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Andrews V, Pinholt M, Schneider UV, Schønning K, Søes LM, Lisby G. Performance of PCR-based syndromic testing compared to bacterial culture in patients with suspected pneumonia applying microscopy for quality assessment. APMIS 2022; 130:417-426. [PMID: 35499302 DOI: 10.1111/apm.13232] [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: 04/22/2022] [Accepted: 04/28/2022] [Indexed: 11/29/2022]
Abstract
Syndromic testing for lower respiratory tract infections with BioFire® FilmArray® Pneumonia Panel Plus (BF) detects 27 pathogens with a turn-around-time of one hour. We compared the performance of BF with culture. Samples from 298 hospitalized patients with suspected pneumonia routinely sent for culture were also analyzed using BF. Retrospectively, patients were clinically categorized as having "pneumonia" or "no pneumonia." BF and culture were compared by analytical performance, which was evaluated by pathogen concordance, and by clinical performance by comparing pathogen detections in patients with and without pneumonia. The BF results for viruses and atypical bacteria were not included in the performance analysis. In 298 patient samples, BF and culture detected 285 and 142 potential pathogens, respectively. Positive percent agreement (PPA) was 88% (125/142). In patients with community-acquired pneumonia (CAP), clinical sensitivity was 70% and 51%, and specificity was 43% and 71% for BF and culture, respectively. In patients with hospital-acquired pneumonia, the corresponding numbers were 55% and 23%, and 47% and 68%. There was no significant improvement of performance, when only high-quality sputum samples were considered. Efficacy of both BF and culture was low. Both tests are best used in CAP patients for whom the diagnosis has already been clinically established. Indiscriminate use may be clinically misleading and a cause of improper use of antibiotics.
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Affiliation(s)
- Vigith Andrews
- Department of Clinical Microbiology, Copenhagen University Hospital - Amager and Hvidovre, Copenhagen, Denmark
| | - Mette Pinholt
- Department of Clinical Microbiology, Copenhagen University Hospital - Amager and Hvidovre, Copenhagen, Denmark
| | - Uffe Vest Schneider
- Department of Clinical Microbiology, Copenhagen University Hospital - Amager and Hvidovre, Copenhagen, Denmark
| | - Kristian Schønning
- Department of Clinical Microbiology, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Lillian Marie Søes
- Department of Clinical Microbiology, Copenhagen University Hospital - Amager and Hvidovre, Copenhagen, Denmark
| | - Gorm Lisby
- Department of Clinical Microbiology, Copenhagen University Hospital - Amager and Hvidovre, Copenhagen, Denmark
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Skodvin B, Wathne JS, Lindemann PC, Harthug S, Nilsen RM, Charani E, Syre H, Kittang BR, Kleppe LKS, Smith I. Use of microbiology tests in the era of increasing AMR rates- a multicentre hospital cohort study. Antimicrob Resist Infect Control 2019; 8:28. [PMID: 30740221 PMCID: PMC6360791 DOI: 10.1186/s13756-019-0480-z] [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: 11/29/2018] [Accepted: 01/29/2019] [Indexed: 01/10/2023] Open
Abstract
Background Effective use of microbiology test results may positively influence patient outcomes and limit the use of broad-spectrum antibiotics. However, studies indicate that their potential is not fully utilized. We investigated microbiology test ordering practices and the use of test results for antibiotic decision-making in hospitals. Methods A multicentre cohort study was conducted during five months in 2014 in Medical departments across three hospitals in Western Norway. Patients treated with antibiotics for sepsis, urinary tract infections, skin and soft tissue infections, lower respiratory tract infections or acute exacerbations of chronic obstructive pulmonary disease were included in the analysis. Primary outcome measures were degree of microbiology test ordering, compliance with microbiology testing recommendations in the national antibiotic guideline and proportion of microbiology test results used to inform antibiotic treatment. Data was obtained from electronic- and paper medical records and charts and laboratory information systems. Results Of the 1731 patient admissions during the study period, mean compliance with microbiology testing recommendations in the antibiotic guideline was 89%, ranging from 81% in patients with acute exacerbations of chronic obstructive pulmonary disease to 95% in patients with sepsis. Substantial additional testing was performed beyond the recommendations with 298/606 (49%) of patients with lower respiratory tract infections having urine cultures and 42/194 (22%) of patients with urinary tract infections having respiratory tests. Microbiology test results from one of the hospitals showed that 18% (120/672) of patient admissions had applicable test results, but only half of them were used for therapy guidance, i.e. in total, 9% (63/672) of patient admissions had test results informing prescription of antibiotic therapy. Conclusions This study showed that despite a large number of microbiology test orders, only a limited number of tests informed antibiotic treatment. To ensure that microbiology tests are used optimally, there is a need to review the utility of existing microbiology tests, test ordering practices and use of test results through a more targeted and overarching approach.
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Affiliation(s)
- Brita Skodvin
- 1Norwegian Advisory Unit for Antibiotic Use in Hospitals, Department of Research and Development, Haukeland University Hospital, Haukelandsveien 22, 5021 Bergen, Norway.,2Department of Clinical Science, University of Bergen, Jonas Lies vei 87, 5020 Bergen, Norway
| | - Jannicke S Wathne
- 1Norwegian Advisory Unit for Antibiotic Use in Hospitals, Department of Research and Development, Haukeland University Hospital, Haukelandsveien 22, 5021 Bergen, Norway.,2Department of Clinical Science, University of Bergen, Jonas Lies vei 87, 5020 Bergen, Norway.,Department of Quality and Development, Hospital Pharmacies Enterprise in Western Norway, Møllendalsbakken 9, 5021 Bergen, Norway
| | - P Christoffer Lindemann
- 2Department of Clinical Science, University of Bergen, Jonas Lies vei 87, 5020 Bergen, Norway.,4Department of Microbiology, Haukeland University Hospital, Haukelandsveien 22, 5021 Bergen, Norway
| | - Stig Harthug
- 1Norwegian Advisory Unit for Antibiotic Use in Hospitals, Department of Research and Development, Haukeland University Hospital, Haukelandsveien 22, 5021 Bergen, Norway.,2Department of Clinical Science, University of Bergen, Jonas Lies vei 87, 5020 Bergen, Norway
| | - Roy M Nilsen
- 5Western Norway University of Applied Sciences, Inndalsveien 28, 5063 Bergen, Norway
| | - Esmita Charani
- 6NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, 8th Floor Commonwealth Building, Imperial College London, Du Cane Road, London, W12 ONN UK
| | - Heidi Syre
- 7Department of Medical Microbiology, Stavanger University Hospital, Gerd Ragna Bloch Thorsens gate 8, 4011 Stavanger, Norway
| | - Baard R Kittang
- 8Department of Medicine, Haraldsplass Deaconess Hospital, Ulriksdal 8, 5009 Bergen, Norway
| | - Lars K S Kleppe
- 9Department of Infectious Diseases and Unit for Infection Prevention and Control, Department of Research and Education, Stavanger University Hospital, Gerd Ragna Bloch Thorsens gate 8, 4011 Stavanger, Norway
| | - Ingrid Smith
- 10Department of Essential Medicines and Health Products, World Health Organization (WHO), Avenue Appia 20, 1211 Geneva 27, Switzerland
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Murdoch DR, Morpeth SC, Hammitt LL, Driscoll AJ, Watson NL, Baggett HC, Brooks WA, Deloria Knoll M, Feikin DR, Kotloff KL, Levine OS, Madhi SA, O'Brien KL, Scott JAG, Thea DM, Adrian PV, Ahmed D, Alam M, Awori JO, DeLuca AN, Higdon MM, Karron RA, Kwenda G, Machuka EM, Makprasert S, McLellan J, Moore DP, Mwaba J, Mwarumba S, Park DE, Prosperi C, Sangwichian O, Sissoko S, Tapia MD, Zeger SL, Howie SRC. The Diagnostic Utility of Induced Sputum Microscopy and Culture in Childhood Pneumonia. Clin Infect Dis 2017; 64:S280-S288. [PMID: 28575362 PMCID: PMC5447842 DOI: 10.1093/cid/cix090] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND. Sputum microscopy and culture are commonly used for diagnosing the cause of pneumonia in adults but are rarely performed in children due to difficulties in obtaining specimens. Induced sputum is occasionally used to investigate lower respiratory infections in children but has not been widely used in pneumonia etiology studies. METHODS. We evaluated the diagnostic utility of induced sputum microscopy and culture in patients enrolled in the Pneumonia Etiology Research for Child Health (PERCH) study, a large study of community-acquired pneumonia in children aged 1-59 months. Comparisons were made between induced sputum samples from hospitalized children with radiographically confirmed pneumonia and children categorized as nonpneumonia (due to the absence of prespecified clinical and laboratory signs and absence of infiltrate on chest radiograph). RESULTS. One induced sputum sample was available for analysis from 3772 (89.1%) of 4232 suspected pneumonia cases enrolled in PERCH. Of these, sputum from 2608 (69.1%) met the quality criterion of <10 squamous epithelial cells per low-power field, and 1162 (44.6%) had radiographic pneumonia. Induced sputum microscopy and culture results were not associated with radiographic pneumonia, regardless of prior antibiotic use, stratification by specific bacteria, or interpretative criteria used. CONCLUSIONS. The findings of this study do not support the culture of induced sputum specimens as a diagnostic tool for pneumonia in young children as part of routine clinical practice.
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Affiliation(s)
- David R Murdoch
- Department of Pathology, University of Otago, and
- Microbiology Unit, Canterbury Health Laboratories, Christchurch, New Zealand
| | - Susan C Morpeth
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi
- Department of Infectious Disease Epidemiology London School of Hygiene & Tropical Medicine, United Kingdom
- Microbiology Laboratory, Middlemore Hospital, Counties Manukau District Health Board, Auckland, New Zealand
| | - Laura L Hammitt
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, and
| | - Amanda J Driscoll
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, and
| | | | - Henry C Baggett
- Global Disease Detection Center, Thailand Ministry of Public Health-US Centers for Disease Control and Prevention Collaboration, Nonthaburi
- Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - W Abdullah Brooks
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka and Matlab
| | - Maria Deloria Knoll
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, and
| | - Daniel R Feikin
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, and
- Division of Viral Diseases, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Karen L Kotloff
- Division of Infectious Disease and Tropical Pediatrics, Department of Pediatrics, Center for Vaccine Development, Institute of Global Health, University of Maryland School of Medicine, Baltimore
| | - Orin S Levine
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, and
- Bill & Melinda Gates Foundation, Seattle, Washington
| | - Shabir A Madhi
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, and
- Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Katherine L O'Brien
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, and
| | - J Anthony G Scott
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi
- Department of Infectious Disease Epidemiology London School of Hygiene & Tropical Medicine, United Kingdom
| | - Donald M Thea
- Center for Global Health and Development, Boston University School of Public Health, Massachusetts
| | - Peter V Adrian
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, and
- Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Dilruba Ahmed
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka and Matlab
| | - Muntasir Alam
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka and Matlab
| | - Juliet O Awori
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi
| | - Andrea N DeLuca
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, and
- Epidemiology, and
| | - Melissa M Higdon
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, and
| | - Ruth A Karron
- International Health, Center for Immunization Research, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Geoffrey Kwenda
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, and
- Zambia Center for Applied Health Research and Development, Lusaka
| | | | - Sirirat Makprasert
- Global Disease Detection Center, Thailand Ministry of Public Health-US Centers for Disease Control and Prevention Collaboration, Nonthaburi
| | - Jessica McLellan
- Medical Research Council Unit, Basse, The Gambia
- University of Calgary Cummings School of Medicine, Alberta, Canada
| | - David P Moore
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, and
- Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases Unit, University of the Witwatersrand, Johannesburg, South Africa
- Department of Paediatrics & Child Health, Chris Hani Baragwanath Academic Hospital and University of the Witwatersrand, Johannesburg, South Africa
| | - John Mwaba
- Zambia Center for Applied Health Research and Development, Lusaka
- Department of Pathology and Microbiology, University Teaching Hospital, Lusaka, Zambia
| | - Salim Mwarumba
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi
| | - Daniel E Park
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, and
- Milken Institute School of Public Health, Department of Epidemiology and Biostatistics, George Washington University
| | - Christine Prosperi
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, and
| | - Ornuma Sangwichian
- Global Disease Detection Center, Thailand Ministry of Public Health-US Centers for Disease Control and Prevention Collaboration, Nonthaburi
| | - Seydou Sissoko
- Centre pour le Développement des Vaccins (CVD-Mali), Bamako
| | - Milagritos D Tapia
- Division of Infectious Disease and Tropical Pediatrics, Department of Pediatrics, Center for Vaccine Development, Institute of Global Health, University of Maryland School of Medicine, Baltimore
| | - Scott L Zeger
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Stephen R C Howie
- Medical Research Council Unit, Basse, The Gambia
- Department of Paediatrics, University of Auckland, and
- Centre for International Health, University of Otago, Dunedin, New Zealand
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