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Sedik S, Wolfgruber S, Hoenigl M, Kriegl L. Diagnosing fungal infections in clinical practice: a narrative review. Expert Rev Anti Infect Ther 2024:1-15. [PMID: 39268795 DOI: 10.1080/14787210.2024.2403017] [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: 07/26/2024] [Revised: 09/02/2024] [Accepted: 09/07/2024] [Indexed: 09/15/2024]
Abstract
BACKGROUND Invasive fungal infections (IFI) present a major medical challenge, with an estimated 6.5 million cases annually, resulting in 3.8 million deaths. Pathogens such as Aspergillus spp. Candida spp. Mucorales spp. Cryptococcus spp. and other fungi species contribute to these infections, posing risks to immunocompromised individuals. Early and accurate diagnosis is crucial for effective treatment and better patient outcomes. AREAS COVERED This narrative review provides an overview of the current methods and challenges associated with diagnosing fungal diseases, including invasive aspergillosis and invasive candidiasis, as well as rare and endemic fungal infections. Various diagnostic techniques, including microscopy, culture, molecular diagnostics, and serological tests, are reviewed, highlighting their respective advantages and limitations and role in clinical guidelines. To illustrate, the need for improved diagnostic strategies to overcome existing challenges, such as the low sensitivity and specificity of current tests and the time-consuming nature of traditional culture-based methods, is addressed. EXPERT OPINION Current advancements in fungal infection diagnostics have significant implications for healthcare outcomes. Improved strategies like molecular testing and antigen detection promise early detection of fungal pathogens, enhancing patient management. Challenges include global access to advanced technologies and the need for standardized, user-friendly point-of-care diagnostics to improve diagnosis of fungal infections globally.
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Affiliation(s)
- Sarah Sedik
- Division of Infectious Diseases, Department of Internal Medicine, Medical University of Graz, ECMM Excellence Center Graz, Austria
- Translational Mycology, Medical University of Graz, Graz, Austria
| | - Stella Wolfgruber
- Division of Infectious Diseases, Department of Internal Medicine, Medical University of Graz, ECMM Excellence Center Graz, Austria
- Translational Mycology, Medical University of Graz, Graz, Austria
| | - Martin Hoenigl
- Division of Infectious Diseases, Department of Internal Medicine, Medical University of Graz, ECMM Excellence Center Graz, Austria
- Translational Mycology, Medical University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | - Lisa Kriegl
- Division of Infectious Diseases, Department of Internal Medicine, Medical University of Graz, ECMM Excellence Center Graz, Austria
- Translational Mycology, Medical University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
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2
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Zolotareva M, Cascalheira F, Caneiras C, Bárbara C, Caetano DM, Teixeira MC. In the flow of molecular miniaturized fungal diagnosis. Trends Biotechnol 2024:S0167-7799(24)00157-4. [PMID: 38987118 DOI: 10.1016/j.tibtech.2024.06.010] [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: 03/21/2024] [Revised: 06/03/2024] [Accepted: 06/18/2024] [Indexed: 07/12/2024]
Abstract
The diagnosis of fungal infections presents several challenges and limitations, stemming from the similarities in symptomatology, diversity of underlying pathogenic species, complexity of fungal biology, and scarcity of rapid, affordable, and point-of-care approaches. In this review, we assess technological advances enabling the conversion of cutting-edge laboratory molecular diagnostic methods to cost-effective microfluidic devices. The most promising strategies toward the design of DNA sequence-based fungal diagnostic systems, capable of capturing and deciphering the highly informative DNA of the pathogen and adapted for resource-limited settings, are discussed, bridging fungal biology, molecular genetics, microfluidics, and biosensors.
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Affiliation(s)
- Maria Zolotareva
- Instituto de Engenharia de Sistemas e Computadores - Microsistemas e Nanotecnologias, INESC-, MN, 1000-029 Lisboa, Portugal; iBB - Institute for Bioengineering and Biosciences, Associate Laboratory Institute for Health and Bioeconomy - i4HB, 1049-001 Lisboa, Portugal
| | - Francisco Cascalheira
- Instituto de Engenharia de Sistemas e Computadores - Microsistemas e Nanotecnologias, INESC-, MN, 1000-029 Lisboa, Portugal; iBB - Institute for Bioengineering and Biosciences, Associate Laboratory Institute for Health and Bioeconomy - i4HB, 1049-001 Lisboa, Portugal
| | - Cátia Caneiras
- Environmental Health Institute (ISAMB), Faculdade de Medicina, Universidade de Lisboa, 1649-026 Lisboa, Portugal; Associate Laboratory TERRA, Faculty of Medicine, Universidade de Lisboa, 1649-026 Lisboa, Portugal; Egas Moniz Center for Interdisciplinary Research, Egas Moniz School of Health and Science, 2829-511 Almada, Portugal; Institute of Preventive Medicine and Public Health, Universidade de Lisboa, 1649-026 Lisboa, Portugal
| | - Cristina Bárbara
- Environmental Health Institute (ISAMB), Faculdade de Medicina, Universidade de Lisboa, 1649-026 Lisboa, Portugal; Associate Laboratory TERRA, Faculty of Medicine, Universidade de Lisboa, 1649-026 Lisboa, Portugal; Centro Hospitalar Universitário Lisboa Norte, 1600-190, Lisboa, Portugal
| | - Diogo Miguel Caetano
- Instituto de Engenharia de Sistemas e Computadores - Microsistemas e Nanotecnologias, INESC-, MN, 1000-029 Lisboa, Portugal; Department of Electrical and Computer Engineering, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisboa, Portugal.
| | - Miguel Cacho Teixeira
- iBB - Institute for Bioengineering and Biosciences, Associate Laboratory Institute for Health and Bioeconomy - i4HB, 1049-001 Lisboa, Portugal; Department of Bioengineering, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisboa, Portugal.
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3
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Alcolea-Medina A, Alder C, Snell LB, Charalampous T, Aydin A, Nebbia G, Williams T, Goldenberg S, Douthwaite S, Batra R, Cliff PR, Mischo H, Neil S, Wilks M, Edgeworth JD. Unified metagenomic method for rapid detection of microorganisms in clinical samples. COMMUNICATIONS MEDICINE 2024; 4:135. [PMID: 38972920 PMCID: PMC11228040 DOI: 10.1038/s43856-024-00554-3] [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: 08/29/2023] [Accepted: 06/18/2024] [Indexed: 07/09/2024] Open
Abstract
BACKGROUND Clinical metagenomics involves the genomic sequencing of all microorganisms in clinical samples ideally after depletion of human DNA to increase sensitivity and reduce turnaround times. Current human DNA depletion methods preferentially preserve either DNA or RNA containing microbes, but not both simultaneously. Here we describe and present data using a practical and rapid mechanical host-depletion method allowing simultaneous detection of RNA and DNA microorganisms linked with nanopore sequencing. METHODS The human cells from respiratory samples are lysed mechanically using 1.4 mm zirconium-silicate spheres and the human DNA is depleted using a nonspecific endonuclease. The RNA is converted to dsDNA to allow the simultaneous sequencing of DNA and RNA. RESULTS The method decreases human DNA concentration by a median of eight Ct values while detecting a broad range of RNA & DNA viruses, bacteria, including atypical pathogens (Legionella, Chlamydia, Mycoplasma) and fungi (Candida, Pneumocystis, Aspergillus). The first automated reports are generated after 30 min sequencing from a 7 h end-to-end workflow. Sensitivity and specificity for bacterial detection are 90% and 100%, respectively, and viral detection are 92% and 100% after 2 h of sequencing. Prospective validation on 33 consecutive lower respiratory tract samples from ventilated patients with suspected pneumonia shows 60% concordance with routine testing, detection of additional pathogens in 21% of samples and pathogen genomic assembly achieve for 42% of viruses and 33% of bacteria. CONCLUSIONS Although further workflow refinement and validation on samples containing a broader range of pathogens is required, it holds promise as a clinically deployable workflow suitable for evaluation in routine microbiology laboratories.
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Affiliation(s)
- Adela Alcolea-Medina
- Infection Sciences, Synnovis, London, UK.
- Center for Clinical Infection and Diagnostics Research, Guys' and St. Thomas' NHS Foundation Trust, London, UK.
- Department of Infectious Diseases, King's College London, London, UK.
| | - Christopher Alder
- Center for Clinical Infection and Diagnostics Research, Guys' and St. Thomas' NHS Foundation Trust, London, UK
| | - Luke B Snell
- Center for Clinical Infection and Diagnostics Research, Guys' and St. Thomas' NHS Foundation Trust, London, UK
- Department of Infectious Diseases, King's College London, London, UK
| | | | - Alp Aydin
- Quadram Institute Bioscience, Norwich, UK
| | - Gaia Nebbia
- Department of Infectious Diseases, Guys' and St Thomas' NHS Foundation Trust, London, UK
| | - Tom Williams
- Department of Infectious Diseases, Guys' and St Thomas' NHS Foundation Trust, London, UK
| | - Simon Goldenberg
- Department of Infectious Diseases, Guys' and St Thomas' NHS Foundation Trust, London, UK
| | - Sam Douthwaite
- Department of Infectious Diseases, Guys' and St Thomas' NHS Foundation Trust, London, UK
| | - Rahul Batra
- Center for Clinical Infection and Diagnostics Research, Guys' and St. Thomas' NHS Foundation Trust, London, UK
| | | | - Hannah Mischo
- Department of Infectious Diseases, King's College London, London, UK
| | - Stuart Neil
- Department of Infectious Diseases, King's College London, London, UK
| | - Mark Wilks
- Queen Mary, University of London, London, UK
| | - Jonathan D Edgeworth
- Center for Clinical Infection and Diagnostics Research, Guys' and St. Thomas' NHS Foundation Trust, London, UK
- Department of Infectious Diseases, King's College London, London, UK
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Ji J, Hu C, Pang X, Liang J, Huang Q, Hu S, Mei Q, Ma H. Open Thermal Control System for Stable Polymerase Chain Reaction on a Digital Microfluidic Chip. ACS OMEGA 2024; 9:10937-10944. [PMID: 38463286 PMCID: PMC10918803 DOI: 10.1021/acsomega.3c10312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 01/31/2024] [Accepted: 02/07/2024] [Indexed: 03/12/2024]
Abstract
In this paper, a digital microfluidic thermal control system was introduced for the stable polymerase chain reaction (PCR). The system consists of a thermoelectric cooler unit, a thermal control board, and graphical-user-interface software capable of simultaneously achieving temperature control and on-chip droplet observation. A fuzzy proportional-integral-derivative (PID) method was developed for this system. The simulation analysis was performed to evaluate the temperature of different reagents within the chip. Based on the results, applying fuzzy PID control for PCR will enhance the thermal stability by 67.8% and save the time by 1195 s, demonstrating excellent dynamic response capability and thermal robustness. The experimental results are consistent with the simulation results on the planar temperature distribution, with a data consistency rate of over 99%. The PCR validation was carried out on this system, successfully amplifying the rat GAPDH gene at a concentration of 193 copies/μL. This work has the potential to be useful in numerous existing lab-on-a-chip applications.
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Affiliation(s)
- Jiajian Ji
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
- CAS Key Laboratory of Biomedical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences (CAS), Suzhou 215163, China
| | - Chenxuan Hu
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
- CAS Key Laboratory of Biomedical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences (CAS), Suzhou 215163, China
| | - Xinpei Pang
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
- CAS Key Laboratory of Biomedical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences (CAS), Suzhou 215163, China
| | - Jiancong Liang
- Guangdong ACXEL Micro & Nano Tech Co., Ltd, Foshan 528200, China
| | - Qi Huang
- CAS Key Laboratory of Biomedical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences (CAS), Suzhou 215163, China
| | - Siyi Hu
- CAS Key Laboratory of Biomedical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences (CAS), Suzhou 215163, China
| | - Qian Mei
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
- CAS Key Laboratory of Biomedical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences (CAS), Suzhou 215163, China
| | - Hanbin Ma
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
- CAS Key Laboratory of Biomedical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences (CAS), Suzhou 215163, China
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Ho M, Sathishkumar N, Sklavounos AA, Sun J, Yang I, Nichols KP, Wheeler AR. Digital microfluidics with distance-based detection - a new approach for nucleic acid diagnostics. LAB ON A CHIP 2023; 24:63-73. [PMID: 37987330 DOI: 10.1039/d3lc00683b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
There is great enthusiasm for using loop-mediated isothermal amplification (LAMP) in point-of-care nucleic acid amplification tests (POC NAATs), as an alternative to PCR. While isothermal amplification techniques like LAMP eliminate the need for rapid temperature cycling in a portable format, these systems are still plagued by requirements for dedicated optical detection apparatus for analysis and manual off-chip sample processing. Here, we developed a new microfluidic system for LAMP-based POC NAATs to address these limitations. The new system combines digital microfluidics (DMF) with distance-based detection (DBD) for direct signal readout. This is the first report of the use of (i) LAMP or (ii) DMF with DBD - thus, we describe a number of characterization steps taken to determine optimal combinations of reagents, materials, and processes for reliable operation. For example, DBD was found to be quite sensitive to background signals from low molecular weight LAMP products; thus, a Capto™ adhere bead-based clean-up procedure was developed to isolate the desirable high-molecular-weight products for analysis. The new method was validated by application to detection of SARS-CoV-2 in saliva. The method was able to distinguish between saliva containing no virus, saliva containing a low viral load (104 genome copies per mL), and saliva containing a high viral load (108 copies per mL), all in an automated system that does not require detection apparatus for analysis. We propose that the combination of DMF with distance-based detection may be a powerful one for implementing a variety of POC NAATs or for other applications in the future.
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Affiliation(s)
- Man Ho
- Department of Chemistry, University of Toronto, 80. St. George Street, Toronto, Ontario, M5S 3H6, Canada.
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario, M5S 3E1, Canada
| | - N Sathishkumar
- Department of Chemistry, University of Toronto, 80. St. George Street, Toronto, Ontario, M5S 3H6, Canada.
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario, M5S 3E1, Canada
| | - Alexandros A Sklavounos
- Department of Chemistry, University of Toronto, 80. St. George Street, Toronto, Ontario, M5S 3H6, Canada.
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario, M5S 3E1, Canada
| | - Jianxian Sun
- Department of Chemistry, University of Toronto, 80. St. George Street, Toronto, Ontario, M5S 3H6, Canada.
| | - Ivy Yang
- Department of Chemical Engineering & Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, M5S 3E5, Canada
| | | | - Aaron R Wheeler
- Department of Chemistry, University of Toronto, 80. St. George Street, Toronto, Ontario, M5S 3H6, Canada.
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario, M5S 3E1, Canada
- Institute of Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario, M5S 3G9, Canada
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6
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Lorenzo-Villegas DL, Gohil NV, Lamo P, Gurajala S, Bagiu IC, Vulcanescu DD, Horhat FG, Sorop VB, Diaconu M, Sorop MI, Oprisoni A, Horhat RM, Susan M, MohanaSundaram A. Innovative Biosensing Approaches for Swift Identification of Candida Species, Intrusive Pathogenic Organisms. Life (Basel) 2023; 13:2099. [PMID: 37895480 PMCID: PMC10608220 DOI: 10.3390/life13102099] [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: 09/26/2023] [Revised: 10/17/2023] [Accepted: 10/20/2023] [Indexed: 10/29/2023] Open
Abstract
Candida is the largest genus of medically significant fungi. Although most of its members are commensals, residing harmlessly in human bodies, some are opportunistic and dangerously invasive. These have the ability to cause severe nosocomial candidiasis and candidemia that affect the viscera and bloodstream. A prompt diagnosis will lead to a successful treatment modality. The smart solution of biosensing technologies for rapid and precise detection of Candida species has made remarkable progress. The development of point-of-care (POC) biosensor devices involves sensor precision down to pico-/femtogram level, cost-effectiveness, portability, rapidity, and user-friendliness. However, futuristic diagnostics will depend on exploiting technologies such as multiplexing for high-throughput screening, CRISPR, artificial intelligence (AI), neural networks, the Internet of Things (IoT), and cloud computing of medical databases. This review gives an insight into different biosensor technologies designed for the detection of medically significant Candida species, especially Candida albicans and C. auris, and their applications in the medical setting.
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Affiliation(s)
| | - Namra Vinay Gohil
- Department of Internal Medicne, Medical College Baroda, Vadodara 390001, India;
- Department of Internal Medicne, SSG Hospital Vadodara, Gotri, Vadodara 390021, India
| | - Paula Lamo
- Escuela Superior de Ingeniería y Tecnología, Universidad Internacional de La Rioja, 26006 Logroño, Spain;
| | - Swathi Gurajala
- College of Applied Medical Sciences in Jubail, Imam Abdulrahman bin Faisal University, Dammam 31441, Saudi Arabia;
| | - Iulia Cristina Bagiu
- Department of Microbiology, “Victor Babes” University of Medicine and Pharmacy, Eftimie Murgu Square 2, 300041 Timisoara, Romania; (D.D.V.); (F.G.H.)
- Multidisciplinary Research Center on Antimicrobial Resistance (MULTI-REZ), Microbiology Department, “Victor Babes” University of Medicine and Pharmacy, Eftimie Murgu Square 2, 300041 Timisoara, Romania
| | - Dan Dumitru Vulcanescu
- Department of Microbiology, “Victor Babes” University of Medicine and Pharmacy, Eftimie Murgu Square 2, 300041 Timisoara, Romania; (D.D.V.); (F.G.H.)
- Multidisciplinary Research Center on Antimicrobial Resistance (MULTI-REZ), Microbiology Department, “Victor Babes” University of Medicine and Pharmacy, Eftimie Murgu Square 2, 300041 Timisoara, Romania
| | - Florin George Horhat
- Department of Microbiology, “Victor Babes” University of Medicine and Pharmacy, Eftimie Murgu Square 2, 300041 Timisoara, Romania; (D.D.V.); (F.G.H.)
- Multidisciplinary Research Center on Antimicrobial Resistance (MULTI-REZ), Microbiology Department, “Victor Babes” University of Medicine and Pharmacy, Eftimie Murgu Square 2, 300041 Timisoara, Romania
| | - Virgiliu Bogdan Sorop
- Department of Obstetrics and Gynecology, “Victor Babes” University of Medicine and Pharmacy, Eftimie Murgu Square, No. 2, 300041 Timisoara, Romania; (V.B.S.); (M.D.)
| | - Mircea Diaconu
- Department of Obstetrics and Gynecology, “Victor Babes” University of Medicine and Pharmacy, Eftimie Murgu Square, No. 2, 300041 Timisoara, Romania; (V.B.S.); (M.D.)
| | - Madalina Ioana Sorop
- Doctoral School, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania;
| | - Andrada Oprisoni
- Department of Pediatrics, Discipline of Pediatric Oncology and Hematology, “Victor Babes” University of Medicine and Pharmacy, Eftimie Murgu Square, No. 2, 300041 Timisoara, Romania;
| | - Razvan Mihai Horhat
- Department of Conservative Dentistry and Endodontics, Faculty of Dental Medicine, “Victor Babes” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square 2, 300041 Timisoara, Romania;
| | - Monica Susan
- Centre for Preventive Medicine, Department of Internal Medicine, “Victor Babes” University of Medicine and Pharmacy, Eftimie Murgu Square, No. 2, 300041 Timisoara, Romania;
| | - ArunSundar MohanaSundaram
- School of Pharmacy, Sathyabama Institute of Science and Technology, Jeppiaar Nagar, Rajiv Gandhi Salai, Chennai 600119, India;
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Jenks JD, White PL, Kidd SE, Goshia T, Fraley SI, Hoenigl M, Thompson GR. An update on current and novel molecular diagnostics for the diagnosis of invasive fungal infections. Expert Rev Mol Diagn 2023; 23:1135-1152. [PMID: 37801397 PMCID: PMC10842420 DOI: 10.1080/14737159.2023.2267977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 10/04/2023] [Indexed: 10/08/2023]
Abstract
BACKGROUND Invasive fungal infections cause millions of infections annually, but diagnosis remains challenging. There is an increased need for low-cost, easy to use, highly sensitive and specific molecular assays that can differentiate between colonized and pathogenic organisms from different clinical specimens. AREAS COVERED We reviewed the literature evaluating the current state of molecular diagnostics for invasive fungal infections, focusing on current and novel molecular tests such as polymerase chain reaction (PCR), digital PCR, high-resolution melt (HRM), and metagenomics/next generation sequencing (mNGS). EXPERT OPINION PCR is highly sensitive and specific, although performance can be impacted by prior/concurrent antifungal use. PCR assays can identify mutations associated with antifungal resistance, non-Aspergillus mold infections, and infections from endemic fungi. HRM is a rapid and highly sensitive diagnostic modality that can identify a wide range of fungal pathogens, including down to the species level, but multiplex assays are limited and HRM is currently unavailable in most healthcare settings, although universal HRM is working to overcome this limitation. mNGS offers a promising approach for rapid and hypothesis-free diagnosis of a wide range of fungal pathogens, although some drawbacks include limited access, variable performance across platforms, the expertise and costs associated with this method, and long turnaround times in real-world settings.
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Affiliation(s)
- Jeffrey D Jenks
- Durham County Department of Public Health, Durham, North Carolina, USA
- Division of Infectious Diseases, Department of Medicine, Duke University, Durham, North Carolina, USA
| | - P Lewis White
- Public Health Wales Microbiology Cardiff, UHW, United Kingdom and Centre for trials research/Division of Infection/Immunity, Cardiff University, Cardiff, UK
| | - Sarah E Kidd
- National Mycology Reference Centre, SA Pathology, Adelaide, Australia
- School of Biological Sciences, Faculty of Sciences, University of Adelaide, Adelaide, Australia
| | - Tyler Goshia
- Department of Bioengineering, University of California, San Diego, CA, USA
| | - Stephanie I Fraley
- Department of Bioengineering, University of California, San Diego, CA, USA
| | - Martin Hoenigl
- Division of Infectious Diseases, Medical University of Graz, Graz, Austria
- BioTechMed, Graz, Austria
| | - George R Thompson
- University of California Davis Center for Valley Fever, Sacramento, CA, USA
- Department of Internal Medicine, Division of Infectious Diseases, University of California Davis Medical Center, Sacramento, CA, USA
- Department of Medical Microbiology and Immunology, University of California Davis, Davis, CA, USA
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8
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Felix GN, de Freitas VLT, da Silva Junior AR, Magri MMC, Rossi F, Sejas ONE, Abdala E, Malbouisson LMS, Guimarães T, Benard G, Del Negro GMB. Performance of a Real-Time PCR Assay for the Detection of Five Candida Species in Blood Samples from ICU Patients at Risk of Candidemia. J Fungi (Basel) 2023; 9:635. [PMID: 37367571 DOI: 10.3390/jof9060635] [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: 03/19/2023] [Revised: 04/22/2023] [Accepted: 05/13/2023] [Indexed: 06/28/2023] Open
Abstract
The gold standard for diagnosing invasive candidiasis still relies on blood cultures, which are inefficient and time-consuming to analyze. We developed an in-house qPCR assay to identify the 5 major Candida species in 78 peripheral blood (PB) samples from ICU patients at risk of candidemia. Blood cultures and (1,3)-β-D-glucan (BDG) testing were performed concurrently to evaluate the performance of the qPCR. The qPCR was positive for DNA samples from all 20 patients with proven candidemia (positive PB cultures), showing complete concordance with Candida species identification in blood cultures, except for detection of dual candidemia in 4 patients, which was missed by blood cultures. Additionally, the qPCR detected Candida species in six DNA samples from patients with positive central venous catheters blood (CB) but negative PB cultures. BDG values were similarly high in these six samples and the ones with proven candidemia, strongly suggesting the diagnosis of a true candidemia episode despite the negative PB cultures. Samples from patients neither infected nor colonized yielded negative results in both the qPCR and BDG testing. Our qPCR assay was at least as sensitive as blood cultures, but with a shorter turnaround time. Furthermore, negative results from the qPCR provided strong evidence for the absence of candidemia caused by the five major Candida species.
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Affiliation(s)
- Gabriel N Felix
- Laboratory of Medical Mycology (LIM 53), Instituto de Medicina Tropical, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (HC-FMUSP), São Paulo 05403-000, Brazil
| | - Vera L T de Freitas
- Laboratório de Investigação Médica em Imunologia (LIM 48), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (HC-FMUSP), São Paulo 05403-000, Brazil
| | - Afonso R da Silva Junior
- Central Laboratory Division (LIM 03), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (HC-FMUSP), São Paulo 05403-010, Brazil
| | - Marcello M C Magri
- Central Laboratory Division (LIM 03), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (HC-FMUSP), São Paulo 05403-010, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-010, Brazil
| | - Flavia Rossi
- Central Laboratory Division (LIM 03), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (HC-FMUSP), São Paulo 05403-010, Brazil
| | - Odeli N E Sejas
- Cancer Institute of São Paulo State (ICESP), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (HC-FMUSP), São Paulo 01246-000, Brazil
| | - Edson Abdala
- Cancer Institute of São Paulo State (ICESP), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (HC-FMUSP), São Paulo 01246-000, Brazil
| | - Luiz M S Malbouisson
- Discipline of Anesthesiology, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-010, Brazil
| | - Thais Guimarães
- Infectious Diseases Department, Hospital do Servidor Público Estadual de São Paulo (IAMSPE), São Paulo 04029-000, Brazil
| | - Gil Benard
- Laboratory of Medical Mycology (LIM 53), Instituto de Medicina Tropical, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (HC-FMUSP), São Paulo 05403-000, Brazil
| | - Gilda M B Del Negro
- Laboratory of Medical Mycology (LIM 53), Instituto de Medicina Tropical, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (HC-FMUSP), São Paulo 05403-000, Brazil
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9
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Koc Ö, Kessler HH, Hoenigl M, Wagener J, Suerbaum S, Schubert S, Dichtl K. Performance of Multiplex PCR and β-1,3-D-Glucan Testing for the Diagnosis of Candidemia. J Fungi (Basel) 2022; 8:jof8090972. [PMID: 36135696 PMCID: PMC9504845 DOI: 10.3390/jof8090972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/05/2022] [Accepted: 09/15/2022] [Indexed: 11/28/2022] Open
Abstract
Bloodstream infections caused by Candida yeasts (candidemia) are associated with high morbidity and mortality. Diagnosis remains challenging, with the current gold standard—isolation from blood culture (BC)—being limited by low sensitivity and long turnaround time. This study evaluated the performance of two nonculture methods: PCR and β-1,3-D-glucan (BDG) testing. The sera of 103 patients with BC-proven candidemia and of 46 controls were analyzed with the Fungiplex Candida Real-Time PCR and the Wako β-Glucan Test. The BDG assay demonstrated higher sensitivity than the multiplex PCR (58% vs. 33%). This was particularly evident in ICU patients (60% vs. 28%) and in C. albicans candidemia (57% vs. 37%). The earlier prior to BC sampling the sera were obtained, the more the PCR sensitivity decreased (46% to 18% in the periods of 0−2 and 3−5 days before BC, respectively), while BDG testing was independent of the sampling date. No positive PCR results were obtained in sera sampled more than five days before BC. Specificities were 89% for BDG and 93% for PCR testing. In conclusion, BDG testing demonstrated several advantages over PCR testing for the diagnosis of candidemia, including higher sensitivity and earlier diagnosis. However, BC remains essential, as BDG does not allow for species differentiation.
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Affiliation(s)
- Özlem Koc
- Max von Pettenkofer-Institut für Hygiene und Medizinische Mikrobiologie, Medizinische Fakultät, LMU München, 80336 Munich, Germany
| | - Harald H. Kessler
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, 8010 Graz, Austria
| | - Martin Hoenigl
- Division of Infectious Diseases, Department of Internal Medicine, Medical University of Graz, 8010 Graz, Austria
| | - Johannes Wagener
- Microbiology Department, St. James’s Hospital, D08 RX0X Dublin, Ireland
- Department of Clinical Microbiology, School of Medicine, Trinity College Dublin, The University of Dublin, St. James’s Hospital Campus, D08 RX0X Dublin, Ireland
| | - Sebastian Suerbaum
- Max von Pettenkofer-Institut für Hygiene und Medizinische Mikrobiologie, Medizinische Fakultät, LMU München, 80336 Munich, Germany
| | - Sören Schubert
- Max von Pettenkofer-Institut für Hygiene und Medizinische Mikrobiologie, Medizinische Fakultät, LMU München, 80336 Munich, Germany
- Correspondence: (S.S.); (K.D.)
| | - Karl Dichtl
- Max von Pettenkofer-Institut für Hygiene und Medizinische Mikrobiologie, Medizinische Fakultät, LMU München, 80336 Munich, Germany
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, 8010 Graz, Austria
- Correspondence: (S.S.); (K.D.)
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Wu J, Tang B, Qiu Y, Tan R, Liu J, Xia J, Zhang J, Huang J, Qu J, Sun J, Wang X, Qu H. Clinical validation of a multiplex droplet digital PCR for diagnosing suspected bloodstream infections in ICU practice: a promising diagnostic tool. Crit Care 2022; 26:243. [PMID: 35941654 PMCID: PMC9358819 DOI: 10.1186/s13054-022-04116-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 07/31/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Droplet digital PCR (ddPCR) has emerged as a promising tool of pathogen detection in bloodstream infections (BSIs) in critical care medicine. However, different ddPCR platforms have variable sensitivity and specificity for diverse microorganisms at various infection sites. There is still a lack of prospective clinical studies aimed at validating and interpreting the discrepant ddPCR results for diagnosing BSI in intensive care unit (ICU) practice.
Methods
A prospective diagnostic study of multiplex ddPCR panels was conducted in a general ICU from May 21, 2021, to December 22, 2021. Paired blood cultures (BCs) and ddPCRs (2.5 h) were obtained synchronously to detect the 12 most common BSI pathogens and three antimicrobial resistance (AMR) genes. Firstly, ddPCR performance was compared to definite BSI. Secondly, clinical validation of ddPCR was compared to composite clinical diagnosis. Sensitivity, specificity, and positive and negative predictive values were calculated. Thirdly, the positive rate of AMR genes and related analysis was presented.
Results
A total of 438 episodes of suspected BSIs occurring in 150 critical patients were enrolled. BC and ddPCR were positive for targeted bacteria in 40 (9.1%) and 180 (41.1%) cases, respectively. There were 280 concordant and 158 discordant. In comparison with BCs, the sensitivity of ddPCR ranged from 58.8 to 86.7% with an aggregate of 72.5% in different species, with corresponding specificity ranging from 73.5 to 92.2% with an aggregate of 63.1%. Furthermore, the rate of ddPCR+/BC− results was 33.6% (147/438) with 87.1% (128 of 147) cases was associated with probable (n = 108) or possible (n = 20) BSIs. When clinically diagnosed BSI was used as true positive, the final sensitivity and specificity of ddPCR increased to 84.9% and 92.5%, respectively. In addition, 40 blaKPC, 3blaNDM, and 38 mecA genes were detected, among which 90.5% were definitely positive for blaKPC. Further, 65.8% specimens were predicted to be mecA-positive in Staphylococcus sp. according to all microbiological analysis.
Conclusions
The multiplexed ddPCR is a flexible and universal platform, which can be used as an add-on complementary to conventional BC. When combined with clinical infection evidence, ddPCR shows potential advantages for rapidly diagnosing suspected BSIs and AMR genes in ICU practice.
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Goralczyk A, Bhagwat S, Mayoussi F, Nekoonam N, Sachsenheimer K, Hou P, Kotz-Helmer F, Helmer D, Rapp BE. Application of Micro/Nanoporous Fluoropolymers with Reduced Bioadhesion in Digital Microfluidics. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 12:2201. [PMID: 35808037 PMCID: PMC9268009 DOI: 10.3390/nano12132201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/24/2022] [Accepted: 06/25/2022] [Indexed: 02/01/2023]
Abstract
Digital microfluidics (DMF) is a versatile platform for conducting a variety of biological and chemical assays. The most commonly used set-up for the actuation of microliter droplets is electrowetting on dielectric (EWOD), where the liquid is moved by an electrostatic force on a dielectric layer. Superhydrophobic materials are promising materials for dielectric layers, especially since the minimum contact between droplet and surface is key for low adhesion of biomolecules, as it causes droplet pinning and cross contamination. However, superhydrophobic surfaces show limitations, such as full wetting transition between Cassie and Wenzel under applied voltage, expensive and complex fabrication and difficult integration into already existing devices. Here we present Fluoropor, a superhydrophobic fluorinated polymer foam with pores on the micro/nanoscale as a dielectric layer in DMF. Fluoropor shows stable wetting properties with no significant changes in the wetting behavior, or full wetting transition, until potentials of 400 V. Furthermore, Fluoropor shows low attachment of biomolecules to the surface upon droplet movement. Due to its simple fabrication process, its resistance to adhesion of biomolecules and the fact it is capable of being integrated and exchanged as thin films into commercial DMF devices, Fluoropor is a promising material for wide application in DMF.
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Affiliation(s)
- Andreas Goralczyk
- Laboratory of Process Technology, NeptunLab, Department of Microsystem Engineering (IMTEK), University of Freiburg, 79110 Freiburg im Breisgau, Germany; (A.G.); (S.B.); (F.M.); (N.N.); (K.S.); (P.H.); (F.K.-H.); (B.E.R.)
| | - Sagar Bhagwat
- Laboratory of Process Technology, NeptunLab, Department of Microsystem Engineering (IMTEK), University of Freiburg, 79110 Freiburg im Breisgau, Germany; (A.G.); (S.B.); (F.M.); (N.N.); (K.S.); (P.H.); (F.K.-H.); (B.E.R.)
| | - Fadoua Mayoussi
- Laboratory of Process Technology, NeptunLab, Department of Microsystem Engineering (IMTEK), University of Freiburg, 79110 Freiburg im Breisgau, Germany; (A.G.); (S.B.); (F.M.); (N.N.); (K.S.); (P.H.); (F.K.-H.); (B.E.R.)
| | - Niloofar Nekoonam
- Laboratory of Process Technology, NeptunLab, Department of Microsystem Engineering (IMTEK), University of Freiburg, 79110 Freiburg im Breisgau, Germany; (A.G.); (S.B.); (F.M.); (N.N.); (K.S.); (P.H.); (F.K.-H.); (B.E.R.)
| | - Kai Sachsenheimer
- Laboratory of Process Technology, NeptunLab, Department of Microsystem Engineering (IMTEK), University of Freiburg, 79110 Freiburg im Breisgau, Germany; (A.G.); (S.B.); (F.M.); (N.N.); (K.S.); (P.H.); (F.K.-H.); (B.E.R.)
| | - Peilong Hou
- Laboratory of Process Technology, NeptunLab, Department of Microsystem Engineering (IMTEK), University of Freiburg, 79110 Freiburg im Breisgau, Germany; (A.G.); (S.B.); (F.M.); (N.N.); (K.S.); (P.H.); (F.K.-H.); (B.E.R.)
| | - Frederik Kotz-Helmer
- Laboratory of Process Technology, NeptunLab, Department of Microsystem Engineering (IMTEK), University of Freiburg, 79110 Freiburg im Breisgau, Germany; (A.G.); (S.B.); (F.M.); (N.N.); (K.S.); (P.H.); (F.K.-H.); (B.E.R.)
- Freiburg Materials Research Center (FMF), University of Freiburg, 79104 Freiburg im Breisgau, Germany
| | - Dorothea Helmer
- Laboratory of Process Technology, NeptunLab, Department of Microsystem Engineering (IMTEK), University of Freiburg, 79110 Freiburg im Breisgau, Germany; (A.G.); (S.B.); (F.M.); (N.N.); (K.S.); (P.H.); (F.K.-H.); (B.E.R.)
- Freiburg Materials Research Center (FMF), University of Freiburg, 79104 Freiburg im Breisgau, Germany
- Freiburg Center of Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, 79110 Freiburg im Breisgau, Germany
| | - Bastian E. Rapp
- Laboratory of Process Technology, NeptunLab, Department of Microsystem Engineering (IMTEK), University of Freiburg, 79110 Freiburg im Breisgau, Germany; (A.G.); (S.B.); (F.M.); (N.N.); (K.S.); (P.H.); (F.K.-H.); (B.E.R.)
- Freiburg Materials Research Center (FMF), University of Freiburg, 79104 Freiburg im Breisgau, Germany
- Freiburg Center of Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, 79110 Freiburg im Breisgau, Germany
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Zhang Y, Zhao Y, Cole T, Zheng J, Bayinqiaoge, Guo J, Tang SY. Microfluidic flow cytometry for blood-based biomarker analysis. Analyst 2022; 147:2895-2917. [PMID: 35611964 DOI: 10.1039/d2an00283c] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Flow cytometry has proven its capability for rapid and quantitative analysis of individual cells and the separation of targeted biological samples from others. The emerging microfluidics technology makes it possible to develop portable microfluidic diagnostic devices for point-of-care testing (POCT) applications. Microfluidic flow cytometry (MFCM), where flow cytometry and microfluidics are combined to achieve similar or even superior functionalities on microfluidic chips, provides a powerful single-cell characterisation and sorting tool for various biological samples. In recent years, researchers have made great progress in the development of the MFCM including focusing, detecting, and sorting subsystems, and its unique capabilities have been demonstrated in various biological applications. Moreover, liquid biopsy using blood can provide various physiological and pathological information. Thus, biomarkers from blood are regarded as meaningful circulating transporters of signal molecules or particles and have great potential to be used as non (or minimally)-invasive diagnostic tools. In this review, we summarise the recent progress of the key subsystems for MFCM and its achievements in blood-based biomarker analysis. Finally, foresight is offered to highlight the research challenges faced by MFCM in expanding into blood-based POCT applications, potentially yielding commercialisation opportunities.
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Affiliation(s)
- Yuxin Zhang
- Department of Electronic, Electrical and Systems Engineering, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
| | - Ying Zhao
- National Chengdu Centre of Safety Evaluation of Drugs, West China Hospital of Sichuan University, Chengdu, China
| | - Tim Cole
- Department of Electronic, Electrical and Systems Engineering, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
| | - Jiahao Zheng
- Department of Electronic, Electrical and Systems Engineering, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
| | - Bayinqiaoge
- Department of Electronic, Electrical and Systems Engineering, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
| | - Jinhong Guo
- The M.O.E. Key Laboratory of Laboratory Medical Diagnostics, The College of Laboratory Medicine, Chongqing Medical University, #1 Yixueyuan Road, Yuzhong District, Chongqing, 400016, China.
| | - Shi-Yang Tang
- Department of Electronic, Electrical and Systems Engineering, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
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Yano J, Fidel PL. Methods Related to the Immunopathogenesis of Vulvovaginal Candidiasis and Associated Neutrophil Anergy. Methods Mol Biol 2022; 2542:193-218. [PMID: 36008666 DOI: 10.1007/978-1-0716-2549-1_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Vulvovaginal candidiasis (VVC) is a common mucosal disease, caused primarily by Candida albicans that affects up to 75% of women of childbearing age. The pathogenesis of VVC and recurrent VVC (RVVC) is largely understood after decades of research. In this regard, an immunopathological response involving the migration of neutrophils that become dysfunctional (anergic) in the vaginal environment leads to the symptomatic conditions. However, immunotherapeutic strategies to correct the immunopathogenesis are still elusive. Much of the mechanistic discoveries have been uncovered using the established mouse model of chronic VVC. This chapter details the methods widely used for the mouse model of experimental VVC and associated outcome measures of the immunopathologic response and resulting symptomatic condition and focuses further on assays used to demonstrate "neutrophil anergy" in the model. These methods may serve as a source or resource for further experimentation with the ultimate goal to reduce or eliminate VVC/RVVC.
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Affiliation(s)
- Junko Yano
- Louisiana State University Health, New Orleans, LA, USA
| | - Paul L Fidel
- Louisiana State University Health, New Orleans, LA, USA.
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14
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Biosensors for Fungal Detection. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2021. [DOI: 10.22207/jpam.15.4.02] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Due to the serious threat of invasive fungal infections, there is an emergent need for improved a sensitive and more accurate diagnostic tests for detection of systemic pathogenic fungi and plant health. Traditional fungal diagnosis can only be achieved at later growing phases. The complex and difficult immunodiagnostic is also widely employed. Enzyme-based immunoassays which lead to cross-interaction with different fungi still also obeyed. A polymerase chain reactions (PCRs)- based molecular diagnosis are does not enable precise identification of fungal pathogens, or the ability to test isolates for drug sensitivity. In the future, biosensing technologies and nanotechnological tools, will improve diagnosis of pathogenic fungi through a specific and sensitive pathogen detection. This report systematically reviews the most prominent biosensor trends for fungi detection.
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15
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Recent Advances and Novel Approaches in Laboratory-Based Diagnostic Mycology. J Fungi (Basel) 2021; 7:jof7010041. [PMID: 33440757 PMCID: PMC7827937 DOI: 10.3390/jof7010041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 12/31/2020] [Accepted: 01/01/2021] [Indexed: 12/16/2022] Open
Abstract
What was once just culture and microscopy the field of diagnostic mycology has significantly advanced in recent years and continues to incorporate novel assays and strategies to meet the changes in clinical demand. The emergence of widespread resistance to antifungal therapy has led to the development of a range of molecular tests that target mutations associated with phenotypic resistance, to complement classical susceptibility testing and initial applications of next-generation sequencing are being described. Lateral flow assays provide rapid results, with simplicity allowing the test to be performed outside specialist centres, potentially as point-of-care tests. Mycology has responded positively to an ever-diversifying patient population by rapidly identifying risk and developing diagnostic strategies to improve patient management. Nowadays, the diagnostic repertoire of the mycology laboratory employs classical, molecular and serological tests and should be keen to embrace diagnostic advancements that can improve diagnosis in this notoriously difficult field.
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Malik A, Fatma T, Shamsi W, Khan HA, Gul A, Jamal A, Bhatti MF. Molecular Characterization of Medically Important Fungi: Current Research and Future Prospects. Fungal Biol 2021. [DOI: 10.1007/978-3-030-60659-6_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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17
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Chen B, Xie Y, Zhang N, Li W, Liu C, Li D, Bian S, Jiang Y, Yang Z, Li R, Feng Y, Zhang X, Shi D. Evaluation of Droplet Digital PCR Assay for the Diagnosis of Candidemia in Blood Samples. Front Microbiol 2021; 12:700008. [PMID: 34603226 PMCID: PMC8480469 DOI: 10.3389/fmicb.2021.700008] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 07/26/2021] [Indexed: 12/14/2022] Open
Abstract
Numerous studies have shown that droplet digital PCR (ddPCR) is a promising tool for the diagnosis of pathogens, especially in samples with low concentrations of pathogenic DNA. An early diagnosis of candidemia is critical for the effective treatment of patients. In this study, we evaluated the sensitivity and specificity of ddPCR assay for Candida DNA detection both in vitro by mixing fungal cells with human blood and in vivo by analyzing blood samples from infected mice and patients with suspected candidemia. The results showed that ddPCR assay could detect a minimum of 4.5 DNA copies per reaction in blood samples. ddPCR showed higher sensitivity and specificity for Candida DNA detection than traditional culture and quantitative PCR (qPCR) methods and also exhibited significantly better positive and negative predictive values than the culture and qPCR methods that were commonly used in clinical practice. Hence, our study demonstrates that ddPCR assay is a promising method for the timely diagnosis of candidemia and could be useful for monitoring the treatment of candidemia.
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Affiliation(s)
- Biao Chen
- The Laboratory of Medical Mycology, Jining No. 1 People's Hospital, Jining, China
- Postdoctoral Mobile Station of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yingguang Xie
- Intensive Care Unit, Jining No. 1 People’s Hospital, Jining, China
| | - Ning Zhang
- The Laboratory of Medical Mycology, Jining No. 1 People's Hospital, Jining, China
| | - Wenqiang Li
- Intensive Care Unit, Jining No. 1 People’s Hospital, Jining, China
| | - Chen Liu
- The Laboratory of Medical Mycology, Jining No. 1 People's Hospital, Jining, China
| | - Dongmei Li
- Department of Microbiology and Immunology, Georgetown University Medical Center, Washington, DC, United States
| | - Shaodong Bian
- The Laboratory of Medical Mycology, Jining No. 1 People's Hospital, Jining, China
| | - Yufeng Jiang
- Postdoctoral Mobile Station of Shandong University of Traditional Chinese Medicine, Jinan, China
- Clinical Laboratory, Jining No. 1 People’s Hospital, Jining, China
| | - Zhiya Yang
- The Laboratory of Medical Mycology, Jining No. 1 People's Hospital, Jining, China
| | - Renzhe Li
- Clinical Laboratory, Jining No. 1 People’s Hospital, Jining, China
| | - Yahui Feng
- Clinical Medicine College, Jining Medical College, Jining, China
| | - Xiaojie Zhang
- Postdoctoral Mobile Station of Shandong University of Traditional Chinese Medicine, Jinan, China
- Xiaojie Zhang,
| | - Dongmei Shi
- The Laboratory of Medical Mycology, Jining No. 1 People's Hospital, Jining, China
- Department of Dermatology, Jining No. 1 People’s Hospital, Jining, China
- *Correspondence: Dongmei Shi,
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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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A Routing-Based Repair Method for Digital Microfluidic Biochips Based on an Improved Dijkstra and Improved Particle Swarm Optimization Algorithm. MICROMACHINES 2020; 11:mi11121052. [PMID: 33260565 PMCID: PMC7761094 DOI: 10.3390/mi11121052] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/25/2020] [Accepted: 11/26/2020] [Indexed: 11/17/2022]
Abstract
Digital microfluidic biochips (DMFBs) are attractive instruments for obtaining modern molecular biology and chemical measurements. Due to the increasingly complex measurements carried out on a DMFB, such chips are more prone to failure. To compensate for the shortcomings of the module-based DMFB, this paper proposes a routing-based fault repair method. The routing-based synthesis methodology ensures a much higher chip utilization factor by removing the virtual modules on the chip, as well as removing the extra electrodes needed as guard cells. In this paper, the routing problem is identified as a dynamic path-planning problem and mixed path design problem under certain constraints, and an improved Dijkstra and improved particle swarm optimization (ID-IPSO) algorithm is proposed. By introducing a cost function into the Dijkstra algorithm, the path-planning problem under dynamic obstacles is solved, and the problem of mixed path design is solved by redefining the position and velocity vectors of the particle swarm optimization. The ID-IPSO routing-based fault repair method is applied to a multibody fluid detection experiment. The proposed design method has a stronger optimization ability than the greedy algorithm. The algorithm is applied to 8×9, 8×8, and 7×8 fault-free chips. The proposed ID-IPSO routing-based chip design method saves 13.9%, 14.3%, and 14.5% of the experiment completion time compared with the greedy algorithm. Compared with a modular fault repair method based on the genetic algorithm, the ID-IPSO routing-based fault repair method has greater advantages and can save 39.3% of the completion time on average in the completion of complex experiments. When the ratio of faulty electrodes is less than 12% and 23%, the modular and ID-IPSO routing-based fault repair methods, respectively, can guarantee a 100% failure repair rate. The utilization rate of the electrodes is 18% higher than that of the modular method, and the average electrode usage time is 17%. Therefore, the ID-IPSO routing-based fault repair method can accommodate more faulty electrodes for the same fault repair rate; the experiment completion time is shorter, the average number of electrodes is lower, and the security performance is better.
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Wang Y, Zhao H, Liu X, Lin W, Jiang Y, Li J, Zhang Q, Zheng G. An integrated digital microfluidic bioreactor for fully automatic screening of microalgal growth and stress-induced lipid accumulation. Biotechnol Bioeng 2020; 118:294-304. [PMID: 32946108 DOI: 10.1002/bit.27570] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/06/2020] [Accepted: 09/15/2020] [Indexed: 01/25/2023]
Abstract
Algae are the promising feedstock of biofuel. The screening of competent species and proper fertilizer supply is of the most important tasks. To accelerate this rather slow and laborious step, we developed an integrated high-throughput digital microfluidic (DMF) system that uses a discrete droplet to serve as a microbioreactor, encapsulating microalgal cells. On the basis of fundamental understanding of various droplet hydrodynamics induced by the existence of different sorts of ions and biological species, incorporation of capacitance-based position estimator, electrode-saving-based compensation, and deterministic splitting approach, was performed to optimize the DMF bioreactor. Thus, it enables all processes (e.g., nutrient gradient generation, algae culturing, and analyzing of growth and lipid accumulation) occurring automatically on-chip especially in a high-fidelity way. The ability of the system to compare different microalgal strains on-chip was investigated. Also, the Chlorella sp. were stressed by various conditions and then growth and oil accumulation were analyzed and compared, which demonstrated its potential as a powerful tool to investigate microalgal lipid accumulation at significantly lower laborites and reduced time.
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Affiliation(s)
- Yunhua Wang
- Institute of Environmental and Chemical Engineering, Dalian University, Dalian, China
| | - Hongyu Zhao
- Institute of Environmental and Chemical Engineering, Dalian University, Dalian, China
| | - Xianming Liu
- Department of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Wang Lin
- Institute of Environmental and Chemical Engineering, Dalian University, Dalian, China
| | - Youwei Jiang
- Department of Materials Science and Engineering, South University of Science and Technology, Shenzhen, China
| | - Jianfeng Li
- Department of R&D, Jiangsu Celyee Cell Technology Research Institute, Nanjing, China
| | - Qian Zhang
- Institute of Environmental and Chemical Engineering, Dalian University, Dalian, China
| | - Guoxia Zheng
- Institute of Environmental and Chemical Engineering, Dalian University, Dalian, China
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22
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Busser FD, Coelho VC, Fonseca CDA, Del Negro GMB, Shikanai-Yasuda MA, Lopes MH, Magri MMC, Freitas VLTD. A Real Time PCR strategy for the detection and quantification of Candida albicans in human blood. Rev Inst Med Trop Sao Paulo 2020; 62:e9. [PMID: 32049260 PMCID: PMC7014565 DOI: 10.1590/s1678-9946202062009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 01/08/2020] [Indexed: 12/01/2022] Open
Abstract
Candidemia is a significant cause of bloodstream infections (BSI) in nosocomial settings. The identification of species can potentially improve the quality of care and decrease human mortality. Quantitative PCR (qPCR) was evaluated for Candida albicans detection using culture suspensions containing C. albicans , spiked human blood, the cloned qPCR target fragment (ITS2 region) and the results of these assays were compared. The assays showed a good detection limit: C. albicans DNA extracted from yeast (sensitivity 0.2 CFU/µL), spiked human blood (sensitivity 10 CFU/mL), and cloned fragment of ITS2 region (sensitivity 20 target copies/μL). The efficiency of ITS2 fragment-qPCR ranged from 89.67 to 97.07, and the linearity (R2) of the standard curve ranged from 0.992 to 0.999. The results showed that this ITS2-qPCR has a great potential as a molecular prototype model for the development of a test to be applied in clinical practice, greatly reducing the time of candidemia diagnosis, which is extremely important in this clinical setting.
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Affiliation(s)
- Felipe Delatorre Busser
- Universidade de São Paulo, Faculdade de Medicina, Hospital das Clínicas, Laboratório de Investigação Médica em Imunologia (LIM 48), São Paulo, São Paulo, Brazil
| | - Vivian Caso Coelho
- Universidade de São Paulo, Faculdade de Medicina, Hospital das Clínicas, Laboratório de Investigação Médica em Imunologia (LIM 48), São Paulo, São Paulo, Brazil
| | - Claudia de Abreu Fonseca
- Universidade de São Paulo, Faculdade de Medicina, Hospital das Clínicas, Laboratório de Investigação Médica em Imunologia (LIM 48), São Paulo, São Paulo, Brazil
| | - Gilda Maria Barbaro Del Negro
- Universidade de São Paulo, Faculdade de Medicina, Hospital das Clínicas, Laboratório de Investigação Médica em Micologia (LIM 53), São Paulo, São Paulo, Brazil.,Universidade de São Paulo, Instituto de Medicina Tropical de São Paulo, São Paulo, São Paulo, Brazil
| | - Maria Aparecida Shikanai-Yasuda
- Universidade de São Paulo, Faculdade de Medicina, Hospital das Clínicas, Laboratório de Investigação Médica em Imunologia (LIM 48), São Paulo, São Paulo, Brazil.,Universidade de São Paulo, Faculdade de Medicina, Departamento de Moléstias Infecciosas e Parasitárias, São Paulo, São Paulo, Brazil
| | - Marta Heloisa Lopes
- Universidade de São Paulo, Faculdade de Medicina, Hospital das Clínicas, Laboratório de Investigação Médica em Imunologia (LIM 48), São Paulo, São Paulo, Brazil.,Universidade de São Paulo, Faculdade de Medicina, Departamento de Moléstias Infecciosas e Parasitárias, São Paulo, São Paulo, Brazil
| | - Marcello Mihailenko Chaves Magri
- Universidade de São Paulo, Faculdade de Medicina, Hospital das Clínicas, Laboratório de Investigação Médica em Imunologia (LIM 48), São Paulo, São Paulo, Brazil
| | - Vera Lucia Teixeira de Freitas
- Universidade de São Paulo, Faculdade de Medicina, Departamento de Moléstias Infecciosas e Parasitárias, São Paulo, São Paulo, Brazil
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23
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Update on the Diagnosis of Candidemia and Invasive Candidiasis. CURRENT FUNGAL INFECTION REPORTS 2019. [DOI: 10.1007/s12281-019-00367-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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24
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Asghar W, Sher M, Khan NS, Vyas JM, Demirci U. Microfluidic Chip for Detection of Fungal Infections. ACS OMEGA 2019; 4:7474-7481. [PMID: 31080939 PMCID: PMC6504191 DOI: 10.1021/acsomega.9b00499] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 03/27/2019] [Indexed: 05/08/2023]
Abstract
Fungal infections can lead to severe clinical outcomes such as multiple organ failure and septic shock. Rapid detection of fungal infections allows clinicians to treat patients in a timely manner and improves clinical outcomes. Conventional detection methods include blood culture followed by plate culture and polymerase chain reaction. These methods are time-consuming and require expensive equipment, hence, they are not suitable for point-of-care and clinical settings. There is an unmet need to develop a rapid and inexpensive detection method for fungal infections such as candidemia. We developed an innovative immuno-based microfluidic device that can rapidly detect and capture Candida albicans from phosphate-buffered saline (PBS) and human whole blood. Our microchip technology showed an efficient capture of C. albicans in PBS with an efficiency of 61-78% at various concentrations ranging from 10 to 105 colony-forming units per milliliter (cfu/mL). The presented microfluidic technology will be useful to screen for various pathogens at the point-of-care and clinical settings.
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Affiliation(s)
- Waseem Asghar
- Ashgar
Lab, Micro and Nanotechnology in Medicine, College of Engineering and Computer Science, Boca Raton, Florida 33431, United States
- Department
of Computer & Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, Florida 33431, United States
- E-mail: (W.A.)
| | - Mazhar Sher
- Ashgar
Lab, Micro and Nanotechnology in Medicine, College of Engineering and Computer Science, Boca Raton, Florida 33431, United States
- Department
of Computer & Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, Florida 33431, United States
| | - Nida S. Khan
- Division
of Infectious Disease, Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts 02115, United States
| | - Jatin M. Vyas
- Division
of Infectious Disease, Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts 02115, United States
| | - Utkan Demirci
- Bio-Acoustic
MEMS in Medicine (BAMM) Laboratory, Canary Center at Stanford for
Cancer Early Detection, Department of Radiology, School of Medicine, Stanford University, Palo Alto, California 94305, United States
- E-mail: (U.D.)
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25
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Zhou W, Le J, Chen Y, Cai Y, Hong Z, Chai Y. Recent advances in microfluidic devices for bacteria and fungus research. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2018.12.024] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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26
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Zou F, Ruan Q, Lin X, Zhang M, Song Y, Zhou L, Zhu Z, Lin S, Wang W, Yang CJ. Rapid, real-time chemiluminescent detection of DNA mutation based on digital microfluidics and pyrosequencing. Biosens Bioelectron 2019; 126:551-557. [DOI: 10.1016/j.bios.2018.09.092] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 09/17/2018] [Accepted: 09/27/2018] [Indexed: 02/07/2023]
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27
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Millington D, Norton S, Singh R, Sista R, Srinivasan V, Pamula V. Digital microfluidics comes of age: high-throughput screening to bedside diagnostic testing for genetic disorders in newborns. Expert Rev Mol Diagn 2018; 18:701-712. [PMID: 30004274 PMCID: PMC6481615 DOI: 10.1080/14737159.2018.1495076] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Digital microfluidics (DMF) is an emerging technology with the appropriate metrics for application to newborn and high-risk screening for inherited metabolic disease and other conditions that benefit from early treatment. Areas covered: This review traces the development of electrowetting-based DMF technology toward the fulfillment of its promise to provide an inexpensive platform to conduct enzymatic assays and targeted biomarker assays at the bedside. The high-throughput DMF platform, referred to as SEEKER®, was recently authorized by the United States Food and Drug Administration to screen newborns for four lysosomal storage disorders (LSDs) and is deployed in newborn screening programs in the United States. The development of reagents and methods for LSD screening and results from screening centers are reviewed. Preliminary results from a more compact DMF device, to perform disease-specific test panels from small volumes of blood, are also reviewed. Literature for this review was sourced using principal author and subject searches in PubMed. Expert commentary: Newborn screening is a vital and highly successful public health program. DMF technology adds value to the current testing platforms that will benefit apparently healthy newborns with underlying genetic disorders and infants at-risk for conditions that present with symptoms in the newborn period.
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Affiliation(s)
- David Millington
- Department of Pediatrics, Duke University Medical Center, Durham, NC
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28
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Kwasny D, Tehrani SE, Almeida C, Schjødt I, Dimaki M, Svendsen WE. Direct Detection of Candida albicans with a Membrane Based Electrochemical Impedance Spectroscopy Sensor. SENSORS 2018; 18:s18072214. [PMID: 29996525 PMCID: PMC6069365 DOI: 10.3390/s18072214] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 06/25/2018] [Accepted: 07/06/2018] [Indexed: 01/04/2023]
Abstract
Candidemia and invasive candidiasis is a cause of high mortality and morbidity rates among hospitalized patients worldwide. The occurrence of the infections increases due to the complexity of the patients and overuse of the antifungal therapy. The current Candida detection method includes blood culturing which is a lengthy procedure and thus delays the administration of the antifungal therapy. Even though the results are available after 48 h it is still the gold standard in pathogen detection in a hospital setting. In this work we present an electrochemical impedance sensor that is capable of detecting Candida albicans yeast. The yeast cells are captured on electrodes specifically functionalized with anti-Candida antibodies and detection is achieved by electrochemical impedance spectroscopy. The sensor allows for detection of the yeast cells at clinically relevant concentrations in less than 1 h.
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Affiliation(s)
- Dorota Kwasny
- Department of Micro- and Nanotechnology, Technical University of Denmark, rsteds Plads, Building 345 B, 2800 Kgs. Lyngby, Denmark.
| | - Sheida Esmail Tehrani
- Department of Micro- and Nanotechnology, Technical University of Denmark, rsteds Plads, Building 345 B, 2800 Kgs. Lyngby, Denmark.
| | - Catarina Almeida
- Department of Micro- and Nanotechnology, Technical University of Denmark, rsteds Plads, Building 345 B, 2800 Kgs. Lyngby, Denmark.
| | - Ida Schjødt
- Department of Haematology, Copenhagen University Hospital, Rigshospitalet, 2100 Copenhagen, Denmark.
| | - Maria Dimaki
- Department of Micro- and Nanotechnology, Technical University of Denmark, rsteds Plads, Building 345 B, 2800 Kgs. Lyngby, Denmark.
| | - Winnie E Svendsen
- Department of Micro- and Nanotechnology, Technical University of Denmark, rsteds Plads, Building 345 B, 2800 Kgs. Lyngby, Denmark.
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29
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López LF, Muñoz CO, Cáceres DH, Tobón ÁM, Loparev V, Clay O, Chiller T, Litvintseva A, Gade L, González Á, Gómez BL. Standardization and validation of real time PCR assays for the diagnosis of histoplasmosis using three molecular targets in an animal model. PLoS One 2017; 12:e0190311. [PMID: 29287097 PMCID: PMC5747470 DOI: 10.1371/journal.pone.0190311] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 12/12/2017] [Indexed: 12/04/2022] Open
Abstract
Histoplasmosis is considered one of the most important endemic and systemic mycoses worldwide. Until now few molecular techniques have been developed for its diagnosis. The aim of this study was to develop and evaluate three real time PCR (qPCR) protocols for different protein-coding genes (100-kDa, H and M antigens) using an animal model. Fresh and formalin-fixed and paraffin-embedded (FFPE) lung tissues from BALB/c mice inoculated i.n. with 2.5x106Histoplasma capsulatum yeast or PBS were obtained at 1, 2, 3, 4, 8, 12 and 16 weeks post-infection. A collection of DNA from cultures representing different clades of H. capsulatum (30 strains) and other medically relevant pathogens (36 strains of related fungi and Mycobacterium tuberculosis) were used to analyze sensitivity and specificity. Analytical sensitivity and specificity were 100% when DNAs from the different strains were tested. The highest fungal burden occurred at first week post-infection and complete fungal clearance was observed after the third week; similar results were obtained when the presence of H. capsulatum yeast cells was demonstrated in histopathological analysis. In the first week post-infection, all fresh and FFPE lung tissues from H. capsulatum-infected animals were positive for the qPCR protocols tested except for the M antigen protocol, which gave variable results when fresh lung tissue samples were analyzed. In the second week, all qPCR protocols showed variable results for both fresh and FFPE tissues. Samples from the infected mice at the remaining times post-infection and uninfected mice (controls) were negative for all protocols. Good agreement was observed between CFUs, histopathological analysis and qPCR results for the 100-kDa and H antigen protocols. We successfully standardized and validated three qPCR assays for detecting H. capsulatum DNA in fresh and FFPE tissues, and conclude that the 100-kDa and H antigen molecular assays are promising tests for diagnosing this mycosis.
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Affiliation(s)
- Luisa F. López
- Medical and Experimental Mycology Group, Corporación para Investigaciones Biológicas (CIB), Medellín, Colombia
| | - César O. Muñoz
- Medical and Experimental Mycology Group, Corporación para Investigaciones Biológicas (CIB), Medellín, Colombia
| | - Diego H. Cáceres
- Medical and Experimental Mycology Group, Corporación para Investigaciones Biológicas (CIB), Medellín, Colombia
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Ángela M. Tobón
- Medical and Experimental Mycology Group, Corporación para Investigaciones Biológicas (CIB), Medellín, Colombia
| | - Vladimir Loparev
- Biotechnology Core Facility Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Oliver Clay
- School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
- Cell and Molecular Biology Group, Corporación para Investigaciones Biológicas (CIB), Medellín, Colombia
| | - Tom Chiller
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Anastasia Litvintseva
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Lalitha Gade
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Ángel González
- Basic and Applied Microbiology Research Group (MICROBA), School of Microbiology, Universidad de Antioquia, Medellín, Colombia
| | - Beatriz L. Gómez
- Medical and Experimental Mycology Group, Corporación para Investigaciones Biológicas (CIB), Medellín, Colombia
- School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
- * E-mail:
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30
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Li C, Cao J, Wang L, Jia X, He J, Zhang L. Up-regulation of chemokine CXCL13 in systemic candidiasis. Clin Immunol 2017; 191:1-9. [PMID: 29198822 DOI: 10.1016/j.clim.2017.11.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 10/12/2017] [Accepted: 11/29/2017] [Indexed: 02/07/2023]
Abstract
Candida albicans is the leading cause of healthcare associated bloodstream infections. Chemokine CXCL13 is well-known involved in inflammation, but its role in candidemia has not been assessed. Our study firstly demonstrated that serum CXCL13 levels were significantly elevated in candidemic patients compared with bacteremic patients and control subjects by ELISA, and CXCL13 concentrations were positively and significantly correlated with clinical Sequential Organ Failure Assessment (SOFA) scores and several laboratory parameters in patients. Moreover, ROC curve analysis showed the diagnostic efficiency of CXCL13 was superior to CRP and PCT. To further study the role of CXCL13, a mouse model was established. Importantly, the data showed the dramatically elevated levels of CXCL13 in mice serum and infected kidney, were significantly correlated with renal fungal burden and pathology scores. In conclusion, our results indicated that CXCL13 had strong potential as a novel biomarker of diagnosis and prognosis for candidemia.
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Affiliation(s)
- Congya Li
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Ju Cao
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Lifang Wang
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Xiaojiong Jia
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Jianchun He
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Liping Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.
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31
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Posch W, Heimdörfer D, Wilflingseder D, Lass-Flörl C. Invasive candidiasis: future directions in non-culture based diagnosis. Expert Rev Anti Infect Ther 2017; 15:829-838. [PMID: 28829207 DOI: 10.1080/14787210.2017.1370373] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION Delayed initial antifungal therapy is associated with high mortality rates caused by invasive candida infections, since accurate detection of the opportunistic pathogenic yeast and its identification display a diagnostic challenge. diagnosis of candida infections relies on time-consuming methods such as blood cultures, serologic and histopathologic examination. to allow for fast detection and characterization of invasive candidiasis, there is a need to improve diagnostic tools. trends in diagnostics switch to non-culture-based methods, which allow specified diagnosis within significantly shorter periods of time in order to provide early and appropriate antifungal treatment. Areas covered: within this review comprise novel pathogen- and host-related testing methods, e.g. multiplex-PCR analyses, T2 magnetic resonance, fungus-specific DNA microarrays, microRNA characterization or analyses of IL-17 as biomarker for early detection of invasive candidiasis. Expert commentary: Early recognition and diagnosis of fungal infections is a key issue for improved patient management. As shown in this review, a broad range of novel molecular based tests for the detection and identification of Candida species is available. However, several assays are in-house assays and lack standardization, clinical validation as well as data on sensitivity and specificity. This underscores the need for the development of faster and more accurate diagnostic tests.
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Affiliation(s)
- Wilfried Posch
- a Division of Hygiene and Medical Microbiology , Medical University of Innsbruck , Innsbruck , Austria
| | - David Heimdörfer
- a Division of Hygiene and Medical Microbiology , Medical University of Innsbruck , Innsbruck , Austria
| | - Doris Wilflingseder
- a Division of Hygiene and Medical Microbiology , Medical University of Innsbruck , Innsbruck , Austria
| | - Cornelia Lass-Flörl
- a Division of Hygiene and Medical Microbiology , Medical University of Innsbruck , Innsbruck , Austria
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32
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Digital Microfluidics for Nucleic Acid Amplification. SENSORS 2017; 17:s17071495. [PMID: 28672827 PMCID: PMC5539496 DOI: 10.3390/s17071495] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Revised: 06/17/2017] [Accepted: 06/22/2017] [Indexed: 01/08/2023]
Abstract
Digital Microfluidics (DMF) has emerged as a disruptive methodology for the control and manipulation of low volume droplets. In DMF, each droplet acts as a single reactor, which allows for extensive multiparallelization of biological and chemical reactions at a much smaller scale. DMF devices open entirely new and promising pathways for multiplex analysis and reaction occurring in a miniaturized format, thus allowing for healthcare decentralization from major laboratories to point-of-care with accurate, robust and inexpensive molecular diagnostics. Here, we shall focus on DMF platforms specifically designed for nucleic acid amplification, which is key for molecular diagnostics of several diseases and conditions, from pathogen identification to cancer mutations detection. Particular attention will be given to the device architecture, materials and nucleic acid amplification applications in validated settings.
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33
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Safavieh M, Coarsey C, Esiobu N, Memic A, Vyas JM, Shafiee H, Asghar W. Advances in Candida detection platforms for clinical and point-of-care applications. Crit Rev Biotechnol 2017; 37:441-458. [PMID: 27093473 PMCID: PMC5083221 DOI: 10.3109/07388551.2016.1167667] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Invasive candidiasis remains one of the most serious community and healthcare-acquired infections worldwide. Conventional Candida detection methods based on blood and plate culture are time-consuming and require at least 2-4 days to identify various Candida species. Despite considerable advances for candidiasis detection, the development of simple, compact and portable point-of-care diagnostics for rapid and precise testing that automatically performs cell lysis, nucleic acid extraction, purification and detection still remains a challenge. Here, we systematically review most prominent conventional and nonconventional techniques for the detection of various Candida species, including Candida staining, blood culture, serological testing and nucleic acid-based analysis. We also discuss the most advanced lab on a chip devices for candida detection.
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Affiliation(s)
- Mohammadali Safavieh
- Division of Biomedical Engineering, Division of Renal medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Cambridge, MA, USA
| | - Chad Coarsey
- Department of Computer Engineering and Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL, USA
- College of Engineering and Computer Science, Asghar-Lab, Micro and Nanotechnologies for Medicine, Boca Raton, FL, USA
| | - Nwadiuto Esiobu
- Biological Sciences Department, Florida Atlantic University, Davie, FL, USA
| | - Adnan Memic
- Center of Nanotechnology, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Jatin Mahesh Vyas
- Department of Medicine, Division of Infectious Disease, Massachusetts General Hospital, Boston, MA, USA
| | - Hadi Shafiee
- Division of Biomedical Engineering, Division of Renal medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Cambridge, MA, USA
| | - Waseem Asghar
- Department of Computer Engineering and Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL, USA
- College of Engineering and Computer Science, Asghar-Lab, Micro and Nanotechnologies for Medicine, Boca Raton, FL, USA
- Biological Sciences Department, Florida Atlantic University, Davie, FL, USA
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34
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Libert X, Packeu A, Bureau F, Roosens NH, De Keersmaecker SCJ. Development and performance assessment of a luminex xMAP® direct hybridization assay for the detection and identification of indoor air fungal contamination. PLoS One 2017; 12:e0173390. [PMID: 28278219 PMCID: PMC5344485 DOI: 10.1371/journal.pone.0173390] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 02/20/2017] [Indexed: 12/30/2022] Open
Abstract
Considered as a public health problem, indoor fungal contamination is generally monitored using classical protocols based on culturing. However, this culture dependency could influence the representativeness of the fungal population detected in an analyzed sample as this includes the dead and uncultivable fraction. Moreover, culture-based protocols are often time-consuming. In this context, molecular tools are a powerful alternative, especially those allowing multiplexing. In this study a Luminex xMAP® assay was developed for the simultaneous detection of 10 fungal species which are most frequently in indoor air and that may cause health problems. This xMAP® assay was found to be sensitive, i.e. its limit of detection is ranging between 0.05 and 0.01 ng of gDNA. The assay was subsequently tested with environmental air samples which were also analyzed with a classical protocol. All the species identified with the classical method were also detected with the xMAP® assay, however in a shorter time frame. These results demonstrate that the Luminex xMAP® fungal assay developed in this study could contribute to the improvement of public health and specifically to the indoor fungal contamination treatment.
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Affiliation(s)
- Xavier Libert
- Platform Biotechnology and Molecular Biology, Scientific Institute of Public Health (WIV-ISP), Brussels, Belgium
- Cellular and Molecular Immunology, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA), Université de Liège (ULg), Sart-Tilman, Belgium
| | - Ann Packeu
- Mycology and Aerobiology, Scientific Institute of Public Health (WIV-ISP), Brussels, Belgium
| | - Fabrice Bureau
- Cellular and Molecular Immunology, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA), Université de Liège (ULg), Sart-Tilman, Belgium
| | - Nancy H. Roosens
- Platform Biotechnology and Molecular Biology, Scientific Institute of Public Health (WIV-ISP), Brussels, Belgium
| | - Sigrid C. J. De Keersmaecker
- Platform Biotechnology and Molecular Biology, Scientific Institute of Public Health (WIV-ISP), Brussels, Belgium
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35
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Dong C, Jia Y, Gao J, Chen T, Mak PI, Vai MI, Martins RP. A 3D microblade structure for precise and parallel droplet splitting on digital microfluidic chips. LAB ON A CHIP 2017; 17:896-904. [PMID: 28194461 DOI: 10.1039/c6lc01539e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Existing digital microfluidic (DMF) chips exploit the electrowetting on dielectric (EWOD) force to perform droplet splitting. However, the current splitting methods are not flexible and the volume of the droplets suffers from a large variation. Herein, we propose a DMF chip featuring a 3D microblade structure to enhance the droplet-splitting performance. By exploiting the EWOD force for shaping and manipulating the mother droplet, we obtain an average dividing error of <2% in the volume of the daughter droplets for a number of fluids such as deionized water, DNA solutions and DNA-protein mixtures. Customized droplet splitting ratios of up to 20 : 80 are achieved by positioning the blade at the appropriate position. Additionally, by fabricating multiple 3D microblades on one electrode, two to five uniform daughter droplets can be generated simultaneously. Finally, by taking synthetic DNA targets and their corresponding molecular beacon probes as a model system, multiple potential pathogens that cause sepsis are detected rapidly on the 3D-blade-equipped DMF chip, rendering it as a promising tool for parallel diagnosis of diseases.
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Affiliation(s)
- Cheng Dong
- State-Key Laboratory of Analog and Mixed-Signal VLSI, University of Macau, Macao, China. and Faculty of Science and Technology - ECE, University of Macau, Macao, China
| | - Yanwei Jia
- State-Key Laboratory of Analog and Mixed-Signal VLSI, University of Macau, Macao, China.
| | - Jie Gao
- State-Key Laboratory of Analog and Mixed-Signal VLSI, University of Macau, Macao, China.
| | - Tianlan Chen
- State-Key Laboratory of Analog and Mixed-Signal VLSI, University of Macau, Macao, China.
| | - Pui-In Mak
- State-Key Laboratory of Analog and Mixed-Signal VLSI, University of Macau, Macao, China. and Faculty of Science and Technology - ECE, University of Macau, Macao, China
| | - Mang-I Vai
- State-Key Laboratory of Analog and Mixed-Signal VLSI, University of Macau, Macao, China. and Faculty of Science and Technology - ECE, University of Macau, Macao, China
| | - Rui P Martins
- State-Key Laboratory of Analog and Mixed-Signal VLSI, University of Macau, Macao, China. and Faculty of Science and Technology - ECE, University of Macau, Macao, China
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36
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Development of Capillary Loop Convective Polymerase Chain Reaction Platform with Real-Time Fluorescence Detection. INVENTIONS 2017. [DOI: 10.3390/inventions2010003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Moore JA, Nemat-Gorgani M, Madison AC, Sandahl MA, Punnamaraju S, Eckhardt AE, Pollack MG, Vigneault F, Church GM, Fair RB, Horowitz MA, Griffin PB. Automated electrotransformation of Escherichia coli on a digital microfluidic platform using bioactivated magnetic beads. BIOMICROFLUIDICS 2017; 11:014110. [PMID: 28191268 PMCID: PMC5291792 DOI: 10.1063/1.4975391] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 01/20/2017] [Indexed: 05/06/2023]
Abstract
This paper reports on the use of a digital microfluidic platform to perform multiplex automated genetic engineering (MAGE) cycles on droplets containing Escherichia coli cells. Bioactivated magnetic beads were employed for cell binding, washing, and media exchange in the preparation of electrocompetent cells in the electrowetting-on-dieletric (EWoD) platform. On-cartridge electroporation was used to deliver oligonucleotides into the cells. In addition to the optimization of a magnetic bead-based benchtop protocol for generating and transforming electrocompetent E. coli cells, we report on the implementation of this protocol in a fully automated digital microfluidic platform. Bead-based media exchange and electroporation pulse conditions were optimized on benchtop for transformation frequency to provide initial parameters for microfluidic device trials. Benchtop experiments comparing electrotransformation of free and bead-bound cells are presented. Our results suggest that dielectric shielding intrinsic to bead-bound cells significantly reduces electroporation field exposure efficiency. However, high transformation frequency can be maintained in the presence of magnetic beads through the application of more intense electroporation pulses. As a proof of concept, MAGE cycles were successfully performed on a commercial EWoD cartridge using variations of the optimal magnetic bead-based preparation procedure and pulse conditions determined by the benchtop results. Transformation frequencies up to 22% were achieved on benchtop; this frequency was matched within 1% (21%) by MAGE cycles on the microfluidic device. However, typical frequencies on the device remain lower, averaging 9% with a standard deviation of 9%. The presented results demonstrate the potential of digital microfluidics to perform complex and automated genetic engineering protocols.
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Affiliation(s)
- J A Moore
- Stanford Genome Technology Center , 3165 Porter Drive, Palo Alto, California 94304, USA
| | - M Nemat-Gorgani
- Stanford Genome Technology Center , 3165 Porter Drive, Palo Alto, California 94304, USA
| | - A C Madison
- Department of Electrical Engineering, Duke University , Durham, North Carolina 27560, USA
| | - M A Sandahl
- Advanced Liquid Logic , 615 Davis Drive #800, Morrisville, North Carolina 27560, USA
| | - S Punnamaraju
- Advanced Liquid Logic , 615 Davis Drive #800, Morrisville, North Carolina 27560, USA
| | - A E Eckhardt
- Advanced Liquid Logic , 615 Davis Drive #800, Morrisville, North Carolina 27560, USA
| | - M G Pollack
- Advanced Liquid Logic , 615 Davis Drive #800, Morrisville, North Carolina 27560, USA
| | - F Vigneault
- Wyss Institute, Harvard University , Boston, Massachusetts 02115, USA
| | - G M Church
- Department of Genetics, Harvard Medical School , Boston, Massachusetts 02115, USA
| | - R B Fair
- Department of Electrical Engineering, Duke University , Durham, North Carolina 27560, USA
| | - M A Horowitz
- Department of Electrical Engineering, Stanford University , Stanford, California 94305, USA
| | - P B Griffin
- Stanford Genome Technology Center , 3165 Porter Drive, Palo Alto, California 94304, USA
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He ZX, Shi LC, Ran XY, Li W, Wang XL, Wang FK. Development of a Lateral Flow Immunoassay for the Rapid Diagnosis of Invasive Candidiasis. Front Microbiol 2016; 7:1451. [PMID: 27679622 PMCID: PMC5020066 DOI: 10.3389/fmicb.2016.01451] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 08/30/2016] [Indexed: 12/11/2022] Open
Abstract
Early and accurate diagnosis of invasive candidiasis (IC) is very important. In this study, a lateral flow immunoassay (LFIA) was developed to detect antibody against Candida albicans enolase (Eno). Colloidal gold particle labeled mouse anti human IgG (1.0 mg/L) was used as the detector reagent. Recombinant enolase (rEno, 1.0 mg/L) and goat anti IgG (1.0 mg/L) were immobilized in test and control lines, respectively, of a nitrocellulose membrane, acting as the capture reagents. The LFIA was used to detect anti Eno in 38 sera from clinically proven IC patients, as well as in 50 healthy control subjects. Compared with an indirect ELISA designed as a reference test, the specificity and sensitivity of the LFIA were 98.2 and 84.8%, respectively. Excellent agreement between the results obtained by ELISA and the LFIA (κ = 0.851) was observed in this study. In addition, the agreement between the blood culture results and LFIA test is strong (κ = 0.658). The data presented in the study indicate that the LFIA test is a suitable tool for the serological surveillance of IC in the field or in poorly equipped laboratories.
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Affiliation(s)
- Zheng-Xin He
- Department of Clinical Laboratory, Bethune International Peace Hospital of PLA Shijiazhuang, China
| | - Lan-Chun Shi
- Department of Biochemistry, Bethune Medical NCO School of PLA Shijiazhuang, China
| | - Xiang-Yang Ran
- Department of Clinical Laboratory, Bethune International Peace Hospital of PLA Shijiazhuang, China
| | - Wei Li
- Department of Clinical Laboratory, Bethune International Peace Hospital of PLA Shijiazhuang, China
| | - Xian-Ling Wang
- Department of Clinical Laboratory, Bethune International Peace Hospital of PLA Shijiazhuang, China
| | - Fu-Kun Wang
- Department of Clinical Laboratory, Bethune International Peace Hospital of PLA Shijiazhuang, China
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Pappas PG, Kauffman CA, Andes DR, Clancy CJ, Marr KA, Ostrosky-Zeichner L, Reboli AC, Schuster MG, Vazquez JA, Walsh TJ, Zaoutis TE, Sobel JD. Clinical Practice Guideline for the Management of Candidiasis: 2016 Update by the Infectious Diseases Society of America. Clin Infect Dis 2016; 62:e1-50. [PMID: 26679628 PMCID: PMC4725385 DOI: 10.1093/cid/civ933] [Citation(s) in RCA: 1888] [Impact Index Per Article: 236.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 11/02/2015] [Indexed: 02/06/2023] Open
Abstract
It is important to realize that guidelines cannot always account for individual variation among patients. They are not intended to supplant physician judgment with respect to particular patients or special clinical situations. IDSA considers adherence to these guidelines to be voluntary, with the ultimate determination regarding their application to be made by the physician in the light of each patient's individual circumstances.
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Affiliation(s)
| | - Carol A Kauffman
- Veterans Affairs Ann Arbor Healthcare System and University of Michigan Medical School, Ann Arbor
| | | | | | - Kieren A Marr
- Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | | | | | | | - Thomas J Walsh
- Weill Cornell Medical Center and Cornell University, New York, New York
| | | | - Jack D Sobel
- Harper University Hospital and Wayne State University, Detroit, Michigan
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Microfluidic Organ/Body-on-a-Chip Devices at the Convergence of Biology and Microengineering. SENSORS 2015; 15:31142-70. [PMID: 26690442 PMCID: PMC4721768 DOI: 10.3390/s151229848] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 11/16/2015] [Accepted: 12/04/2015] [Indexed: 12/24/2022]
Abstract
Recent advances in biomedical technologies are mostly related to the convergence of biology with microengineering. For instance, microfluidic devices are now commonly found in most research centers, clinics and hospitals, contributing to more accurate studies and therapies as powerful tools for drug delivery, monitoring of specific analytes, and medical diagnostics. Most remarkably, integration of cellularized constructs within microengineered platforms has enabled the recapitulation of the physiological and pathological conditions of complex tissues and organs. The so-called “organ-on-a-chip” technology, which represents a new avenue in the field of advanced in vitro models, with the potential to revolutionize current approaches to drug screening and toxicology studies. This review aims to highlight recent advances of microfluidic-based devices towards a body-on-a-chip concept, exploring their technology and broad applications in the biomedical field.
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Digital Microfluidics for Manipulation and Analysis of a Single Cell. Int J Mol Sci 2015; 16:22319-32. [PMID: 26389890 PMCID: PMC4613310 DOI: 10.3390/ijms160922319] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Revised: 08/12/2015] [Accepted: 08/18/2015] [Indexed: 12/31/2022] Open
Abstract
The basic structural and functional unit of a living organism is a single cell. To understand the variability and to improve the biomedical requirement of a single cell, its analysis has become a key technique in biological and biomedical research. With a physical boundary of microchannels and microstructures, single cells are efficiently captured and analyzed, whereas electric forces sort and position single cells. Various microfluidic techniques have been exploited to manipulate single cells through hydrodynamic and electric forces. Digital microfluidics (DMF), the manipulation of individual droplets holding minute reagents and cells of interest by electric forces, has received more attention recently. Because of ease of fabrication, compactness and prospective automation, DMF has become a powerful approach for biological application. We review recent developments of various microfluidic chips for analysis of a single cell and for efficient genetic screening. In addition, perspectives to develop analysis of single cells based on DMF and emerging functionality with high throughput are discussed.
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Molecular and nonmolecular diagnostic methods for invasive fungal infections. Clin Microbiol Rev 2015; 27:490-526. [PMID: 24982319 DOI: 10.1128/cmr.00091-13] [Citation(s) in RCA: 207] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Invasive fungal infections constitute a serious threat to an ever-growing population of immunocompromised individuals and other individuals at risk. Traditional diagnostic methods, such as histopathology and culture, which are still considered the gold standards, have low sensitivity, which underscores the need for the development of new means of detecting fungal infectious agents. Indeed, novel serologic and molecular techniques have been developed and are currently under clinical evaluation. Tests like the galactomannan antigen test for aspergillosis and the β-glucan test for invasive Candida spp. and molds, as well as other antigen and antibody tests, for Cryptococcus spp., Pneumocystis spp., and dimorphic fungi, have already been established as important diagnostic approaches and are implemented in routine clinical practice. On the other hand, PCR and other molecular approaches, such as matrix-assisted laser desorption ionization (MALDI) and fluorescence in situ hybridization (FISH), have proved promising in clinical trials but still need to undergo standardization before their clinical use can become widespread. The purpose of this review is to highlight the different diagnostic approaches that are currently utilized or under development for invasive fungal infections and to identify their performance characteristics and the challenges associated with their use.
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Teles F, Seixas J. The future of novel diagnostics in medical mycology. J Med Microbiol 2014; 64:315-322. [PMID: 25418735 DOI: 10.1099/jmm.0.082297-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 11/17/2014] [Indexed: 11/18/2022] Open
Abstract
Several fungal diseases have become serious threats to human health and life, especially upon the advent of human immunodeficiency virus/AIDS epidemics and of other typical immunosuppressive conditions of modern life. Accordingly, the burden posed by these diseases and, concurrently, by intensive therapeutic regimens against these diseases has increased worldwide. Existing and available rapid tests for point-of-care diagnosis of important fungal diseases could enable the limitations of current laboratory methods for detection and identification of medically important fungi to be surpassed, both in low-income countries and for first-line diagnosis (screening) in richer countries. As with conventional diagnostic methods and devices, former immunodiagnostics have been challenged by molecular biology-based platforms, as a way to enhance the sensitivity and shorten the assay time, thus enabling early and more accurate diagnosis. Most of these tests have been developed in-house, without adequate validation and standardization. Another challenge has been the DNA extraction step, which is especially critical when dealing with fungi. In this paper, we have identified three major research trends in this field: (1) the application of newer biorecognition techniques, often applied in analytical chemistry; (2) the development of new materials with improved physico-chemical properties; and (3) novel bioanalytical platforms, allowing fully automated testing. Keeping up to date with the fast technological advances registered in this field, primarily at the proof-of-concept level, is essential for wise assessment of those that are likely to be more cost effective and, as already observed for bacterial and viral pathogens, may provide leverage to the current tepid developmental status of novel and improved diagnostics for medical mycology.
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Affiliation(s)
- Fernando Teles
- Centre for Malaria and Other Tropical Diseases, Institute of Hygiene and Tropical Medicine, Universidade Nova de Lisboa, 100 Rua da Junqueira, 1349-008 Lisbon, Portugal.,Mycology Group/Unit of Medical Microbiology, Institute of Hygiene and Tropical Medicine, Universidade Nova de Lisboa, 100 Rua da Junqueira, 1349-008 Lisbon, Portugal
| | - Jorge Seixas
- Tropical Clinic Unit, Institute of Hygiene and Tropical Medicine (IHMT), Universidade Nova de Lisboa, 100 Rua da Junqueira, 1349-008 Lisbon, Portugal.,Centre for Malaria and Other Tropical Diseases, Institute of Hygiene and Tropical Medicine, Universidade Nova de Lisboa, 100 Rua da Junqueira, 1349-008 Lisbon, Portugal
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Rival A, Jary D, Delattre C, Fouillet Y, Castellan G, Bellemin-Comte A, Gidrol X. An EWOD-based microfluidic chip for single-cell isolation, mRNA purification and subsequent multiplex qPCR. LAB ON A CHIP 2014; 14:3739-49. [PMID: 25080028 DOI: 10.1039/c4lc00592a] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Single cell analysis circumvents the need to average data from large populations by observing each cell individually, thus enabling the analysis of cell-to-cell variability. The ability to work on this scale presents many new opportunities for the life sciences and biomedical applications. Microfluidics has become a tool of choice for such studies and electrowetting on dielectric (EWOD) technology is well adapted for samples with reduced size and biological studies at the single cell level. In the present manuscript, for the first time, we present an integrated and automated system based on EWOD that can process the complete workflow on a single device, from the isolation of a single cell to mRNA purification and gene expression analysis.
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Affiliation(s)
- A Rival
- CEA, IRTSV, Laboratoire de Biologie à Grande Echelle, F-38054 Grenoble Cedex 9, France.
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Clancy CJ, Nguyen MH. Undiagnosed invasive candidiasis: incorporating non-culture diagnostics into rational prophylactic and preemptive antifungal strategies. Expert Rev Anti Infect Ther 2014; 12:731-4. [DOI: 10.1586/14787210.2014.919853] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Cornelius J Clancy
- VA Pittsburgh Healthcare System, Division of Infectious Diseases, University of Pittsburgh,
Scaife 867, 3550 Terrace St, Pittsburgh, PA 15261, USA
- Department of Medicine, University of Pittsburgh,
M240 Scaife Hall, 3550 Terrace St, Pittsburgh, PA 15261, USA
| | - Minh Hong Nguyen
- Department of Medicine, University of Pittsburgh,
M240 Scaife Hall, 3550 Terrace St, Pittsburgh, PA 15261, USA
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Schultz A, Papautsky I, Heikenfeld J. Investigation of Laplace barriers for arrayed electrowetting lab-on-a-chip. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:5349-5356. [PMID: 24738982 DOI: 10.1021/la500314v] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Partial-post Laplace barriers have been postulated as a means to allow electrowetting transport and geometrical reshaping of fluids, followed by the preservation of fluid geometry after the electrowetting voltage is removed. Reported here is the first investigation of Laplace barriers with the arrayed electrodes and splitting/merging transport functions for an electrowetting lab-on-a-chip. Laplace barriers optimized for 500 × 500 μm(2) electrodes and 78 μm channel height are shown to provide geometrical control of fluid shape down to radii of curvature of ~70 μm. The Laplace barriers increase the splitting volume error, but with proper electrical control, the average error in the split volume is reduced to 5%. Improved programmable fluid storage in droplets or reservoirs and continuous channel flow are also shown. This work confirms the potential benefits of Laplace barriers for lab-on-a-chip and also reveals the unique challenges and operation requirements for Laplace barriers in lab-on-a-chip applications.
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Affiliation(s)
- A Schultz
- Department of Electrical Engineering and Computing Systems, University of Cincinnati , Cincinnati, Ohio 45221, United States
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Kersaudy-Kerhoas M, Sollier E. Micro-scale blood plasma separation: from acoustophoresis to egg-beaters. LAB ON A CHIP 2013; 13:3323-46. [PMID: 23824514 DOI: 10.1039/c3lc50432h] [Citation(s) in RCA: 124] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Plasma is a rich mine of various biomarkers including proteins, metabolites and circulating nucleic acids. The diagnostic and therapeutic potential of these analytes has been quite recently uncovered, and the number of plasma biomarkers will still be growing in the coming years. A significant part of the blood plasma preparation is still handled manually, off-chip, via centrifugation or filtration. These batch methods have variable waiting times, and are often performed under non-reproducible conditions that may impair the collection of analytes of interest, with variable degradation. The development of miniaturised modules capable of automated and reproducible blood plasma separation would aid in the translation of lab-on-a-chip devices to the clinical market. Here we propose a systematic review of major plasma analytes and target applications, alongside existing solutions for micro-scale blood plasma extraction, focusing on the approaches that have been biologically validated for specific applications.
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Affiliation(s)
- Maïwenn Kersaudy-Kerhoas
- Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh Campus, Edinburgh EH14 4AS, United Kingdom.
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Abstract
BACKGROUND Morbidity and mortality remain high for patients with invasive fungal infections (IFIs) despite an increasing number of antifungals and other treatments. Many studies indicate that delayed or inaccurate diagnosis and treatment are major causes of poor outcomes in patients with IFIs. OBJECTIVE The aim of the current paper is to provide a review of traditional and newer approaches to the diagnosis of IFIs, with a particular focus on invasive candidiasis (IC) and aspergillosis (IA). Recent studies from the author's institution are highlighted, along with an advancement in cryptococcal meningitis diagnosis that should improve the care of AIDS and its opportunistic infection in many developing countries. FINDINGS Currently available tools for the diagnosis of IFIs include traditional methods like histopathology, culture, and radiology, and newer antigen- and PCR-based diagnostic assays. Attempts have also been made to predict IFIs based on colonization or other factors, including genetic polymorphisms impacting IFI susceptibility in high-risk patients. Biopsy with histopathologic analysis is often not possible in patients suspected of pulmonary aspergillosis due to increased bleeding risk, and blood cultures for IC, IA, or other IFIs are hindered by poor sensitivity and slow turnaround time which delays diagnosis. Radiology is often used to predict IFI but suffers from inability to differentiate certain pathogens and does not generally provide certainty of IFI diagnosis. Newer antigen-based diagnostics for early diagnosis include the β-glucan assay for IFIs, galactomannan assay for IA, and a recent variation on the traditional cryptococcal antigen (CRAG) test with a Lateral Flow Assay for invasive cryptococcosis. PCR-based diagnostics represent additional tools with high sensitivity for the rapid diagnosis of IFIs, although better standardization of these methods is still required for their routine clinical use. CONCLUSION Better understanding of the strengths and weaknesses of currently available diagnostic tools, and further devising linked strategies to best implement them either alone or in combination, would greatly improve early and accurate diagnosis of IFIs and improve their successful management.
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Clancy CJ, Nguyen MH. Finding the “Missing 50%” of Invasive Candidiasis: How Nonculture Diagnostics Will Improve Understanding of Disease Spectrum and Transform Patient Care. Clin Infect Dis 2013; 56:1284-92. [DOI: 10.1093/cid/cit006] [Citation(s) in RCA: 424] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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50
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Straub T, Baird C, Bartholomew RA, Colburn H, Seiner D, Victry K, Zhang L, Bruckner-Lea CJ. Estimated copy number of Bacillus anthracis plasmids pXO1 and pXO2 using digital PCR. J Microbiol Methods 2012; 92:9-10. [PMID: 23142659 DOI: 10.1016/j.mimet.2012.10.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Revised: 10/23/2012] [Accepted: 10/29/2012] [Indexed: 10/27/2022]
Abstract
We evaluated digital PCR (dPCR) to directly enumerate plasmid and chromosome copies in three strains of Bacillus anthracis. Copy number estimates based on conventional quantitative PCR (qPCR) highlighted the variability of using qPCR to measure copy number whereas estimates based on direct sequencing are comparable to dPCR.
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Affiliation(s)
- Timothy Straub
- Chemical and Biological Signature Sciences Group, National Security Directorate, Pacific Northwest National Laboratory, Richland, WA 99354, United States.
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