, Bergen Integrated Diagnostic Stewardship Cluster, Faculty of Medicine, University of Bergen, Bergen, Norway; Department of Microbiology, Haukeland University Hospital, Bergen, Norway
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Serigstad S, Knoop ST, Markussen DL, Ulvestad E, Bjørneklett RO, Ebbesen MH, Kommedal Ø, Grewal HMS. Diagnostic utility of oropharyngeal swabs as an alternative to lower respiratory tract samples for PCR-based syndromic testing in patients with community-acquired pneumonia. J Clin Microbiol 2023; 61:e0050523. [PMID: 37585220 PMCID: PMC10512787 DOI: 10.1128/jcm.00505-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 07/06/2023] [Indexed: 08/17/2023] Open
Abstract
Syndromic PCR-based analysis of lower respiratory tract (LRT) samples in patients with community-acquired pneumonia (CAP) improves the bacterial yield and time-to-results compared to culture-based methods. However, obtaining adequate sputum samples can be challenging and is frequently not prioritized in the emergency department (ED). In this study, we assess the concordance of microbiological detections between oropharyngeal- (OP) and LRT samples from patients presenting to the ED with CAP using a syndromic PCR-based respiratory panel [Biofire FilmArray Pneumonia plus (FAP plus)]. Paired OP- and high-quality LRT samples were collected from 103 patients with confirmed CAP, who had been included in a randomized controlled trial (NCT04660084) or a subsequent observational study at Haukeland University Hospital, and analyzed using the FAP plus. The LRT samples were obtained mainly by sputum induction (88%). Using the LRT samples as a reference standard, the positive percent agreement (PPA), negative percent agreement (NPA), and overall percent agreement for the most common bacterial pathogens in CAP, Streptococcus pneumoniae and Haemophilus influenzae, were 85%, 99% and 95%, and 86%, 98% and 93%, respectively. For Moraxella catarrhalis, the PPA was lower (74%), while the NPA was 100%. For bacteria that are less likely causes of uncomplicated CAP (e.g., Staphylococcus aureus and Enterobacterales) the results were more divergent. In conclusion, the FAP plus detects the most common CAP pathogens S. pneumoniae and H. influenzae from OP samples with high PPAs and excellent NPAs when compared with LRT samples. For these pathogens, the PPAs for OP samples were higher than previous reports for nasopharyngeal samples. This suggests that analysis of OP samples with syndromic PCR panels could represent an alternative approach for rapid microbiological testing in the ED, especially in patients where LRT samples are difficult to obtain. Divergent results for bacteria that are less likely to cause uncomplicated CAP do, however, emphasize the need for clinical evaluation of positive test results.
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Affiliation(s)
- Sondre Serigstad
- Emergency Care Clinic, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Siri T. Knoop
- Department of Clinical Science, Bergen Integrated Diagnostic Stewardship Cluster, University of Bergen, Bergen, Norway
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Dagfinn L. Markussen
- Emergency Care Clinic, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Science, Bergen Integrated Diagnostic Stewardship Cluster, University of Bergen, Bergen, Norway
| | - Elling Ulvestad
- Department of Clinical Science, Bergen Integrated Diagnostic Stewardship Cluster, University of Bergen, Bergen, Norway
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Rune O. Bjørneklett
- Emergency Care Clinic, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Marit H. Ebbesen
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Øyvind Kommedal
- Department of Clinical Science, Bergen Integrated Diagnostic Stewardship Cluster, University of Bergen, Bergen, Norway
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Harleen M. S. Grewal
- Department of Clinical Science, Bergen Integrated Diagnostic Stewardship Cluster, University of Bergen, Bergen, Norway
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
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Debes S, Haug JB, De Blasio BF, Lindstrøm JC, Jonassen CM, Dudman SG. Antibiotic Consumption in a Cohort of Hospitalized Adults with Viral Respiratory Tract Infection. Antibiotics (Basel) 2023; 12:788. [PMID: 37107150 PMCID: PMC10135008 DOI: 10.3390/antibiotics12040788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/14/2023] [Accepted: 04/17/2023] [Indexed: 04/29/2023] Open
Abstract
Development of antibiotic resistance, a threat to global health, is driven by inappropriate antibiotic usage. Respiratory tract infections (RTIs) are frequently treated empirically with antibiotics, despite the fact that a majority of the infections are caused by viruses. The purpose of this study was to determine the prevalence of antibiotic treatment in hospitalized adults with viral RTIs, and to investigate factors influencing the antibiotic decision-making. We conducted a retrospective observational study of patients ≥ 18 years, hospitalized in 2015-2018 with viral RTIs. Microbiological data were taken from the laboratory information system and information on antibiotic treatment drawn from the hospital records. To investigate decisions for prescribing antibiotic treatment, we evaluated relevant factors such as laboratory and radiological results, in addition to clinical signs. In 951 cases without secondary bacterial RTIs (median age 73 years, 53% female), 720 (76%) were prescribed antibiotic treatment, most frequently beta-lactamase-sensitive penicillins, but cephalosporins were prescribed as first-line in 16% of the cases. The median length of treatment (LOT) in the patients treated with antibiotics was seven days. Patients treated with antibiotics had an average of two days longer hospital stay compared to patients with no such treatment, but no difference in mortality was found. Our study revealed that there is still a role for antimicrobial stewardship to further improve antibiotic use in patients admitted for viral RTIs in a country with relatively low antibiotic consumption.
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Affiliation(s)
- Sara Debes
- Center for Laboratory Medicine, Østfold Hospital Trust Kalnes, 1714 Grålum, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, 0372 Oslo, Norway
| | - Jon Birger Haug
- Department of Infection Control, Østfold Hospital Trust Kalnes, 1714 Grålum, Norway
| | - Birgitte Freiesleben De Blasio
- Division of Infection Control and Environmental Health, Department of Methods Development and Analytics, Norwegian Institute of Public Health, 0213 Oslo, Norway
- Institute of Basic Medical Sciences, Department of Biostatistics, Centre for Biostatistics and Epidemiology, University of Oslo, 0372 Oslo, Norway
| | - Jonas Christoffer Lindstrøm
- Division of Infection Control and Environmental Health, Department of Methods Development and Analytics, Norwegian Institute of Public Health, 0213 Oslo, Norway
| | | | - Susanne Gjeruldsen Dudman
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, 0372 Oslo, Norway
- Department of Microbiology, Oslo University Hospital, 0372 Oslo, Norway
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Domnich A, Orsi A, Trombetta CS, Costa E, Guarona G, Lucente M, Ricucci V, Bruzzone B, Icardi G. Comparative Diagnostic Accuracy of the STANDARD M10 Assay for the Molecular Diagnosis of SARS-CoV-2 in the Point-of-Care and Critical Care Settings. J Clin Med 2022; 11:2465. [PMID: 35566591 PMCID: PMC9105343 DOI: 10.3390/jcm11092465] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 04/25/2022] [Accepted: 04/27/2022] [Indexed: 02/06/2023] Open
Abstract
Accurate and rapid molecular diagnosis of COVID-19 is a crucial step to tackle the ongoing pandemic. The primary objective of this study was to estimate the real-world performance of the novel RT-PCR STANDARD M10 SARS-CoV-2 assay in a large number of nasopharyngeal (NP) specimens eluted in universal transport medium. The secondary objective was to evaluate the compatibility of this kit in testing NP samples eluted in an inactivated transport medium (essential for point-of-care testing) and lower respiratory tract (LRT) specimens, which are commonly collected in critical care. A total of 591 samples were analyzed. Compared with the standard extraction-based RT-PCR Allplex 2019-nCoV (time-to-result of 270 min), the sensitivities of the STANDARD M10 were 100% (95% CI: 98.1-100%), 95.5% (95% CI: 91.7-97.6%), and 99.5% (95% CI: 97.2-99.9%) for ≥1 gene, the ORF1ab gene, and the E gene, respectively, while the specificity was 100% (95% CI: 98.7-100%). The diagnostic accuracy was 100% in testing both NP samples eluted in an inactivated transport medium and LRT specimens. STANDARD M10 reliably detects SARS-CoV-2 in 60 min, may be used as a POC tool, and is suitable for testing LRT specimens in the critical care setting.
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Affiliation(s)
- Alexander Domnich
- Hygiene Unit, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, 16132 Genoa, Italy; (A.O.); (G.G.); (M.L.); (V.R.); (B.B.); (G.I.)
| | - Andrea Orsi
- Hygiene Unit, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, 16132 Genoa, Italy; (A.O.); (G.G.); (M.L.); (V.R.); (B.B.); (G.I.)
- Department of Health Sciences (DISSAL), University of Genoa, 16132 Genoa, Italy; (C.-S.T.); (E.C.)
| | - Carlo-Simone Trombetta
- Department of Health Sciences (DISSAL), University of Genoa, 16132 Genoa, Italy; (C.-S.T.); (E.C.)
| | - Elisabetta Costa
- Department of Health Sciences (DISSAL), University of Genoa, 16132 Genoa, Italy; (C.-S.T.); (E.C.)
| | - Giulia Guarona
- Hygiene Unit, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, 16132 Genoa, Italy; (A.O.); (G.G.); (M.L.); (V.R.); (B.B.); (G.I.)
| | - Miriana Lucente
- Hygiene Unit, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, 16132 Genoa, Italy; (A.O.); (G.G.); (M.L.); (V.R.); (B.B.); (G.I.)
| | - Valentina Ricucci
- Hygiene Unit, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, 16132 Genoa, Italy; (A.O.); (G.G.); (M.L.); (V.R.); (B.B.); (G.I.)
| | - Bianca Bruzzone
- Hygiene Unit, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, 16132 Genoa, Italy; (A.O.); (G.G.); (M.L.); (V.R.); (B.B.); (G.I.)
| | - Giancarlo Icardi
- Hygiene Unit, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, 16132 Genoa, Italy; (A.O.); (G.G.); (M.L.); (V.R.); (B.B.); (G.I.)
- Department of Health Sciences (DISSAL), University of Genoa, 16132 Genoa, Italy; (C.-S.T.); (E.C.)
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