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Dähne T, Bauer W, Essig A, Schaaf B, Barten-Neiner G, Spinner CD, Pletz MW, Rohde G, Rupp J, Witzenrath M, Panning M. Resurgence of common respiratory viruses in patients with community-acquired pneumonia (CAP)-A prospective multicenter study. J Clin Virol 2024; 173:105694. [PMID: 38781632 DOI: 10.1016/j.jcv.2024.105694] [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: 02/08/2024] [Revised: 04/26/2024] [Accepted: 05/13/2024] [Indexed: 05/25/2024]
Abstract
BACKGROUND Community-acquired pneumonia (CAP) is a major global cause of death and hospitalization. Bacteria or community-acquired viruses (CARVs) cause CAP. COVID-19 associated restrictions effectively reduced the circulation of CARVs. OBJECTIVES The aim of this study was to analyze the proportion of CARVs in adult patients with CAP from mid-2020 to mid-2023. Specifically, we aimed to compare the rate of influenza virus, SARS-CoV-2, and RSV detections in patients aged 18-59 years and ≥60 years. STUDY DESIGN We analyze the proportion of 21 community-acquired respiratory viruses (CARVs) and three atypical bacteria (Bordetella pertussis, Legionella pneumophila, and Mycoplasma pneumoniae) in nasopharyngeal swab samples using molecular multiplex methods within the prospective, multicentre, multinational study of the German study Group CAPNETZ. We used stringent inclusion criteria throughout the study. RESULTS We identified CARVs in 364/1,388 (26.2 %) patients. In detail, we detected SARS-CoV-2 in 210/1,388 (15.1 %), rhino-/enterovirus in 64/1,388 (4.6 %), influenza virus in 23/1,388 (1.6 %) and RSV in 17/1,388 (1.2 %) of all patients. We detected RSV and influenza more frequently in patients ≥60 years, especially in 22/23 compared to the previous season. None of the atypical bacteria were detected. CONCLUSIONS Beginning in 2023, we demonstrate a re-emergence of CARVs in CAP patients. Effective vaccines or specific antiviral therapies for more than two thirds of the detected viral infections are currently available. High detection rates of vaccine-preventable viruses in older age groups support targeted vaccination campaigns.
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Affiliation(s)
- Theo Dähne
- Institute of Virology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Berta-Ottenstein-Programme for Clinician Scientists, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Wolfgang Bauer
- Department of Emergency Medicine, Charité-Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Andreas Essig
- Institute of Medical Microbiology and Hygiene, University Hospital of Ulm, Ulm, Germany
| | | | - Grit Barten-Neiner
- CAPNETZ STIFTUNG, Hannover, Germany; Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), Hannover, Germany
| | - Christoph D Spinner
- TUM School of Medicine and Health, Department of Clinical Medicine - Clinical Department for Internal Medicine II, University Medical Center, Technical University of Munich, Germany
| | - Mathias W Pletz
- CAPNETZ STIFTUNG, Hannover, Germany; Institute of Infectious Diseases and Infection Control, Jena University Hospital / Friedrich-Schiller-University Jena, Jena, Germany
| | - Gernot Rohde
- CAPNETZ STIFTUNG, Hannover, Germany; Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), Hannover, Germany; Department of Respiratory Medicine, Medical Clinic I, Goethe University Hospital, Frankfurt, Main, Germany
| | - Jan Rupp
- CAPNETZ STIFTUNG, Hannover, Germany; Department of Infectious Diseases and Microbiology, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Martin Witzenrath
- CAPNETZ STIFTUNG, Hannover, Germany; Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany; German Center for Lung Research (DZL), Berlin, Germany
| | - Marcus Panning
- Institute of Virology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
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Medrano PG, Weerasinghe N, Nagahawatte A, Vanderburg S, Park LP, Wijayaratne GB, Devasiri V, Dilshan B, Sheng T, Kurukulasooriya R, Anderson J, Nicholson BP, Woods CW, Bodinayake CK, Tillekeratne LG. Prevalence and predictors of antibiotic prescription among patients hospitalized with viral lower respiratory tract infections in Southern Province, Sri Lanka. PLoS One 2024; 19:e0304690. [PMID: 38861513 PMCID: PMC11166322 DOI: 10.1371/journal.pone.0304690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 05/16/2024] [Indexed: 06/13/2024] Open
Abstract
BACKGROUND Antimicrobial overprescription is common for lower respiratory tract infections (LRTI), as viral and bacterial infections generally present with similar clinical features. Overprescription is associated with downstream antimicrobial resistance. This study aims to identify the prevalence and predictors of antibiotic prescription among patients hospitalized with viral LRTI. METHODS A prospective cohort study was conducted among patients aged ≥1 year hospitalized with viral LRTI in a tertiary care hospital in Southern Province, Sri Lanka from 2018-2021. Demographic, clinical, and laboratory data were recorded. Nasopharyngeal and blood samples were collected for multiplex polymerase chain reaction testing for 21 respiratory pathogens and procalcitonin (PCT) detection, respectively. Demographic and clinical features associated with antibiotic prescription were identified using Chi Square and t-tests; significant variables (p<0.05) were further included in multivariable logistic regression models. The potential impact of biomarker testing on antibiotic prescription was simulated using standard c-reactive protein (CRP) and PCT cut-offs. RESULTS Of 1217 patients enrolled, 438 (36.0%) had ≥1 respiratory virus detected, with 48.4% of these patients being male and 30.8% children. Influenza A (39.3%) and human rhinovirus/ enterovirus (28.3%) were most commonly detected. A total of 114 (84.4%) children and 266 (87.8%) adults with respiratory viruses were treated with antibiotics. Among children, neutrophil percentage (median 63.6% vs 47.6%, p = 0.04) was positively associated with antibiotic prescription. Among adults, headache (60.6% vs 35.1%, p = 0.003), crepitations/crackles (55.3% vs 21.6%, p<0.001), rhonchi/wheezing (42.9% vs 18.9%, p = 0.005), and chest x-ray opacities (27.4% vs 8.1%, p = 0.01) were associated with antibiotic prescription. Access to CRP and procalcitonin test results could have potentially decreased inappropriate antibiotic prescription in this study by 89.5% and 83.3%, respectively. CONCLUSIONS High proportions of viral detection and antibiotic prescription were observed among a large inpatient cohort with LRTI. Increased access to point-of-care biomarker testing may improve antimicrobial prescription.
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Affiliation(s)
- Perla G. Medrano
- Duke University, Durham, North Carolina, United States of America
- Duke Global Health Institute, Durham, North Carolina, United States of America
| | | | - Ajith Nagahawatte
- Duke Global Health Institute, Durham, North Carolina, United States of America
- Faculty of Medicine, University of Ruhuna, Galle, Sri Lanka
| | - Sky Vanderburg
- University of California, San Francisco, California, United States of America
| | - Lawrence P. Park
- Duke University, Durham, North Carolina, United States of America
- Duke Global Health Institute, Durham, North Carolina, United States of America
| | | | | | | | - Tianchen Sheng
- Duke University, Durham, North Carolina, United States of America
- Duke Global Health Institute, Durham, North Carolina, United States of America
| | | | - Jack Anderson
- Duke University, Durham, North Carolina, United States of America
| | - Bradly P. Nicholson
- Institute for Medical Research, Durham, North Carolina, United States of America
| | - Christopher W. Woods
- Duke University, Durham, North Carolina, United States of America
- Duke Global Health Institute, Durham, North Carolina, United States of America
| | - Champica K. Bodinayake
- Duke Global Health Institute, Durham, North Carolina, United States of America
- Faculty of Medicine, University of Ruhuna, Galle, Sri Lanka
| | - L. Gayani Tillekeratne
- Duke University, Durham, North Carolina, United States of America
- Duke Global Health Institute, Durham, North Carolina, United States of America
- Faculty of Medicine, University of Ruhuna, Galle, Sri Lanka
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Pickens CI, Gao CA, Morales-Nebreda L, Wunderink RG. Microbiology of Severe Community-Acquired Pneumonia and the Role of Rapid Molecular Techniques. Semin Respir Crit Care Med 2024; 45:158-168. [PMID: 38196061 DOI: 10.1055/s-0043-1777770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
The microbiology of severe community acquired pneumonia (SCAP) has implications on management, clinical outcomes and public health policy. Therefore, knowledge of the etiologies of SCAP and methods to identify these microorganisms is key. Bacteria including Streptococcus pneumoniae, Staphylococcus aureus and Enterobacteriaceae continue to be important causes of SCAP. Viruses remain the most commonly identified etiology of SCAP. Atypical organisms are also important etiologies of SCAP and are critical to identify for public health. With the increased number of immunocompromised individuals, less common pathogens may also be found as the causative agent of SCAP. Traditional diagnostic tests, including semi-quantitative respiratory cultures, blood cultures and urinary antigens continue to hold an important role in the evaluation of patients with SCAP. Many of the limitations of the aforementioned tests are addressed by rapid, molecular diagnostic tests. Molecular diagnostics utilize culture-independent technology to identify species-specific genetic sequences. These tests are often semi-automated and provide results within hours, which provides an opportunity for expedient antibiotic stewardship. The existing literature suggests molecular diagnostic techniques may improve antibiotic stewardship in CAP, and future research should investigate optimal methods for implementation of these assays into clinical practice.
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Affiliation(s)
- Chiagozie I Pickens
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Catherine A Gao
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Luisa Morales-Nebreda
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Richard G Wunderink
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
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Hong Q, Chen W, Zhang Z, Chen Q, Wei G, Huang H, Yu Y. Nasopharyngeal carcinoma cell screening based on the electroporation-SERS spectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 308:123747. [PMID: 38091653 DOI: 10.1016/j.saa.2023.123747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 11/12/2023] [Accepted: 12/08/2023] [Indexed: 01/13/2024]
Abstract
Nasopharyngeal carcinoma (NPC) is a malignant tumor in head and neck. Early diagnosis can effectively improve the survival rate of patients. Nasopharyngeal exfoliative cytology, as a convenient and noninvasive auxiliary diagnostic method, is suitable for the population screening of NPC, but its diagnostic sensitivity is low. In this study, an electroporation-based SERS technique was proposed to detect and screen the clinical nasopharyngeal exfoliated cell samples. Firstly, nasopharyngeal swabs was used to collected the nasopharyngeal exfoliated cell samples from NPC patients (n = 54) and healthy volunteers (n = 60). Then, gold nanoparticles, as the Raman scattering enhancing substrates, were rapidly introduced into cells by electroporation technique for surface-enhanced Raman scattering (SERS) detection. Finally, SERS spectra combined with principal component analysis (PCA) and linear discriminant analysis (LDA) were employed to diagnose and distinguish NPC cell samples. Raman peak assignments combined with spectral differences reflected the biochemical changes associated with NPC, including nucleic acid, amino acid and carbohydrates. Based on the PCA-LDA approach, the sensitivity, specificity and accuracy of 98.15 %, 96.67 % and 97.37 %, respectively, were achieved for screening NPC. This study offers valuable assistance for noninvasive NPC auxiliary diagnosis, and has grate potential in expanding the application of the SERS technique in clinical cell sample testing.
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Affiliation(s)
- Quanxing Hong
- College of Integrative Medicine, Laboratory of Pathophysiology, Key Laboratory of Integrative Medicine on Chronic Diseases (Fujian Province University), Synthesized Laboratory of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China
| | - Weiwei Chen
- Department of Medical Technology, Fujian Health College, Fuzhou 350101, China
| | - Zhongping Zhang
- The Third Affiliated People's Hospital Affiliated to Fujian University of Traditional Chinese Medicine, Fuzhou 350108, China
| | - Qin Chen
- The Second Affiliated People's Hospital Affiliated to Fujian University of Traditional Chinese Medicine, Fuzhou 350003, China
| | - Guoqiang Wei
- College of Integrative Medicine, Laboratory of Pathophysiology, Key Laboratory of Integrative Medicine on Chronic Diseases (Fujian Province University), Synthesized Laboratory of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China
| | - Hao Huang
- College of Integrative Medicine, Laboratory of Pathophysiology, Key Laboratory of Integrative Medicine on Chronic Diseases (Fujian Province University), Synthesized Laboratory of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China.
| | - Yun Yu
- College of Integrative Medicine, Laboratory of Pathophysiology, Key Laboratory of Integrative Medicine on Chronic Diseases (Fujian Province University), Synthesized Laboratory of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China.
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Claessens YE. Response to 'Integrating clinical judgment, advanced radiology, and molecular diagnosis: the modern ways of pneumonia management'. Eur J Emerg Med 2023; 30:301. [PMID: 37387635 DOI: 10.1097/mej.0000000000001040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2023]
Affiliation(s)
- Yann-Erick Claessens
- Department of Emergency Medicine, Princesse Grace Hospital Center, Avenue Pasteur, Monte Carlo, Monaco
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