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Jose Lucar, Rebecca Yee. Diagnostic Stewardship for Multiplex Respiratory Testing: What We Know and What Needs to Be Done. Clin Lab Med 2024; 44:45-61. [PMID: 38280797 DOI: 10.1016/j.cll.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2024]
Abstract
Syndromic respiratory panels are now widely available in clinical microbiology laboratories and health care institutions. These panels can rapidly diagnose infections and detect antimicrobial resistance genes allowing for more rapid therapeutic optimization compared to standard microbiology approaches. However, given reimbursement concerns and limitations of multiplex molecular testing and results interpretation, maximum clinical utility and positive clinical outcomes depend on active diagnostic stewardship. Here, the authors review clinical outcomes of both upper and lower respiratory panels and present diagnostic stewardship strategies for optimal use of respiratory panels.
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Affiliation(s)
- Jose Lucar
- Division of Infectious Diseases, George Washington University School of Medicine and Health Sciences, 2150 Pennsylvania Avenue Northeast, Washington, DC 20037, USA
| | - Rebecca Yee
- Department of Pathology, George Washington University School of Medicine and Health Sciences, 900 23rd Street Northwest, Washington, DC 20037, USA.
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Cojuc-Konigsberg G, Moscona-Nissan A, Guijosa A, Mireles Dávalos CD, Martínez MEJ, Mújica Sánchez MA, Hernández Huizar VF, Durán Barrón MA, Gómez KV, Andrade-Galindo R, Ordóñez-Oviedo M, Brito GD, Vargas EB. Diagnostic accuracy of the BioFire® FilmArray® pneumonia panel in COVID-19 patients with ventilator-associated pneumonia. BMC Infect Dis 2023; 23:524. [PMID: 37559032 PMCID: PMC10413519 DOI: 10.1186/s12879-023-08486-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 07/26/2023] [Indexed: 08/11/2023] Open
Abstract
BACKGROUND Ventilator-Associated pneumonia (VAP) is one of the leading causes of morbidity and mortality in critically ill COVID-19 patients in lower-and-middle-income settings, where timely access to emergency care and accurate diagnostic testing is not widely available. Therefore, rapid microbiological diagnosis is essential to improve effective therapy delivery to affected individuals, preventing adverse outcomes and reducing antimicrobial resistance. METHODS We conducted a cross-sectional study of patients with suspected VAP and COVID-19, evaluating the diagnostic performance of the BioFire® FilmArray® Pneumonia Panel (FA-PP). Respiratory secretion samples underwent standard microbiological culture and FA-PP assays, and the results were compared. RESULTS We included 252 samples. The traditional culture method detected 141 microorganisms, and FA-PP detected 277, resulting in a sensitivity of 95% and specificity of 60%, with a positive predictive value of 68% and negative predictive value of 93%. In samples with high levels of genetic material (> 10^5 copies/mL), the panel had a sensitivity of 94% and specificity of 86%. In addition, 40% of the culture-negative samples had positive FA-PP® results, of which 35% had > 10^5 copies/mL of genetic material. The most prevalent bacteria were Gram-negative bacilli, followed by Gram-positive cocci. The panel identified 98 genes associated with antimicrobial resistance, predominantly extended-spectrum beta-lactamases (28%). CONCLUSION The FA-PP is a sensitive assay for identifying bacteria causing VAP in patients with COVID-19, with a greater capacity to detect bacteria than the conventional method. The timely microbiological recognition offered by this panel could lead to optimized decision-making processes, earlier tailored treatment initiation, and improved antibiotic stewardship practices.
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Affiliation(s)
- Gabriel Cojuc-Konigsberg
- Clinical Microbiology Laboratory, National Institute of Respiratory Diseases, Mexico City, Mexico
- Health Sciences Faculty, Universidad Anahuac Mexico, Mexico City, Mexico
| | - Alberto Moscona-Nissan
- School of Medicine, Universidad Panamericana, Insurgentes Mixcoac, Donatello 59, 03920, Mexico City, Mexico
| | - Alberto Guijosa
- School of Medicine, Universidad Panamericana, Insurgentes Mixcoac, Donatello 59, 03920, Mexico City, Mexico
| | | | - María E Jiménez Martínez
- Clinical Microbiology Laboratory, National Institute of Respiratory Diseases, Mexico City, Mexico
| | - Mario A Mújica Sánchez
- Clinical Microbiology Laboratory, National Institute of Respiratory Diseases, Mexico City, Mexico
| | | | - Martha A Durán Barrón
- Clinical Microbiology Laboratory, National Institute of Respiratory Diseases, Mexico City, Mexico
| | - Karen Villarreal Gómez
- Clinical Microbiology Laboratory, National Institute of Respiratory Diseases, Mexico City, Mexico
| | | | - Montserrat Ordóñez-Oviedo
- School of Medicine, Universidad Panamericana, Insurgentes Mixcoac, Donatello 59, 03920, Mexico City, Mexico
| | - Grecia Deloya Brito
- Clinical Microbiology Laboratory, National Institute of Respiratory Diseases, Mexico City, Mexico
| | - Eduardo Becerril Vargas
- Clinical Microbiology Laboratory, National Institute of Respiratory Diseases, Mexico City, Mexico.
- Health Sciences Faculty, Universidad Anahuac Mexico, Mexico City, Mexico.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Vila J, Bosch J, Muñoz-Almagro C. Molecular diagnosis of the central nervous system (CNS) infections. ACTA ACUST UNITED AC 2021; 39:403-410. [PMID: 34620475 DOI: 10.1016/j.eimce.2020.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 03/09/2020] [Indexed: 11/17/2022]
Abstract
Central nervous system (CNS) infections such as meningitis and encephalitis are medical emergencies that require rapid diagnosis of the causative pathogen to guide early and adequate treatment since a delay in implementing an adequate antimicrobial therapy can lead to death. The current microbiological diagnostic methods based on culture or antigen detection have important limitations in their capacity to accurately identify the different potential pathogens causing CNS and, in the time, to obtaining results. Rapid syndromic molecular arrays have been developed. The main advantage of using a meningoencephalitis panel based in a multiplex test is that includes bacteria, viruses and fungi, covering the most prevalent microorganisms causing meningitis and encephalitis and the turn-around time is circa 1h. The use of these multiplex-PCR based tools is reviewed and the advantages and disadvantages of this technique are discussed.
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Affiliation(s)
- Jordi Vila
- Department of Clinical Microbiology, Hospital Clinic, University of Barcelona, Barcelona, Spain; Institute of Global Health of Barcelona (ISGlobal), Barcelona, Spain; Spanish Network for Research in Infectious Diseases, REIPI, Instituto de Salud Carlos III, Madrid, Spain.
| | - Jordi Bosch
- Department of Clinical Microbiology, Hospital Clinic, University of Barcelona, Barcelona, Spain; Institute of Global Health of Barcelona (ISGlobal), Barcelona, Spain; Spanish Network for Research in Infectious Diseases, REIPI, Instituto de Salud Carlos III, Madrid, Spain
| | - Carmen Muñoz-Almagro
- Department of Molecular Microbiology, Hospital Sant Joan de Deu, Barcelona, Spain; School of Medicine, Universitat Internacional de Catalunya, Barcelona, Spain; Spanish Network of Epidemiology and Public Health, CIBERESP, Instituto de Salud Carlos III, Madrid, Spain
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Vila J, Bosch J, Muñoz-Almagro C. Molecular diagnosis of the central nervous system (CNS) infections. Enferm Infecc Microbiol Clin 2020; 39:S0213-005X(20)30168-3. [PMID: 32345489 DOI: 10.1016/j.eimc.2020.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 02/27/2020] [Accepted: 03/09/2020] [Indexed: 10/24/2022]
Abstract
Central nervous system (CNS) infections such as meningitis and encephalitis are medical emergencies that require rapid diagnosis of the causative pathogen to guide early and adequate treatment since a delay in implementing an adequate antimicrobial therapy can lead to death. The current microbiological diagnostic methods based on culture or antigen detection have important limitations in their capacity to accurately identify the different potential pathogens causing CNS and, in the time, to obtaining results. Rapid syndromic molecular arrays have been developed. The main advantage of using a meningoencephalitis panel based in a multiplex test is that includes bacteria, viruses and fungi, covering the most prevalent microorganisms causing meningitis and encephalitis and the turn-around time is circa 1h. The use of these multiplex-PCR based tools is reviewed and the advantages and disadvantages of this technique are discussed.
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Affiliation(s)
- Jordi Vila
- Department of Clinical Microbiology, Hospital Clinic, University of Barcelona, Barcelona, Spain; Institute of Global Health of Barcelona (ISGlobal), Barcelona, Spain; Spanish Network for Research in Infectious Diseases, REIPI, Instituto de Salud Carlos III, Madrid, Spain.
| | - Jordi Bosch
- Department of Clinical Microbiology, Hospital Clinic, University of Barcelona, Barcelona, Spain; Institute of Global Health of Barcelona (ISGlobal), Barcelona, Spain; Spanish Network for Research in Infectious Diseases, REIPI, Instituto de Salud Carlos III, Madrid, Spain
| | - Carmen Muñoz-Almagro
- Department of Molecular Microbiology, Hospital Sant Joan de Deu, Barcelona, Spain; School of Medicine, Universitat Internacional de Catalunya, Barcelona, Spain; Spanish Network of Epidemiology and Public Health, CIBERESP, Instituto de Salud Carlos III, Madrid, Spain
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Abstract
Purpose of Review Major technologic advances in two main areas of molecular infectious disease diagnostics have resulted in accelerated adoption or ordering, outpacing implementation, and clinical utility studies. Physicians must understand the limitations to and appropriate utilization of these technologies in order to provide cost-effective and well-informed care for their patients. Recent Findings Rapid molecular testing and, to a lesser degree, clinical metagenomics are now being routinely used in clinical practice. While these tests allow for a breadth of interrogation not possible with conventional microbiology, they pose new challenges for diagnostic and antimicrobial stewardship programs. This review will summarize the most recent literature on these two categories of technologic advances and discuss the few studies that have looked at utilization and stewardship approaches. This review also highlights the future directions for both of these technologies. Summary The appropriate utilization of rapid molecular testing and clinical metagenomics has not been well established. More studies are needed to assess their prospective impacts on patient management and antimicrobial stewardship efforts as the future state of infectious disease diagnostics will see continued expansion of these technologic advances.
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Zimmermann S, Horner S, Altwegg M, Dalpke AH. Workflow optimization for syndromic diarrhea diagnosis using the molecular Seegene Allplex™ GI-Bacteria(I) assay. Eur J Clin Microbiol Infect Dis 2020; 39:1245-50. [PMID: 32026192 DOI: 10.1007/s10096-020-03837-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 01/29/2020] [Indexed: 12/24/2022]
Abstract
Syndromic panel-based molecular testing has been suggested to improve and accelerate microbiological diagnosis. We aimed to analyze workflow improvements when using the multiplex Seegene Allplex™ GI-Bacteria(I) assay as a first-line assay for bacterial diarrhea. Technical assay evaluation was done using spiked stool samples and stored patient samples. After implementation of the assay in the routine clinical workflow, an analysis of 5032 clinical samples analyzed by the Seegene assay and 4173 control samples examined by culture in a similar time period 1 year earlier was performed. Sensitivity of the assay was shown to be between 0.4 and 95.9 genome equivalents/PCR. For 159 positive patient samples with a composite reference of culture and/or a molecular assay, the sensitivity of the assay was 100% for Campylobacter, 92% for Salmonella, 89% for Aeromonas, and 83% for Shigella. Sensitivity for C. difficile toxin B detection was 93.9%. The comparison of clinical samples obtained in two 8-month periods showed increased detection rates for Aeromonas (2.90%vs. 0.34%), Campylobacter spp. (2.25% vs. 1.34%), Shigella spp. (0.42% vs. 0.05%) whereas detection of Salmonella was slightly decreased (0.46% vs. 0.67%) when using the Seegene assay. An analysis of the time-to-result showed that the median dropped from 52.7 to 26.4 h when using the molecular panel testing. The Seegene Allplex™ GI-Bacteria(I) assay allows accelerated, reliable detection of major gastrointestinal bacteria roughly within 1 day. Workload is reduced, specifically in a low-prevalence setting.
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