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E L, Zhao B, Liu H, Zheng C, Song X, Cai Y, Liang H. Image-based deep learning in diagnosing the etiology of pneumonia on pediatric chest X-rays. Pediatr Pulmonol 2021; 56:1036-1044. [PMID: 33331678 DOI: 10.1002/ppul.25229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 12/07/2020] [Accepted: 12/13/2020] [Indexed: 11/12/2022]
Abstract
PURPOSE Comparing the efficacy of a deep-learning model in classifying the etiology of pneumonia on pediatric chest X-rays (CXRs) with that of human readers. METHODS We built a clinical-pediatric CXR set containing 4035 patients to exploit a deep-learning model called Resnet-50 for differentiating viral from bacterial pneumonia. The dataset was split into training (80%) and validation (20%). Model performance was assessed by receiver operating characteristic curve and area under the curve (AUC) on the first test set of 400 CXRs collected from different studies. For the second test set composed of 100 independent examinations obtained from the daily clinical practice at our institution, the kappa coefficient was selected to measure the interrater agreement in a pairwise fashion for the reference standard, all reviewers, and the model. Gradient-weighted class activation mapping was used to visualize the significant areas contributing to the model prediction. RESULTS On the first test set, the best-performing classifier achieved an AUC of 0.919 (p < .001), with a sensitivity of 79.0% and specificity of 88.9%. On the second test set, the classifier achieved performance similar to that of human experts, which resulted in a sensitivity of 74.3% and specificity of 90.8%, positive and negative likelihood ratios of 8.1 and 0.3, respectively. Contingence tables and kappa values further revealed that expert reviewers and model reached substantial agreements on differentiating the etiology of pediatric pneumonia. CONCLUSIONS This study demonstrated that the model performed similarly as human reviewers and recognized the regions of pathology on CXRs.
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Affiliation(s)
- Longjiang E
- Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Baisong Zhao
- Department of Anesthesiology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Hongsheng Liu
- Department of Radiology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Changmeng Zheng
- Department of Software Engineering, School of Software Engineering, South China University of Technology, Guangzhou, Guangdong, China
| | - Xingrong Song
- Department of Anesthesiology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Yi Cai
- Department of Software Engineering, School of Software Engineering, South China University of Technology, Guangzhou, Guangdong, China.,The Key Laboratory of Big Data and Intelligent Robot (South China University of Technology), Ministry of Education, Guangzhou, Guangdong, China
| | - Huiying Liang
- Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
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Increased Detection of Viruses in Children with Respiratory Tract Infection Using PCR. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17020564. [PMID: 31952364 PMCID: PMC7013517 DOI: 10.3390/ijerph17020564] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 01/06/2020] [Accepted: 01/12/2020] [Indexed: 01/06/2023]
Abstract
Respiratory viruses are a common cause of respiratory tract infection (RTI), particularly in neonates and children. Rapid and accurate diagnosis of viral infections could improve clinical outcomes and reduce the use of antibiotics and treatment sessions. Advances in diagnostic technology contribute to the accurate detection of viruses. We performed a multiplex real-time polymerase chain reaction (PCR) to investigate the viral etiology in pediatric patients and compared the detection rates with those determined using traditional antigen tests and virus cultures. Fifteen respiratory viruses were included in our investigation: respiratory syncytial virus A/B (RSV), influenza virus A (FluA) and influenza virus B (FluB), human metapneumovirus (MPV), enterovirus (EV), human parainfluenza virus (PIV) types 1-4, human rhinovirus (RV), human coronavirus OC43, NL63, and 229E, human adenovirus (ADV), and human bocavirus (Boca). In total, 474 specimens were collected and tested. Respiratory viruses were detected more frequently by PCR (357, 75.3%) than they were by traditional tests (229, 49.3%). The leading pathogens were RSV (113, 23.8%), RV (72, 15.2%), PIV3 (53, 11.2%), FluA (51, 10.8%), and ADV (48, 10.1%). For children younger than 5 years, RSV and RV were most prevalent; for children older than 5 years, FluA and ADV were the most frequently detected. Of the specimens, 25.8% (92/357) were coinfected with two or more viruses. RV, Boca, PIV2, FluB, and PIV4 had higher rates of coinfection; MPV and PIV1 had the lowest rates of coinfection (9.1% and 5.3%). To conclude, the detection power of PCR was better than that of traditional antigen tests and virus cultures when considering the detection of respiratory viruses. RSV and RV were the leading viral pathogens identified in the respiratory specimens. One-quarter of the positive specimens were coinfected with two or more viruses. In the future, further application of PCR may contribute to the rapid and accurate diagnosis of respiratory viruses and could improve patient outcomes.
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Gkika E, Psaroulaki A, Tselentis Y, Angelakis E, Kouikoglou VS. Can point-of-care testing shorten hospitalization length of stay? An exploratory investigation of infectious agents using regression modelling. Health Informatics J 2018; 25:1606-1617. [PMID: 30179068 DOI: 10.1177/1460458218796612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
This retrospective study investigates the potential benefits from the introduction of point-of-care tests for rapid diagnosis of infectious diseases. We analysed a sample of 441 hospitalized patients who had received a final diagnosis related to 18 pathogenic agents. These pathogens were mostly detected by standard tests but were also detectable by point-of-care testing. The length of hospital stay was partitioned into pre- and post-laboratory diagnosis stages. Regression analysis and elementary queueing theory were applied to estimate the impact of quick diagnosis on the mean length of stay and the utilization of healthcare resources. The analysis suggests that eliminating the pre-diagnosis times through point-of-care testing could shorten the mean length of hospital stay for infectious diseases by up to 34 per cent and result in an equal reduction in bed occupancy and other resources. Regression and other more sophisticated models can aid the financing decision-making of pilot point-of-care laboratories in healthcare systems.
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Sun X, Song L, Feng S, Li L, Yu H, Wang Q, Wang X, Hou Z, Li X, Li Y, Zhang Q, Li K, Cui C, Wu J, Qin Z, Wu Q, Chen H. Fatty Acid Metabolism is Associated With Disease Severity After H7N9 Infection. EBioMedicine 2018; 33:218-229. [PMID: 29941340 PMCID: PMC6085509 DOI: 10.1016/j.ebiom.2018.06.019] [Citation(s) in RCA: 25] [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: 05/15/2018] [Revised: 06/15/2018] [Accepted: 06/15/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Human infections with the H7N9 virus could lead to lung damage and even multiple organ failure, which is closely associated with a high mortality rate. However, the metabolic basis of such systemic alterations remains unknown. METHODS This study included hospitalized patients (n = 4) with laboratory-confirmed H7N9 infection, healthy controls (n = 9), and two disease control groups comprising patients with pneumonia (n = 9) and patients with pneumonia who received steroid treatment (n = 10). One H7N9-infected patient underwent lung biopsy for histopathological analysis and expression analysis of genes associated with lung homeostasis. H7N9-induced systemic alterations were investigated using metabolomic analysis of sera collected from the four patients by using ultra-performance liquid chromatography-mass spectrometry. Chest digital radiography and laboratory tests were also conducted. FINDINGS Two of the four patients did not survive the clinical treatments with antiviral medication, steroids, and oxygen therapy. Biopsy revealed disrupted expression of genes associated with lung epithelial integrity. Histopathological analysis demonstrated severe lung inflammation after H7N9 infection. Metabolomic analysis indicated that fatty acid metabolism may be inhibited during H7N9 infection. Serum levels of palmitic acid, erucic acid, and phytal may negatively correlate with the extent of lung inflammation after H7N9 infection. The changes in fatty acid levels may not be due to steroid treatment or pneumonia. INTERPRETATION Altered structural and secretory properties of the lung epithelium may be associated with the severity of H7N9-infection-induced lung disease. Moreover, fatty acid metabolism level may predict a fatal outcome after H7N9 virus infection.
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Affiliation(s)
- Xin Sun
- Department of Basic Medicine, Haihe Clinical College of Tianjin Medical University, Tianjin 300070, China
| | - Lijia Song
- Department of Respiratory Medicine, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Shuang Feng
- Department of Clinical Laboratory, Tianjin Haihe Hospital, Tianjin 300350, China
| | - Li Li
- Department of Respiratory Medicine, Tianjin Haihe Hospital, Tianjin 300350, China
| | - Hongzhi Yu
- Department of Respiratory Medicine, Tianjin Haihe Hospital, Tianjin 300350, China
| | - Qiaoxing Wang
- Department of Clinical Laboratory, Tianjin Haihe Hospital, Tianjin 300350, China
| | - Xing Wang
- Department of Respiratory Medicine, Tianjin Haihe Hospital, Tianjin 300350, China
| | - Zhili Hou
- Department of Tuberculosis, Tianjin Haihe Hospital, Tianjin 300350, China
| | - Xue Li
- Department of Basic Medicine, Haihe Clinical College of Tianjin Medical University, Tianjin 300070, China
| | - Yu Li
- Department of Basic Medicine, Haihe Clinical College of Tianjin Medical University, Tianjin 300070, China
| | - Qiuyang Zhang
- Department of Basic Medicine, Haihe Clinical College of Tianjin Medical University, Tianjin 300070, China
| | - Kuan Li
- Department of Basic Medicine, Haihe Clinical College of Tianjin Medical University, Tianjin 300070, China
| | - Chao Cui
- Department of Thoracic Surgery, Tianjin Haihe Hospital, Tianjin 300350, China
| | - Junping Wu
- Department of Respiratory Medicine, Tianjin Haihe Hospital, Tianjin 300350, China
| | - Zhonghua Qin
- Department of Clinical Laboratory, Tianjin Haihe Hospital, Tianjin 300350, China
| | - Qi Wu
- Department of Basic Medicine, Haihe Clinical College of Tianjin Medical University, Tianjin 300070, China; Department of Respiratory Medicine, Tianjin Medical University General Hospital, Tianjin 300052, China; Key Research Laboratory for Infectious Disease Prevention for State Administration of Traditional Chinese Medicine, Tianjin Institute of Respiratory Diseases, Tianjin 300350, China.
| | - Huaiyong Chen
- Department of Basic Medicine, Haihe Clinical College of Tianjin Medical University, Tianjin 300070, China; Key Research Laboratory for Infectious Disease Prevention for State Administration of Traditional Chinese Medicine, Tianjin Institute of Respiratory Diseases, Tianjin 300350, China.
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Ko DH, Kim HS, Hyun J, Kim HS, Kim JS, Park KU, Song W. Comparison of the Luminex xTAG Respiratory Viral Panel Fast v2 Assay With Anyplex II RV16 Detection Kit and AdvanSure RV Real-Time RT-PCR Assay for the Detection of Respiratory Viruses. Ann Lab Med 2018. [PMID: 28643489 PMCID: PMC5500739 DOI: 10.3343/alm.2017.37.5.408] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Background The accurate and rapid identification of the causative viruses is important for the timely diagnosis and management of respiratory infections. Multiplex molecular diagnostic techniques have been widely adopted to detect respiratory viruses. We compared the results of a newly upgraded, multiplex, molecular bead-based respiratory viral panel (RVP) assay with the results of Anyplex II RV16 detection kit and AdvanSure RV real-time RT-PCR assay. Methods We tested 254 respiratory specimens and cultured viral strains using the Luminex xTAG RVP Fast v2 assay (Luminex Molecular Diagnostics, Canada) and Anyplex II RV16 detection kit and compared the results. Specimens showing discordant results between the two assays were tested with a AdvanSure RV real-time RT-PCR assay. Results Of the 254 respiratory specimens, there was total agreement in the results between the xTAG RVP Fast v2 assay and the other real-time PCR assay in 94.1–100% of the specimens. The agreement levels were relatively low (94.1–97.6%) for specimens of adenovirus, coronavirus NL63, and parainfluenza type 3. In comparison to the other assay, the xTAG RVP Fast v2 assay detected a higher number of parainfluenza type 3 (4 cases) and metapneumovirus (9 cases). Conclusions The xTAG RVP Fast v2 assay showed comparable capabilities compared with the other assays; it will be useful for identifying respiratory viral infections in patients with respiratory symptoms. Clinicians should be aware of the characteristics of the assays they use, since different assays show different detectability for each virus.
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Affiliation(s)
- Dae Hyun Ko
- Department of Laboratory Medicine, Hallym University College of Medicine, Hwaseong, Korea
| | - Hyun Soo Kim
- Department of Laboratory Medicine, Hallym University College of Medicine, Hwaseong, Korea.
| | - Jungwon Hyun
- Department of Laboratory Medicine, Hallym University College of Medicine, Hwaseong, Korea
| | - Han Sung Kim
- Department of Laboratory Medicine, Hallym University College of Medicine, Hwaseong, Korea
| | - Jae Seok Kim
- Department of Laboratory Medicine, Hallym University College of Medicine, Hwaseong, Korea
| | - Kyoung Un Park
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Wonkeun Song
- Department of Laboratory Medicine, Hallym University College of Medicine, Hwaseong, Korea
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Abstract
Introduction: Successful treatment outcomes for viral respiratory tract infections presenting from primary health care to quaternary hospitals will only be achieved with rapid, sensitive and specific identification of pathogens to allow effective pathogen-specific antiviral therapy and infection control measures. Areas covered: This review aims to explore the different point-of-care tests currently available to diagnose viral respiratory tract infections, discuss the advantages and limitations of point-of-care testing, and provide insights into the future of point-of-care tests. The following databases were searched: Medline (January 1996 to 30 September 2017) and Embase (1988 to 30 September 2017), using the following keywords: ‘point of care’, ‘respiratory virus’, ‘influenza’, ‘RSV’, ‘diagnostics’, ‘nucleic acid test’ and ‘PCR’. Expert commentary: Viral respiratory tract infections cause significant morbidity and mortality worldwide, and point-of-care tests are facilitating the rapid identification of the pathogen responsible given the similarities in clinical presentation.
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Affiliation(s)
- Kerri Basile
- a Centre for Infectious Diseases and Microbiology Laboratory Services , Institute of Clinical Pathology and Medical Research, NSW Health Pathology , Westmead , Australia.,b Marie Bashir Institute for Emerging Infections and Biosecurity , University of Sydney, Westmead Hospital , Westmead , Australia
| | - Jen Kok
- a Centre for Infectious Diseases and Microbiology Laboratory Services , Institute of Clinical Pathology and Medical Research, NSW Health Pathology , Westmead , Australia.,b Marie Bashir Institute for Emerging Infections and Biosecurity , University of Sydney, Westmead Hospital , Westmead , Australia
| | - Dominic E Dwyer
- a Centre for Infectious Diseases and Microbiology Laboratory Services , Institute of Clinical Pathology and Medical Research, NSW Health Pathology , Westmead , Australia.,b Marie Bashir Institute for Emerging Infections and Biosecurity , University of Sydney, Westmead Hospital , Westmead , Australia
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Guía de consenso para el abordaje de la neumonía adquirida en la comunidad en el paciente anciano. Rev Esp Geriatr Gerontol 2014; 49:279-91. [PMID: 24873864 PMCID: PMC7103352 DOI: 10.1016/j.regg.2014.04.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 04/11/2014] [Indexed: 11/29/2022]
Abstract
La incidencia de la neumonía adquirida en la comunidad se incrementa con la edad y se asocia a una elevada morbimortalidad debido a los cambios fisiológicos asociados al envejecimiento y a una mayor presencia de enfermedades crónicas. Debido a la importancia que tiene desde un punto de epidemiológico y pronóstico, y a la enorme heterogeneidad descrita en el manejo clínico, creemos que existía la necesidad de realizar un documento de consenso específico para este perfil de paciente. El propósito de este fue realizar una revisión de las evidencias en relación con los factores de riesgo para la etiología, la presentación clínica, el manejo y el tratamiento de la neumonía adquirida en la comunidad en los ancianos con el fin de elaborar una serie de recomendaciones específicas basadas en el análisis crítico de la literatura. Este documento es fruto de la colaboración de diferentes especialistas en representación de la Sociedad Española de Medicina de Urgencias y Emergencias (SEMES), Sociedad Española de Geriatría y Gerontología (SEGG), Sociedad Española de Quimioterapia (SEQ), Sociedad Española de Medicina Interna (SEMI), Sociedad Española de Neumología y Cirugía Torácica (SEPAR), Sociedad Española de Hospitalización a Domicilio (SEHAD) y Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica (SEIMC).
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Svensson MJ, Lind I, Wirgart BZ, Östlund MR, Albert J. Performance of the Simplexa™ Flu A/B & RSV Direct Kit on respiratory samples collected in saline solution. ACTA ACUST UNITED AC 2014; 46:825-31. [PMID: 25195649 DOI: 10.3109/00365548.2014.946444] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND Molecular assays for diagnosis of influenza A, influenza B, and respiratory syncytial virus (RSV) with short turnaround time are of considerable clinical importance. We have evaluated the diagnostic performance of the Simplexa(™) Flu A/B & RSV Direct Kit, which has a run time of 60 min, using different types of respiratory samples collected from patients with a suspected respiratory tract infection, including materials not previously evaluated on this kit. METHODS In total, 210 clinical respiratory samples were analyzed using both the Simplexa direct assay and a laboratory-developed assay (LDA). The 210 clinical samples included 99 nasopharyngeal aspirates collected in 0.9% saline, 91 nasopharyngeal swabs in Σ-Virocult transport medium, 9 tracheal secretions, 8 bronchoalveolar lavages (BAL), and 3 other respiratory sample materials. RESULTS The specificity of the Simplexa assay, using the LDA as gold standard and excluding secondary viral findings, was 100% for all three viruses, whereas the sensitivity was 94.0% for influenza A (47/50), 90.7% for influenza B (49/54), and 90.1% for RSV (46/51), respectively. Discordant results were only observed for samples with cycle threshold values (Ct) > 31 in the LDA. The Simplexa assay generated higher Ct values than the LDA for all three viruses and performed equally well on nasopharyngeal swabs and aspirates. CONCLUSIONS The short run time of the Simplexa direct assay, in combination with high specificity and good sensitivity regarding the sample materials used in this study, make it an interesting option for rapid detection of these three important viral respiratory pathogens in a variety of clinical sample materials.
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Affiliation(s)
- Malin J Svensson
- From the Department of Clinical Microbiology, Karolinska University Hospital , Stockholm , Sweden
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9
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Kaman WE, Andrinopoulou ER, Hays JP. Perceptions of point-of-care infectious disease testing among European medical personnel, point-of-care test kit manufacturers, and the general public. Patient Prefer Adherence 2013; 7:559-77. [PMID: 23814465 PMCID: PMC3693915 DOI: 10.2147/ppa.s44889] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND The proper development and implementation of point-of-care (POC) diagnostics requires knowledge of the perceived requirements and barriers to their implementation. To determine the current requirements and perceived barriers to the introduction of POC diagnostics in the field of medical microbiology (MM)-POC a prospective online survey (TEMPOtest-QC) was established. METHODS AND RESULTS The TEMPOtest-QC survey was online between February 2011 and July 2012 and targeted the medical community, POC test diagnostic manufacturers, general practitioners, and the general public. In total, 293 individuals responded to the survey, including 91 (31%) medical microbiologists, 39 (13%) nonmedical microbiologists, 25 (9%) employees of POC test manufacturers, and 138 (47%) members of the general public. Responses were received from 18 different European countries, with the largest percentage of these living in The Netherlands (52%). The majority (>50%) of medical specialists regarded the development of MM-POC for blood culture and hospital acquired infections as "absolutely necessary", but were much less favorable towards their use in the home environment. Significant differences in perceptions between medical specialists and the general public included the: (1) Effect on quality of patient care; (2) Ability to better monitor patients; (3) Home testing and the doctor-patient relationship; and (4) MM-POC interpretation. Only 34.7% of the general public is willing to pay more than a€10 ($13) for a single MM-POC test, with 85.5% preferring to purchase their MM-POC test from a pharmacy. CONCLUSION The requirements for the proper implementation of MM-POC were found to be generally similar between medical specialists and POC test kit manufacturers. The general public was much more favorable with respect to a perceived improvement in the quality of healthcare that these tests would bring to the hospital and home environment.
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Affiliation(s)
- Wendy E Kaman
- Department of Medical Microbiology and Infectious Diseases, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - John P Hays
- Department of Medical Microbiology and Infectious Diseases, Erasmus Medical Center, Rotterdam, The Netherlands
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Abstract
Aims Diagnostic microbiology for community acquired pneumonia (CAP) provides useful information for patient management, infection control and epidemiological surveillance. Newer techniques enhance that information and the time interval for obtaining results. An audit of diagnostic microbiology utilisation, microbiological aetiology, and influence of results on prescribing practices in CAP in a regional Australian hospital setting was performed. Methods Clinical, microbiological and outcome data were collected by medical record review of patients discharged from Ballarat Hospital with a diagnosis of CAP over a 12 month period. Results Of 184 identified CAP episodes, 47 (25.5%) had no diagnostic microbiology performed. Respiratory virus polymerase chain reaction (PCR) was rarely performed (2.7% of all episodes). Acute serology was frequently requested, however paired acute and convalescent serology was infrequently performed (5/75 testing episodes; 6.7%). CAP severity was not correlated with microbiological investigation intensity. The most common pathogens identified were Streptococcus pneumoniae and Mycoplasma pneumoniae (5.4% and 2.2%, respectively). Diagnostic testing appeared to rarely influence antimicrobial prescribing. Conclusions In this setting, diagnostic microbiological tests such as respiratory virus PCR and urinary antigen tests are under-utilised. In contrast, sputum and serological investigations are commonly requested, however rarely influence practice. Interventions to facilitate efficient usage of diagnostic microbiology are required.
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Poritz MA, Blaschke AJ, Byington CL, Allen L, Nilsson K, Jones DE, Thatcher SA, Robbins T, Lingenfelter B, Amiott E, Herbener A, Daly J, Dobrowolski SF, Teng DHF, Ririe KM. FilmArray, an automated nested multiplex PCR system for multi-pathogen detection: development and application to respiratory tract infection. PLoS One 2011; 6:e26047. [PMID: 22039434 PMCID: PMC3198457 DOI: 10.1371/journal.pone.0026047] [Citation(s) in RCA: 262] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Accepted: 09/16/2011] [Indexed: 12/19/2022] Open
Abstract
The ideal clinical diagnostic system should deliver rapid, sensitive, specific and reproducible results while minimizing the requirements for specialized laboratory facilities and skilled technicians. We describe an integrated diagnostic platform, the "FilmArray", which fully automates the detection and identification of multiple organisms from a single sample in about one hour. An unprocessed biologic/clinical sample is subjected to nucleic acid purification, reverse transcription, a high-order nested multiplex polymerase chain reaction and amplicon melt curve analysis. Biochemical reactions are enclosed in a disposable pouch, minimizing the PCR contamination risk. FilmArray has the potential to detect greater than 100 different nucleic acid targets at one time. These features make the system well-suited for molecular detection of infectious agents. Validation of the FilmArray technology was achieved through development of a panel of assays capable of identifying 21 common viral and bacterial respiratory pathogens. Initial testing of the system using both cultured organisms and clinical nasal aspirates obtained from children demonstrated an analytical and clinical sensitivity and specificity comparable to existing diagnostic platforms. We demonstrate that automated identification of pathogens from their corresponding target amplicon(s) can be accomplished by analysis of the DNA melting curve of the amplicon.
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Affiliation(s)
- Mark A Poritz
- Idaho Technology, Inc., Salt Lake City, Utah, United States of America.
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12
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Hung YP, Wu CJ, Chen CZ, Lee HC, Chang CM, Lee NY, Chung CH, Ko WC. Comparisons of clinical characters in patients with pneumococcal and Legionella pneumonia. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2011; 43:215-21. [PMID: 21291849 DOI: 10.1016/s1684-1182(10)60034-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2008] [Revised: 03/27/2009] [Accepted: 07/23/2009] [Indexed: 11/30/2022]
Abstract
BACKGROUND/PURPOSE The etiology of pneumonia is usually unknown, but the availability of urinary pneumococcal and Legionella antigen tests can improve the diagnostic yield. Our aim was to provide clinical clues to help clinicians perform the appropriate urinary antigen tests. METHODS A retrospective study of patients admitted to the National Cheng Kung University Hospital between July 2006 and June 2008 was conducted. Patients aged over 18 years presenting with clinical symptoms and signs, radiological findings compatible with pneumonia, and a positive pneumococcal or Legionella pneumophila urinary antigen test, were included. Medical records were reviewed for data collection. RESULTS Overall, 55 adults with pneumonia, including 42 with pneumococcal pneumonia (PP) and 13 with Legionella pneumonia (LP), were enrolled. On admission, patients with PP tended to be older (73.5 years vs. 59.1 years; p=0.001), had lower body weights (52.0 kg vs. 69.7 kg; p < 0.001), more frequent respiratory symptoms (59.5%vs. 0%; p < 0.001), and lower systolic (123.0 mmHg vs. 141.0 mmHg; p=0.004) and diastolic blood pressures (68.3 mmHg vs. 81.7 mmHg; p=0.008), compared with patients with LP. However, those with LP had higher body temperatures (39.0°C vs. 37.5°C; p < 0.001), a higher incidence of relative bradycardia (45.5%vs. 0%; p < 0.001), diarrhea (15.4%vs. 0%; p= 0.053), and lower platelet counts (178.5 × 10(3)/mm(3)vs. 233.7 × 10(3)/mm(3); p= 0.026). Radiological findings showed that the major abnormality, lobar consolidation, was indistinguishable between LP and PP. The percentage of patients requiring intensive care (35.7%vs. 38.5%) or ventilator support (31%vs. 23.1%) and in-hospital crude mortality rates (9.5%vs. 7.7%) was similar in both groups. CONCLUSION Some clinical and laboratory characteristics may be regarded as important clues indicating the need for an appropriate urinary antigen test in patients with pneumonia.
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Affiliation(s)
- Yuan-Pin Hung
- Division of Infectious Diseases, Department of Internal Medicine, National Cheng Kung University Hospital, Tainan, Taiwan
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13
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Tenover FC. Developing molecular amplification methods for rapid diagnosis of respiratory tract infections caused by bacterial pathogens. Clin Infect Dis 2011; 52 Suppl 4:S338-45. [PMID: 21460293 DOI: 10.1093/cid/cir049] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Current diagnostic methods for bacterial respiratory tract infections are slow and often of marginal value for patient management if the adequacy of the specimen is not confirmed before culture. Molecular amplification tests, which are highly sensitive, can provide results in hours rather than days but may not distinguish colonization from infection unless a quantification step is included. Defining the reference method to be used for evaluating a novel molecular assay, with input from the US Food and Drug Administration (FDA), is critical before initiating development of a potential product. Although expectorated sputum may be the clinician's specimen of choice for testing because of ease of collection, the poor quality of such specimens may pose problems for clinical trials of novel amplification tests. There are still many gaps in our understanding of the interplay between colonization and infection and of the role that amplification tests may play in guiding anti-infective therapy. Thus, the performance parameters of a new diagnostic method should be closely matched to a precisely defined intended use statement.
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Bissonnette L, Bergeron MG. Diagnosing infections--current and anticipated technologies for point-of-care diagnostics and home-based testing. Clin Microbiol Infect 2010; 16:1044-53. [PMID: 20670286 DOI: 10.1111/j.1469-0691.2010.03282.x] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In recent years, we have witnessed many transitions in healthcare systems around the globe. For example, population expansion and ageing, and the human immunodeficiency virus (HIV)-AIDS epidemics, have exerted pressure to decentralize the practice of healthcare outside of traditional settings to bring care to those in need. Upstream of patient management, diagnosis is aimed at adequately orienting medical decisions, and considerable efforts have been made to make this process faster and more efficient. However, there are several diseases and medical conditions that may/will benefit from technologies and tests that can be performed closer to the patient, at the point of care or even in the home. In this review, and in light of the paradox that technology and assay developers and healthcare officials must take into consideration for advancing human health in developed and developing countries, we present an overview of rapid diagnosis of infectious diseases at the point of care and of technologies that may contribute to enhancement of the worldwide point-of-care testing market.
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Affiliation(s)
- L Bissonnette
- Département microbiologie-infectiologie et immunologie, Faculté de médecine, Université Laval, Montreal, Quebec, Canada
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Roger PM, Risso K, Hyvernat H, Landraud L, Vassallo M, Dellamonica J, de Salvador F, Cua É, Bernardin G. Antigènuries pneumocoque ou Legionella et antibiothérapie à spectre restreint au cours des pneumonies aiguës communautaires. Med Mal Infect 2010; 40:347-51. [DOI: 10.1016/j.medmal.2010.01.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2009] [Revised: 12/01/2009] [Accepted: 01/06/2010] [Indexed: 11/27/2022]
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te Witt R, van Leeuwen WB, van Belkum A. Specific Diagnostic Tests for Atypical Respiratory Tract Pathogens. Infect Dis Clin North Am 2010. [DOI: 10.1016/j.idc.2009.10.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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Community-Acquired Legionnaires Disease in Croatia. INFECTIOUS DISEASES IN CLINICAL PRACTICE 2010. [DOI: 10.1097/ipc.0b013e3181b7f809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Segonds C, Le Goff A, Chabanon G. [Assessment of the contribution of the immunochromatographic pneumococcal urinary antigen test to the etiological diagnosis of pneumonia in hospitalized adults]. ACTA ACUST UNITED AC 2009; 58:117-22. [PMID: 19875240 DOI: 10.1016/j.patbio.2009.07.037] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2009] [Accepted: 07/21/2009] [Indexed: 11/28/2022]
Abstract
AIM OF THE STUDY To assess the usefulness and prescription practices of the Binax Now Streptococcus pneumoniae urinary antigen test in hospitalized adults. PATIENTS AND METHODS The results of the pneumococcal urinary antigen tests (UAT) performed from January 2002 to September 2004 were related to that of microbiological cultures, and in positive patients to radiographic findings and C-reactive protein (CRP) levels. The evolution of the number of prescriptions and positivity rate in 2007 versus 2002-2004 was analyzed. RESULTS The pneumococcal UAT was positive in 32 of the 278 patients included from 2002 to 2004 (11.5%). Results were concordant with that of microbiological cultures in 90% of the 247 documented cases. Pneumococcal etiology was considered to be definite in 19 patients (isolation of S. pneumoniae from blood, 17 patients; or pleural fluid, two patients), of whom 15 had a positive UAT (sensitivity: 79%); to be probable in 22 patients (positive UAT, 17 patients and/or isolation of S. pneumoniae from respiratory samples, six patients), and was retained in 39 of the 41 patients (positive predictive value: 93.7%). CRP was greater than 100mg/L in 34 of 39 documented patients and lobar alveolar radiographic opacities observed in 25 of 28 documented patients. In 2007, the dramatic increase in the number of UAT prescriptions and the diversification of prescribing units were associated to a decreased positivity rate (8.1%). CONCLUSION Whereas the pneumococcal UAT clearly increases etiological diagnosis, pneumococcal pneumonia cannot be ruled out if negative. Indications for its use need to be refined to improve the cost-effectiveness of this test.
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Affiliation(s)
- C Segonds
- Laboratoire de bactériologie-hygiène, institut fédératif de biologie, hôpital Purpan, CHU de Toulouse, 330, avenue de Grande-Bretagne, TSA 40031, 31059 Toulouse cedex 9, France.
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Weile J, Knabbe C. Current applications and future trends of molecular diagnostics in clinical bacteriology. Anal Bioanal Chem 2009; 394:731-42. [PMID: 19377839 PMCID: PMC7079892 DOI: 10.1007/s00216-009-2779-8] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2008] [Revised: 03/03/2009] [Accepted: 03/30/2009] [Indexed: 01/09/2023]
Abstract
Molecular diagnostics of infectious diseases, in particular, nucleic-acid-based methods, are the fastest growing field in clinical laboratory diagnostics. These applications are stepwise replacing or complementing culture-based, biochemical, and immunological assays in microbiology laboratories. The first-generation nucleic acid assays were monoparametric such as conventional tests, determining only a single parameter. Improvements and new approaches in technology now open the possibility for the development of multiparameter assays using microarrays, multiplex nucleic acid amplification techniques, or mass spectrometry, while the introduction of closed-tube systems has resulted in rapid microbial diagnostics with a subsequently reduced contamination risk. Whereas the first assays were focused on the detection and identification of microbial pathogens, these new technologies paved the way for the parallel determination of multiple antibiotic resistance determinants or to perform microbial epidemiology and surveillance on a genetic level.
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Affiliation(s)
- Jan Weile
- Department of Laboratory Medicine and Molecular Diagnostics, Robert-Bosch-Hospital, Auerbachstrasse 110, 70376, Stuttgart, Germany.
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Brouqui P, Puro V, Fusco FM, Bannister B, Schilling S, Follin P, Gottschalk R, Hemmer R, Maltezou HC, Ott K, Peleman R, Perronne C, Sheehan G, Siikamäki H, Skinhoj P, Ippolito G. Infection control in the management of highly pathogenic infectious diseases: consensus of the European Network of Infectious Disease. THE LANCET. INFECTIOUS DISEASES 2009; 9:301-11. [PMID: 19393960 PMCID: PMC7106353 DOI: 10.1016/s1473-3099(09)70070-2] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The European Network for Infectious Diseases (EUNID) is a network of clinicians, public health epidemiologists, microbiologists, infection control, and critical-care doctors from the European member states, who are experienced in the management of patients with highly infectious diseases. We aim to develop a consensus recommendation for infection control during clinical management and invasive procedures in such patients. After an extensive literature review, draft recommendations were amended jointly by 27 partners from 15 European countries. Recommendations include repetitive training of staff to ascertain infection control, systematic use of cough and respiratory etiquette at admission to the emergency department, fluid sampling in the isolation room, and analyses in biosafety level 3/4 laboratories, and preference for point-of-care bedside laboratory tests. Children should be cared for by paediatricians and intensive-care patients should be cared for by critical-care doctors in high-level isolation units (HLIU). Invasive procedures should be avoided if unnecessary or done in the HLIU, as should chest radiography, ultrasonography, and renal dialysis. Procedures that require transport of patients out of the HLIU should be done during designated sessions or hours in secure transport. Picture archiving and communication systems should be used. Post-mortem examination should be avoided; biopsy or blood collection is preferred.
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Affiliation(s)
- Philippe Brouqui
- Department of Infectious Diseases and Tropical Medicine, CHU Nord and URMITE IRD-CNRS UMR 6236, Marseille, France
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Analytical and clinical sensitivity of the 3M rapid detection influenza A+B assay. J Clin Microbiol 2008; 46:3804-7. [PMID: 18832133 DOI: 10.1128/jcm.01779-08] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The performance of the 3M rapid detection influenza A+B (3M flu) assay was compared to the performance of other immunochromatographic assays. The clinical and analytical performance of the 3M flu assay was superior to that of BinaxNOW and Directigen EZ assays and equivalent to that of the QuickVue assay. The 3M flu assay offers an objective output and direct linkage to laboratory information systems.
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