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Erba A, Franzeck FC, Hinic V, Egli A, Osthoff M. Utilization of a Meningitis/Encephalitis PCR panel at the University Hospital Basel - a retrospective study to develop a diagnostic decision rule. Front Med (Lausanne) 2024; 11:1351903. [PMID: 38695026 PMCID: PMC11061443 DOI: 10.3389/fmed.2024.1351903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 04/05/2024] [Indexed: 05/04/2024] Open
Abstract
Background The Biofire® FilmArray® Meningitis/Encephalitis (ME) PCR panel covers 14 viral, bacterial, and fungal pathogens and has been implemented in many institutions worldwide. Post-marketing studies indicate a reduced sensitivity and overutilization underscoring the need for a more targeted usage. The aim of our study is to describe the utilization of the ME panel and to develop a diagnostic-stewardship based decision rule. Materials Adult patients, who underwent CSF analysis with the ME panel between August 2016 and June 2021 at the University Hospital Basel, were included. Demographic, clinical, microbiological, and laboratory data were extracted from the electronic health record. Factors associated with a positive ME panel result were identified, and a decision rule was developed to potentially optimize the diagnostic yield and reduce the number of unnecessary tests. Results 1,236 adult patients received at least one panel in the observed period, of whom 106 panels tested positive (8.6%). The most frequently observed pathogens were Varicella Zoster Virus (VZV, 27%), Streptococcus pneumoniae (19%), Enterovirus (16%), Herpes simplex Virus 1/2 (16%), and Human Herpesvirus 6 (HHV-6, 13%). Fever, vomiting, headache, and photophobia were more frequently present in test positive patients as were significantly higher CSF leukocytes and protein concentrations. When simulating a decision rule based on CSF leukocytes and protein concentration, only 35% of all patients would have qualified for a ME panel tests, thereby increasing the positivity rate to 22.7%. 10 of 106 positive ME panels would have been missed, only involving HHV-6 and VZV (6 and 4 cases, respectively). As these subjects were either severely immunocompromised or had clinical features of shingles we propose extending the testing algorithm by including those criteria. Conclusion The ME panel positivity rate at our institution was similar as previously published. Our results highlight the need for diagnostic-stewardship interventions when utilizing this assay by implementing a stepwise approach based on a limited number of clinical and laboratory features. This decision rule may improve the pretest probability of a positive test result, increase the quality of test utilization, and reduce costs.
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Affiliation(s)
- Andrea Erba
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Fabian C. Franzeck
- Clinical Data Warehouse, Research and Analytics Services, University Hospital Basel, Basel, Switzerland
| | - Vladimira Hinic
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
| | - Adrian Egli
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
| | - Michael Osthoff
- Department of Internal Medicine, University Hospital Basel, Basel, Switzerland
- Department of Internal Medicine, Cantonal Hospital Winterthur, Winterthur, Switzerland
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Barros N, Rosenblatt RE, Phipps MM, Fomin V, Mansour MK. Invasive fungal infections in liver diseases. Hepatol Commun 2023; 7:e0216. [PMID: 37639701 PMCID: PMC10462082 DOI: 10.1097/hc9.0000000000000216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 06/07/2023] [Indexed: 08/31/2023] Open
Abstract
Patients with liver diseases, including decompensated cirrhosis, alcohol-associated hepatitis, and liver transplant recipients are at increased risk of acquiring invasive fungal infections (IFIs). These infections carry high morbidity and mortality. Multiple factors, including host immune dysfunction, barrier failures, malnutrition, and microbiome alterations, increase the risk of developing IFI. Candida remains the most common fungal pathogen causing IFI. However, other pathogens, including Aspergillus, Cryptococcus, Pneumocystis, and endemic mycoses, are being increasingly recognized. The diagnosis of IFIs can be ascertained by the direct observation or isolation of the pathogen (culture, histopathology, and cytopathology) or by detecting antigens, antibodies, or nucleic acid. Here, we provide an update on the epidemiology, pathogenesis, diagnosis, and management of IFI in patients with liver disease and liver transplantation.
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Affiliation(s)
- Nicolas Barros
- Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Division of Infectious Diseases, Department of Medicine, Indiana University Health, Indianapolis, Indiana, USA
| | - Russell E. Rosenblatt
- Department of Gastroenterology and Hepatology, Weill Cornell Medicine, New York, New York, USA
| | - Meaghan M. Phipps
- Division of Digestive and Liver Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Vladislav Fomin
- Department of Gastroenterology and Hepatology, Weill Cornell Medicine, New York, New York, USA
| | - Michael K. Mansour
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
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Berkhout A, Cheng DR, McNab S, Lee LY, Daley AJ, Clifford V. Clinical and Health System Impact of Biofire Filmarray Meningitis/Encephalitis Routine Testing of CSF in a Pediatric Hospital: An Observational Study. Pediatr Infect Dis J 2023; 42:281-285. [PMID: 36728816 DOI: 10.1097/inf.0000000000003812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
BACKGROUND Rapid cartridge-based molecular test panels targeting multiple pathogens are increasingly available, improve pathogen detection and reduce turn-around-time but are more expensive than standard testing. Confirmation that these test panels contribute to improved patient or health service outcomes is required. METHODS In March 2021, our pediatric hospital laboratory implemented the BioFire Filmarray™ meningitis/encephalitis (M/E) panel as an additional routine test for all cerebrospinal fluid (CSF) samples collected from infants <90 days or from any patient in the emergency department. A retrospective chart review was done to ascertain changes in clinical outcomes, antimicrobial prescribing practices, and hospital length of stay, comparing two discrete 6-month periods: preimplementation (March-August 2019) and postimplementation (March-August 2021). RESULTS Both pre- and postimplementation groups were similar at baseline, except the preimplementation group had a higher proportion of infants with enterovirus and parechovirus meningitis. There was no significant difference between the groups in terms of median length of stay (2.94 vs 3.47 days, p = 0.41), duration of antibiotic treatment (2.0 vs 2.3 days, p = 0.25), need for central venous access (12.9% vs 17%, p = 0.38) or hospital-in-the-home admission (9.4% vs 9%, p = 0.92). A similar proportion of infants received aciclovir (33% vs 31%), however, a reduction in duration was observed (1.36 vs 0.90 days, p = 0.03) in the postimplementation period. CONCLUSIONS Introduction of the Biofire Filmarray™ M/E panel for routine testing of CSF samples reduced the duration of antiviral prescribing but had only a minor impact on antibiotic prescribing practices or health service outcomes in our pediatric hospital. The introduction of new laboratory testing needs to be supported by a comprehensive stewardship program to see optimal outcomes from new testing platforms.
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Affiliation(s)
- Angela Berkhout
- Laboratory Services, Royal Children's Hospital, Parkville, Victoria, Australia
- Murdoch Children's Research Institute, Parkville, Victoria, Australia
- General Medicine, Royal Children's Hospital, Parkville, Victoria, Australia
- The University of Queensland, Faculty of Medicine, Brisbane. Queensland, Australia
- Department of Paediatrics, University of Melbourne, Victoria, Australia
- Infection Management & Prevention Service, The Queensland Children's Hospital, Brisbane, Queensland, Australia
| | - Daryl R Cheng
- General Medicine, Royal Children's Hospital, Parkville, Victoria, Australia
- The University of Queensland, Faculty of Medicine, Brisbane. Queensland, Australia
- Department of Paediatrics, University of Melbourne, Victoria, Australia
| | - Sarah McNab
- General Medicine, Royal Children's Hospital, Parkville, Victoria, Australia
- The University of Queensland, Faculty of Medicine, Brisbane. Queensland, Australia
- Department of Paediatrics, University of Melbourne, Victoria, Australia
| | - Lai-Yang Lee
- Laboratory Services, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Andrew J Daley
- Laboratory Services, Royal Children's Hospital, Parkville, Victoria, Australia
- General Medicine, Royal Children's Hospital, Parkville, Victoria, Australia
- The University of Queensland, Faculty of Medicine, Brisbane. Queensland, Australia
| | - Vanessa Clifford
- Laboratory Services, Royal Children's Hospital, Parkville, Victoria, Australia
- Murdoch Children's Research Institute, Parkville, Victoria, Australia
- General Medicine, Royal Children's Hospital, Parkville, Victoria, Australia
- The University of Queensland, Faculty of Medicine, Brisbane. Queensland, Australia
- Department of Paediatrics, University of Melbourne, Victoria, Australia
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Tay E, Chen SCA, Green W, Lopez R, Halliday CL. Development of a Real-Time PCR Assay to Identify and Distinguish between Cryptococcus neoformans and Cryptococcus gattii Species Complexes. J Fungi (Basel) 2022; 8:jof8050462. [PMID: 35628719 PMCID: PMC9144077 DOI: 10.3390/jof8050462] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/25/2022] [Accepted: 04/27/2022] [Indexed: 02/04/2023] Open
Abstract
Cryptococcus neoformans and Cryptococcus gattii are the principle causative agents of cryptococcosis. Differences in epidemiological and clinical features, and also treatment, mean it is important for diagnostic laboratories to distinguish between the two species. Molecular methods are potentially more rapid than culture and cryptococcal antigen (CRAG) detection; however, commercial PCR-based assays that target Cryptococcus do not distinguish between species. Here, we developed a real-time PCR assay targeting the multicopy mitochondrial cytochrome b (cyt b) gene to detect C. neoformans and C. gattii in clinical specimens. Assay performance was compared with culture, histopathology, CRAG and panfungal PCR/DNA sequencing. The cyt b-directed assay accurately detected and identified all eight C. neoformans/gattii genotypes. High-resolution melt curve analysis unambiguously discriminated between the two species. Overall, assay sensitivity (96.4%) compared favorably with panfungal PCR (76.9%) and culture (14.5%); assay specificity was 100%. Of 25 fresh frozen paraffin embedded (FFPE) specimens, assay sensitivity was 96% (76% for panfungal PCR; 68% for histopathology). The Cryptococcus-specific PCR is a rapid (~4 h) sensitive method to diagnose (or exclude) cryptococcosis and differentiate between the two major species. It is suitable for use on diverse clinical specimens and may be the preferred molecular method for FFPE specimens where clinical suspicion of cryptococcosis is high.
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Affiliation(s)
- Enoch Tay
- Research Education Network, Western Sydney Local Health District, Westmead Hospital, Westmead, NSW 2145, Australia;
| | - Sharon C-A. Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, NSW 2145, Australia; (S.C.-A.C.); (W.G.); (R.L.)
| | - Wendy Green
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, NSW 2145, Australia; (S.C.-A.C.); (W.G.); (R.L.)
| | - Ronald Lopez
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, NSW 2145, Australia; (S.C.-A.C.); (W.G.); (R.L.)
| | - Catriona L. Halliday
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, NSW 2145, Australia; (S.C.-A.C.); (W.G.); (R.L.)
- Correspondence: ; Tel.: +61-2-8890-6255
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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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Bridge S, Hullsiek KH, Nerima C, Evans EE, Nuwagira E, Stadelman AM, Tran T, Kim G, Tadeo KK, Kwizera R, Mwesigye J, Ellis J, Cresswell FV, Meya DB, Muzoora C, Boulware DR, Rhein J. Evaluation of the BioFire® FilmArray® Meningitis/Encephalitis panel in an adult and pediatric Ugandan population. J Mycol Med 2021; 31:101170. [PMID: 34246087 PMCID: PMC9983612 DOI: 10.1016/j.mycmed.2021.101170] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 06/06/2021] [Accepted: 06/22/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Meningitis causes significant mortality in sub-Saharan Africa and limited diagnostics exist. We evaluated the utility of the BioFire® FilmArray® Meningitis/Encephalitis multiplex PCR panel (BioFire ME) in HIV-infected adults and HIV-infected and uninfected children presenting with suspected meningitis in Uganda. METHODS We tested cerebrospinal fluid (CSF) using a stepwise meningitis diagnostic algorithm including BioFire ME. We determined the diagnostic performance of BioFire ME for cryptococcal meningitis, using cryptococcal antigen (CrAg) and CSF culture as reference standards, and assessed other central nervous system (CNS) pathogens identified by the panel. RESULTS We evaluated 328 adult and 42 pediatric CSF specimens using BioFire ME. Of the adult CSF samples tested, 258 were obtained at baseline, and 70 were obtained from repeat lumbar punctures in cryptococcal meningitis. For Cryptococcus, sensitivity was 82%, specificity was 98%, PPV was 98%, and NPV was 79% in baseline specimens using CSF CrAg as the reference standard. Among follow-up specimens, a negative BioFire ME for Cryptococcus predicted CSF culture sterility with 84% NPV. Overall sensitivity was decreased at low fungal burdens: 29% for 0-99 Cryptococcus CFU/mL compared to 94% for ≥100 CFU/mL in baseline specimens. Other pathogens detected included E. Coli, H. influenzae, S. pneumoniae, CMV, enterovirus, HSV, HHV-6, and VZV. Two specimens tested positive for S. pneumoniae and one for Cryptococcus in the pediatric population. CONCLUSIONS Multiplex PCR is a promising rapid diagnostic test for meningitis in adults and children in resource-limited settings. Cryptococcus at low fungal burdens in CSF may be missed by BioFire ME.
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Affiliation(s)
- Sarah Bridge
- Mbarara University of Science and Technology, P.O Box 1410, Mbarara, Uganda; University of Minnesota, 689 23rd Ave SE, Minneapolis 55455, MN, United States; University of Virginia, Charlottesville, VA, United States.
| | | | - Carol Nerima
- Mbarara University of Science and Technology, P.O Box 1410, Mbarara, Uganda
| | - Emily E Evans
- Mbarara University of Science and Technology, P.O Box 1410, Mbarara, Uganda; University of Minnesota, 689 23rd Ave SE, Minneapolis 55455, MN, United States
| | - Edwin Nuwagira
- Mbarara University of Science and Technology, P.O Box 1410, Mbarara, Uganda
| | - Anna M Stadelman
- Mbarara University of Science and Technology, P.O Box 1410, Mbarara, Uganda; University of Minnesota, 689 23rd Ave SE, Minneapolis 55455, MN, United States
| | - Tu Tran
- Mbarara University of Science and Technology, P.O Box 1410, Mbarara, Uganda; University of Minnesota, 689 23rd Ave SE, Minneapolis 55455, MN, United States
| | - Grace Kim
- University of Virginia, Charlottesville, VA, United States
| | - Kiiza K Tadeo
- Infectious Disease Institute, College of Health Sciences, Makerere University, PO Box 22418, Kampala, Uganda
| | - Richard Kwizera
- Infectious Disease Institute, College of Health Sciences, Makerere University, PO Box 22418, Kampala, Uganda
| | - James Mwesigye
- Mbarara University of Science and Technology, P.O Box 1410, Mbarara, Uganda
| | - Jayne Ellis
- Infectious Disease Institute, College of Health Sciences, Makerere University, PO Box 22418, Kampala, Uganda; Hospital for Tropical Diseases, University College London, NHS Foundation Trust, London, United Kingdom
| | - Fiona V Cresswell
- Infectious Disease Institute, College of Health Sciences, Makerere University, PO Box 22418, Kampala, Uganda; Clinical Research Department, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E, 7HT, United Kingdom; UVRI-MRC London School of Hygiene and Tropical Medicine Research Unit, Entebbe, Uganda
| | - David B Meya
- Infectious Disease Institute, College of Health Sciences, Makerere University, PO Box 22418, Kampala, Uganda
| | - Conrad Muzoora
- Mbarara University of Science and Technology, P.O Box 1410, Mbarara, Uganda
| | - David R Boulware
- University of Minnesota, 689 23rd Ave SE, Minneapolis 55455, MN, United States.
| | - Joshua Rhein
- University of Minnesota, 689 23rd Ave SE, Minneapolis 55455, MN, United States; Infectious Disease Institute, College of Health Sciences, Makerere University, PO Box 22418, Kampala, Uganda
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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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Chong BSW, Kennedy KJ. Comparison of a commercial real-time PCR panel to routine laboratory methods for the diagnosis of meningitis-encephalitis. Pathology 2021; 53:635-638. [PMID: 33472744 DOI: 10.1016/j.pathol.2020.09.029] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 09/08/2020] [Accepted: 09/20/2020] [Indexed: 11/26/2022]
Abstract
Meningitis-encephalitis can range from a mild, self limiting illness to a life threatening disease. Rapid microbial diagnosis allows for early targeted management. This study aimed to compare the BioFire FilmArray Meningitis/Encephalitis multiplex PCR panel (ME panel) to traditional testing algorithms for accuracy and turnaround time in the diagnosis of meningitis-encephalitis. From April to November 2018, cerebrospinal fluid (CSF) samples meeting existing laboratory testing criteria for suspected community acquired meningitis-encephalitis were tested on the ME panel and by routine laboratory methods. The methods were compared for accuracy of diagnosis and turnaround time. Where an organism was not identified, the study investigators came to a consensus on whether an infective aetiology was likely based on CSF parameters, clinical features, management and final discharge diagnosis. A total of 147 CSF samples met criteria for testing. Results were concordant in 143 (97%) of cases, including 27 samples where the same organism was identified by both methods. Of the four discordant samples, three organisms identified by the ME panel alone were considered clinically insignificant. One sample, which was culture and antigen positive for Cryptococcus neoformans, was not detected on the ME panel. The ME panel and routine methods identified an organism in 55% and 58% of clinically compatible cases of infection, respectively. The median turnaround time for the ME panel was 2.9 hours, compared to 21.1 hours for routine testing. The ME panel showed high concordance with traditional testing, simplified laboratory workflow, and significantly reduced turnaround time. The failure of the ME panel to detect Cryptococcus spp. is concerning. When cryptococcal meningitis is suspected, we would recommend using culture and cryptococcal antigen testing as the investigations of choice. Despite the availability of molecular assays targeting the common causes of CNS infection, the diagnostic yield remains suboptimal.
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Affiliation(s)
- B S W Chong
- Department of Clinical Microbiology, ACT Pathology, Canberra Hospital, Garran, ACT, Australia.
| | - K J Kennedy
- Department of Clinical Microbiology, ACT Pathology, Canberra Hospital, Garran, ACT, Australia; Department of Infectious Diseases, Canberra Hospital, Garran, ACT, Australia; Australian National University Medical School, Canberra Hospital, Canberra, ACT, Australia
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Lewis PO, Lanier CG, Patel PD, Krolikowski WD, Krolikowski MA. False negative diagnostic errors with polymerase chain reaction for the detection of cryptococcal meningoencephalitis. Med Mycol 2020; 58:408-410. [PMID: 31212317 DOI: 10.1093/mmy/myz064] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 05/13/2019] [Accepted: 05/20/2019] [Indexed: 01/22/2023] Open
Abstract
The accuracy of the BioFire FilmArray Meningitis/Encephalitis (ME) panel for the identification of Cryptococcus has recently been called into question. The primary objective of this study was to assess the agreement between the BioFire ME polymerase chain reaction (PCR) and other markers of cryptococcal infection. This retrospective review identified five patients with cryptococcal meningoencephalitis, 4 of whom had a negative ME panel for Cryptococcus. All five cases had positive serum cryptococcal antigens, and three of five had a positive cerebrospinal fluid (CSF) culture for Cryptococcus. The BioFire ME panel does not appear to be reliable for ruling out Cryptococcus meningoencephalitis; multiple testing methods are recommended.
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Affiliation(s)
- Paul O Lewis
- Johnson City Medical Center, Department of Pharmacy, Johnson City, TN, 37604, USA
| | - Cameron G Lanier
- Bill Gatton College of Pharmacy at East Tennessee State University, Department of Pharmacy Practice, Johnson City, TN, 37614, USA
| | - Paras D Patel
- East Tennessee State University, Quillen College of Medicine, Division of Infectious Diseases, Johnson City TN, 37614, USA
| | - Whitney D Krolikowski
- East Tennessee State University, Quillen College of Medicine, Division of Infectious Diseases, Johnson City TN, 37614, USA
| | - Matthew A Krolikowski
- East Tennessee State University, Quillen College of Medicine, Division of Infectious Diseases, Johnson City TN, 37614, USA
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10
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Update on fungal infections of the central nervous system: emerging pathogens and emerging diagnostics. Curr Opin Infect Dis 2020; 32:277-284. [PMID: 30921084 DOI: 10.1097/qco.0000000000000541] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
PURPOSE OF REVIEW Fungal infections of the central nervous system (CNS) are relatively uncommon but associated with significant morbidity and mortality. We reviewed recent literature highlighting new approaches to management of these complex patients. RECENT FINDINGS Fungal infections are increasingly recognized as important causes of CNS disease in both immunocompromised and immunocompetent hosts. Globally, cryptococcal meningitis remains a leading cause of death in HIV-infected persons in resource-limited settings. Emerging fungal pathogens with increased virulence and resistance to numerous classes of antifungal agents have been identified and represent a management challenge. Newer diagnostic techniques focused on antigen detection or molecular amplification of fungal pathogens offer promise in the expediated diagnosis and treatment of CNS fungal infections. SUMMARY Meningitis and brain abscess because of invasive fungal pathogens are frequently fatal infections. Newer laboratory tests allowing antigen detection or molecular amplification from cerebrospinal fluid are more sensitive than culture and allow earlier initiation of effective therapy.
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11
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Van TT, Kim TH, Butler-Wu SM. Evaluation of the Biofire FilmArray meningitis/encephalitis assay for the detection of Cryptococcus neoformans/gattii. Clin Microbiol Infect 2020; 26:1375-1379. [PMID: 31972318 DOI: 10.1016/j.cmi.2020.01.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 01/06/2020] [Accepted: 01/07/2020] [Indexed: 01/09/2023]
Abstract
OBJECTIVES Cryptococcal meningitis (CM) remains an important cause of morbidity and mortality among immunocompromised patients. Laboratory diagnostics for CM includes antigen detection, staining and culture. Data on the performance of the Biofire® FilmArray® meningitis/encephalitis (ME) panel for detecting Cryptococcus neoformans/gattii is limited, with several reports describing false negativity for this target. METHODS A retrospective analysis of 1384 physician-ordered ME panel tests ordered between January 2017 to October 2018 was performed. ME panel results were compared to cerebrospinal fluid (CSF) cryptococcal antigen (CrAg) and CSF culture testing and clinical significance of cryptococcal detection was determined. RESULTS There were 34 patients positive for cryptococcal detection by either ME panel, CSF CrAg or CSF culture in 2.7% of CSF specimens tested (38/1384). Of the 34 patients positive for cryptococcal detection, 85.3% were human immunodeficiency virus positive (29/34). The ME panel detected 32/38 (84.2%) cryptococcal-positive specimens, culture detected 28/38 (73.7%) and CSF CrAg was positive in 37/38 specimens (97.4%). The ME panel had a sensitivity and specificity of 96.4% (95% CI 81.7-99.9%) and 99.6% (95% CI 99.2-99.9%) compared with culture, and 83.8% (95% CI 68.0-93.8%) and 99.9% (95% CI 99.6-100.0%) compared to CSF CrAg testing, respectively. CrAg titres were lower among ME panel-negative, culture-negative specimens compared with ME panel-positive, culture-negative specimens (reciprocal median end-point titres of 128 ± 60 vs. 1920 ± 1730, p 0.04). All five CrAg-positive, ME panel- and culture-negative specimens were obtained from previously treated CM patients. DISCUSSION The ME panel had high correlation with CSF culture and a somewhat lower correlation with CSF CrAg testing. The potential utility of using negative ME panel test results to predict culture sterility among patients undergoing treatment for CM warrants further study.
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Affiliation(s)
- T T Van
- Department of Pathology, Harbor-UCLA Medical Center, Torrance, CA, USA; Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - T H Kim
- Department of Pathology and Laboratory Medicine, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - S M Butler-Wu
- Department of Pathology and Laboratory Medicine, Keck School of Medicine of USC, Los Angeles, CA, USA.
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Vetter P, Schibler M, Herrmann JL, Boutolleau D. Diagnostic challenges of central nervous system infection: extensive multiplex panels versus stepwise guided approach. Clin Microbiol Infect 2019; 26:706-712. [PMID: 31899336 DOI: 10.1016/j.cmi.2019.12.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 12/20/2019] [Accepted: 12/22/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND Cerebrospinal fluid (CSF) testing is a key component for the diagnosis of central nervous system (CNS) infections. Current meningitis and encephalitis management guidelines agree on the need for CSF molecular testing in combination with other direct and indirect biological testing, both in CSF and blood. Multiplex molecular tests have been developed to reduce turnaround times and facilitate the diagnostic approach. OBJECTIVES We aim to discuss the role of multiplex molecular panels in the management of CNS infections. SOURCES The MEDLINE database and the grey literature have been searched for relevant articles. CONTENT New molecular multiplex panels are being developed to simultaneously detect a large array of neuropathogens in CSF. Although one of these assays has been US Food and Drug Administration-approved, extensive analytical and clinical validation is still missing, and suboptimal performance related issues have been raised. Its use has been associated with decreased costs, reduced length of hospital stay and reduced antiviral therapy administration in retrospective, industry-sponsored studies. The pros and cons of this multiplex syndromic approach are discussed in this narrative review. IMPLICATIONS Molecular multiplex CNS infection diagnosis panels have been developed and present several attractive features, including ease of use and low turnaround time. However, suboptimal analytical performances render these tests difficult to use without additional confirmatory tests. Such panels are not comprehensive nor adapted to all situations, depending on the epidemiological or clinical context. Overall, available data in the literature currently do not support the use of a multiplex PCR panel in clinical routine as a 'stand-alone' molecular assay. Except in restricted laboratory capacity settings where such easy-to-use multiplex panels offer the diagnostic means that would otherwise not be available, the stepwise testing approach remains a more rational option. Serological testing both in blood and CSF should not be neglected, but it represents essential complementary tools regarding some neuropathogens.
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Affiliation(s)
- P Vetter
- Laboratory of Virology, Geneva University Hospitals, Geneva, Switzerland; Infectious Diseases Division, Geneva University Hospitals, Geneva, Switzerland.
| | - M Schibler
- Laboratory of Virology, Geneva University Hospitals, Geneva, Switzerland; Infectious Diseases Division, Geneva University Hospitals, Geneva, Switzerland
| | - J L Herrmann
- 2I, UVSQ, INSERM, Université Paris Saclay, Versailles France; AP-HP, GHU Paris Saclay, Hôpital Raymond Poincaré, Garches, France
| | - D Boutolleau
- Sorbonne Université, INSERM, Institut Pierre Louis D'Epidémiologie et de Santé Publique (iPLESP), Paris, France; AP-HP, GHU AP-HP. Sorbonne Université, Hôpitaux Universitaires Pitié-Salpêtrière - Charles Foix, Virology Department, National Reference Center for Herpesviruses (associate Laboratory), Paris, France
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Abstract
Patients with central nervous system (CNS) infection experience very high levels of morbidity and mortality, in part because of the many challenges inherent to the diagnosis of CNS infection and identification of a causative pathogen. The clinical presentation of CNS infection is nonspecific, so clinicians must often order and interpret many diagnostic tests in parallel. This can be a daunting task given the large number of potential pathogens and the availability of different testing modalities. Here, we review traditional diagnostic techniques including Gram stain and culture, serology, and polymerase chain reaction (PCR). We highlight which of these are recommended for the pathogens most commonly tested among U.S. patients with suspected CNS infection. Finally, we describe the newer broad-range diagnostic approaches, multiplex PCR and metagenomic sequencing, which are increasingly used in clinical practice.
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Affiliation(s)
- Sanjat Kanjilal
- Division of Infectious Diseases, Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts.,Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts
| | - Tracey A Cho
- Department of Neurology, University of Iowa Hospitals and Clinics, Iowa City, Iowa
| | - Anne Piantadosi
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts
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