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van der Westhuizen C, Newton-Foot M, Nel P. Performance comparison of three commercial multiplex molecular panels for respiratory viruses at a South African academic hospital. Afr J Lab Med 2024; 13:2415. [PMID: 39228900 PMCID: PMC11369576 DOI: 10.4102/ajlm.v13i1.2415] [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: 01/24/2024] [Accepted: 05/29/2024] [Indexed: 09/05/2024] Open
Abstract
Background Respiratory infections are a major contributor to hospital admissions. Identification of respiratory pathogens by means of conventional culture and serology methods remains challenging. Multiplex molecular assays are an appealing alternative that endeavours to be rapid, more accurate and less arduous. Objective The study aimed to compare the clinical performance of three commercial multiplex molecular assays for respiratory viruses. Methods Forty-eight respiratory specimens obtained from patients at Tygerberg Hospital in the Western Cape province of South Africa were studied. These specimens were collected between May 2020 and August 2020. The results of the Seegene Anyplex™ II RV16, FilmArray® Respiratory 2.1 plus Panel (FARP), and QIAstat-Dx® Respiratory SARS-CoV-2 Panel (QRP) were analysed based on the overlapping targets. A composite reference standard was applied to provide a standard reference for comparison. Results The overall sensitivity of the Seegene Anyplex™ II RV16 was 96.6% (57/59), the FARP 98.2% (56/57) and the QRP 80.7% (46/57). The overall specificities were 99.8% (660/661), 99.0% (704/711) and 99.7% (709/711), respectively. The QRP failed to detect coronaviruses and parainfluenza viruses in 41.7% (5/12) and 28.6% (4/14) of positive specimens, respectively, while the FARP produced the lowest target specificity of 88.4% (38/43) for rhinovirus/enterovirus. Conclusion The overall specificity of all three platforms was comparable; however, the sensitivity of the QRP was inferior to that of the ARV and FARP. What this study adds This study adds to the body of performance characteristics described for respiratory multiplex panels, especially in the African context where molecular diagnostics for infectious diseases are gaining momentum.
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Affiliation(s)
- Clinton van der Westhuizen
- Division of Medical Microbiology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Department of Medical Microbiology, Tygerberg Hospital, National Health Laboratory Service, Cape Town, South Africa
| | - Mae Newton-Foot
- Division of Medical Microbiology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Department of Medical Microbiology, Tygerberg Hospital, National Health Laboratory Service, Cape Town, South Africa
| | - Pieter Nel
- Division of Medical Microbiology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Department of Medical Microbiology, Tygerberg Hospital, National Health Laboratory Service, Cape Town, South Africa
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Khilnani GC, Tiwari P, Mittal S, Kulkarni AP, Chaudhry D, Zirpe KG, Todi SK, Mohan A, Hegde A, Jagiasi BG, Krishna B, Rodrigues C, Govil D, Pal D, Divatia JV, Sengar M, Gupta M, Desai M, Rungta N, Prayag PS, Bhattacharya PK, Samavedam S, Dixit SB, Sharma S, Bandopadhyay S, Kola VR, Deswal V, Mehta Y, Singh YP, Myatra SN. Guidelines for Antibiotics Prescription in Critically Ill Patients. Indian J Crit Care Med 2024; 28:S104-S216. [PMID: 39234229 PMCID: PMC11369928 DOI: 10.5005/jp-journals-10071-24677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 03/20/2024] [Indexed: 09/06/2024] Open
Abstract
How to cite this article: Khilnani GC, Tiwari P, Mittal S, Kulkarni AP, Chaudhry D, Zirpe KG, et al. Guidelines for Antibiotics Prescription in Critically Ill Patients. Indian J Crit Care Med 2024;28(S2):S104-S216.
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Affiliation(s)
- Gopi C Khilnani
- Department of Pulmonary, Critical Care and Sleep Medicine, PSRI Hospital, New Delhi, India
| | - Pawan Tiwari
- Department of Pulmonary, Critical Care and Sleep Medicine, AIIMS, New Delhi, India
| | - Saurabh Mittal
- Department of Pulmonary, Critical Care and Sleep Medicine, AIIMS, New Delhi, India
| | - Atul P Kulkarni
- Division of Critical Care Medicine, Department of Anaesthesia, Critical Care and Pain, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, Maharashtra, India
| | - Dhruva Chaudhry
- Department of Pulmonary and Critical Care Medicine, University of Health Sciences, Rohtak, Haryana, India
| | - Kapil G Zirpe
- Department of Neuro Trauma Unit, Grant Medical Foundation, Pune, Maharashtra, India
| | - Subhash K Todi
- Department of Critical Care, AMRI Hospital, Kolkata, West Bengal, India
| | - Anant Mohan
- Department of Pulmonary, Critical Care and Sleep Medicine, AIIMS, New Delhi, India
| | - Ashit Hegde
- Department of Medicine & Critical Care, P D Hinduja National Hospital, Mumbai, India
| | - Bharat G Jagiasi
- Department of Critical Care, Kokilaben Dhirubhai Ambani Hospital, Navi Mumbai, Maharashtra, India
| | - Bhuvana Krishna
- Department of Critical Care Medicine, St John's Medical College and Hospital, Bengaluru, India
| | - Camila Rodrigues
- Department of Microbiology, P D Hinduja National Hospital, Mumbai, India
| | - Deepak Govil
- Department of Critical Care and Anesthesia, Medanta – The Medicity, GuruGram, Haryana, India
| | - Divya Pal
- Department of Critical Care and Anesthesia, Medanta – The Medicity, GuruGram, Haryana, India
| | - Jigeeshu V Divatia
- Department of Anaesthesiology, Critical Care and Pain, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, Maharashtra, India
| | - Manju Sengar
- Department of Medical Oncology, Tata Memorial Center, Homi Bhabha National Institute, Mumbai, Maharashtra, India
| | - Mansi Gupta
- Department of Pulmonary Medicine, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Mukesh Desai
- Department of Immunology, Pediatric Hematology and Oncology Bai Jerbai Wadia Hospital for Children, Mumbai, Maharashtra, India
| | - Narendra Rungta
- Department of Critical Care & Anaesthesiology, Rajasthan Hospital, Jaipur, India
| | - Parikshit S Prayag
- Department of Transplant Infectious Diseases, Deenanath Mangeshkar Hospital, Pune, Maharashtra, India
| | - Pradip K Bhattacharya
- Department of Critical Care Medicine, Rajendra Institute of Medical Sciences, Ranchi, Jharkhand, India
| | - Srinivas Samavedam
- Department of Critical Care, Ramdev Rao Hospital, Hyderabad, Telangana, India
| | - Subhal B Dixit
- Department of Critical Care, Sanjeevan and MJM Hospital, Pune, Maharashtra, India
| | - Sudivya Sharma
- Department of Anaesthesiology, Critical Care and Pain, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, Maharashtra, India
| | - Susruta Bandopadhyay
- Department of Critical Care, AMRI Hospitals Salt Lake, Kolkata, West Bengal, India
| | - Venkat R Kola
- Department of Critical Care Medicine, Yashoda Hospitals, Hyderabad, Telangana, India
| | - Vikas Deswal
- Consultant, Infectious Diseases, Medanta - The Medicity, Gurugram, Haryana, India
| | - Yatin Mehta
- Department of Critical Care and Anesthesia, Medanta – The Medicity, GuruGram, Haryana, India
| | - Yogendra P Singh
- Department of Critical Care, Max Super Speciality Hospital, Patparganj, New Delhi, India
| | - Sheila N Myatra
- Department of Anaesthesiology, Critical Care and Pain, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, Maharashtra, India
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Schoffelen T, Papan C, Carrara E, Eljaaly K, Paul M, Keuleyan E, Martin Quirós A, Peiffer-Smadja N, Palos C, May L, Pulia M, Beovic B, Batard E, Resman F, Hulscher M, Schouten J. European society of clinical microbiology and infectious diseases guidelines for antimicrobial stewardship in emergency departments (endorsed by European association of hospital pharmacists). Clin Microbiol Infect 2024:S1198-743X(24)00251-9. [PMID: 39029872 DOI: 10.1016/j.cmi.2024.05.014] [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: 02/29/2024] [Revised: 05/24/2024] [Accepted: 05/26/2024] [Indexed: 07/21/2024]
Abstract
SCOPE This European Society of Clinical Microbiology and Infectious Diseases guideline provides evidence-based recommendations to support a selection of appropriate antibiotic use practices for patients seen in the emergency department (ED) and guidance for their implementation. The topics addressed in this guideline are (a) Do biomarkers or rapid pathogen tests improve antibiotic prescribing and/or clinical outcomes? (b) Does taking blood cultures in common infectious syndromes improve antibiotic prescribing and/or clinical outcomes? (c) Does watchful waiting without antibacterial therapy or with delayed antibiotic prescribing reduce antibiotic prescribing without worsening clinical outcomes in patients with specific infectious syndromes? (d) Do structured culture follow-up programs in patients discharged from the ED with cultures pending improve antibiotic prescribing? METHODS An expert panel was convened by European Society of Clinical Microbiology and Infectious Diseases and the guideline chair. The panel selected in consensus the four most relevant antimicrobial stewardship topics according to pre-defined relevance criteria. For each main question for the four topics, a systematic review was performed, including randomized controlled trials and observational studies. Both clinical outcomes and stewardship process outcomes related to antibiotic use were deemed relevant. The literature searches were conducted between May 2021 and March 2022. In April 2022, the panel members were formally asked to suggest additional studies that were not identified in the initial searches. Data were summarized in a meta-analysis if possible or otherwise summarized narratively. The certainty of the evidence was classified according to the Grading of Recommendations Assessment, Development and Evaluation criteria. The guideline panel reviewed the evidence per topic critically appraising the evidence and formulated recommendations through a consensus-based process. The strength of the recommendations was classified as strong or weak. To substantiate the implementation process, implementation trials or observational studies describing facilitators/barriers for implementation were identified from the same searches and were summarized narratively. RECOMMENDATIONS The recommendations on the use of biomarkers and rapid pathogen diagnostic tests focus on the initiation of antibiotics in patients admitted through the ED. Their effect on the discontinuation or de-escalation of antibiotics during hospital stay was not reported, neither was their effect on hospital infection prevention and control practices. The recommendations on watchful waiting (i.e. withholding antibiotics with some form of follow-up) focus on specific infectious syndromes for which the primary care literature was also included. The recommendations on blood cultures focus on the indication in three common infectious syndromes in the ED explicitly excluding patients with sepsis or septic shock. Most recommendations are based on very low and low certainty of evidence, leading to weak recommendations or, when no evidence was available, to best practice statements. Implementation of these recommendations needs to be adapted to the specific settings and circumstances of the ED. The scarcity of high-quality studies in the area of antimicrobial stewardship in the ED highlights the need for future research in this field.
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Affiliation(s)
- Teske Schoffelen
- Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Internal Medicine, Radboud University Medical Center, Nijmegen, the Netherlands.
| | - Cihan Papan
- Institute for Hygiene and Public Health, University Hospital Bonn, Bonn, Germany; Centre for Infectious Diseases, Institute of Medical Microbiology and Hygiene, Saarland University, Homburg, Germany
| | - Elena Carrara
- Division of Infectious Diseases, Department of Diagnostic and Public Health, University of Verona, Verona, Italy
| | - Khalid Eljaaly
- Department of Pharmacy Practice, College of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia; Department of Pharmacy, King Abdulaziz University Hospital, Jeddah, Saudi Arabia
| | - Mical Paul
- Infectious Diseases, Rambam Health Care Campus, Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Emma Keuleyan
- Department of Clinical Microbiology and Virology, University Hospital Lozenetz, Sofia, Bulgaria; Ministry of Health, Sofia, Bulgaria
| | | | - Nathan Peiffer-Smadja
- Infectious Diseases Department, Bichat-Claude Bernard Hospital, Assistance-Publique Hôpitaux de Paris, Paris, France; Université Paris Cité, INSERM, IAME, Paris, France; National Institute for Health Research, Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, London, UK
| | - Carlos Palos
- Infection Control and Antimicrobial Resistance Committee, Hospital da Luz, Lisbon, Portugal
| | - Larissa May
- Department of Emergency Medicine, University of California Davis, Sacramento, CA, USA
| | - Michael Pulia
- BerbeeWalsh Department of Emergency Medicine, University of Wisconsin Madison School of Medicine and Public Health, Madison, WI, USA
| | - Bojana Beovic
- Faculty of Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Eric Batard
- Emergency Department, CHU Nantes, Nantes, France; Cibles et Médicaments des Infections et du Cancer, IICiMed UR1155, Nantes Université, Nantes, France
| | - Fredrik Resman
- Clinical Infection Medicine, Department of Translational Medicine, Lund University, Malmö, Sweden
| | - Marlies Hulscher
- IQ Health Science Department, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Jeroen Schouten
- Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Intensive Care Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
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Mills DC, Huder JB, Bloemberg GV, Huber M. Comparison of three cartridge-based platforms for syndromic testing for respiratory viruses. Diagn Microbiol Infect Dis 2024; 109:116308. [PMID: 38688147 DOI: 10.1016/j.diagmicrobio.2024.116308] [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: 08/16/2023] [Revised: 04/17/2024] [Accepted: 04/17/2024] [Indexed: 05/02/2024]
Abstract
Syndromic testing, the simultaneous testing for multiple pathogens causing similar symptoms, has recently gained ground in clinical diagnostics. This approach can significantly shorten time to diagnosis and speed up decision-making, leading to an improved outcome for the patient. Here, we compared three automated multiplex PCR platforms for syndromic testing of respiratory samples in a retrospective study, and assessed their relative sensitivities. The PPA between BioFire and QIAstat compared to ePlex was 98.4 % and 93.8 %, respectively, and 6 discrepant results were observed. The BioFire was identified as the platform with the highest relative sensitivity. Overall, the platforms performed similarly and are all suitable for syndromic testing of respiratory samples.
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Affiliation(s)
| | - Jon Barduot Huder
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | | | - Michael Huber
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
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5
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Deng S, Chang W, Liu Q, Zhao Y, Liu J, Wang H. Development and application of multiplex PCR for the rapid identification of four Fusarium spp. associated with Fusarium crown rot in wheat. PeerJ 2024; 12:e17656. [PMID: 38948216 PMCID: PMC11214737 DOI: 10.7717/peerj.17656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 06/08/2024] [Indexed: 07/02/2024] Open
Abstract
Fusarium crown rot (FCR), caused by Fusarium spp., is a devastating disease in wheat growing areas. Previous studies have shown that FCR is caused by co-infection of F. graminearum, F. pseudograminearum, F. proliferatum and F. verticillioides in Hubei Province, China. In this study, a method was developed to simultaneously detected DNAs of F. graminearum, F. pseudograminearum, F. proliferatum and F. verticillioides that can efficiently differentiate them. Whole genome sequence comparison of these four Fusarium spp. was performed and a 20 bp sequence was designed as an universal upstream primer. Specific downstream primers of each pathogen was also designed, which resulted in a 206, 482, 680, and 963 bp amplicon for each pathogen, respectively. Multiplex PCR specifically identified F. graminearum, F. pseudograminearum, F. proliferatum and F. verticillioides but not from other 46 pathogens, and the detection limit of target pathogens is about 100 pg/μl. Moreover, we accurately determined the FCR pathogen species in wheat samples using the optimized multiplex PCR method. These results demonstrate that the multiplex PCR method established in this study can efficiently and rapidly identify F. graminearum, F. pseudograminearum, F. proliferatum, and F. verticillioides, which should provide technical support for timely and targeted prevention and control of FCR.
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Affiliation(s)
- Siyi Deng
- Institute of Plant Protection and Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan, China
- Hubei Key Laboratory of Crop Disease, Insect Pests and Weeds Control, Wuhan, China
- Key Laboratory of Integrated Pest Management on Crops in Central China, Ministry of Agriculture, Wuhan, China
| | - Wei Chang
- Institute of Plant Protection and Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan, China
- Hubei Key Laboratory of Crop Disease, Insect Pests and Weeds Control, Wuhan, China
- Key Laboratory of Integrated Pest Management on Crops in Central China, Ministry of Agriculture, Wuhan, China
| | - Quanke Liu
- General Plant Protection Station of Hubei Province, Wuhan, China
| | - Youfu Zhao
- Department of Plant Pathology, Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, United States
| | - Jun Liu
- Institute of Plant Protection and Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan, China
- Hubei Key Laboratory of Crop Disease, Insect Pests and Weeds Control, Wuhan, China
- Key Laboratory of Integrated Pest Management on Crops in Central China, Ministry of Agriculture, Wuhan, China
| | - Hua Wang
- Institute of Plant Protection and Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan, China
- Hubei Key Laboratory of Crop Disease, Insect Pests and Weeds Control, Wuhan, China
- Key Laboratory of Integrated Pest Management on Crops in Central China, Ministry of Agriculture, Wuhan, China
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6
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Saarela E, Renko M, Uhari M, Pokka T, Kauma H, Ruuska TS. Multiplex PCR for respiratory bacteria in acute care. APMIS 2024; 132:444-451. [PMID: 38482705 DOI: 10.1111/apm.13403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 03/04/2024] [Indexed: 05/09/2024]
Abstract
The purpose of the study was to evaluate the clinical utility of multiplex PCR for detecting bacterial respiratory pathogens in nasopharyngeal samples. Acutely ill adults in the emergency department with respiratory infection symptoms, fever, chest pain or poor general condition were enrolled for this cohort study. Samples were stored at -70 °C until being analysed with multiplex PCR for seven respiratory bacteria. Of the 912 patients enrolled, those with positive bacterial samples (n = 130, 14%) were significantly younger than those with a negative finding (55.5 years vs 62.2 years, p < 0.001), and their mean C-reactive protein (CRP) concentration was higher (110 mg/L vs 59 mg/L, p < 0.0001). Patients with a positive respiratory bacterial finding had a higher probability of pneumonia (35% vs 13%, p < 0.001) and a higher likelihood of receiving a prescription for antibiotics than those with a negative finding (79% vs 59%, p < 0.0001). Positive detection of Streptococcus pneumoniae was associated with a 4.5-fold risk of pneumonia in a multivariate model and detection of an atypical respiratory pathogen with a 9-fold risk. Bacterial PCR performed on nasopharyngeal samples appeared to offer a valuable addition to the diagnostics of infections in adults in acute care.
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Affiliation(s)
- Elina Saarela
- Research Unit of Biomedicine and Internal Medicine, University of Oulu and Medical Research Center Oulu, Oulu University Hospital, Oulu, Finland
| | - Marjo Renko
- Department of Pediatrics, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
- Research Unit of Clinical Medicine, University of Oulu, Oulu, Finland
| | - Matti Uhari
- Research Unit of Clinical Medicine, University of Oulu, Oulu, Finland
| | - Tytti Pokka
- Research Unit of Clinical Medicine, University of Oulu, Oulu, Finland
- Research Service Unit, Oulu University Hospital, Oulu, Finland
| | - Heikki Kauma
- Research Unit of Biomedicine and Internal Medicine, University of Oulu and Medical Research Center Oulu, Oulu University Hospital, Oulu, Finland
| | - Terhi S Ruuska
- Research Unit of Clinical Medicine, University of Oulu, Oulu, Finland
- Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland
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Abbs SE, Armstrong-Buisseret L, Eastwood K, Granier S, Lane A, Lui M, Metcalfe C, Mitchell P, Muir P, Ridd M, Taylor J, Yardley L, Young G, Hay AD. Rapid respiratory microbiological point-of-care-testing and antibiotic prescribing in primary care: Protocol for the RAPID-TEST randomised controlled trial. PLoS One 2024; 19:e0302302. [PMID: 38768129 PMCID: PMC11104596 DOI: 10.1371/journal.pone.0302302] [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: 03/21/2024] [Accepted: 03/28/2024] [Indexed: 05/22/2024] Open
Abstract
BACKGROUND Antibiotics are prescribed for over 50% of respiratory tract infections in primary care, despite good evidence of there being no benefit to the patient, and evidence of over prescribing driving microbial resistance. The high treatment rates are attributed to uncertainty regarding microbiological cause and clinical prognosis. Point-of-care-tests have been proposed as potential antibiotic stewardship tools, with some providing microbiological results in 15 minutes. However, there is little research on their impact on antibiotic use and clinical outcomes in primary care. METHODS This is a multi-centre, individually randomised controlled trial with mixed-methods investigation of microbial, behavioural and antibiotic mechanisms on outcomes in patients aged 12 months and over presenting to primary care in the UK with a suspected respiratory tract infection, where the clinician and/or patient thinks antibiotic treatment may be, or is, necessary. Once consented, all participants are asked to provide a combined nose and throat swab sample and randomised to have a rapid microbiological point-of-care-test or no point-of-care-test. For intervention patients, clinicians review the result of the test, before contacting the patient to finalise treatment. Treatment decisions are made as per usual care in control group patients. The primary outcome is whether an antibiotic is prescribed at this point. All swab samples are sent to the central laboratory for further testing. Patients are asked to complete a diary to record the severity and duration of symptoms until resolution or day 28, and questionnaires at 2 months about their beliefs and intention to consult for similar future illnesses. Primary care medical records are also reviewed at 6-months to collect further infection consultations, antibiotic prescribing and hospital admissions. The trial aims to recruit 514 patients to achieve 90% power with 5% significance to detect a 15% absolute reduction in antibiotic prescribing. Qualitative interviews are being conducted with approximately 20 clinicians and 30 participants to understand any changes in beliefs and behaviour resulting from the point-of-care-test and generate attributes for clinician and patient discrete choice experiments. DISCUSSION This trial will provide evidence of efficacy, acceptability and mechanisms of action of a rapid microbiological point-of-care test on antibiotic prescribing and patient symptoms in primary care. TRIAL REGISTRATION ISRCTN16039192, prospectively registered on 08/11/2022.
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Affiliation(s)
- Samantha Elizabeth Abbs
- Bristol Trials Centre, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | | | | | | | - Athene Lane
- Bristol Trials Centre, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Mandy Lui
- Bristol Trials Centre, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Chris Metcalfe
- Bristol Trials Centre, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Paul Mitchell
- Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Peter Muir
- UKHSA South West Regional Laboratory, Southmead Hospital, Bristol, United Kingdom
| | - Matthew Ridd
- Centre for Academic Primary Care, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Jodi Taylor
- Bristol Trials Centre, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Lucy Yardley
- School of Psychological Science, University of Bristol, Bristol, United Kingdom
- School of Psychology, University of Southampton, Southampton, United Kingdom
| | - Grace Young
- Bristol Trials Centre, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Alastair D. Hay
- Centre for Academic Primary Care, Bristol Medical School, University of Bristol, Bristol, United Kingdom
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8
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Berry GJ, Jhaveri TA, Larkin PMK, Mostafa H, Babady NE. ADLM Guidance Document on Laboratory Diagnosis of Respiratory Viruses. J Appl Lab Med 2024; 9:599-628. [PMID: 38695489 DOI: 10.1093/jalm/jfae010] [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: 01/08/2024] [Accepted: 01/12/2024] [Indexed: 06/06/2024]
Abstract
Respiratory viral infections are among the most frequent infections experienced worldwide. The COVID-19 pandemic has highlighted the need for testing and currently several tests are available for the detection of a wide range of viruses. These tests vary widely in terms of the number of viral pathogens included, viral markers targeted, regulatory status, and turnaround time to results, as well as their analytical and clinical performance. Given these many variables, selection and interpretation of testing requires thoughtful consideration. The current guidance document is the authors' expert opinion based on the preponderance of available evidence to address key questions related to best practices for laboratory diagnosis of respiratory viral infections including who to test, when to test, and what tests to use. An algorithm is proposed to help laboratories decide on the most appropriate tests to use for the diagnosis of respiratory viral infections.
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Affiliation(s)
- Gregory J Berry
- Columbia University Vagelos College of Physicians and Surgeons, New York-Presbyterian-Columbia University Irving Medical Center, New York, NY, United States
| | - Tulip A Jhaveri
- Department of Internal Medicine, Division of Infectious Diseases, University of Mississippi Medical Center, Jackson, MS, United States
| | - Paige M K Larkin
- University of Chicago Pritzker School of Medicine, NorthShore University Health System, Chicago, IL, United States
| | - Heba Mostafa
- Johns Hopkins School of Medicine, Department of Pathology, Baltimore, MD, United States
| | - N Esther Babady
- Clinical Microbiology and Infectious Disease Services, Department of Pathology and Laboratory Medicine and Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, United States
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9
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Liu J, Deng S, Chang W, Yu D, Wang H. Development of a Multiplex PCR Assay for the Detection of Tomato Wilt Caused by Coinfection of Fusarium brachygibbosum, Fusarium oxysporum, and Ralstonia solanacearum Based on Comparative Genomics. PLANT DISEASE 2024; 108:1128-1138. [PMID: 37953228 DOI: 10.1094/pdis-05-23-0962-sr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2023]
Abstract
Tomato is consumed worldwide as fresh or processed food products. However, soilborne diseases of tomato plants caused by coinfection of various pathogens result in great economic losses to the tomato industry. It is difficult to accurately identify and diagnose soilborne diseases of tomato plants caused by pathogen complexes. In this study, we investigated field diseases of tomato plants by pathogen isolation and molecular identification and found that tomato wilt was caused by coinfection of Fusarium brachygibbosum, F. oxysporum, and Ralstonia solanacearum. Therefore, developing a method for simultaneous detection of DNA from F. brachygibbosum, F. oxysporum, and R. solanacearum is of great importance to efficiently and accurately monitor disease development at different growth stages of tomato plants. In this study, we performed a comparative genomic analysis of F. brachygibbosum, F. oxysporum, and R. solanacearum and determined the primer sets for simultaneous detection of DNA from these target pathogens. Then, we tested the reagent and condition parameters of multiplex PCR, including primers, dNTP and Mg2+ concentrations, and annealing temperatures, to determine the optimal parameters of a multiplex PCR system. We evaluated the specificity, sensitivity, and stability of the multiplex PCR system based on the optimized reaction conditions. The multiplex PCR system can specifically identify 13 target pathogens from 57 different fungal and bacterial pathogens, at the lower detection limit of the three target pathogens at concentrations of 100 pg/μl. In addition, we can accurately identify the three pathogens in tomato plants using the optimized multiplex PCR method. These results demonstrated that the multiplex PCR method developed in this study can simultaneously detect DNA from F. brachygibbosum, F. oxysporum, and R. solanacearum in a single PCR system to accurately identify and diagnose the pathogen causing tomato wilt.
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Affiliation(s)
- Jun Liu
- Institute of Plant Protection and Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
- Hubei Key Laboratory of Crop Disease, Insect Pests and Weeds Control, Wuhan 430064, China
- Key Laboratory of Integrated Pest Management on Crops in Central China, Ministry of Agriculture, Wuhan 430064, China
| | - Siyi Deng
- Institute of Plant Protection and Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
- Hubei Key Laboratory of Crop Disease, Insect Pests and Weeds Control, Wuhan 430064, China
- Key Laboratory of Integrated Pest Management on Crops in Central China, Ministry of Agriculture, Wuhan 430064, China
| | - Wei Chang
- Institute of Plant Protection and Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
- Hubei Key Laboratory of Crop Disease, Insect Pests and Weeds Control, Wuhan 430064, China
- Key Laboratory of Integrated Pest Management on Crops in Central China, Ministry of Agriculture, Wuhan 430064, China
| | - Dazhao Yu
- Institute of Plant Protection and Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
- Hubei Key Laboratory of Crop Disease, Insect Pests and Weeds Control, Wuhan 430064, China
- Key Laboratory of Integrated Pest Management on Crops in Central China, Ministry of Agriculture, Wuhan 430064, China
| | - Hua Wang
- Institute of Plant Protection and Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
- Hubei Key Laboratory of Crop Disease, Insect Pests and Weeds Control, Wuhan 430064, China
- Key Laboratory of Integrated Pest Management on Crops in Central China, Ministry of Agriculture, Wuhan 430064, China
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10
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Sapozhnikov J, Albarillo FS, Pulia MS. Optimizing Antimicrobial Stewardship in the Emergency Department. Emerg Med Clin North Am 2024; 42:443-459. [PMID: 38641398 DOI: 10.1016/j.emc.2024.02.003] [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] [Indexed: 04/21/2024]
Abstract
Antibiotic stewardship is a core component of emergency department (ED) practice and impacts patient safety, clinical outcomes, and public health. The unique characteristics of ED practice, including crowding, time pressure, and diagnostic uncertainty, need to be considered when implementing antibiotic stewardship interventions in this setting. Rapid advances in pathogen detection and host response biomarkers promise to revolutionize the diagnosis of infectious diseases in the ED, but such tests are not yet considered standard of care. Presently, clinical decision support embedded in the electronic health record and pharmacist-led interventions are the most effective ways to improve antibiotic prescribing in the ED.
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Affiliation(s)
- Julia Sapozhnikov
- Medical Science Liaison, Karius Inc, 975 Island Drive, Redwood City, CA 94065, USA
| | - Fritzie S Albarillo
- Department of Medicine, Infectious Diseases Division, Loyola University Medical Center, Loyola University Medical Center is 2160 South First Avenue, Maywood, IL 60153, USA
| | - Michael S Pulia
- BerbeeWalsh Department of Emergency Medicine, University of Wisconsin School of Medicine and Public Health, 800 University Bay Drive, Suite 300, Madison, WI 53705, USA.
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11
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Levin S, Mayer D, Puius YA, Arora S, Gileles-Hillel A. Things We Do for No Reason™: Routine respiratory pathogen panels for emergency department and hospitalized patients. J Hosp Med 2024. [PMID: 38599820 DOI: 10.1002/jhm.13365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 03/20/2024] [Accepted: 03/31/2024] [Indexed: 04/12/2024]
Affiliation(s)
- Samara Levin
- Division of General Internal Medicine, Section of Hospital Medicine, Weill Cornell Medicine, New York, New York, USA
| | - David Mayer
- Pediatric Division, Hadassah Medical Center, & Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | - Yoram A Puius
- Division of Infectious Diseases, Department of Internal Medicine, Montefiore Medical Center, Bronx, New York, USA
| | - Shitij Arora
- Division of Hospital Medicine, Department of Internal Medicine, Montefiore Medical Center, Bronx, New York, USA
| | - Alex Gileles-Hillel
- Pediatric Division, Hadassah Medical Center, & Faculty of Medicine, The Hebrew University, Jerusalem, Israel
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12
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Lu J, Butler-Wu SM. Home and Clinical Laboratory Improvement Amendments-Waived Testing for Infectious Diseases-How Do These Fit in the Testing Landscape? Clin Lab Med 2024; 44:13-21. [PMID: 38280794 DOI: 10.1016/j.cll.2023.10.005] [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] [Indexed: 01/29/2024]
Abstract
Though testing for infectious diseases has long been performed in traditional clincial laboratory settings, more widespread availability of waived testing is expanding accessibility of patients to rapid test results. This is being further expanded to home testing. Nevertheless, with this greater democratization and availability of clinical testing there are important limitations that need to be balanced. In this article, we review the current test landscape for infectious diseases waived testing and opportunities for assuring optimal quality testing.
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Affiliation(s)
- Jacky Lu
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, 4650 Sunset Boulevard, Los Angeles, CA 90027, USA
| | - Susan M Butler-Wu
- Department of Pathology, Keck School of Medicine of the University of Southern California, HMR 211, 2011 Zonal Avenue, Los Angeles, CA 90033, USA.
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13
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Matic N, Lawson T, Ritchie G, Lowe CF, Romney MG. Testing the limits of multiplex respiratory virus assays for SARS-CoV-2 at high cycle threshold values: Comparative performance of cobas 6800/8800 SARS-CoV-2 & Influenza A/B, Xpert Xpress SARS-CoV-2/Flu/RSV, and cobas Liat SARS-CoV-2 & Influenza A/B. JOURNAL OF THE ASSOCIATION OF MEDICAL MICROBIOLOGY AND INFECTIOUS DISEASE CANADA = JOURNAL OFFICIEL DE L'ASSOCIATION POUR LA MICROBIOLOGIE MEDICALE ET L'INFECTIOLOGIE CANADA 2024; 8:328-335. [PMID: 38250621 PMCID: PMC10797767 DOI: 10.3138/jammi-2022-0039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 03/21/2023] [Accepted: 03/26/2023] [Indexed: 01/23/2024]
Abstract
Background Multiplex real-time RT-PCR assays for respiratory pathogens are valuable tools to optimize laboratory workflow and turnaround time. At a time when resurgence of influenza and respiratory syncytial virus (RSV) cases have been widely observed along with continued transmission of SARS-CoV-2, timely identification of all circulating respiratory viruses is crucial. This study evaluates the detection of low viral loads of SARS-CoV-2 by four multiplex molecular assays: Roche cobas 6800/8800 SARS-CoV-2 & Influenza A/B Test, Cepheid Xpert Xpress SARS-CoV-2/Flu/RSV, cobas Liat SARS-CoV-2 & Influenza A/B, and a laboratory-developed test (LDT). Methods Retrospective upper respiratory tract specimens positive for various respiratory viruses at a range of cycle threshold (Ct) values (18-40) were tested by four multiplex assays. Positive and negative percent agreement (PPA and NPA) with validated RT-PCR assays were calculated. Results A total of 82 samples were assessed, with discordant results observed in a portion of the samples (10/82, 12.2%) where Ct values were >33. The majority of the discordant results (6/10, 60%) were false negatives. Overall, PPA was 100% (58/58) for cobas 6800, 97.4% (38/39) for GeneXpert, 100% (17/17) for Liat, and 90.5% (57/63) for the LDT. PPA for the LDT increased to 92.1% after manual review of amplification curves. Conclusions Commercial multiplex respiratory virus assays have good performance for samples with medium to high viral loads (Ct values <33). Laboratories should consider appropriate test result review and confirmation protocols to optimize sensitivity, and may consider reporting samples with additional interpretive comments when low viral loads are detected.
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Affiliation(s)
- Nancy Matic
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Tanya Lawson
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
| | - Gordon Ritchie
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Christopher F Lowe
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Marc G Romney
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
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14
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Bergese S, Fox B, García-Allende N, Elisiri ME, Schneider AE, Ruiz J, Gonzalez-Fraga S, Rodriguez V, Fernandez-Canigia L. Impact of the multiplex molecular FilmArray Respiratory Panel on antibiotic prescription and clinical management of immunocompromised adults with suspected acute respiratory tract infections: A retrospective before-after study. Rev Argent Microbiol 2023; 55:337-344. [PMID: 37127474 DOI: 10.1016/j.ram.2023.03.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 12/17/2022] [Accepted: 03/27/2023] [Indexed: 05/03/2023] Open
Abstract
This study aimed to assess the impact of the implementation of a rapid multiplex molecular FilmArray Respiratory Panel (FRP) on the medical management of immunocompromised patients from a community general hospital. We conducted a single-center, retrospective, and before-after study. Two periods were evaluated: before the implementation of the FRP (pre-FRP) from April 2017 to May 2018 and after the implementation of the FRP (post-FRP) from January to July 2019. The inclusion criteria were immunocompromised patients over 18 years of age with suspected acute respiratory illness tested by conventional diagnostic methods (pre-FRP) or the FilmArray™ Respiratory Panel v1.7 (post-FRP). A total of 142 patients were included, 64 patients in the pre-FRP and 78 patients in the post-FRP. The positive detection rate was significantly higher in the post-FRP (63% vs. 10%, p<0.01). There were more patients receiving antimicrobial treatment in the pre-FRP compared with the post-FRP period (94% vs. 68%, p<0.01). A decrease in beta-lactam (89% vs. 61%, p<0.01) and macrolide (44% vs. 13%, p<0.01) prescriptions were observed in the post-FRP. No differences were observed in oseltamivir use (22% vs. 13%, p=0.14), changes in antimicrobial treatment, hospital admission rate, days-reduction in droplet isolation precautions, hospital length of stay (LOS), admission to intensive care unit (ICU), LOS in ICU, treatment failure and 30-day mortality. The implementation of the FRP impacted patient care by improving diagnostic yield and optimizing antimicrobial treatment in immunocompromised adult patients.
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Affiliation(s)
- Silvina Bergese
- Sector de Microbiología, Laboratorio Central Hospital Alemán, Ciudad de Buenos Aires, Argentina.
| | - Bárbara Fox
- Sector de Microbiología, Laboratorio Central Hospital Alemán, Ciudad de Buenos Aires, Argentina
| | - Natalia García-Allende
- Servicio de Infectología y Epidemiología Hospitalaria, Hospital Alemán, Ciudad de Buenos Aires, Argentina
| | - María Elisa Elisiri
- Sector de Microbiología, Laboratorio Central Hospital Alemán, Ciudad de Buenos Aires, Argentina
| | - Ana Elizabeth Schneider
- Sector de Microbiología, Laboratorio Central Hospital Alemán, Ciudad de Buenos Aires, Argentina
| | - Juan Ruiz
- Servicio de Clínica Médica, Hospital Alemán, Ciudad Autónoma de Buenos Aires, Argentina
| | - Sol Gonzalez-Fraga
- Sector de Microbiología, Laboratorio Central Hospital Alemán, Ciudad de Buenos Aires, Argentina
| | - Viviana Rodriguez
- Servicio de Infectología y Epidemiología Hospitalaria, Hospital Alemán, Ciudad de Buenos Aires, Argentina
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15
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Lissajoux A, Denis B, Gault E, Pépin M, Herr M, Duran C, Teillet L, Lechowski L, Dinh A. Real-life impact of respiratory panel PCR assay on antibiotic prescription in geriatric acute care in the pre-COVID-19 era. Infect Dis Now 2023; 53:104737. [PMID: 37331699 PMCID: PMC10275648 DOI: 10.1016/j.idnow.2023.104737] [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: 04/10/2023] [Revised: 05/30/2023] [Accepted: 06/10/2023] [Indexed: 06/20/2023]
Abstract
OBJECTIVES In this era of bacterial resistance, avoiding inappropriate use of antibiotic treatments is of major importance. Respiratory tract infections are frequent among older patients, and differentiating viral from bacterial infections is a challenge. The aim of our study was to evaluate the impact of recently available respiratory PCR testing on antimicrobial prescription in geriatric acute care. METHODS We performed a retrospective study, including all hospitalized geriatric patients who had had multiplex respiratory PCR testing prescribed from 1st October 2018 to 30th September 2019. The PCR test comprised a respiratory viral panel (RVP) and a respiratory bacterial panel (RBP). PCR testing could be prescribed at any time during hospitalization by geriatricians. Our primary endpoint was antibiotic prescription after viral multiplex PCR testing results. RESULTS All in all, 193 patients were included, 88 (45.6%) of whom had positive RVP, while none had positive RBP. Patients with positive RVP had significantly fewer antibiotic prescriptions following test results than patients with negative RVP (odds ratio (OR) 0.41, 95% confidence interval (CI) 0.22-0.77; p = 0.004). Among positive-RVP patients, factors associated with antibiotic continuation were presence of radiological infiltrate (OR 12.02, 95%CI 3.07-30.29), and detected Respiratory Syncytial Virus (OR 7.54, 95%CI 1.74-32.65). That said, discontinuation of antibiotic treatment seems safe. CONCLUSION In this population, the impact of viral detection by respiratory multiplex PCR on antibiotic therapy was low. It could be optimized by means of clearly formulated local guidelines, qualified staff and specific training by infectious disease specialists. Cost-effectiveness studies are necessary.
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Affiliation(s)
- Agathe Lissajoux
- Geriatric Unit, Sainte-Périne Hospital, AP-HP Paris Saclay University, Paris, France
| | - Bertrand Denis
- Geriatric Unit, Sainte-Périne Hospital, AP-HP Paris Saclay University, Paris, France
| | - Elyanne Gault
- Université de Versailles Saint-Quentin-en-Yvelines, Université de Paris Saclay, INSERM U1173, APHP, Ambroise Paré Hospital, Department of Microbiology, Boulogne-Billancourt, France
| | - Marion Pépin
- Acute Geriatric Unit, Ambroise-Paré University Hospital, AP-HP Paris Saclay University, Boulogne-Billancourt, France
| | - Marie Herr
- Epidemiology and Public Health Department, AP-HP Université Paris-Saclay, Raymond-Poincaré Hospital, Garches 92380, France
| | - Clara Duran
- Infectious Disease Department, Raymond-Poincaré University Hospital, AP-HP Paris Saclay University, Garches, France
| | - Laurent Teillet
- Acute Geriatric Unit, Ambroise-Paré University Hospital, AP-HP Paris Saclay University, Boulogne-Billancourt, France
| | - Laurent Lechowski
- Geriatric Unit, Sainte-Périne Hospital, AP-HP Paris Saclay University, Paris, France
| | - Aurélien Dinh
- Infectious Disease Department, Raymond-Poincaré University Hospital, AP-HP Paris Saclay University, Garches, France.
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16
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Upadhyay P, Reddy J, Proctor T, Sorel O, Veereshlingam H, Gandhi M, Wang X, Singh V. Expanded PCR Panel Testing for Identification of Respiratory Pathogens and Coinfections in Influenza-like Illness. Diagnostics (Basel) 2023; 13:2014. [PMID: 37370910 DOI: 10.3390/diagnostics13122014] [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: 05/16/2023] [Revised: 05/30/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
While COVID-19 has dominated Influenza-like illness (ILI) over the past few years, there are many other pathogens responsible for ILI. It is not uncommon to have coinfections with multiple pathogens in patients with ILI. The goal of this study was to identify the different organisms in symptomatic patients presenting with ILI using two different high throughput multiplex real time PCR platforms. Specimens were collected from 381 subjects presenting with ILI symptoms. All samples (nasal and nasopharyngeal swabs) were simultaneously tested on two expanded panel PCR platforms: Applied Biosystems™ TrueMark™ Respiratory Panel 2.0, OpenArray™ plate (OA) (32 viral and bacterial targets); and Applied Biosystems™ TrueMark™ Respiratory Panel 2.0, TaqMan™ Array card (TAC) (41 viral, fungal, and bacterial targets). Results were analyzed for concordance between the platforms and for identification of organisms responsible for the clinical presentation including possible coinfections. Very good agreement was observed between the two PCR platforms with 100% agreement for 12 viral and 3 bacterial pathogens. Of 381 specimens, approximately 58% of the samples showed the presence of at least one organism with an important incidence of co-infections (~36-40% of positive samples tested positive for two and more organisms). S. aureus was the most prevalent detected pathogen (~30%) followed by SARS-CoV-2 (~25%), Rhinovirus (~15%) and HHV6 (~10%). Co-infections between viruses and bacteria were the most common (~69%), followed by viral-viral (~23%) and bacterial-bacterial (~7%) co-infections. These results showed that coinfections are common in RTIs suggesting that syndromic panel based multiplex PCR tests could enable the identification of pathogens contributing to coinfections, help guide patient management thereby improving clinical outcomes and supporting antimicrobial stewardship.
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Affiliation(s)
| | - Jairus Reddy
- HealthTrackRx R&D Division, Denton, TX 76207, USA
| | - Teddie Proctor
- Thermo Fisher Scientific, 180 Oyster Point Blvd, South San Francisco, CA 94080, USA
| | - Oceane Sorel
- Thermo Fisher Scientific, 180 Oyster Point Blvd, South San Francisco, CA 94080, USA
| | - Harita Veereshlingam
- Thermo Fisher Scientific, 180 Oyster Point Blvd, South San Francisco, CA 94080, USA
| | - Manoj Gandhi
- Thermo Fisher Scientific, 180 Oyster Point Blvd, South San Francisco, CA 94080, USA
| | - Xuemei Wang
- Thermo Fisher Scientific, 180 Oyster Point Blvd, South San Francisco, CA 94080, USA
| | - Vijay Singh
- HealthTrackRx R&D Division, Denton, TX 76207, USA
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17
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Zhang J, Yang T, Zou M, Wang L, Sai L. The epidemiological features of respiratory tract infection using the multiplex panels detection during COVID-19 pandemic in Shandong province, China. Sci Rep 2023; 13:6319. [PMID: 37072619 PMCID: PMC10112310 DOI: 10.1038/s41598-023-33627-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 04/16/2023] [Indexed: 05/03/2023] Open
Abstract
Respiratory tract infection is one of the most common reasons for both morbidity and mortality worldwide. High attention has been paid to the etiological tracing of respiratory tract infection since the advent of COVID-19. In this study, we aimed to evaluate the epidemiological features of pathogens in respiratory tract infection, especially during COVID-19 pandemic. A total of 7668 patients with respiratory tract infection who admitted to Qilu Hospital of Shandong University from March 2019 to Dec 2021 were retrospectively included. The respiratory tract specimens were detected using a commercial multiplex PCR-based panel assay for common respiratory pathogens including influenza A virus (Flu-A), influenza A virus H1N1 (H1N1), influenza A virus H3N2 (H3N2), influenza B virus (Flu-B), parainfluenza virus (PIV), respiratory syncytial virus (RSV), adenovirus (ADV), Boca virus (Boca), human Rhinovirus (HRV), Metapneumovirus (MPV), Coronavirus (COV), Mycoplasma pneumoniae (MP), and Chlamydia (Ch). The positive rates were compared using a chi-square test. Compared with 2019, the positive rate of pathogen detection during from January 2020 to December 2021 was significantly lower, especially the detection of Flu-A. The positive rate of respiratory pathogen strains was 40.18% during COVID-19 pandemic, and a total of 297 cases (4.69%) of mixed infection with two or more pathogens were detected. There was no statistical difference in the positive rate between male and female patients. However, the positive rates of infection were different among different age groups, with higher incidence of RSV in infancy and toddler group, and MP infection in children and teenager group. While, HRV was the most common pathogen in the adult patients. Moreover, Flu-A and Flu-B were higher in winter, and MP and RSV were higher in spring, autumn and winter. The pathogens such as ADV, BOCA, PIV, and COV were detected without significant seasonal distribution. In conclusion, respiratory pathogen infection rates may vary by age and season, regardless of gender. During the COVID-19 epidemic, blocking transmission routes could help reduce the incidence of respiratory tract infection. The current prevalence of respiratory tract infection pathogens is of great significance for clinical prevention, diagnosis and treatment.
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Affiliation(s)
- Jie Zhang
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, 107 Wenhuaxi Road, Jinan, 250012, Shandong, China
- Shandong Engineering Research Center of Biomarker and Artificial Intelligence Application, Jinan, Shandong, China
| | - Tao Yang
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, 107 Wenhuaxi Road, Jinan, 250012, Shandong, China
| | - Mingjin Zou
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, 107 Wenhuaxi Road, Jinan, 250012, Shandong, China
| | - Lili Wang
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, 107 Wenhuaxi Road, Jinan, 250012, Shandong, China.
- Shandong Engineering Research Center of Biomarker and Artificial Intelligence Application, Jinan, Shandong, China.
| | - Lintao Sai
- Department of Infectious Diseases, Qilu Hospital of Shandong University, Jinan, Shandong, China.
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18
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Rapid Multiplex PCR for Respiratory Viruses Reduces Time to Result and Improves Clinical Care: Results of a Systematic Review and Meta-Analysis. J Infect 2023; 86:462-475. [PMID: 36906153 DOI: 10.1016/j.jinf.2023.03.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 02/23/2023] [Accepted: 03/02/2023] [Indexed: 03/13/2023]
Abstract
OBJECTIVES The clinical impact of rapid sample-to-answer 'syndromic' multiplex polymerase chain reaction (PCR) testing for respiratory viruses is not clearly established. We performed a systematic literature review and meta-analysis to evaluate this impact for patients with possible acute respiratory tract infection in the hospital setting. METHODS We searched EMBASE, MEDLINE, and Cochrane databases from 2012 to present and conference proceedings from 2021 for studies comparing clinical impact outcomes between multiplex PCR testing and standard testing. RESULTS Twenty-seven studies with 17,321 patient encounters were included in this review. Rapid multiplex PCR testing was associated with a reduction of -24.22hours (95% CI -28.70 to -19.74hours) in the time to results. Hospital length of stay was decreased by -0.82 days (95% CI -1.52 to -0.11 days). Among influenza positive patients, antivirals were more likely to be given (RR 1.25, 95% CI 1.06 to 1.48) and appropriate infection control facility use was more common with rapid multiplex PCR testing (RR 1.55, 95% CI 1.16 to 2.07). CONCLUSIONS Our systematic review and meta-analysis demonstrates a reduction in time to results and length of stay for patients overall along with improvements in appropriate antiviral and infection control management among influenza positive patients. This evidence supports the routine use of rapid sample-to-answer multiplex PCR testing for respiratory viruses in the hospital setting.
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19
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Antimicrobial Stewardship Techniques for Critically Ill Patients with Pneumonia. Antibiotics (Basel) 2023; 12:antibiotics12020295. [PMID: 36830205 PMCID: PMC9952097 DOI: 10.3390/antibiotics12020295] [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: 12/30/2022] [Revised: 01/24/2023] [Accepted: 01/27/2023] [Indexed: 02/04/2023] Open
Abstract
Pneumonia is common in the intensive care unit (ICU), infecting 27% of all critically ill patients. Given the high prevalence of this disease state in the ICU, optimizing antimicrobial therapy while minimizing toxicities is of utmost importance. Inappropriate antimicrobial use can increase the risk of antimicrobial resistance, Clostridiodes difficile infection, allergic reaction, and other complications from antimicrobial use (e.g., QTc prolongation, thrombocytopenia). This review article aims to discuss methods to optimize antimicrobial treatment in patients with pneumonia, including the following: procalcitonin use, utilization of methicillin-resistant Staphylococcus aureus nares testing to determine need for vancomycin therapy, utilization of the Biofire® FilmArray® pneumonia polymerase chain reaction (PCR), and microbiology reporting techniques.
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20
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Measuring clinical outcomes of highly multiplex molecular diagnostics for respiratory infections: A systematic review and conceptual framework. ANTIMICROBIAL STEWARDSHIP & HEALTHCARE EPIDEMIOLOGY : ASHE 2023; 3:e9. [PMID: 36714285 PMCID: PMC9879901 DOI: 10.1017/ash.2022.362] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 11/22/2022] [Accepted: 11/26/2022] [Indexed: 01/11/2023]
Abstract
Objectives To review methodologies and outcomes reporting among these studies and to develop a conceptual framework of outcomes to assist in guiding studies and production of clinical metrics. Data sources PubMed and Embase from January 1, 2012, thru December 1, 2021. Study eligibility criteria Studies evaluating highly multiplex molecular respiratory diagnostics and their impact on either clinical or economic outcomes. Methods A systematic literature review (SLR) of methodologies and outcomes reporting was performed. A qualitative synthesis of identified SLRs and associated primary studies was conducted to develop conceptual framework for outcomes. Results Ultimately, 4 systemic literature reviews and their 12 associated primary studies were selected for review. Most primary studies included patient outcomes focusing on antimicrobial exposure changes such as antibiotic (80%) and antiviral use (50%) or occupancy changes such as hospital length of stay (60%). Economic outcomes were infrequently reported, and societal outcomes, such as antibiotic resistance impact, were absent from the reviewed literature. Qualitative evidence synthesis of reported outcomes yielded a conceptual framework of outcomes to include operational, patient, economic, and societal domains. Conclusions Our review highlights the significant heterogeneity in outcomes reporting among clinical impact studies for highly multiplex molecular respiratory diagnostics. Furthermore, we developed a conceptual framework of outcomes domains that may act as a guide to improve considerations in outcomes selection and reporting when evaluating clinical impact of these tests. These improvements may be important in synthesizing the evidence for informing clinical decision making, guidelines, and financial reimbursement.
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21
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Relich RF, Abbott AN. Syndromic and Point-of-Care Molecular Testing. Clin Lab Med 2022; 42:507-531. [PMID: 36368779 DOI: 10.1016/j.cll.2022.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ryan F Relich
- Division of Clinical Microbiology, Indiana University Health Pathology Laboratory, Indiana University Health and Indiana University School of Medicine, Suite 6027E, 350 West 11th Street, Indianapolis, IN 46202, USA.
| | - April N Abbott
- Department of Laboratory Medicine, Deaconess Hospital, 600 Mary Street, Evansville, IN 47747, USA
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22
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Bibby HL, de Koning L, Seiden-Long I, Zelyas N, Church DL, Berenger BM. A pragmatic randomized controlled trial of rapid on-site influenza and respiratory syncytial virus PCR testing in paediatric and adult populations. BMC Infect Dis 2022; 22:854. [PMID: 36384484 PMCID: PMC9667852 DOI: 10.1186/s12879-022-07796-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 10/14/2022] [Indexed: 11/17/2022] Open
Abstract
Background Rapid/point-of-care respiratory virus nucleic acid tests (NAT) may improve oseltamivir, antibiotic, diagnostic test, and hospital bed utilization. Previous randomized controlled trials (RCT) on this topic have not used standard procedures of an accredited healthcare and laboratory system. Methods We conducted a parallel RCT at two hospitals [paediatric = Alberta Children’s Hospital (ACH); primarily adult = Peter Lougheed Centre (PLC)]. Patients with a respiratory viral testing order were randomized to testing at either a central accredited laboratory (standard arm) or with a rapid polymerase chain reaction test at an on-site accredited laboratory followed by standard testing [rapid on-site test (ROST) arm] based on day of specimen receipt at the laboratory. Patients and clinicians were blinded to assignment. The primary outcome for ACH was inpatient length of stay (LOS) and for PLC was the proportion of inpatients prescribed oseltamivir. Results 706 patient encounters were included at ACH; 322 assigned to ROST (181 inpatients) and 384 to the standard arm (194 inpatients). 422 patient encounters were included at PLC; 200 assigned to ROST (157 inpatients) and 222 to the standard arm (175 inpatients). The rate of oseltamivir prescription and number of doses given was reduced in PLC inpatients negative for influenza in the ROST arm compared to standard arm [mean 14.9% (95% CI 9.87–21.9) vs. 27.5% (21.0–35.2), p = 0.0135; mean 2.85 doses (SEM 2.39–3.32) vs. 4.17 doses (3.85–4.49) p = 0.022, respectively]. ROST also significantly reduced oseltamivir use at ACH, reduced chest radiographs (ACH), and laboratory test ordering (PLC), but not antibiotic prescriptions. ROST also reduced the median turnaround time by > 24 h (ACH and PLC). The LOS at ACH was not significantly different between the ROST and standard arms [median 4.05 days (SEM 1.79–18.2) vs 4.89 days (2.07–22.9), p = 0.062, respectively]. No adverse events were reported. Conclusions In a RCT representing implementation of ROST in an accredited laboratory system, we found that a ROST improved oseltamivir utilization and is the first RCT to show reduced ancillary testing in both paediatric and adult populations. A larger study is required to assess reduction in paediatric LOS as ACH was underpowered. These findings help justify the implementation of rapid on-site respiratory virus testing for inpatients. Trial registration ISRCTN, number 10110119, Retrospectively Registered, 01/12/2021. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-022-07796-3.
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Huang H, Huang K, Sun Y, Luo D, Wang M, Chen T, Li M, Duan J, Huang L, Dong C. A Digital Microfluidic RT-qPCR Platform for Multiple Detections of Respiratory Pathogens. MICROMACHINES 2022; 13:mi13101650. [PMID: 36296002 PMCID: PMC9611846 DOI: 10.3390/mi13101650] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/24/2022] [Accepted: 09/27/2022] [Indexed: 05/30/2023]
Abstract
The coronavirus disease 2019 pandemic has spread worldwide and caused more than six million deaths globally. Therefore, a timely and accurate diagnosis method is of pivotal importance for controlling the dissemination and expansions. Nucleic acid detection by the reverse transcription-polymerase chain reaction (RT-PCR) method generally requires centralized diagnosis laboratories and skilled operators, significantly restricting its use in rural areas and field settings. The digital microfluidic (DMF) technique provides a better option for simultaneous detections of multiple pathogens with fewer specimens and easy operation. In this study, we developed a novel digital microfluidic RT-qPCR platform for multiple detections of respiratory pathogens. This method can simultaneously detect eleven respiratory pathogens, namely, mycoplasma pneumoniae (MP), chlamydophila pneumoniae (CP), streptococcus pneumoniae (SP), human respiratory syncytial virus A (RSVA), human adenovirus (ADV), human coronavirus (HKU1), human coronavirus 229E (HCoV-229E), human metapneumovirus (HMPV), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza A virus (FLUA) and influenza B virus (FLUB). The diagnostic performance was evaluated using positive plasmids samples and clinical specimens compared with off-chip individual RT-PCR testing. The results showed that the limit of detections was around 12 to 150 copies per test. The true positive rate, true negative rate, positive predictive value, negative predictive value, and accuracy of DMF on-chip method were 93.33%, 100%, 100%, 99.56%, and 99.85%, respectively, as validated by the off-chip RT-qPCR counterpart. Collectively, this study reported a cost-effective, high sensitivity and specificity on-chip DMF RT-qPCR system for detecting multiple respiratory pathogens, which will greatly contribute to timely and effective clinical management of respiratory infections in medical resource-limited settings.
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Affiliation(s)
- Huitao Huang
- Zhuhai Center for Disease Control and Prevention, Zhuhai 519087, China
| | - Kaisong Huang
- Zhuhai Center for Disease Control and Prevention, Zhuhai 519087, China
| | - Yun Sun
- Digifluidic Biotech Ltd., Zhuhai 519000, China
| | - Dasheng Luo
- Digifluidic Biotech Ltd., Zhuhai 519000, China
| | - Min Wang
- Digifluidic Biotech Ltd., Zhuhai 519000, China
| | - Tianlan Chen
- Digifluidic Biotech Ltd., Zhuhai 519000, China
- Guangzhou Nansha IT Park Postdoctoral Programme, Guangzhou 511466, China
| | - Mingzhong Li
- State Key Laboratory of Analog and Mixed-Signal VLSI, University of Macau, Macao 999078, China
| | - Junwei Duan
- College of Information Science and Technology, Jinan University, Guangzhou 510632, China
| | - Liqun Huang
- Zhuhai Center for Disease Control and Prevention, Zhuhai 519087, China
| | - Cheng Dong
- School of Intelligent Systems Science and Engineering/JNU-Industry School of Artificial Intelligence, Jinan University, Zhuhai 519000, China
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Calderaro A, Buttrini M, Farina B, Montecchini S, De Conto F, Chezzi C. Respiratory Tract Infections and Laboratory Diagnostic Methods: A Review with A Focus on Syndromic Panel-Based Assays. Microorganisms 2022; 10:microorganisms10091856. [PMID: 36144458 PMCID: PMC9504108 DOI: 10.3390/microorganisms10091856] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 08/20/2022] [Accepted: 09/11/2022] [Indexed: 11/16/2022] Open
Abstract
Respiratory tract infections (RTIs) are the focus of developments in public health, given their widespread distribution and the high morbidity and mortality rates reported worldwide. The clinical spectrum ranges from asymptomatic or mild infection to severe or fatal disease. Rapidity is required in diagnostics to provide adequate and prompt management of patients. The current algorithm for the laboratory diagnosis of RTIs relies on multiple approaches including gold-standard conventional methods, among which the traditional culture is the most used, and innovative ones such as molecular methods, mostly used to detect viruses and atypical bacteria. The implementation of molecular methods with syndromic panels has the potential to be a powerful decision-making tool for patient management despite requiring appropriate use of the test in different patient populations. Their use radically reduces time-to-results and increases the detection of clinically relevant pathogens compared to conventional methods. Moreover, if implemented wisely and interpreted cautiously, syndromic panels can improve antimicrobial use and patient outcomes, and optimize laboratory workflow. In this review, a narrative overview of the main etiological, clinical, and epidemiological features of RTI is reported, focusing on the laboratory diagnosis and the potentialities of syndromic panels.
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25
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Pichlinski EM, Chong PP, Prokesch BC. Impact of Respiratory Viral Panel Results on Piperacillin-Tazobactam Use in a Medical Intensive Care Unit: A Single-Center Retrospective Study. Clin Ther 2022; 44:e97-e103. [PMID: 36075750 DOI: 10.1016/j.clinthera.2022.08.007] [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: 01/27/2022] [Revised: 04/15/2022] [Accepted: 08/17/2022] [Indexed: 11/29/2022]
Abstract
PURPOSE In critically ill patients with acute respiratory infection, antibiotic stewardship can be challenging given the acuity and complexities of such patients, and the associated high mortality. This study determined the impact of respiratory viral panel (RVP) testing on piperacillin-tazobactam (PT) use in patients admitted to a medical intensive care unit (MICU). METHODS This retrospective chart review used data from adults admitted to a MICU between January 1, 2017, and January 31, 2018, and with findings from at least one RVP available. FINDINGS RVP testing was performed on samples from 90 patients admitted to the MICU. RVP was positive in 41% (37/90) of patients, and 53.3% (48/90) received PT during their MICU stay. PT was discontinued in 25.5% (23/90) of patients, 16.2% (6/37) with a positive RVP and 32.1% (17/53) with a negative RVP. Overall mortality was significantly lower in the positive RVP group versus the negative RVP group (odds ratio = 0.28; P = 0.001). In a multivariate Cox proportional hazards model (adjusted for acute kidney injury and culture positivity), the risk for PT discontinuation was significantly less in patients with a positive RVP compared to those with a negative RVP (primary outcome). Overall mortality rate and median length of stay were significantly lower in patients with a positive RVP compared to those in patients with a negative RVP (secondary outcomes). The 30-day hospital readmission rate and the risk for AKI were not significantly different between those with positive versus negative RVP. IMPLICATIONS Reasons for these observations are currently unclear, but deserve further exploration in future studies. It is hypothesized that the treating providers were concerned about the presence of concurrent bacterial infections along with the diagnosed viral infections given that the patients were critically ill. This suggests that RVP results did not impact PT-prescribing practices in the MICU, and thus that the routine use of RVP solely for guiding antimicrobial-stewardship practices may not be effective.
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Affiliation(s)
- Elisa M Pichlinski
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Pearlie P Chong
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Bonnie C Prokesch
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas; Parkland Health and Hospital System, Dallas, Texas.
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Tse J, Near AM, Cheng M, Karichu J, Lee B, Chang SN. Outpatient Antibiotic and Antiviral Utilization Patterns in Patients Tested for Respiratory Pathogens in the United States: A Real-World Database Study. Antibiotics (Basel) 2022; 11:1058. [PMID: 36009927 PMCID: PMC9405217 DOI: 10.3390/antibiotics11081058] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 12/10/2022] Open
Abstract
This retrospective observational study evaluated outpatient treatment patterns among patients with molecular-based viral diagnostic testing for suspected upper respiratory tract infections in the United States. Patients with a respiratory viral test were identified from 1 August 2016 to 1 July 2019 in a large national reference laboratory database linked to IQVIA's prescription and medical claims databases. Antibiotic and influenza antiviral treatment patterns were reported up to 7 days post-test result. Predictors of antibiotic utilization were assessed using multivariable logistic regression. Among 9561 patients included in the study, 24.6% had evidence of ≥1 filled antibiotic prescription. Antibiotic utilization was higher in patients who tested negative for all viral targets (odds ratio [OR], 1.33; 95% confidence interval [CI], 1.17-1.50) and patients positive for non-influenza viruses (OR, 1.28; 95% CI, 1.09-1.51) compared with those influenza-positive only. Age ≥ 50 years and location outside of the northeast United States also predicted antibiotic utilization. Influenza antivirals were more common in influenza-positive patients compared with patients with other test results (32.5% vs. 3.6-9.0%). Thus, in this real-world study, antibiotic utilization was elevated in patients positive for non-influenza viruses, although antibiotics would generally not be indicated. Further research on pairing diagnostic tools with outpatient antibiotic stewardship programs is needed.
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Affiliation(s)
| | | | - Mindy Cheng
- Roche Diagnostics Solutions, 4300 Hacienda Drive, Pleasanton, CA 94588, USA
| | - James Karichu
- Roche Diagnostics Solutions, 4300 Hacienda Drive, Pleasanton, CA 94588, USA
| | - Brian Lee
- Roche Diagnostics Solutions, 4300 Hacienda Drive, Pleasanton, CA 94588, USA
| | - Susan N. Chang
- Roche Diagnostics Solutions, 4300 Hacienda Drive, Pleasanton, CA 94588, USA
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Comparative Performance of the Luminex NxTAG Respiratory Pathogen Panel, GenMark eSensor Respiratory Viral Panel, and BioFire FilmArray Respiratory Panel. Microbiol Spectr 2022; 10:e0124822. [PMID: 35766513 PMCID: PMC9431521 DOI: 10.1128/spectrum.01248-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
This study compares three of the most inclusive and widely used panels for respiratory syndromic testing in the United States, namely, Luminex NxTAG Respiratory Pathogen Panel (RPP), BioFire FilmArray Respiratory Panel (RP), and GenMark eSensor Respiratory Viral Panel (RVP). We compared the three assays using nasopharyngeal swab samples (n = 350) collected from symptomatic patients (n = 329) in the pre-coronavirus disease 2019 (COVID-19) era. There was no significant difference in the overall accuracies of BioFire and Luminex assays (P = 0.6171); however, significant differences were found between BioFire and GenMark (P = 0.0003) and between GenMark and Luminex (P = 0.0009). The positive percent agreement of the BioFire RP assay was 94.1%, compared to 97.3% for GenMark RVP and 96.5% for Luminex RPP. Overall negative percent agreement values were high for all three assays, i.e., 99.9% for BioFire and Luminex and 99.5% for GenMark. The three assays were equivalent for adenovirus, human metapneumovirus, influenza A, and respiratory syncytial virus. Increased false-positive results were seen with BioFire for the endemic coronaviruses and with GenMark for influenza B and the parainfluenza viruses. IMPORTANCE Clinical laboratories have multiple choices when it is comes to syndromic respiratory testing. Here, the Luminex NxTAG RPP is compared to the BioFire FilmArray RP and GenMark eSensor RVP for overall and per-target accuracy. As new tests come to market, it is important to ascertain their performance characteristics, compared to other widely used in vitro diagnostic products.
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28
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Burillo A, Candel FJ, Canut-Blasco A. Value of syndromic panels in the management of severe community-acquired pneumonia. REVISTA ESPANOLA DE QUIMIOTERAPIA : PUBLICACION OFICIAL DE LA SOCIEDAD ESPANOLA DE QUIMIOTERAPIA 2022; 35 Suppl 1:15-20. [PMID: 35488818 PMCID: PMC9106196 DOI: 10.37201/req/s01.03.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Community-acquired pneumonia requiring hospital admission is a prevalent and potentially serious infection, especially in high-risk patients (e.g., those requiring ICU admission or immunocompromised). International guidelines recommend early aetiological diagnosis to improve prognosis and reduce mortality. Syndromic panels that detect causative pathogens by molecular methods are here to stay. They are highly sensitive and specific for detecting the targets included in the test. A growing number of studies measuring their clinical impact have observed increased treatment appropriateness and decreased turnaround time to aetiological diagnosis, need for admission, length of hospital stay, days of isolation, adverse effects of medication and hospital costs. Its use is recommended a) per a pre-established protocol on making the diagnosis and managing the patient, b) together with an antimicrobial stewardship programme involving both the Microbiology Service and the clinicians responsible for the patient, and c) the final evaluation of the whole process. However, we recall that microbiological diagnosis with traditional methods remains mandatory due to the possibility that the aetiological agent is not included among the molecular targets and to determine the antimicrobial susceptibility of the pathogens detected.
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Affiliation(s)
- A Burillo
- Almudena Burillo, Clinical Microbiology and Infectious Diseases Department, Doctor Esquerdo 46, 28007 Madrid, Spain.
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29
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Multipathogen Detection in Patients with Respiratory Tract Infection: Identification of Non-respiratory Viruses Using Multiplex Real-time Polymerase Reaction. Jundishapur J Microbiol 2022. [DOI: 10.5812/jjm.120553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background: Due to the overlapping clinical characteristics of respiratory tract infections (RTIs) and the unavailability of appropriate diagnostic techniques, the diagnosis of RTIs is controversial. Objectives: The study aimed to prompt the diagnosis of RTIs using commercial multiplex real-time PCR. Methods: The survey undertook for two years (2019 - 2020) on 144 flu-negative immunocompetent outpatients. Respiratory samples were examined by multiplex PCR assays. Results: Study population consisted of females (n = 77, 53.5%) and males (n = 67, 46.5%). The mean age was 42.8 ± 23.7 years. Thirty-one (21.5%) patients were infected with only one viral or bacterial infection. Eighty-two (57%) were infected with more than one pathogen. Ninety-five (37%) and 161 (62%) tests were positive for bacterial and viral pathogens, respectively. Community-acquired Pneumonia (CAP) and atypical CAP pathogens included 17% and 10% of respiratory specimens, respectively. The predominant pathogens consisted of Human Herpes Virus 7 (HHV-7) (n = 38, 15.5%), Epstein-Barr Virus (EBV) (n = 34, 13.8%), Mycoplasma pneumoniae (n = 24, 9.8%), and Human Herpes Virus 6 (HHV-6) (n = 21, 8.5%). There were associations between pathogen findings and special age categories. Fever, cough, dyspnea, and hemoptysis were associated with certain pathogens. There was no substantial difference between viral and bacterial Ct concerning gender, age group, and comorbidities. Conclusions: Multiplex diagnostic assays significantly increased the rate of appropriate diagnosis of respiratory pathogens. However, further investigation is needed to find non-respiratory viruses' significance in respiratory specimens of immunocompetent symptomatic patients.
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Abstract
Influenza infection causes severe illness in 3 to 5 million people annually, with up to an estimated 650,000 deaths per annum. As such, it represents an ongoing burden to health care systems and human health. Severe acute respiratory infection can occur, resulting in respiratory failure requiring intensive care support. Herein we discuss diagnostic approaches, including development of CLIA-waived point of care tests that allow rapid diagnosis and treatment of influenza. Bacterial and fungal coinfections in severe influenza pneumonia are associated with worse outcomes, and we summarize the approach and treatment options for diagnosis and treatment of bacterial and Aspergillus coinfection. We discuss the available drug options for the treatment of severe influenza, and treatments which are no longer supported by the evidence base. Finally, we describe the supportive management and ventilatory approach to patients with respiratory failure as a result of severe influenza in the intensive care unit.
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Affiliation(s)
- Liam S O'Driscoll
- Department of Intensive Care Medicine, St. James's University Hospital, Multidisciplinary Intensive Care Research Organization (MICRO), Trinity Centre for Health Sciences, Dublin, Ireland
| | - Ignacio Martin-Loeches
- Department of Intensive Care Medicine, St. James's University Hospital, Multidisciplinary Intensive Care Research Organization (MICRO), Trinity Centre for Health Sciences, Dublin, Ireland.,Respiratory Medicine, Hospital Clinic, IDIBAPS, Universidad de Barcelona, CIBERes, Barcelona, Spain
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31
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Markussen DL, Grewal HMS, Knoop ST, Serigstad S, Kommedal Ø, Ebbesen M, Ulvestad E, Bjørneklett R. Comparison of rapid molecular testing methods for detecting respiratory viruses in emergency care: a prospective study. Infect Dis (Lond) 2021; 54:247-254. [PMID: 34847841 DOI: 10.1080/23744235.2021.2003857] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Respiratory tract infections (RTIs) caused by contagious viruses are common among patients presenting to the emergency department (ED). Early detection of these viruses can help prevent nosocomial transmission. AIM To investigate the efficacy of three rapid molecular methods, namely FilmArray® Pneumonia Panel plus (FAP plus), ID NOW™ Influenza A and B 2 (ID NOW2) point-of-care test, and an in-house real-time polymerase chain reaction (RT-PCR) test, to identify patients with viral RTIs requiring isolation in an emergency setting. METHODS We included a FilmArray® Pneumonia Panel plus in the initial workup of patients with suspected RTIs during a flu season. The RT-PCR and the influenza point-of-care test were performed as part of routine diagnostics, on demand from the treating physicians. We compared viral detections and compared time to positive test results for each method. FINDINGS The FAP plus significantly reduced the turnaround time and was able to identify 95% patients with potential contagious viral RTI. Routine diagnostics ordered by the treating physician had a turnaround time of a median 22 h and detected 87% of patients with potential contagious viral RTI. In patients that had all three tests, the ID NOW2 detected 62% of patients with influenza. CONCLUSIONS The FAP plus was able to rapidly and reliably identify patients with potential contagious viral RTIs; its use was feasible in the ED setting. Failing to test patients with viral RTI and using tests with long turnaround time may lead to nosocomial transmission of viral infections and adverse patient outcomes.
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Affiliation(s)
| | - 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
| | - Siri Tandberg Knoop
- Emergency Care Clinic, Haukeland University Hospital, Bergen, Norway.,Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Sondre Serigstad
- Emergency Care Clinic, Haukeland University Hospital, Bergen, Norway.,Department of Clinical Science, Bergen Integrated Diagnostic Stewardship Cluster, University of Bergen, Bergen, Norway.,Department of Clinical Medicine, Faculty of Medicine, University of Bergen, 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
| | - Marit Ebbesen
- Department of Microbiology, Haukeland University Hospital, 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 Bjørneklett
- Emergency Care Clinic, Haukeland University Hospital, Bergen, Norway.,Department of Clinical Medicine, Faculty of Medicine, University of Bergen, Bergen, Norway
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Impact of multiplexed respiratory viral panels on infection control measures and antimicrobial stewardship: a review of the literature. Eur J Clin Microbiol Infect Dis 2021; 41:187-202. [PMID: 34799754 PMCID: PMC8604699 DOI: 10.1007/s10096-021-04375-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 11/03/2021] [Indexed: 11/25/2022]
Abstract
Multiplexed respiratory viral panels (MRVP) have recently been added to the diagnostic work-up of respiratory infections. This review provides a summary of the main literature of MRVP for patients with regard to 3 different topics. Can the results of MRVP reduce the inappropriate use of antibiotics, can they guide the use of appropriate antiviral therapy and do they have an added value with respect to infection control measures? Literature was searched for based on a defined search string using both the PubMed and Embase database. Twenty-five articles report on the impact of MRVP on antibiotic therapy. In all the articles where active antimicrobial stewardship was performed (e.g., education/advice on interpreting results of MRVP) (N = 9), a reduction in antibiotic therapy was shown (with exception of 2 studies). Three studies evaluating the effect of MRVP on antimicrobial use in a population that is not suspected of having bacterial pneumonia (e.g., absence of radiology suggestive for bacterial infection or low PCT) found a positive impact on antibiotic therapy. Eight studies with a short TAT (< 7 h) had a positive impact on use of antibiotic therapy. Eleven studies focused on the impact of MRVP on antiviral use. In contrast to antibiotic reduction, all studies systematically objectified improved antiviral use as a consequence of MRVP results. With regard to the impact of MRVP on infection control, eleven articles were withheld. All these studies led to a more accurate use of infection control measures by detecting unidentified pathogens or stopping isolation precautions in case of a negative MRVP result. MRVP don’t reduce antibiotic therapy in all populations. Reduction seems more likely if the following factors are present: active antimicrobial stewardship, low likelihood of a bacterial infection, and a short turnaround time to result. With respect to antiviral therapy, all studies have an impact but the targeted use of antivirals is so far not that evidence based for all viral respiratory pathogens. Regarding infection control measures, the potential impact of MRVP is high because of the need of additional isolation precautions for many respiratory viruses, although logistical problems can occur.
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Khalid TY, Duncan LJ, Thornton HV, Lasseter G, Muir P, Toney ZA, Hay AD. Novel multi-virus rapid respiratory microbiological point-of-care testing in primary care: a mixed-methods feasibility evaluation. Fam Pract 2021; 38:598-605. [PMID: 33684208 DOI: 10.1093/fampra/cmab002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND AND OBJECTIVES Rapid multi-viral respiratory microbiological point-of-care tests (POCTs) have not been evaluated in UK primary care. The aim of this study was to evaluate the use of a multi-viral microbiological POCT for suspected respiratory tract infections (RTIs). METHODS In this observational, mixed-methods feasibility study practices were provided with a POCT machine for any patient aged ≥3 months with suspected RTI. Dual throat/nose swabs tested for 17 respiratory viruses and three atypical bacteria, 65 minutes per sample. RESULTS Twenty clinicians recruited 93 patients (estimated 1:3 of all RTI cases). Patient's median age was 29, 57% female, and 44% with co-morbidities. Pre-test diagnoses: upper RTI (48%); lower RTI (30%); viral/influenza-like illness (18%); other (4%). Median set-up time was 2.72 minutes, with 72% swabs processed <4 hours, 90% <24 hours. Tests detected ≥1 virus in 58%, no pathogen 37% and atypical bacteria 2% (3% inconclusive). Antibiotics were prescribed pre-test to 35% of patients with no pathogen detected and 25% with a virus. Post-test diagnoses changed in 20%, and diagnostic certainty increased (P = 0.02), more so when the test was positive rather than negative (P < 0.001). Clinicians predicted decreased antibiotic benefit post-test (P = 0.02). Interviews revealed the POCT has clear potential, was easy to use and well-liked, but limited by time-to-result and the absence of testing for typical respiratory bacteria. CONCLUSIONS This POCT was acceptable and appeared to influence clinical reasoning. Clinicians wanted faster time-to-results and more information about bacteria. Randomized trials are needed to understand the safety, efficacy and patient perceptions of these POCTs.
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Affiliation(s)
- Tanzeela Y Khalid
- Centre for Academic Primary Care, Bristol Medical School: Population Health Sciences
| | - Lorna J Duncan
- Centre for Academic Primary Care, Bristol Medical School: Population Health Sciences
| | - Hannah V Thornton
- Centre for Academic Primary Care, Bristol Medical School: Population Health Sciences
| | - Gemma Lasseter
- NIHR Health Protection Research Unit in Behavioural Science and Evaluation, University of Bristol, Bristol, UK
| | - Peter Muir
- Public Health Laboratory Bristol, National Infection Service, Public Health England, Bristol, UK
| | - Zara Abigail Toney
- St George's, University of London MBBS Programme at the University of Nicosia Medical School, Nicosia, Cyprus
| | - Alastair D Hay
- Centre for Academic Primary Care, Bristol Medical School: Population Health Sciences.,NIHR Health Protection Research Unit in Behavioural Science and Evaluation, University of Bristol, Bristol, UK
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Cassidy H, Van Genne M, Lizarazo-Forero E, Gard L, Niesters HGM. A discussion of syndromic molecular testing for clinical care. J Antimicrob Chemother 2021; 76:iii58-iii66. [PMID: 34555161 PMCID: PMC8460109 DOI: 10.1093/jac/dkab243] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Current molecular detection methods for single or multiplex pathogens by real-time PCR generally offer great sensitivity and specificity. However, many infectious pathogens often result in very similar clinical presentations, complicating the test-order for physicians who have to narrow down the causative agent prior to in-house PCR testing. As a consequence, the intuitive response is to start empirical therapy to treat a broad spectrum of possible pathogens. Syndromic molecular testing has been increasingly integrated into routine clinical care, either to provide diagnostic, epidemiological or patient management information. These multiplex panels can be used to screen for predefined infectious disease pathogens simultaneously within a 1 h timeframe, creating opportunities for rapid diagnostics. Conversely, syndromic panels have their own challenges and must be adaptable to the evolving demands of the clinical setting. Firstly, questions have been raised regarding the clinical relevance of some of the targets included in the panels and secondly, there is the added expense of integration into the clinical laboratory. Here, we aim to discuss some of the factors that should be considered before performing syndromic testing rather than traditional low-plex in-house PCR.
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Affiliation(s)
- Hayley Cassidy
- The University of Groningen, University Medical Centre Groningen, Department of Medical Microbiology and Infection Prevention, Division of Clinical Virology, Groningen, The Netherlands
| | - Mart Van Genne
- The University of Groningen, University Medical Centre Groningen, Department of Medical Microbiology and Infection Prevention, Division of Clinical Virology, Groningen, The Netherlands
| | - Erley Lizarazo-Forero
- The University of Groningen, University Medical Centre Groningen, Department of Medical Microbiology and Infection Prevention, Division of Clinical Virology, Groningen, The Netherlands
| | - Lilli Gard
- The University of Groningen, University Medical Centre Groningen, Department of Medical Microbiology and Infection Prevention, Division of Clinical Virology, Groningen, The Netherlands
| | - Hubert G M Niesters
- The University of Groningen, University Medical Centre Groningen, Department of Medical Microbiology and Infection Prevention, Division of Clinical Virology, Groningen, The Netherlands
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Dumkow LE, Worden LJ, Rao SN. Syndromic diagnostic testing: a new way to approach patient care in the treatment of infectious diseases. J Antimicrob Chemother 2021; 76:iii4-iii11. [PMID: 34555157 PMCID: PMC8460095 DOI: 10.1093/jac/dkab245] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Advanced microbiology technologies such as multiplex molecular assays (i.e. syndromic diagnostic tests) are a novel approach to the rapid diagnosis of common infectious diseases. As the global burden of antimicrobial resistance continues to rise, the judicious use of antimicrobials is of utmost importance. Syndromic panels are now being recognized in some clinical practice guidelines as a 'game-changer' in the diagnosis of infectious diseases. These syndromic panels, if implemented thoughtfully and interpreted carefully, have the potential to improve patient outcomes through improved clinical decision making, optimized laboratory workflow, and enhanced antimicrobial stewardship. This paper reviews the potential benefits of and considerations regarding various infectious diseases syndromic panels, and highlights how to maximize impact through collaboration between clinical microbiology laboratory and antimicrobial stewardship programmes.
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Affiliation(s)
- Lisa E Dumkow
- Mercy Health Saint Mary's Hospital, Grand Rapids, MI, USA
| | - Lacy J Worden
- Mercy Health Saint Mary's Hospital, Grand Rapids, MI, USA
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36
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Samuel LP, Hansen GT, Kraft CS, Pritt BS. The Need for Dedicated Microbiology Leadership in the Clinical Microbiology Laboratory. J Clin Microbiol 2021; 59:e0154919. [PMID: 33597258 PMCID: PMC8288296 DOI: 10.1128/jcm.01549-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Clinical microbiology laboratories play a crucial role in patient care using traditional and innovative diagnostics. Challenges faced by laboratories include emerging pathogens, rapidly evolving technologies, health care-acquired infections, antibiotic-resistant organisms, and diverse patient populations. Despite these challenges, many clinical microbiology laboratories in the United States are not directed by doctoral level microbiology-trained individuals with sufficient time dedicated to laboratory leadership. The manuscript highlights the need for medical microbiology laboratory directors with appropriate training and qualifications.
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Affiliation(s)
- Linoj P. Samuel
- Department of Pathology and Laboratory Medicine, Henry Ford Health System, Detroit, Michigan, USA
| | - Glen T. Hansen
- Department of Pathology and Laboratory Medicine, Hennepin County Medical Center, Minneapolis, Minnesota, USA
- Department of Pathology and Laboratory Medicine, University of Minnesota, Minneapolis, Minnesota, USA
- Department of Medicine, Division of Infectious Diseases, University of Minnesota, Minneapolis, Minnesota, USA
| | - Colleen S. Kraft
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, USA
- Department Medicine, Division of Infectious Diseases, Emory University, Atlanta, Georgia, USA
| | - Bobbi S. Pritt
- Department of Laboratory Medicine and Pathology, Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
- Department of Internal Medicine, Division of Infectious Diseases, Mayo Clinic, Rochester, Minnesota, USA
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37
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Wabe N, Li L, Lindeman R, Post JJ, Dahm MR, Li J, Westbrook JI, Georgiou A. Evaluation of the accuracy of diagnostic coding for influenza compared to laboratory results: the availability of test results before hospital discharge facilitates improved coding accuracy. BMC Med Inform Decis Mak 2021; 21:168. [PMID: 34022851 PMCID: PMC8141245 DOI: 10.1186/s12911-021-01531-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 05/19/2021] [Indexed: 11/10/2022] Open
Abstract
Background Assessing the accuracy of diagnostic coding is essential to ensure the validity and reliability of administrative coded data. The aim of the study was to evaluate the accuracy of assigned International Classification of Diseases version 10-Australian Modification (ICD-10-AM) codes for influenza by comparing with patients’ results of their polymerase chain reaction (PCR)-based laboratory tests. Method A retrospective study was conducted across seven public hospitals in New South Wales, Australia. A total of 16,439 patients who were admitted and tested by either cartridge-based rapid PCR or batched multiplex PCR between January 2016 and December 2017 met the inclusion criteria. We calculated the sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of ICD-10-AM coding using laboratory results as a gold standard. Separate analyses were conducted to determine whether the availability of test results at the time of hospital discharge influenced diagnostic coding accuracy. Results Laboratory results revealed 2759 positive influenza cases, while ICD-10-AM coding identified 2527 patients. Overall, 13.7% (n = 378) of test positive patients were not assigned an ICD-10-AM code for influenza. A further 5.8% (n = 146) patients with negative test results were incorrectly assigned an ICD-10-AM code for influenza. The sensitivity, specificity, PPV and NPV of ICD-10-AM coding were 93.1%; 98.9%; 94.5% and 98.6% respectively when test results were received before discharge and 32.7%; 99.2%; 87.8% and 89.8% respectively when test results were not available at discharge. The sensitivity of ICD-10-AM coding varied significantly across hospitals. The use of rapid PCR or hospitalisation during the influenza season were associated with greater coding accuracy. Conclusion Although ICD-10-AM coding for influenza demonstrated high accuracy when laboratory results were received before discharge, its sensitivity was substantially lower for patients whose test results were not available at discharge. The timely availability of laboratory test results during the episode of care could contribute to improved coding accuracy. Supplementary Information The online version contains supplementary material available at 10.1186/s12911-021-01531-9.
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Affiliation(s)
- Nasir Wabe
- Centre for Health Systems and Safety Research, Australian Institute of Health Innovation, Macquarie University, North Ryde, NSW, 2109, Australia.
| | - Ling Li
- Centre for Health Systems and Safety Research, Australian Institute of Health Innovation, Macquarie University, North Ryde, NSW, 2109, Australia
| | - Robert Lindeman
- New South Wales Health Pathology, St Leonards, NSW, 2065, Australia
| | - Jeffrey J Post
- Department of Infectious Diseases, Prince of Wales Hospital, Randwick, NSW, 2031, Australia.,Prince of Wales Clinical School, University of New South Wales, Kensington, NSW, 2052, Australia
| | - Maria R Dahm
- Institute for Communication in Health Care, The Australian National University, 110 Ellery Crescent, Acton, ACT, 2601, Australia
| | - Julie Li
- Centre for Health Systems and Safety Research, Australian Institute of Health Innovation, Macquarie University, North Ryde, NSW, 2109, Australia
| | - Johanna I Westbrook
- Centre for Health Systems and Safety Research, Australian Institute of Health Innovation, Macquarie University, North Ryde, NSW, 2109, Australia
| | - Andrew Georgiou
- Centre for Health Systems and Safety Research, Australian Institute of Health Innovation, Macquarie University, North Ryde, NSW, 2109, Australia
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Evans SE, Jennerich AL, Azar MM, Cao B, Crothers K, Dickson RP, Herold S, Jain S, Madhavan A, Metersky ML, Myers LC, Oren E, Restrepo MI, Semret M, Sheshadri A, Wunderink RG, Dela Cruz CS. Nucleic Acid-based Testing for Noninfluenza Viral Pathogens in Adults with Suspected Community-acquired Pneumonia. An Official American Thoracic Society Clinical Practice Guideline. Am J Respir Crit Care Med 2021; 203:1070-1087. [PMID: 33929301 PMCID: PMC8314899 DOI: 10.1164/rccm.202102-0498st] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Background: This document provides evidence-based clinical practice guidelines on the diagnostic utility of nucleic acid–based testing of respiratory samples for viral pathogens other than influenza in adults with suspected community-acquired pneumonia (CAP). Methods: A multidisciplinary panel developed a Population–Intervention–Comparison–Outcome question, conducted a pragmatic systematic review, and applied Grading of Recommendations, Assessment, Development, and Evaluation methodology for clinical recommendations. Results: The panel evaluated the literature to develop recommendations regarding whether routine diagnostics should include nucleic acid–based testing of respiratory samples for viral pathogens other than influenza in suspected CAP. The evidence addressing this topic was generally adjudicated to be of very low quality because of risk of bias and imprecision. Furthermore, there was little direct evidence supporting a role for routine nucleic acid–based testing of respiratory samples in improving critical outcomes such as overall survival or antibiotic use patterns. However, on the basis of direct and indirect evidence, recommendations were made for both outpatient and hospitalized patients with suspected CAP. Testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection was not addressed in the literature at the time of the evidence review. Conclusions: The panel formulated and provided their rationale for recommendations on nucleic acid–based diagnostics for viral pathogens other than influenza for patients with suspected CAP.
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Moradi T, Bennett N, Shemanski S, Kennedy K, Schlachter A, Boyd S. Use of Procalcitonin and a Respiratory Polymerase Chain Reaction Panel to Reduce Antibiotic Use via an Electronic Medical Record Alert. Clin Infect Dis 2021; 71:1684-1689. [PMID: 31637442 PMCID: PMC7108168 DOI: 10.1093/cid/ciz1042] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 10/17/2019] [Indexed: 12/23/2022] Open
Abstract
Background Respiratory tract infections are often viral and but are frequently treated with antibiotics, providing a significant opportunity for antibiotic de-escalation in patients. We sought to determine whether an automated electronic medical record best practice alert (BPA) based on procalcitonin and respiratory polymerase chain reaction (PCR) results could help reduce inappropriate antibiotic use in patients with likely viral respiratory illness. Methods This multisite, pre–post, quasi-experimental study included patients 18 years and older with a procalcitonin level <0.25 ng/mL and a virus identified on respiratory PCR within 48 hours of each other, and 1 or more systemic antibiotics ordered. In the study group, a BPA alerted providers of the diagnostic results suggesting viral infection and prompted them to reassess the need for antibiotics. The primary outcome measured was total antibiotic-days of therapy. Results The BPA reduced inpatient antibiotic-days of therapy by a mean of 2.2 days compared with patients who met criteria but did not have the alert fire (8.0 vs 5.8 days, respectively, P < .001). The BPA also reduced the percentage of patients prescribed antibiotics on discharge (20% vs 47.8%, P < .001), whereas there was no difference in need for antibiotic escalation after initial discontinuation (7.6% vs 4.3%, P = .198). Conclusions The automated antimicrobial stewardship BPA effectively reduced antibiotic use and discharge prescribing rates when diagnostics suggested viral respiratory tract infection, without a higher rate for reinitiation of antibiotics after discontinuation.
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Affiliation(s)
- Tony Moradi
- Department of Pharmacy, University of Kansas Health System, Kansas City, Missouri, USA
| | - Nicholas Bennett
- Antimicrobial Stewardship Program, Saint Luke's Health System, Kansas City, Missouri, USA
| | - Shelby Shemanski
- Department of Pharmacy, Saint Luke's Hospital, Kansas City, Missouri, USA
| | - Kevin Kennedy
- Department of Biostatistics, Saint Luke's Hospital, Kansas City, Missouri, USA
| | - Andrew Schlachter
- Department of Pulmonary and Critical Care Medicine, Saint Luke's Hospital, Kansas City, Missouri, USA
| | - Sarah Boyd
- Department of Infectious Disease, Saint Luke's Health System, Kansas City, Missouri, USA
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40
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Rader TS, Stevens MP, Bearman G. Syndromic Multiplex Polymerase Chain Reaction (mPCR) Testing and Antimicrobial Stewardship: Current Practice and Future Directions. Curr Infect Dis Rep 2021; 23:5. [PMID: 33679252 PMCID: PMC7909367 DOI: 10.1007/s11908-021-00748-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/27/2021] [Indexed: 02/07/2023]
Abstract
PURPOSE OF REVIEW Syndromic multiplex polymerase chain reaction (mPCR) panels offer the antimicrobial steward a rapid tool for optimizing and de-escalating antimicrobials. In this review, we analyze the role of syndromic mPCR in respiratory, gastrointestinal, and central nervous system infections within the context of antimicrobial stewardship efforts. RECENT FINDINGS For all mPCR syndromic panels, multiple studies analyzed the pre-and-post implementation impact of mPCR on antimicrobial utilization. Prospective studies and trials of respiratory mPCR stewardship interventions, including diagnostic algorithms, educational efforts, co-testing with procalcitonin, and targeted provider feedback currently exist. For gastrointestinal and cerebrospinal fluid mPCR, fewer peer-reviewed reports exist for the use of mPCR in antimicrobial stewardship. These studies demonstrated an inconsistent trend towards decreasing antibiotic use with mPCR. This is further limited by a lack of statistical significance, the absence of controlled, prospective trials, and issues with data generalizability. SUMMARY Antibiotic overuse may improve when mPCR is coupled with electronic medical record algorithm-based approaches and direct provider feedback by an antimicrobial stewardship professional. mPCR may prove a useful tool for antimicrobial stewardship but future studies are needed to define the best practice for its utilization.
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Affiliation(s)
- Theodore S. Rader
- Department of Internal Medicine, Virginia Commonwealth University Health System, 1250 E MARSHALL ST # 980509, Richmond, VA 23298-0019 USA
| | - Michael P. Stevens
- Division of Infectious Diseases, Virginia Commonwealth University Health System, Richmond, VA USA
| | - Gonzalo Bearman
- Division of Infectious Diseases, Virginia Commonwealth University Health System, Richmond, VA USA
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41
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[Virological diagnosis of lower respiratory tract infections]. Rev Mal Respir 2021; 38:58-73. [PMID: 33461842 DOI: 10.1016/j.rmr.2020.11.002] [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: 11/15/2019] [Accepted: 08/06/2020] [Indexed: 11/21/2022]
Abstract
INTRODUCTION The etiological diagnosis of bronchopulmonary infections cannot be assessed with clinical, radiological and epidemiological data alone. Viruses have been demonstrated to cause a large proportion of these infections, both in children and adults. BACKGROUND The diagnosis of viral bronchopulmonary infections is based on the analysis of secretions, collected from the lower respiratory tract when possible, by techniques that detect either influenza and respiratory syncytial viruses, or a large panel of viruses that can be responsible for respiratory disease. The latter, called multiplex PCR assays, allow a syndromic approach to respiratory infection. Their high cost for the laboratory raises the question of their place in the management of patients in terms of antibiotic economy and isolation. In the absence of clear recommendations, the strategy and equipment are very unevenly distributed in France. OUTLOOK Medico-economic analyses need to be performed in France to evaluate the place of these tests in the management of patients. The evaluation of the role of the different viruses often detected in co-infection, especially in children, also deserves the attention of virologists and clinicians. CONCLUSIONS The availability of new diagnostic technologies, the recent emergence of SARS-CoV-2, together with the availability of new antiviral drugs are likely to impact future recommendations for the management of viral bronchopulmonary infections.
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Lee HJ, Park JH, Kim JM, Kim JH, Baek HS. Clinical efficacy of respiratory virus detection by using the FilmArray method in children admitted with respiratory infection. ALLERGY ASTHMA & RESPIRATORY DISEASE 2021. [DOI: 10.4168/aard.2021.9.1.12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Hyun Joo Lee
- Department of Pediatrics, Hallym University Kangdong Sacred Heart Hospital, Seoul, Korea
| | - Jun Hong Park
- Department of Pediatrics, Hallym University Kangdong Sacred Heart Hospital, Seoul, Korea
| | - Jae Min Kim
- Department of Pediatrics, Hallym University Kangdong Sacred Heart Hospital, Seoul, Korea
| | - Ji Hye Kim
- Department of Pediatrics, Hallym University Kangdong Sacred Heart Hospital, Seoul, Korea
| | - Hey-Sung Baek
- Department of Pediatrics, Hallym University Kangdong Sacred Heart Hospital, Seoul, Korea
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43
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Diesner-Treiber SC, Voitl P, Voitl JJM, Langer K, Kuzio U, Riepl A, Patel P, Mühl-Riegler A, Mühl B. Respiratory Infections in Children During a Covid-19 Pandemic Winter. Front Pediatr 2021; 9:740785. [PMID: 34733808 PMCID: PMC8558488 DOI: 10.3389/fped.2021.740785] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 09/21/2021] [Indexed: 01/03/2023] Open
Abstract
Background: The Covid-19 pandemic compelled the implementation of measures to curb the SARS CoV-2 spread, such as social distancing, wearing FFP2 masks, and frequent hand hygiene. One anticipated ramification of these measures was the containment of other pathogens. This prospective, longitudinal study aimed to investigate the spread of 22 common seasonal non-SARS-CoV-2 pathogens, such as RSV and influenza, among children with an acute respiratory infection during a pandemic. Methods: Three hundred ninety children (0-24 months) admitted to Vienna's largest pediatric center with acute respiratory infection (November 2020-April 2021) were included in this study. The researchers tested nasal swabs for 22 respiratory pathogens by Multiplex PCR, documented clinical features and treatment, and evaluated data for a potential connection with the lockdown measures then in force. Results: The 448 smears revealed the most common pathogens to be rhino-/enterovirus (41.4%), adenovirus (2.2%), and coronavirus NL63 (13.6%). While the first two were active throughout the entire season, coronaviruses peaked in the first trimester of 2021 in conjunction with the lift of the lockdown period (OR 4.371, 95%CI 2.34-8.136, P < 0.001). RSV, metapneumovirus, and influenza were absent. Conclusion: This prospective, longitudinal study shows that Covid-19 measures suppressed the seasonal activity of influenza, RSV, and metapneumovirus among very young children, but not of rhino-/enterovirus and adenovirus. The 0-24 month-olds are considered the lowest risk group and were only indirectly affected by the public health measures. Lockdowns were negatively associated with coronaviruses infections.
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Affiliation(s)
- Susanne C Diesner-Treiber
- First Vienna Pediatric Medical Center, Vienna, Austria.,Medical University of Vienna, Vienna, Austria
| | - Peter Voitl
- First Vienna Pediatric Medical Center, Vienna, Austria.,Medical University of Vienna, Vienna, Austria.,Sigmund Freud University Vienna, Vienna, Austria
| | | | - Klara Langer
- First Vienna Pediatric Medical Center, Vienna, Austria
| | - Ulrike Kuzio
- First Vienna Pediatric Medical Center, Vienna, Austria
| | - Angela Riepl
- First Vienna Pediatric Medical Center, Vienna, Austria
| | - Pia Patel
- First Vienna Pediatric Medical Center, Vienna, Austria
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Hanson KE, Azar MM, Banerjee R, Chou A, Colgrove RC, Ginocchio CC, Hayden MK, Holodiny M, Jain S, Koo S, Levy J, Timbrook TT, Caliendo AM. Molecular Testing for Acute Respiratory Tract Infections: Clinical and Diagnostic Recommendations From the IDSA's Diagnostics Committee. Clin Infect Dis 2020; 71:2744-2751. [PMID: 32369578 PMCID: PMC7454374 DOI: 10.1093/cid/ciaa508] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 04/30/2020] [Indexed: 01/08/2023] Open
Abstract
The clinical signs and symptoms of acute respiratory tract infections (RTIs) are not pathogen specific. Highly sensitive and specific nucleic acid amplification tests have become the diagnostic reference standard for viruses, and translation of bacterial assays from basic research to routine clinical practice represents an exciting advance in respiratory medicine. Most recently, molecular diagnostics have played an essential role in the global health response to the novel coronavirus pandemic. How best to use newer molecular tests for RTI in combination with clinical judgment and traditional methods can be bewildering given the plethora of available assays and rapidly evolving technologies. Here, we summarize the current state of the art with respect to the diagnosis of viral and bacterial RTIs, provide a practical framework for diagnostic decision making using selected patient-centered vignettes, and make recommendations for future studies to advance the field.
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Affiliation(s)
- Kimberly E Hanson
- Division of Infectious Diseases, Department of Medicine, University of Utah School of Medicine, Salt Lake City, Utah, USA
- Section of Clinical Microbiology, Department of Pathology, University of Utah and ARUP Laboratories, Salt Lake City, Utah, USA
| | - Marwan M Azar
- Department of Medicine, Section of Infectious Diseases, AIDS Program, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Ritu Banerjee
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Andrew Chou
- Michael E. DeBakey VA Medical Center, Baylor College of Medicine, Houston, Texas, USA
| | - Robert C Colgrove
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Christine C Ginocchio
- Global Medical Affairs, bioMérieux/BioFire Diagnostics, Salt Lake City, Utah, USA
- Department of Pathology and Laboratory Medicine, Hofstra North Shore–Long Island Jewish School of Medicine, Hempstead, New York, USA
| | - Mary K Hayden
- Division of Infectious Diseases, Department of Medicine, Rush University Medical Center, Chicago, Illinois, USA
- Division of Laboratory Medicine, Department of Pathology, Rush University Medical Center, Chicago, Illinois, USA
| | - Mark Holodiny
- VA Palo Alto Health Care System, Palo Alto, California, USA
- Stanford University, Palo Alto, California, USA
| | - Seema Jain
- Disease Investigations Section, Infectious Diseases Branch, California Department of Public Health, Richmond, California, USA
| | - Sophia Koo
- Division of Infectious Diseases, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Jaclyn Levy
- Infectious Diseases Society of America, Arlington, Virginia, USA
| | - Tristan T Timbrook
- Division of Epidemiology, Department of Medicine, University of Utah School of Medicine, Salt Lake City, Utah USA
- Department of Pharmacy, University of Utah Health, Salt Lake City, Utah, USA
| | - Angela M Caliendo
- Division of Infectious Diseases, Department of Medicine, Brown University Warren Alpert School of Medicine, Providence, Rhode Island, USA
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45
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Tripathi S, Al-Sayyed B, Gladfelter TR. Comparative epidemiology, hospital course, and outcomes of viral respiratory infections in hospitalized pediatric patients. Indian J Med Microbiol 2020; 39:24-29. [PMID: 33610252 DOI: 10.1016/j.ijmmb.2020.10.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
PURPOSE Acute respiratory illness is the leading cause of hospitalization for young children. Current guidelines recommend against testing to identify specific viruses due to a lack of data on the benefit of such testing. This study was designed to characterize epidemiology, hospital course, and outcomes of the various common virus -related hospitalization in children. METHOD Single-center retrospective chart review. All patients who had respiratory viral panel sent within 48 h of admission. Comparative demographic and outcome analysis. Statistical analysis using ANOVA and multivariable regression. RESULT 1831 patients met the study criteria. Rhinovirus was the most common virus (55.9%). Coronavirus had the highest proportion of infants (61.2%), while influenza had the least (17.8%). Positive urine culture identified in 8.1% of patients, with blood and urine positivity at 2% each. Rhinovirus and parainfluenza were spread throughout the year, while Corona, RSV, and influenza were more predominant in winter months. Overall PICU admission rate 22.8% and was highest for RSV (28.0%) and lowest for adenovirus (13.5%). No difference in ICU length of stay among different virus. Intubation rate was 5.6% with a median duration of 5 days. Median hospital length of stay was 2 days and differ significantly with different virus (maximum four RSV and metapneumo virus). Mortality in the study population was 0.3%. CONCLUSION The difference in the disease course of different viruses may justify the resources required to test for the respiratory viral panel. This study data can serve as a benchmark for comparison of disease course of COVID-19 compared to other viral infections.
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Affiliation(s)
- Sandeep Tripathi
- Pediatric Intensive Care, University of Illinois College of Medicine at Peoria, IL, USA.
| | - Ban Al-Sayyed
- Pediatric Infectious Diseases, University of Illinois College of Medicine at Peoria, IL, USA
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Li H, Cui X, Sun L, Deng X, Liu S, Zou X, Li B, Wang C, Wang Y, Liu Y, Lu B, Cao B. High concentration of Cas12a effector tolerates more mismatches on ssDNA. FASEB J 2020; 35:e21153. [PMID: 33159392 DOI: 10.1096/fj.202001475r] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 10/05/2020] [Accepted: 10/15/2020] [Indexed: 12/26/2022]
Abstract
Rapid pathogen detection is critical for prompt treatment, interrupting transmission routes, and decreasing morbidity and mortality. The V-type CRISPR system had been used for rapid pathogen detection. However, whether single-stranded DNA in CRISPR system can cause false positives remains undetermined. Herein, we show that high molar concentration of Cas12a effector tolerated more mismatches on ssDNA and activated its trans-cleavage activity at six base matches. Reducing Cas12a and crRNA molar concentration increased the minimal base-match number required for Cas12a ssDNA activation to 11, which reducing nonspecific activation. We then established a Cas12a-based M tuberculosis detection system with a primer having an 8 bp overlap with crRNA. This system did not exhibit primer-induced false positives, and minimum detection copy reached 1 copy/uL (inputting 1-μL sample) in standard strains. The Cas12a-based M tuberculosis detection system showed 80.0% sensitivity and 100.0% specificity in verification using clinical specimens, compared with Xpert MTB/RIF, which showed 72.0% sensitivity and 90.9% specificity. All these results prove that appropriate concentration of cas12a effector can effectively perform nucleic acid detection.
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Affiliation(s)
- Haibo Li
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, Centre for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, P. R. China.,Institute of Respiratory Medicine, Chinese Academy of Medical Science, Beijing, P. R. China.,National Clinical Research Center for Respiratory Diseases, Capital Medical University, Beijing, P. R. China
| | - Xiaojing Cui
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, Centre for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, P. R. China.,Institute of Respiratory Medicine, Chinese Academy of Medical Science, Beijing, P. R. China.,National Clinical Research Center for Respiratory Diseases, Capital Medical University, Beijing, P. R. China
| | - Lingxiao Sun
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, Centre for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, P. R. China.,Institute of Respiratory Medicine, Chinese Academy of Medical Science, Beijing, P. R. China.,National Clinical Research Center for Respiratory Diseases, Capital Medical University, Beijing, P. R. China
| | - Xiaoyan Deng
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, Centre for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, P. R. China.,Clinical Center for Pulmonary Infections, Capital Medical University, Tsinghua University-Peking University Joint Center for Life Sciences, Beijing, P. R. China
| | - Shuai Liu
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, Centre for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, P. R. China.,Institute of Respiratory Medicine, Chinese Academy of Medical Science, Beijing, P. R. China.,National Clinical Research Center for Respiratory Diseases, Capital Medical University, Beijing, P. R. China.,Clinical Center for Pulmonary Infections, Capital Medical University, Tsinghua University-Peking University Joint Center for Life Sciences, Beijing, P. R. China
| | - Xiaohui Zou
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, Centre for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, P. R. China.,Institute of Respiratory Medicine, Chinese Academy of Medical Science, Beijing, P. R. China.,National Clinical Research Center for Respiratory Diseases, Capital Medical University, Beijing, P. R. China
| | - Binbin Li
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, Centre for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, P. R. China.,Institute of Respiratory Medicine, Chinese Academy of Medical Science, Beijing, P. R. China.,National Clinical Research Center for Respiratory Diseases, Capital Medical University, Beijing, P. R. China
| | - Chunlei Wang
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, Centre for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, P. R. China.,Institute of Respiratory Medicine, Chinese Academy of Medical Science, Beijing, P. R. China.,National Clinical Research Center for Respiratory Diseases, Capital Medical University, Beijing, P. R. China
| | - Yeming Wang
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, Centre for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, P. R. China.,Institute of Respiratory Medicine, Chinese Academy of Medical Science, Beijing, P. R. China.,National Clinical Research Center for Respiratory Diseases, Capital Medical University, Beijing, P. R. China.,Clinical Center for Pulmonary Infections, Capital Medical University, Tsinghua University-Peking University Joint Center for Life Sciences, Beijing, P. R. China
| | - Yinmei Liu
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, Centre for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, P. R. China.,Institute of Respiratory Medicine, Chinese Academy of Medical Science, Beijing, P. R. China.,National Clinical Research Center for Respiratory Diseases, Capital Medical University, Beijing, P. R. China
| | - Binghuai Lu
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, Centre for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, P. R. China.,Institute of Respiratory Medicine, Chinese Academy of Medical Science, Beijing, P. R. China.,National Clinical Research Center for Respiratory Diseases, Capital Medical University, Beijing, P. R. China
| | - Bin Cao
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, Centre for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, P. R. China.,Institute of Respiratory Medicine, Chinese Academy of Medical Science, Beijing, P. R. China.,National Clinical Research Center for Respiratory Diseases, Capital Medical University, Beijing, P. R. China.,Clinical Center for Pulmonary Infections, Capital Medical University, Tsinghua University-Peking University Joint Center for Life Sciences, Beijing, P. R. China
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Impact of clinical guidance and rapid molecular pathogen detection on evaluation and outcomes of febrile or hypothermic infants. Infect Control Hosp Epidemiol 2020; 41:1285-1291. [PMID: 32880255 DOI: 10.1017/ice.2020.317] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
OBJECTIVE To quantify the impact of clinical guidance and rapid respiratory and meningitis/encephalitis multiplex polymerase chain reaction (mPCR) testing on the management of infants. DESIGN Before-and-after intervention study. SETTING Tertiary-care children's hospital. PATIENTS Infants ≤90 days old presenting with fever or hypothermia to the emergency department (ED). METHODS The study spanned 3 periods: period 1, January 1, 2011, through December 31, 2014; period 2, January 1, 2015, through April 30, 2018; and period 3, May 1, 2018, through June 15, 2019. During period 1, no standardized clinical guideline had been established and no rapid pathogen testing was available. During period 2, a clinical guideline was implemented, but no rapid testing was available. During period 3, a guideline was in effect, plus mPCR testing using the BioFire FilmArray respiratory panel 2 (RP 2) and the meningitis encephalitis panel (MEP). Outcomes included antimicrobial and ancillary test utilization, length of stay (LOS), admission rate, 30-day mortality. Outcomes were compared across periods using Kruskal-Wallis and Pearson tests and interrupted time series analysis. RESULTS Overall 5,317 patients were included: 2,514 in period 1, 2,082 in period 2, and 721 in period 3. Over the entire study period, we detected reductions in the use of chest radiographs, lumbar punctures, LOS, and median antibiotic duration. After adjusting for temporal trends, we observed that the introduction of the guideline was associated with reductions in ancillary tests and lumbar punctures. Use of mPCR testing with the febrile infant clinical guideline was associated with additional reductions in ancillary testing for all patients and a higher proportion of infants 29-60 days old being managed without antibiotics. CONCLUSIONS Use of mPCR testing plus a guideline for young infant evaluation in the emergency department was associated with less antimicrobial and ancillary test utilization compared to the use of a guideline alone.
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Durant TJS, Kubilay NZ, Reynolds J, Tarabar AF, Dembry LM, Peaper DR. Antimicrobial Stewardship Optimization in the Emergency Department: The Effect of Multiplex Respiratory Pathogen Testing and Targeted Educational Intervention. J Appl Lab Med 2020; 5:1172-1183. [DOI: 10.1093/jalm/jfaa130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 06/13/2020] [Indexed: 11/13/2022]
Abstract
Abstract
Background
Antibacterial agents are often prescribed for patients with suspected respiratory tract infections even though these are most often caused by viruses. In this study, we sought to evaluate the effect of Respiratory Pathogen Panel (RPP) PCR result availability and antimicrobial stewardship education on antibiotic prescription rates in the adult emergency department (ED).
Methods
We compared rates of antibacterial and oseltamivir prescriptions between 2 nonconsecutive influenza seasons among ED visits, wherein the latter season followed the implementation of a comprehensive educational stewardship campaign. In addition, we sought to elucidate the effect of RPP-PCR on antibiotic prescriptions, with focus on result availability prior to the conclusion of emergency department encounters.
Results
Antibiotic prescription rates globally decreased by 17.9% in the FS-17/18 cohort compared to FS-14/15 (P < 0.001), while oseltamivir prescription rates stayed the same overall (P = 0.42). Multivariate regression across both cohorts revealed that patients were less likely to receive antibiotics if RPP-PCR results were available before the end of the ED visit or if the RPP-PCR result was positive for influenza. Patients in the educational intervention cohort were also less likely to receive an antibiotic prescription.
Conclusion
This study provides evidence that RPP-PCR results are most helpful if available prior to the end of the provider-patient interaction. Further, these data suggest that detection of influenza remains an influential result in the context of antimicrobial treatment decision making. In addition, these data contribute to the body of literature which supports comprehensive ASP interventions including leadership and patient engagement.
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Affiliation(s)
| | | | | | - Asim F Tarabar
- Department of Emergency Medicine, Yale University, New Haven, CT
- VA Connecticut Healthcare System, West Haven, CT
| | - Louise M Dembry
- Department of Internal Medicine, Yale University, New Haven, CT
- Yale School of Public Health, New Haven, CT
- VA Connecticut Healthcare System, West Haven, CT
| | - David R Peaper
- Department of Laboratory Medicine, Yale University, New Haven, CT
- VA Connecticut Healthcare System, West Haven, CT
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Abstract
Syndromic panels have allowed clinical microbiology laboratories to rapidly identify bacteria, viruses, fungi, and parasites and are now fully integrated into the standard testing practices of many clinical laboratories. To maximize the benefit of syndromic testing, laboratories must implement strict measures to ensure that syndromic panels are being used responsibly. This article discusses commercially available syndromic panels, the benefits and limitations of testing, and how diagnostic and laboratory stewardship can be used to optimize testing and improve patient care while keeping costs at a minimum.
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Affiliation(s)
- Jennifer Dien Bard
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, 4650 Sunset Boulevard MS#32, Los Angeles, CA 90027, USA; University of Southern California, Keck School of Medicine.
| | - Erin McElvania
- Department of Pathology and Laboratory Medicine, Evanston Hospital, NorthShore University HealthSystem, 2650 Ridge Avenue, Evanston, IL 60201, USA; University of Chicago Pritzker School of Medicine. https://twitter.com/e_mcelvania
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50
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Qavi AJ, McMullen A, Burnham CAD, Anderson NW. Repeat Molecular Testing for Respiratory Pathogens: Diagnostic Gain or Diminishing Returns? J Appl Lab Med 2020; 5:897-907. [PMID: 32674131 PMCID: PMC7454602 DOI: 10.1093/jalm/jfaa029] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 01/02/2020] [Indexed: 01/05/2023]
Abstract
BACKGROUND Upper respiratory tract infections are common, and the ability to accurately and rapidly diagnose the causative pathogen has important implications for patient management. METHODS We evaluated the test-ordering practices for 2 commonly utilized nucleic acid amplification tests (NAATs) for the detection of respiratory pathogens: the Xpert Flu Assay for influenza A/B (Flu assay) and the Biofire FilmArray respiratory panel assay (RP assay), which detects 20 different targets. Our study examined repeat testing; that is, testing within 7 days from an initial test. RESULTS Our study found that repeat testing is common for each of the individual assays: 3.0% of all Flu assays and 10.0% of all RP assays were repeat testing. Of repeat testing, 8/293 (2.7%) of repeat Flu assays and 75/1257 (6.0%) of RP assays resulted diagnostic gains, i.e., new detections. However, for the RP assay, these new detections were not always clinically actionable. The most frequently discrepant organisms were rhinovirus/enterovirus (28/102, 27.5%), followed by respiratory syncytial virus (12/102, 11.8%) and coronavirus OC43 (11/102, 10.8%). Furthermore, there were 3,336 instances in which a patient was tested using both a Flu assay and RP assay, of which only 44 (1.3%) had discrepant influenza results. CONCLUSIONS Our findings suggest opportunities exist to better guide ordering practices for respiratory pathogen testing, including limiting repeat testing, with the goal of optimization of clinical yield, and diagnostic stewardship.
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Affiliation(s)
- Abraham J Qavi
- Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO
| | - Allison McMullen
- Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO
| | - Carey-Ann D Burnham
- Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO
| | - Neil W Anderson
- Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO
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