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Long B, Lacy AJ, Koyfman A, Liang SY. Candida auris: A focused review for emergency clinicians. Am J Emerg Med 2024; 84:162-167. [PMID: 39137491 DOI: 10.1016/j.ajem.2024.07.062] [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: 07/05/2024] [Revised: 07/25/2024] [Accepted: 07/28/2024] [Indexed: 08/15/2024] Open
Abstract
INTRODUCTION Candida auris is an emerging pathogen and human health threat. However, diagnosis and treatment of fungal infection due to C. auris are challenging. OBJECTIVE This narrative review provides a focused overview of C. auris for the emergency clinician. DISCUSSION C. auris was first identified in 2009 and is currently present on all continents except Antarctica. C. auris possesses multiple genetic factors resulting in antimicrobial resistance, increased virulence and survival within the host, and environmental adaptation. It is readily transmitted from person to person and from the environment to a person, resulting in colonization. Infection may develop days to months following colonization, most commonly in those with immunocompromised state, significant comorbidities or other underlying conditions, healthcare exposure, and recent antimicrobial therapy. Candidemia, device infection (e.g., central venous catheter), soft tissue or wound infection, burn infection, osteomyelitis, myocarditis, meningitis, and urinary tract infection have been associated with C. auris. Samples should be obtained from the suspected site of infection for microbiological culture. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) with reference databases to differentiate C. auris from other species is optimal for diagnosis, though other molecular testing methods are available. Treatment is challenging due to antifungal resistance, with over 90% resistant to fluconazole. Echinocandins are most commonly used as the first line therapy. Prevention of colonization and infection are vital and include screening in high-risk populations and strict adherence to infection prevention practices with contact precautions and hand hygiene, as well as appropriate decontamination of patient areas. CONCLUSION An understanding of C. auris can assist emergency clinicians in the care of infected or colonized patients.
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Affiliation(s)
- Brit Long
- SAUSHEC, Emergency Medicine, Brooke Army Medical Center, Fort Sam Houston, TX, United States.
| | - Aaron J Lacy
- Division of Emergency Medicine Washington University School of Medicine, 660 S. Euclid Ave, St. Louis, MO, United States
| | - Alex Koyfman
- Department of Emergency Medicine, UT Southwester, Dallas, TX, United States
| | - Stephen Y Liang
- Divisions of Emergency Medicine and Infectious Diseases, Washington University School of Medicine, 660 S. Euclid Ave, St. Louis, MO, United States.
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Thomas JK, Clark J, Arora V, Burgess DS, Burgess DR, Mynatt RP, VanHoose JD, Wallace KL, Cotner SE. Performance of ePlex® blood culture identification panels in clinical isolates and characterization of antimicrobial stewardship opportunities. Diagn Microbiol Infect Dis 2024; 109:116269. [PMID: 38692201 DOI: 10.1016/j.diagmicrobio.2024.116269] [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: 08/03/2023] [Revised: 03/08/2024] [Accepted: 03/14/2024] [Indexed: 05/03/2024]
Abstract
We assessed the performance of GenMark's ePlex® Blood Culture Identification (BCID) Panels for overall agreement of organism identification and resistance mechanism detection with standard microbiologic methods. This study included patients with a positive blood culture from May 2020 to January 2021. The primary outcomes were to assess concordance of ePlex® organism identification with standard identification methods and concordance of ePlex® genotypic resistance mechanism detection with standard phenotypic susceptibility testing. Secondary outcomes included panel specific performance and characterization of antimicrobial stewardship opportunities. The overall identification concordance rate in 1276 positive blood cultures was 98.1%. The overall concordance for the presence of resistance markers was 98.2% and concordance for the absence of resistance markers was 100%. A majority of ePlex® results (69.5%) represented opportunities for potential antimicrobial stewardship intervention. High concordance rates between the ePlex® BCID panels and standard identification and susceptibility methods enable utilization of results to guide rapid antimicrobial optimization.
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Affiliation(s)
- Jenni K Thomas
- Department of Pharmacy Services, University of Kentucky HealthCare, Lexington, KY, USA
| | - Justin Clark
- University of Kentucky College of Pharmacy, Lexington, KY, USA
| | - Vaneet Arora
- University of Kentucky College of Medicine, Lexington, KY, USA; Department of Pathology and Laboratory Medicine, University of Kentucky HealthCare, Lexington, KY, USA
| | - David S Burgess
- University of Kentucky College of Pharmacy, Lexington, KY, USA
| | - Donna R Burgess
- Department of Pharmacy Services, University of Kentucky HealthCare, Lexington, KY, USA; University of Kentucky College of Pharmacy, Lexington, KY, USA
| | - Ryan P Mynatt
- Department of Pharmacy Services, University of Kentucky HealthCare, Lexington, KY, USA
| | - Jeremy D VanHoose
- Department of Pharmacy Services, University of Kentucky HealthCare, Lexington, KY, USA
| | - Katie L Wallace
- Department of Pharmacy Services, University of Kentucky HealthCare, Lexington, KY, USA; University of Kentucky College of Pharmacy, Lexington, KY, USA
| | - Sarah E Cotner
- Department of Pharmacy Services, University of Kentucky HealthCare, Lexington, KY, USA; University of Kentucky College of Pharmacy, Lexington, KY, USA.
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Caspar Y, Deves A, Richarme C, Le Marechal M, Ponderand L, Mounayar AL, Lejeune S, Arata-Bardet J, Gallouche M, Recule C, Maubon D, Garnaud C, Cornet M, Veloso M, Chabani B, Maurin M, David-Tchouda S, Pavese P. Clinical impact and cost-consequence analysis of ePlex® blood culture identification panels for the rapid diagnosis of bloodstream infections: a single-center randomized controlled trial. Eur J Clin Microbiol Infect Dis 2024; 43:1193-1203. [PMID: 38536524 PMCID: PMC11178566 DOI: 10.1007/s10096-024-04820-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 03/21/2024] [Indexed: 06/15/2024]
Abstract
To assess clinical impact and perform cost-consequence analysis of the broadest multiplex PCR panels available for the rapid diagnosis of bloodstream infections (BSI). Single-center, randomized controlled trial conducted from June 2019 to February 2021 at a French University hospital with an institutional antimicrobial stewardship program. Primary endpoint was the percentage of patients with optimized antimicrobial treatment 12 h after transmission of positivity and Gram stain results from the first positive BC. This percentage was significantly higher in the multiplex PCR (mPCR) group (90/105 = 85.7% %, CI95% [77.5 ; 91.8] vs. 68/107 = 63.6%, CI95% [53.7 ; 72.6]; p < 10- 3) at interim analysis, resulting in the early termination of the study after the inclusion of 309 patients. For patients not optimized at baseline, the median time to obtain an optimized therapy was much shorter in the mPCR group than in the control group (6.9 h, IQR [2.9; 17.8] vs. 26.4 h, IQR [3.4; 47.5]; p = 0.001). Early optimization of antibiotic therapy resulted in a non-statistically significant decrease in mortality from 12.4 to 8.8% (p = 0.306), with a trend towards a shorter median length of stay (18 vs. 20 days; p = 0.064) and a non-significant reduction in the average cost per patient of €3,065 (p = 0.15). mPCR identified all the bacteria present in 88% of the samples. Despite its higher laboratory cost, the use of multiplex PCR for BSI diagnosis leads to early-optimised therapy, seems cost-effective and could reduce mortality and length of stay. Their impact could probably be improved if implemented 24/7.
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Affiliation(s)
- Yvan Caspar
- Laboratoire de Bactériologie-Hygiène Hospitalière, CHU Grenoble Alpes, Grenoble, France.
- Univ. Grenoble Alpes, CNRS, CHU Grenoble Alpes, CEA, IBS, Grenoble, 38000, France.
| | - A Deves
- Laboratoire de Bactériologie-Hygiène Hospitalière, CHU Grenoble Alpes, Grenoble, France
| | - C Richarme
- Laboratoire de Bactériologie-Hygiène Hospitalière, CHU Grenoble Alpes, Grenoble, France
| | - M Le Marechal
- Service des Maladies infectieuses et tropicales, CHU Grenoble Alpes, Grenoble, France
| | - L Ponderand
- Laboratoire de Bactériologie-Hygiène Hospitalière, CHU Grenoble Alpes, Grenoble, France
- Univ. Grenoble Alpes, CNRS, CHU Grenoble Alpes, CEA, IBS, Grenoble, 38000, France
| | - A-L Mounayar
- Service des Maladies infectieuses et tropicales, CHU Grenoble Alpes, Grenoble, France
| | - S Lejeune
- Service des Maladies infectieuses et tropicales, CHU Grenoble Alpes, Grenoble, France
| | - J Arata-Bardet
- Service des Maladies infectieuses et tropicales, CHU Grenoble Alpes, Grenoble, France
| | - M Gallouche
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, CHU Grenoble Alpes, TIMC, Grenoble, 38000, France
- Service d'Hygiène Hospitalière, CHU Grenoble Alpes, Grenoble, France
| | - C Recule
- Laboratoire de Bactériologie-Hygiène Hospitalière, CHU Grenoble Alpes, Grenoble, France
| | - D Maubon
- Laboratoire de Parasitologie-Mycologie, CHU Grenoble Alpes, Grenoble, France
- University Grenoble Alpes, CNRS, CHU Grenoble Alpes, TIMC, Grenoble, 38000, France
| | - C Garnaud
- Laboratoire de Parasitologie-Mycologie, CHU Grenoble Alpes, Grenoble, France
- University Grenoble Alpes, CNRS, CHU Grenoble Alpes, TIMC, Grenoble, 38000, France
| | - M Cornet
- Laboratoire de Parasitologie-Mycologie, CHU Grenoble Alpes, Grenoble, France
- University Grenoble Alpes, CNRS, CHU Grenoble Alpes, TIMC, Grenoble, 38000, France
| | - M Veloso
- Cellule d'ingénierie des données, CHU Grenoble Alpes, Grenoble, France
| | - B Chabani
- Unité d'évaluation médico-économique, Pôle Santé Publique, CHU Grenoble Alpes, Grenoble, France
| | - M Maurin
- Laboratoire de Bactériologie-Hygiène Hospitalière, CHU Grenoble Alpes, Grenoble, France
- University Grenoble Alpes, CNRS, CHU Grenoble Alpes, TIMC, Grenoble, 38000, France
| | - S David-Tchouda
- Unité d'évaluation médico-économique, Pôle Santé Publique, CHU Grenoble Alpes, Grenoble, France
- CIC 1406 Grenoble, INSERM, Grenoble, 38000, France
- Univ. Grenoble Alpes, TIMC-Imag UMR 5525, Grenoble, 38000, France
| | - P Pavese
- Service des Maladies infectieuses et tropicales, CHU Grenoble Alpes, Grenoble, France
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Hamilton-Seth R, Streva V, Gammel N, Campodónico VL, Simner PJ, Zhang SX, Carroll KC. Evaluation of false-positive Rhodotorula detections by a multiplex PCR-based fungal panel performed on positive blood culture bottles. J Clin Microbiol 2024; 62:e0017924. [PMID: 38629843 PMCID: PMC11077967 DOI: 10.1128/jcm.00179-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2024] Open
Affiliation(s)
- Robert Hamilton-Seth
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Vincent Streva
- Pathology and Laboratory Medicine, Northwell Health Laboratories, Queens, New York, USA
| | - Natalie Gammel
- Microbiology Division, Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Victoria L. Campodónico
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Patricia J. Simner
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Microbiology Division, Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Sean X. Zhang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Microbiology Division, Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Karen C. Carroll
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Microbiology Division, Johns Hopkins Hospital, Baltimore, Maryland, USA
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Pintye A, Bacsó R, Kovács GM. Trans-kingdom fungal pathogens infecting both plants and humans, and the problem of azole fungicide resistance. Front Microbiol 2024; 15:1354757. [PMID: 38410389 PMCID: PMC10896089 DOI: 10.3389/fmicb.2024.1354757] [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: 12/12/2023] [Accepted: 01/23/2024] [Indexed: 02/28/2024] Open
Abstract
Azole antifungals are abundantly used in the environment and play an important role in managing fungal diseases in clinics. Due to the widespread use, azole resistance is an emerging global problem for all applications in several fungal species, including trans-kingdom pathogens, capable of infecting plants and humans. Azoles used in agriculture and clinics share the mode of action and facilitating cross-resistance development. The extensive use of azoles in the environment, e.g., for plant protection and wood preservation, contributes to the spread of resistant populations and challenges using these antifungals in medical treatments. The target of azoles is the cytochrome p450 lanosterol 14-α demethylase encoded by the CYP51 (called also as ERG11 in the case of yeasts) gene. Resistance mechanisms involve mainly the mutations in the coding region in the CYP51 gene, resulting in the inadequate binding of azoles to the encoded Cyp51 protein, or mutations in the promoter region causing overexpression of the protein. The World Health Organization (WHO) has issued the first fungal priority pathogens list (FPPL) to raise awareness of the risk of fungal infections and the increasingly rapid spread of antifungal resistance. Here, we review the main issues about the azole antifungal resistance of trans-kingdom pathogenic fungi with the ability to cause serious human infections and included in the WHO FPPL. Methods for the identification of these species and detection of resistance are summarized, highlighting the importance of these issues to apply the proper treatment.
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Affiliation(s)
- Alexandra Pintye
- Centre for Agricultural Research, Plant Protection Institute, HUN-REN, Budapest, Hungary
- Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, Budapest, Hungary
| | - Renáta Bacsó
- Centre for Agricultural Research, Plant Protection Institute, HUN-REN, Budapest, Hungary
| | - Gábor M. Kovács
- Centre for Agricultural Research, Plant Protection Institute, HUN-REN, Budapest, Hungary
- Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, Budapest, Hungary
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Otto C, Babady NE. Epidemiology and Outcomes of Non-albicans Candida Bloodstream Infections in Transplant Recipients and Cancer Patients. Mycopathologia 2023; 188:863-871. [PMID: 37365379 DOI: 10.1007/s11046-023-00765-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 06/10/2023] [Indexed: 06/28/2023]
Abstract
We performed a retrospective survey of non-Candida albicans candidemia in patients with cancer, including those with solid tumors and those with hematological malignancies as well as transplants patients both, solid-organ transplant recipients and hematopoietic stem cell transplant recipients. The study was performed at two healthcare centers in New York City and covered the years 2018-2022. A total of 292 patients (318 isolates) were included in the study. In order of frequency, C. glabrata (38%) was the most common species recovered, followed by C. parapsilosis (19.2%), C. tropicalis (12.6%), C. krusei (10.7%), C. lusitaniae (5.7%), and C. guilliermondii (4.4%). Micafungin was the most common antifungal treatment and 18.5% of patients were on antifungal prophylaxis. The 30-day crude mortality was 40%. 4.5% of patients had more than one non-albicans species detected. In conclusion, this study represents one of the largest surveys of non-albicans species in cancer and transplant patients and provides data on the current epidemiology of these Candida species in this patient population.
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Affiliation(s)
- Caitlin Otto
- Department of Pathology, NYU Langone Health, New York, NY, USA
| | - N Esther Babady
- Department of Pathology and Laboratory Medicine, Department of Medicine, Memorial Sloan Kettering Cancer Center, 327 East 64th Street CLM 522, New York, NY, 10065, USA.
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Lin C, Tang H, Hu X, Li G, Jiang T, Yang W, Xia Z, Zhu Y, Xu H, Zhou J, Shen J. A PCR-Reverse Dot Blot Hybridization Based Microfluidics Detection System for the Rapid Identification of 13 Fungal Pathogens Directly After Blood Cultures Over a Period of Time. Infect Drug Resist 2023; 16:5347-5357. [PMID: 37605759 PMCID: PMC10440108 DOI: 10.2147/idr.s424156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 08/09/2023] [Indexed: 08/23/2023] Open
Abstract
Introduction It is time-consuming to identify fungal pathogens from positive blood cultures using the standard culture-based method. And delayed diagnosis of bloodstream infection leads to significantly increased mortality. Methods We developed a PCR-reverse dot blot hybridization combined with microfluidic chip techniques to rapidly identify 13 fungal pathogens within 3-4 h using the sample of blood cultured over a period of time. Results We performed clinical validation using 43 blood culture-positive samples with a sensitivity of 96.7%, a specificity of 100%, and a concordance rate of 97.7%. Samples with different culture durations were evaluated using our approach, showing a detection rate of 85.2% at 16 h and 96.3% at 24 h; the platform could reach a detection limit of 103cfu/mL for the Candida spp. and 103 copies/mL for Aspergillus spp. Discussion The detection rate of the platform is much higher than the positive rates of concurrent blood cultures. This method bears substantial clinical application potential as it incorporates the microfluidic platform with low reagent consumption, automation, and low cost (about 10 dollars).
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Affiliation(s)
- Chunhui Lin
- Clinical Laboratory, the First Affiliated Hospital of Anhui Medical University, Hefei, People’s Republic of China
- Clinical Laboratory, Anhui Public Health Clinical Center Hefei, Hefei, People’s Republic of China
| | - Hao Tang
- Clinical Laboratory, the Second Affiliated Hospital of Anhui Medical University, Hefei, People’s Republic of China
| | - Xinyi Hu
- Clinical Laboratory, the First Affiliated Hospital of Anhui Medical University, Hefei, People’s Republic of China
- Clinical Laboratory, Anhui Public Health Clinical Center Hefei, Hefei, People’s Republic of China
| | - Ge Li
- Clinical Laboratory, the First Affiliated Hospital of Anhui Medical University, Hefei, People’s Republic of China
- Clinical Laboratory, Anhui Public Health Clinical Center Hefei, Hefei, People’s Republic of China
| | - Tong Jiang
- Clinical Laboratory, the First Affiliated Hospital of Anhui Medical University, Hefei, People’s Republic of China
- Clinical Laboratory, Anhui Public Health Clinical Center Hefei, Hefei, People’s Republic of China
| | - Wensu Yang
- Clinical Laboratory, the First Affiliated Hospital of Anhui Medical University, Hefei, People’s Republic of China
- Clinical Laboratory, Anhui Public Health Clinical Center Hefei, Hefei, People’s Republic of China
| | - Zhaoxin Xia
- Clinical Laboratory, the First Affiliated Hospital of Anhui Medical University, Hefei, People’s Republic of China
- Clinical Laboratory, Anhui Public Health Clinical Center Hefei, Hefei, People’s Republic of China
| | - Yi Zhu
- Clinical Laboratory, the First Affiliated Hospital of Anhui Medical University, Hefei, People’s Republic of China
- Clinical Laboratory, Anhui Public Health Clinical Center Hefei, Hefei, People’s Republic of China
| | - Huaming Xu
- Clinical Laboratory, the First Affiliated Hospital of Anhui University of Traditional Chinese Medicine, Hefei, People’s Republic of China
| | - Jing Zhou
- Clinical Laboratory, the First Affiliated Hospital of Anhui Medical University, Hefei, People’s Republic of China
- Clinical Laboratory, Anhui Public Health Clinical Center Hefei, Hefei, People’s Republic of China
| | - Jilu Shen
- Clinical Laboratory, the First Affiliated Hospital of Anhui Medical University, Hefei, People’s Republic of China
- Clinical Laboratory, Anhui Public Health Clinical Center Hefei, Hefei, People’s Republic of China
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Fang W, Wu J, Cheng M, Zhu X, Du M, Chen C, Liao W, Zhi K, Pan W. Diagnosis of invasive fungal infections: challenges and recent developments. J Biomed Sci 2023; 30:42. [PMID: 37337179 DOI: 10.1186/s12929-023-00926-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 02/13/2023] [Indexed: 06/21/2023] Open
Abstract
BACKGROUND The global burden of invasive fungal infections (IFIs) has shown an upsurge in recent years due to the higher load of immunocompromised patients suffering from various diseases. The role of early and accurate diagnosis in the aggressive containment of the fungal infection at the initial stages becomes crucial thus, preventing the development of a life-threatening situation. With the changing demands of clinical mycology, the field of fungal diagnostics has evolved and come a long way from traditional methods of microscopy and culturing to more advanced non-culture-based tools. With the advent of more powerful approaches such as novel PCR assays, T2 Candida, microfluidic chip technology, next generation sequencing, new generation biosensors, nanotechnology-based tools, artificial intelligence-based models, the face of fungal diagnostics is constantly changing for the better. All these advances have been reviewed here giving the latest update to our readers in the most orderly flow. MAIN TEXT A detailed literature survey was conducted by the team followed by data collection, pertinent data extraction, in-depth analysis, and composing the various sub-sections and the final review. The review is unique in its kind as it discusses the advances in molecular methods; advances in serology-based methods; advances in biosensor technology; and advances in machine learning-based models, all under one roof. To the best of our knowledge, there has been no review covering all of these fields (especially biosensor technology and machine learning using artificial intelligence) with relevance to invasive fungal infections. CONCLUSION The review will undoubtedly assist in updating the scientific community's understanding of the most recent advancements that are on the horizon and that may be implemented as adjuncts to the traditional diagnostic algorithms.
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Affiliation(s)
- Wenjie Fang
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, China
| | - Junqi Wu
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
- Shanghai Engineering Research Center of Lung Transplantation, Shanghai, 200433, China
| | - Mingrong Cheng
- Department of Anorectal Surgery, The Third Affiliated Hospital of Guizhou Medical University, Guizhou, 558000, China
| | - Xinlin Zhu
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, China
| | - Mingwei Du
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, China
| | - Chang Chen
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
- Shanghai Engineering Research Center of Lung Transplantation, Shanghai, 200433, China
| | - Wanqing Liao
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, China
| | - Kangkang Zhi
- Department of Vascular and Endovascular Surgery, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, China.
| | - Weihua Pan
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, China.
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Luethy PM. Point-of-Care Testing for the Diagnosis of Fungal Infections. Clin Lab Med 2023; 43:209-220. [PMID: 37169443 DOI: 10.1016/j.cll.2023.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
Invasive fungal infections are increasing worldwide due to factors such as climate change and immunomodulating therapies. Unfortunately, the detection of these infections is limited due to the low sensitivity and long periods required for laboratory testing. Point-of-care testing could lead to more rapid diagnosis of these often devasting infections. However, there are currently no true point-of-care tests on the market for the detection of fungi. In this article, the current state of fungal antigen and molecular testing is reviewed, with commentary on the potential for development and use in the point-of-care setting.
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A Closer Look at the Laboratory Impact of Utilizing ePlex Blood Culture Identification Panels: a Workflow Analysis Using Rapid Molecular Detection for Positive Blood Cultures. Microbiol Spectr 2022; 10:e0179622. [PMID: 36069598 PMCID: PMC9602361 DOI: 10.1128/spectrum.01796-22] [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] [Indexed: 12/31/2022] Open
Abstract
Rapid identification of pathogens is critical in bloodstream infections. We evaluated the diagnostic performance of the GenMark Dx ePlex blood culture identification (BCID) panels and the adoption of the ePlex system into the clinical laboratory workflow. Nonduplicate remnant specimens of positive blood cultures were prospectively tested using ePlex panels between January and March 2020. A total of 313 unique positive blood culture specimens were tested. The identified organisms consisted of 98 Gram-negative rods (GNR), 90 Gram-positive cocci (GPC) in clusters, 62 GPC in chains, 21 Gram-positive rods, and 20 yeasts; 22 organisms were off panel. The positive percent agreement was 100% across all organisms tested after discordancy resolution, while the negative percent agreement was 100% across all targets except Corynebacterium spp., where it was 99.7%. The ePlex BCID panels accurately detected 5 pan targets and 42 antimicrobial resistance gene markers, including 31 mecA, 4 vanA, 6 CTX-M, and 1 KPC gene. The median times to result were calculated as 2.5 h for Xpert MRSA/SA in GPC in clusters, 9.5 h for Accelerate Pheno (identification and susceptibility) in GNR, 6 h for peptide nucleic acid fluorescent in situ hybridization [PNA-FISH] in yeasts, 27 h for the latex agglutination test in S. aureus, 29 h for Lancefield serotyping in GPC in chains, and 29 h for Vitek-MS in GNR. In our laboratory, the ePlex panels could substantially reduce the time to result for bloodstream infection (BSI) caused by Streptococcus spp., Enterococcus spp., and Candida spp. The highly accurate ePlex panels can help streamline laboratory efficiency in the blood bench workflow, reducing the time to result for identification of BSI pathogens. IMPORTANCE Sepsis is a leading cause of morbidity and mortality worldwide. Rapid identification of the causative agent is of critical importance for the prompt initiation of the appropriate antibiotic treatment. In this study, we evaluated the diagnostic performance of the GenMark Dx ePlex blood culture identification (BCID) panels and their adoption into the clinical laboratory workflow. We prospectively tested 313 blood culture isolates and found that ePlex BCID panels had a positive percent agreement of 100% across all organisms tested after discordancy resolution. The negative percent agreement was 100% across all targets except Corynebacterium spp., where it was 99.7%. This new rapid technology (turnaround time of ~90 min) can help streamline laboratory efficiency in the blood bench workflow, reducing the time to result for identification of BSI pathogens. Adoption should be individualized based on the needs of the patient population and capabilities of the laboratory.
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Matzko ME, Sephton-Clark PCS, Young EL, Jhaveri TA, Martinsen MA, Mojica E, Boykin R, Pierce VM, Cuomo CA, Bhattacharyya RP. A novel rRNA hybridization-based approach to rapid, accurate Candida identification directly from blood culture. Med Mycol 2022; 60:6674770. [PMID: 36002024 PMCID: PMC9989835 DOI: 10.1093/mmy/myac065] [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: 06/21/2022] [Revised: 08/03/2022] [Accepted: 08/22/2022] [Indexed: 01/24/2023] Open
Abstract
Invasive fungal infections are increasingly common and carry high morbidity and mortality, yet fungal diagnostics lag behind bacterial diagnostics in rapidly identifying the causal pathogen. We previously devised a fluorescent hybridization-based assay to identify bacteria within hours directly from blood culture bottles without subculture, called phylogeny-informed rRNA-based strain identification (Phirst-ID). Here, we adapt this approach to unambiguously identify 11 common pathogenic Candida species, including C. auris, with 100% accuracy from laboratory culture (33 of 33 strains in a reference panel, plus 33 of 33 additional isolates tested in a validation panel). In a pilot study on 62 consecutive positive clinical blood cultures from two hospitals that showed yeast on Gram stain, Candida Phirst-ID matched the clinical laboratory result for 58 of 59 specimens represented in the 11-species reference panel, without misclassifying the 3 off-panel species. It also detected mixed Candida species in 2 of these 62 specimens, including the one discordant classification, that were not identified by standard clinical microbiology workflows; in each case the presence of both species was validated by both clinical and experimental data. Finally, in three specimens that grew both bacteria and yeast, we paired our prior bacterial probeset with this new Candida probeset to detect both pathogen types using Phirst-ID. This simple, robust assay can provide accurate Candida identification within hours directly from blood culture bottles, and the conceptual approach holds promise for pan-microbial identification in a single workflow. LAY SUMMARY Candida bloodstream infections cause considerable morbidity and mortality, yet slow diagnostics delay recognition, worsening patient outcomes. We develop and validate a novel molecular approach to accurately identify Candida species directly from blood culture one day faster than standard workflows.
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Affiliation(s)
- Michelle E Matzko
- Infectious Diseases Division, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Poppy C S Sephton-Clark
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Eleanor L Young
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Tulip A Jhaveri
- Microbiology Laboratory, Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Melanie A Martinsen
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Evan Mojica
- Microbiology Laboratory, Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Rich Boykin
- NanoString Technologies, Inc., Seattle, WA 98109, USA
| | - Virginia M Pierce
- Microbiology Laboratory, Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Christina A Cuomo
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Roby P Bhattacharyya
- Infectious Diseases Division, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.,Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
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12
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Richter F, Bindschedler S, Calonne-Salmon M, Declerck S, Junier P, Stanley CE. Fungi-on-a-Chip: microfluidic platforms for single-cell studies on fungi. FEMS Microbiol Rev 2022; 46:6674677. [PMID: 36001464 PMCID: PMC9779915 DOI: 10.1093/femsre/fuac039] [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: 04/29/2022] [Revised: 08/11/2022] [Accepted: 08/22/2022] [Indexed: 01/07/2023] Open
Abstract
This review highlights new advances in the emerging field of 'Fungi-on-a-Chip' microfluidics for single-cell studies on fungi and discusses several future frontiers, where we envisage microfluidic technology development to be instrumental in aiding our understanding of fungal biology. Fungi, with their enormous diversity, bear essential roles both in nature and our everyday lives. They inhabit a range of ecosystems, such as soil, where they are involved in organic matter degradation and bioremediation processes. More recently, fungi have been recognized as key components of the microbiome in other eukaryotes, such as humans, where they play a fundamental role not only in human pathogenesis, but also likely as commensals. In the food sector, fungi are used either directly or as fermenting agents and are often key players in the biotechnological industry, where they are responsible for the production of both bulk chemicals and antibiotics. Although the macroscopic fruiting bodies are immediately recognizable by most observers, the structure, function, and interactions of fungi with other microbes at the microscopic scale still remain largely hidden. Herein, we shed light on new advances in the emerging field of Fungi-on-a-Chip microfluidic technologies for single-cell studies on fungi. We discuss the development and application of microfluidic tools in the fields of medicine and biotechnology, as well as in-depth biological studies having significance for ecology and general natural processes. Finally, a future perspective is provided, highlighting new frontiers in which microfluidic technology can benefit this field.
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Affiliation(s)
- Felix Richter
- Department of Bioengineering, Imperial College London, South Kensington Campus, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Saskia Bindschedler
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Maryline Calonne-Salmon
- Laboratory of Mycology, Université catholique de Louvain, Place Croix du Sud 2, B-1348 Louvain-la-Neuve, Belgium
| | - Stéphane Declerck
- Laboratory of Mycology, Université catholique de Louvain, Place Croix du Sud 2, B-1348 Louvain-la-Neuve, Belgium
| | - Pilar Junier
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Claire E Stanley
- Corresponding author: Department of Bioengineering, Imperial College London, South Kensington Campus, Exhibition Road, London, SW7 2AZ, United Kingdom. E-mail:
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13
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Abstract
Candida auris is an emerging yeast species that has the unique characteristics of patient skin colonization and rapid transmission within healthcare facilities and the ability to rapidly develop antifungal resistance. When C. auris first started appearing in clinical microbiology laboratories, it could only be identified using DNA sequencing. In the decade since its first identification outside of Japan there have been many improvements in the detection of C. auris. These include the expansion of MALDI-TOF databases to include C. auris, the development of both laboratory-developed tests and commercially available kits for its detection, and special CHROMagar for identification from laboratory specimens. Here we discuss the current tools and resources that are available for C. auris identification and detection.
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14
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Mendonça A, Santos H, Franco-Duarte R, Sampaio P. Fungal infections diagnosis - Past, present and future. Res Microbiol 2022; 173:103915. [PMID: 34863883 PMCID: PMC8634697 DOI: 10.1016/j.resmic.2021.103915] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/19/2021] [Accepted: 11/26/2021] [Indexed: 01/07/2023]
Abstract
Despite the scientific advances observed in the recent decades and the emergence of new methodologies, the diagnosis of systemic fungal infections persists as a problematic issue. Fungal cultivation, the standard method that allows a proven diagnosis, has numerous disadvantages, as low sensitivity (only 50% of the patients present positive fungal cultures), and long growth time. These are factors that delay the patient's treatment and, consequently, lead to higher hospital costs. To improve the accuracy and quickness of fungal infections diagnosis, several new methodologies attempt to be implemented in clinical microbiology laboratories. Most of these innovative methods are independent of pathogen isolation, which means that the diagnosis goes from being considered proven to probable. In spite of the advantage of being culture-independent, the majority of the methods lack standardization. PCR-based methods are becoming more and more commonly used, which has earned them an important place in hospital laboratories. This can be perceived now, as PCR-based methodologies have proved to be an essential tool fighting against the COVID-19 pandemic. This review aims to go through the main steps of the diagnosis for systemic fungal infection, from diagnostic classifications, through methodologies considered as "gold standard", to the molecular methods currently used, and finally mentioning some of the more futuristic approaches.
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15
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Dennis EK, Chaturvedi S, Chaturvedi V. So Many Diagnostic Tests, So Little Time: Review and Preview of Candida auris Testing in Clinical and Public Health Laboratories. Front Microbiol 2021; 12:757835. [PMID: 34691009 PMCID: PMC8529189 DOI: 10.3389/fmicb.2021.757835] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 09/13/2021] [Indexed: 01/13/2023] Open
Abstract
The recognition of a new yeast, Candida auris, in 2009 in East Asia, and its rapid global spread, was a reminder of the threats posed by multidrug-resistant fungal pathogens. C. auris had likely remained unrecognized for a long time as accurate tests were not available. The laboratory community responded to the C. auris challenge by publishing 35 new or revised diagnostic methods between 2014 and early 2021. The commercial sector also modified existing diagnostic devices. These C. auris diagnostic tests run the gamut from traditional culture-based differential and selective media, biochemical assimilations, and rapid protein profiles, as well as culture-independent DNA-based diagnostics. We provide an overview of these developments, especially the tests with validation data that were subsequently adopted for common use. We share a workflow developed in our laboratory to process over 37,000 C. auris surveillance samples and 5,000 C. auris isolates from the outbreak in the New York metropolitan area. Our preview covers new devices and diagnostic approaches on the horizon based on microfluidics, optics, and nanotechnology. Frontline laboratories need rapid, cheap, stable, and easy-to-implement tests to improve C. auris diagnosis, surveillance, patient isolation, admission screening, and environmental control. Among the urgent needs is a lateral flow assay or similar device for presumptive C. auris identification. All laboratories will benefit from devices that allow rapid antifungal susceptibility testing, including detection of mutations conferring drug resistance. Hopefully, multiplex test panels are on the horizon for synergy of C. auris testing with ongoing surveillance of other healthcare-associated infections. C. auris genome analysis has a proven role for outbreak investigations, and diagnostic laboratories need quick access to regional and national genome analysis networks.
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Affiliation(s)
- Emily K Dennis
- Mycology Laboratory, Wadsworth Center, New York State Department of Health, Albany, NY, United States
| | - Sudha Chaturvedi
- Mycology Laboratory, Wadsworth Center, New York State Department of Health, Albany, NY, United States.,Department of Biomedical Sciences, University at Albany, Albany, NY, United States
| | - Vishnu Chaturvedi
- Mycology Laboratory, Wadsworth Center, New York State Department of Health, Albany, NY, United States
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16
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A Multicenter Clinical Study To Demonstrate the Diagnostic Accuracy of the GenMark Dx ePlex Blood Culture Identification Gram-Negative Panel. J Clin Microbiol 2021; 59:e0248420. [PMID: 34232066 PMCID: PMC8373019 DOI: 10.1128/jcm.02484-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Bacteremia can progress to septic shock and death without appropriate medical intervention. Increasing evidence supports the role of molecular diagnostic panels in reducing the clinical impact of these infections through rapid identification of the infecting organism and associated antimicrobial resistance genes. We report the results of a multicenter clinical study assessing the performance of the GenMark Dx ePlex investigational-use-only blood culture identification Gram-negative panel (BCID-GN), a rapid diagnostic assay for detection of bloodstream pathogens in positive blood culture (PBC) bottles. Prospective, retrospective, and contrived samples were tested. Results from the BCID-GN were compared to standard-of-care bacterial identification methods. Antimicrobial resistance genes (ARGs) were identified using PCR and sequence analysis. The final BCID-GN analysis included 2,444 PBC samples, of which 926 were clinical samples with negative Gram stain results. Of these, 109 samples had false-negative and/or -positive results, resulting in an overall sample accuracy of 88.2% (817/926). After discordant resolution, overall sample accuracy increased to 92.9% (860/926). Pre- and postdiscordant resolution sample accuracy excludes 37 Gram-negative organisms representing 20 uncommon genera, 10 Gram-positive organisms, and 1 Candida species present in 5% of samples that are not targeted by the BCID-GN. The overall weighted positive percent agreement (PPA), which averages the individual PPAs from the 27 targets (Gram-negative and ARG), was 94.9%. The limit of detection ranged from 104 to 107 CFU/ml, except for one strain of Fusobacterium necrophorum at 108 CFU/ml.
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17
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Recognition of Diagnostic Gaps for Laboratory Diagnosis of Fungal Diseases: Expert Opinion from the Fungal Diagnostics Laboratories Consortium (FDLC). J Clin Microbiol 2021; 59:e0178420. [PMID: 33504591 DOI: 10.1128/jcm.01784-20] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Fungal infections are a rising threat to our immunocompromised patient population, as well as other nonimmunocompromised patients with various medical conditions. However, little progress has been made in the past decade to improve fungal diagnostics. To jointly address this diagnostic challenge, the Fungal Diagnostics Laboratory Consortium (FDLC) was recently created. The FDLC consists of 26 laboratories from the United States and Canada that routinely provide fungal diagnostic services for patient care. A survey of fungal diagnostic capacity among the 26 members of the FDLC was recently completed, identifying the following diagnostic gaps: lack of molecular detection of mucormycosis; lack of an optimal diagnostic algorithm incorporating fungal biomarkers and molecular tools for early and accurate diagnosis of Pneumocystis pneumonia, aspergillosis, candidemia, and endemic mycoses; lack of a standardized molecular approach to identify fungal pathogens directly in formalin-fixed paraffin-embedded tissues; lack of robust databases to enhance mold identification with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry; suboptimal diagnostic approaches for mold blood cultures, tissue culture processing for Mucorales, and fungal respiratory cultures for cystic fibrosis patients; inadequate capacity for fungal point-of-care testing to detect and identify new, emerging or underrecognized, rare, or uncommon fungal pathogens; and performance of antifungal susceptibility testing. In this commentary, the FDLC delineates the most pressing unmet diagnostic needs and provides expert opinion on how to fulfill them. Most importantly, the FDLC provides a robust laboratory network to tackle these diagnostic gaps and ultimately to improve and enhance the clinical laboratory's capability to rapidly and accurately diagnose fungal infections.
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18
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Banerjee R, Humphries R. Rapid Antimicrobial Susceptibility Testing Methods for Blood Cultures and Their Clinical Impact. Front Med (Lausanne) 2021; 8:635831. [PMID: 33777978 PMCID: PMC7987685 DOI: 10.3389/fmed.2021.635831] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/01/2021] [Indexed: 12/29/2022] Open
Abstract
Antimicrobial susceptibility testing (AST) of bacteria isolated in blood cultures is critical for optimal management of patients with sepsis. This review describes new and emerging phenotypic and genotypic AST methods and summarizes the evidence that implementation of these methods can impact clinical outcomes of patients with bloodstream infections.
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Affiliation(s)
- Ritu Banerjee
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Romney Humphries
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, United States
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19
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White PL, Price JS, Cordey A, Backx M. Molecular Diagnosis of Yeast Infections. CURRENT FUNGAL INFECTION REPORTS 2021; 15:67-80. [PMID: 34178207 PMCID: PMC8212580 DOI: 10.1007/s12281-021-00421-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/27/2021] [Indexed: 02/06/2023]
Abstract
PURPOSE OF REVIEW The use of molecular tests to aid the diagnosis of invasive yeast infection, in particular invasive candidosis, has been described for over two decades, yet widespread application is limited, and diagnosis remains heavily dependent on classical microbiology. This article will review developments from the past decade in attempt to build on existing knowledge. It will highlight clinical performance and limitations while reviewing developments on recognized procedures; it will also provide insight into novel approaches incorporated in response to clinical demand (e.g. C. auris and antifungal resistance) or technological advances (e.g. next-generation sequencing). RECENT FINDINGS Limited methodological standardization and, until recently, unavailability of commercial options have hindered the integration of molecular diagnostics for yeasts. The development of certain, novel commercial methods has received considerable evaluation allowing a greater understanding of individual assay performance, but widespread multicentre evaluation of most commercial kits is lacking. The detection of emerging pathogens (e.g. C. auris) has been enhanced by the development of molecular tests. Molecular methods are providing a better understanding of the mycobiome, mechanisms of resistance and epidemiology/phylogeny. SUMMARY Despite over two decades of use, the incorporation of molecular methods to enhance the diagnosis of yeast infections remains limited to certain specialist centres. While the development of commercial tests will provide stimulus for broader application, further validation and reduced costs are required. Over the same period of time, Aspergillus PCR has become more widely accepted driven by international efforts to standardize methodology; it is critical that yeast PCR follows suit. Next-generation sequencing will provide significant information on the mycobiome, antifungal resistance mechanism and even broad-range detection directly from the specimen, which may be critical for the molecular detection of yeasts other than Candida species, which is currently limited.
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Affiliation(s)
- P. Lewis White
- grid.241103.50000 0001 0169 7725Mycology Reference Laboratory, Public Health Wales, Microbiology Cardiff, UHW, Heath Park, Cardiff, CF14 4XW UK
| | - Jessica S. Price
- grid.241103.50000 0001 0169 7725Mycology Reference Laboratory, Public Health Wales, Microbiology Cardiff, UHW, Heath Park, Cardiff, CF14 4XW UK
| | - Alan Cordey
- grid.241103.50000 0001 0169 7725Mycology Reference Laboratory, Public Health Wales, Microbiology Cardiff, UHW, Heath Park, Cardiff, CF14 4XW UK
| | - Matthijs Backx
- grid.241103.50000 0001 0169 7725Mycology Reference Laboratory, Public Health Wales, Microbiology Cardiff, UHW, Heath Park, Cardiff, CF14 4XW UK
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20
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Bryant S, Almahmoud I, Pierre I, Bardet J, Touati S, Maubon D, Cornet M, Richarme C, Maurin M, Pavese P, Caspar Y. Evaluation of Microbiological Performance and the Potential Clinical Impact of the ePlex ® Blood Culture Identification Panels for the Rapid Diagnosis of Bacteremia and Fungemia. Front Cell Infect Microbiol 2020; 10:594951. [PMID: 33324578 PMCID: PMC7726344 DOI: 10.3389/fcimb.2020.594951] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 10/29/2020] [Indexed: 12/18/2022] Open
Abstract
Molecular rapid diagnostic assays associated with antimicrobial stewardship have proven effective for the early adaptation of empiric therapy in bloodstream infections. The ePlex® BCID (GenMark Diagnostics) Panels allow identification of 56 bacteria and fungi and 10 resistance genes in 90 min directly from positive blood cultures. We prospectively evaluated 187 sepsis episodes at Grenoble University Hospital and retrospectively analyzed the cases to measure the potential clinical impact of the ePlex BCID results. Identification of all pathogens was obtained for 164/187 (88%) bloodstream infections with 100% detection of antimicrobial resistance genes (17 blaCTX-M , 1 vanA, and 17 mecA genes). Only 15/209 (7%) strains were not covered by the panels. Sensitivity for detection of micro-organisms targeted by the RUO BCID-GP, BCID-GN, and BCID-FP Panels was respectively 84/84 (100%), 103/107 (96%), and 14/14 (100%). Interestingly, accurate identification of all pathogens was achieved in 15/17 (88%) polymicrobial samples. Retrospective analysis of medical records showed that a modification of antimicrobial treatment would have been done in 45% of the patients. Treatment modifications would have been an optimization of empiric therapy, a de-escalation or an escalation in respectively 16, 17, and 11% of the patients. Moreover, 11% of the samples were classified as contaminants or not clinically relevant and would have led to early de-escalation or withdrawal of any antibiotic. Detection of resistance genes in addition to identification alone increased escalation rate from 4 to 11% of the patients. Absence of the ePlex result was considered a lost opportunity for therapy modification in 28% of patients.
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Affiliation(s)
- Sabrina Bryant
- Laboratoire de bactériologie-hygiène hospitalière, Centre Hospitalier Universitaire Grenoble Alpes, Grenoble, France
| | - Iyad Almahmoud
- Univ. Grenoble Alpes, CNRS, CHU Grenoble Alpes, Grenoble INP, TIMC-IMAG, Grenoble, France
| | - Isabelle Pierre
- Service des maladies infectieuses et tropicales, Centre Hospitalier Universitaire Grenoble Alpes, Grenoble, France
| | - Julie Bardet
- Service des maladies infectieuses et tropicales, Centre Hospitalier Universitaire Grenoble Alpes, Grenoble, France
| | - Saber Touati
- Service des maladies infectieuses et tropicales, Centre Hospitalier Universitaire Grenoble Alpes, Grenoble, France
| | - Daniele Maubon
- Univ. Grenoble Alpes, CNRS, CHU Grenoble Alpes, Grenoble INP, TIMC-IMAG, Grenoble, France
| | - Muriel Cornet
- Univ. Grenoble Alpes, CNRS, CHU Grenoble Alpes, Grenoble INP, TIMC-IMAG, Grenoble, France
| | - Claire Richarme
- Laboratoire de bactériologie-hygiène hospitalière, Centre Hospitalier Universitaire Grenoble Alpes, Grenoble, France
| | - Max Maurin
- Laboratoire de bactériologie-hygiène hospitalière, Centre Hospitalier Universitaire Grenoble Alpes, Grenoble, France.,Univ. Grenoble Alpes, CNRS, CHU Grenoble Alpes, Grenoble INP, TIMC-IMAG, Grenoble, France
| | - Patricia Pavese
- Service des maladies infectieuses et tropicales, Centre Hospitalier Universitaire Grenoble Alpes, Grenoble, France
| | - Yvan Caspar
- Laboratoire de bactériologie-hygiène hospitalière, Centre Hospitalier Universitaire Grenoble Alpes, Grenoble, France.,Univ. Grenoble Alpes, CNRS, CHU Grenoble Alpes, Grenoble INP, TIMC-IMAG, Grenoble, France
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21
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Abstract
Appropriate diagnosis of invasive fungal infections (IFIs) is critical due to the high rates of morbidity and mortality, as well as the substantial economic burden, associated with the management of these diseases. The recognition of IFI and differentiation from other infections with similar clinical presentations can be challenging, which can lead to diagnostic error that not only has an impact on individual patient health outcomes but also on antimicrobial drug usage and the growing threat of antimicrobial resistance in bacteria. Therefore, there is a significant need for improved stewardship related to diagnostic testing for and treatment of IFIs. The purpose of this review is to highlight recent advances related to current fungal diagnostics, as well as explore some of the most innovative technology that has emerged with the potential to shift the paradigm of clinical mycology. In general, this review will discuss research related to enhanced fungal culture utilization and identification techniques, expanded applications of fungal antigen testing, and recently developed molecular assays and other novel nonculture fungal diagnostic approaches. Specifically, the application of mass spectrometry, novel glycobiomarker detection, and detection of fungal-specific volatile organic compounds will be reviewed, along with other key updates, to provide the reader with an updated review that extends beyond the basics of IFI laboratory diagnostics. Where appropriate, the reader will be directed to more comprehensive reviews of certain aspects of clinical mycology laboratory testing to provide a broader context for the critical consideration of these updates.
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