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      Clinical Utility of Advanced Microbiology Testing Tools

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          Abstract

          Advanced microbiology technologies are rapidly changing our ability to diagnose infections, improve patient care, and enhance clinical workflow. These tools are increasing the breadth, depth, and speed of diagnostic data generated per patient, and testing is being moved closer to the patient through rapid diagnostic technologies, including point-of-care (POC) technologies.

          ABSTRACT

          Advanced microbiology technologies are rapidly changing our ability to diagnose infections, improve patient care, and enhance clinical workflow. These tools are increasing the breadth, depth, and speed of diagnostic data generated per patient, and testing is being moved closer to the patient through rapid diagnostic technologies, including point-of-care (POC) technologies. While select stakeholders have an appreciation of the value/importance of improvements in the microbial diagnostic field, there remains a disconnect between clinicians and some payers and hospital administrators in terms of understanding the potential clinical utility of these novel technologies. Therefore, a key challenge for the clinical microbiology community is to clearly articulate the value proposition of these technologies to encourage payers to cover and hospitals to adopt advanced microbiology tests. Specific guidance on how to define and demonstrate clinical utility would be valuable. Addressing this challenge will require alignment on this topic, not just by microbiologists but also by primary care and emergency room (ER) physicians, infectious disease specialists, pharmacists, hospital administrators, and government entities with an interest in public health. In this article, we discuss how to best conduct clinical studies to demonstrate and communicate clinical utility to payers and to set reasonable expectations for what diagnostic manufacturers should be required to demonstrate to support reimbursement from commercial payers and utilization by hospital systems.

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          Most cited references51

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          Ongoing revolution in bacteriology: routine identification of bacteria by matrix-assisted laser desorption ionization time-of-flight mass spectrometry.

          Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry accurately identifies both selected bacteria and bacteria in select clinical situations. It has not been evaluated for routine use in the clinic. We prospectively analyzed routine MALDI-TOF mass spectrometry identification in parallel with conventional phenotypic identification of bacteria regardless of phylum or source of isolation. Discrepancies were resolved by 16S ribosomal RNA and rpoB gene sequence-based molecular identification. Colonies (4 spots per isolate directly deposited on the MALDI-TOF plate) were analyzed using an Autoflex II Bruker Daltonik mass spectrometer. Peptidic spectra were compared with the Bruker BioTyper database, version 2.0, and the identification score was noted. Delays and costs of identification were measured. Of 1660 bacterial isolates analyzed, 95.4% were correctly identified by MALDI-TOF mass spectrometry; 84.1% were identified at the species level, and 11.3% were identified at the genus level. In most cases, absence of identification (2.8% of isolates) and erroneous identification (1.7% of isolates) were due to improper database entries. Accurate MALDI-TOF mass spectrometry identification was significantly correlated with having 10 reference spectra in the database (P=.01). The mean time required for MALDI-TOF mass spectrometry identification of 1 isolate was 6 minutes for an estimated 22%-32% cost of current methods of identification. MALDI-TOF mass spectrometry is a cost-effective, accurate method for routine identification of bacterial isolates in or =10 reference spectra per bacterial species and a 1.9 identification score (Brucker system). It may replace Gram staining and biochemical identification in the near future.
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            Pathogen detection: a perspective of traditional methods and biosensors.

            The detection of pathogenic bacteria is key to the prevention and identification of problems related to health and safety. Legislation is particularly tough in areas such as the food industry, where failure to detect an infection may have terrible consequences. In spite of the real need for obtaining analytical results in the shortest time possible, traditional and standard bacterial detection methods may take up to 7 or 8 days to yield an answer. This is clearly insufficient, and many researchers have recently geared their efforts towards the development of rapid methods. The advent of new technologies, namely biosensors, has brought in new and promising approaches. However, much research and development work is still needed before biosensors become a real and trustworthy alternative. This review not only offers an overview of trends in the area of pathogen detection but it also describes main techniques, traditional methods, and recent developments in the field of pathogen bacteria biosensors.
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              Transforming clinical microbiology with bacterial genome sequencing.

              Whole-genome sequencing of bacteria has recently emerged as a cost-effective and convenient approach for addressing many microbiological questions. Here, we review the current status of clinical microbiology and how it has already begun to be transformed by using next-generation sequencing. We focus on three essential tasks: identifying the species of an isolate, testing its properties, such as resistance to antibiotics and virulence, and monitoring the emergence and spread of bacterial pathogens. We predict that the application of next-generation sequencing will soon be sufficiently fast, accurate and cheap to be used in routine clinical microbiology practice, where it could replace many complex current techniques with a single, more efficient workflow.
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                Author and article information

                Contributors
                On behalf of : on behalf of the ASM Clinical and Public Health Microbiology Committee and the ASM Corporate Council
                Role: Editor
                Journal
                J Clin Microbiol
                J. Clin. Microbiol
                jcm
                jcm
                JCM
                Journal of Clinical Microbiology
                American Society for Microbiology (1752 N St., N.W., Washington, DC )
                0095-1137
                1098-660X
                19 June 2019
                26 August 2019
                September 2019
                26 August 2019
                : 57
                : 9
                : e00495-19
                Affiliations
                [a ]University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
                [b ]Curetis USA Inc, San Diego, California, USA
                [c ]Washington School of Medicine, St. Louis, Missouri, USA
                [d ]Creighton University School of Medicine, Omaha, Nebraska, USA
                [e ]Texas Children’s Hospital, Houston, Texas, USA
                [f ]ClearView Healthcare Partners, Newton, Massachusetts, USA
                [g ]American Society for Microbiology, Washington, DC, USA
                [h ]Accelerate Diagnostics, Inc., Tucson, Arizona, USA
                [i ]Roche Diagnostics Corporation, Indianapolis, Indiana, USA
                [j ]University of Michigan Medical School, Ann Arbor, Michigan, USA
                [k ]Illumina, San Diego, California, USA
                [l ]Becton Dickinson, Diagnostics Systems, Sparks, Maryland, USA
                [m ]Genmark Diagnostics, Inc., Carlsbad, California, USA
                [n ]Children’s National Hospital, Washington, DC, USA
                Emory University
                Author notes
                Address correspondence to Melissa B. Miller, Melissa.Miller@ 123456unchealth.unc.edu , or Charles Mathews, charles.mathews@ 123456clearviewhcp.com .

                Citation Miller MB, Atrzadeh F, Burnham C-AD, Cavalieri S, Dunn J, Jones S, Mathews C, McNult P, Meduri J, Newhouse C, Newton D, Oberholzer M, Osiecki J, Pedersen D, Sweeney N, Whitfield N, Campos J, on behalf of the ASM Clinical and Public Health Microbiology Committee and the ASM Corporate Council. 2019. Clinical utility of advanced microbiology testing tools. J Clin Microbiol 57:e00495-19. https://doi.org/10.1128/JCM.00495-19.

                Article
                00495-19
                10.1128/JCM.00495-19
                6711927
                31217268
                62ac9333-905d-4596-9cb4-e8d05f1318c4
                Copyright © 2019 Miller et al.

                This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

                History
                Page count
                Figures: 2, Tables: 0, Equations: 0, References: 61, Pages: 13, Words: 8847
                Funding
                Funded by: ASM Corporate Council;
                Award Recipient : Award Recipient : Award Recipient :
                Funded by: Curetis;
                Award Recipient :
                Funded by: Accelerate Dx;
                Award Recipient :
                Funded by: Roche Diagnostics;
                Award Recipient : Award Recipient :
                Funded by: Becton Dickinson;
                Award Recipient :
                Funded by: GenMark Dx;
                Award Recipient :
                Funded by: Illumina, https://doi.org/10.13039/100010905;
                Award Recipient :
                Categories
                Minireview
                Custom metadata
                September 2019

                Microbiology & Virology
                clinical utility,evidence,health economics,molecular methods,outcomes research,reimbursement

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