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de Souza ÂC, Pereira DC, Barth PO, Roesch EW, Lutz L, Aquino VR, Goldani LZ. Rapid identification,fluconazole and micafungin susceptibility testing of Candida species from blood culture by a short incubation method. Diagn Microbiol Infect Dis 2024; 109:116271. [PMID: 38522370 DOI: 10.1016/j.diagmicrobio.2024.116271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 02/18/2024] [Accepted: 03/15/2024] [Indexed: 03/26/2024]
Abstract
This study aimed to develop and validate a rapid method for identification by MALDI-TOF system and determination of the susceptibility to Fluconazole and Micafungin by broth microdilution among Candidaspecies causing bloodstream infections. Subcultures from blood culture bottles were incubated for 5 hours (+/- 1h) and used to perform the tests, so that the turnaround time of rapid identification and susceptibility profile was about 5 and 24 hours, respectively. The rapid identification showed agreement of 92.05 %. Regarding the rapid broth microdilution for Fluconazole and Micafungin, the agreement was 97.06 % (p<0.001) and 100 % (p<0.001), and the Kappa coefficient was 0.91 (p<0.001) and 1.0 (p<0.001), respectively. To conclude, both rapid methods showed to be reproducible, inexpensive, easy to perform and time-saving. Thus, these methodologies could be useful to guide and adjust empirical antifungal therapy.
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Affiliation(s)
- Ândrea Celestino de Souza
- Post-graduation Program in Medical Sciences, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brasil.
| | - Dariane Castro Pereira
- Unidade de Microbiologia, Serviço de Diagnóstico Laboratorial - Hospital de Clínicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, Brasil
| | - Patricia Orlandi Barth
- Post-graduation Program in Medical Sciences, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brasil
| | - Eliane Würdig Roesch
- Unidade de Microbiologia, Serviço de Diagnóstico Laboratorial - Hospital de Clínicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, Brasil
| | - Larissa Lutz
- Unidade de Microbiologia, Serviço de Diagnóstico Laboratorial - Hospital de Clínicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, Brasil
| | - Valério Rodrigues Aquino
- Unidade de Microbiologia, Serviço de Diagnóstico Laboratorial - Hospital de Clínicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, Brasil
| | - Luciano Zubaran Goldani
- Post-graduation Program in Medical Sciences, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brasil
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2
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Pezzotti G, Kobara M, Asai T, Nakaya T, Miyamoto N, Adachi T, Yamamoto T, Kanamura N, Ohgitani E, Marin E, Zhu W, Nishimura I, Mazda O, Nakata T, Makimura K. Raman Imaging of Pathogenic Candida auris: Visualization of Structural Characteristics and Machine-Learning Identification. Front Microbiol 2021; 12:769597. [PMID: 34867902 PMCID: PMC8633489 DOI: 10.3389/fmicb.2021.769597] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 10/18/2021] [Indexed: 01/04/2023] Open
Abstract
Invasive fungal infections caused by yeasts of the genus Candida carry high morbidity and cause systemic infections with high mortality rate in both immunocompetent and immunosuppressed patients. Resistance rates against antifungal drugs vary among Candida species, the most concerning specie being Candida auris, which exhibits resistance to all major classes of available antifungal drugs. The presently available identification methods for Candida species face a severe trade-off between testing speed and accuracy. Here, we propose and validate a machine-learning approach adapted to Raman spectroscopy as a rapid, precise, and labor-efficient method of clinical microbiology for C. auris identification and drug efficacy assessments. This paper demonstrates that the combination of Raman spectroscopy and machine learning analyses can provide an insightful and flexible mycology diagnostic tool, easily applicable on-site in the clinical environment.
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Affiliation(s)
- Giuseppe Pezzotti
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Kyoto, Japan
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
- Department of Orthopedic Surgery, Tokyo Medical University, Shinjuku-ku, Tokyo, Japan
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
- The Center for Advanced Medical Engineering and Informatics, Osaka University, Suita, Osaka, Japan
| | - Miyuki Kobara
- Division of Pathological Science, Department of Clinical Pharmacology, Kyoto Pharmaceutical University, Kyoto, Japan
| | - Tenma Asai
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Kyoto, Japan
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Tamaki Nakaya
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Kyoto, Japan
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Nao Miyamoto
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Tetsuya Adachi
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Toshiro Yamamoto
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Narisato Kanamura
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Eriko Ohgitani
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Elia Marin
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Kyoto, Japan
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Wenliang Zhu
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Kyoto, Japan
| | - Ichiro Nishimura
- Division of Advanced Prosthodontics, The Jane and Jerry Weintraub Center for Reconstructive Biotechnology, UCLA School of Dentistry, Los Angeles, CA, United States
| | - Osam Mazda
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Tetsuo Nakata
- Division of Pathological Science, Department of Clinical Pharmacology, Kyoto Pharmaceutical University, Kyoto, Japan
| | - Koichi Makimura
- Medical Mycology, Graduate School of Medicine, Teikyo University, Itabashi-ku, Tokyo, Japan
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3
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Oral Candidosis: Pathophysiology and Best Practice for Diagnosis, Classification, and Successful Management. J Fungi (Basel) 2021; 7:jof7070555. [PMID: 34356934 PMCID: PMC8306613 DOI: 10.3390/jof7070555] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/10/2021] [Accepted: 07/11/2021] [Indexed: 01/12/2023] Open
Abstract
Oral candidosis is the most common fungal infection that frequently occurs in patients debilitated by other diseases or conditions. No candidosis happens without a cause; hence oral candidosis has been branded as a disease of the diseased. Prior research has identified oral candidosis as a mark of systemic diseases, such as hematinic deficiency, diabetes mellitus, leukopenia, HIV/AIDS, malignancies, and carbohydrate-rich diet, drugs, or immunosuppressive conditions. An array of interaction between Candida and the host is dynamic and complex. Candida exhibits multifaceted strategies for growth, proliferation, evasion of host defenses, and survival within the host to induce fungal infection. Oral candidosis presents a variety of clinical forms, including pseudomembranous candidosis, erythematous candidosis, angular cheilitis, median rhomboid glossitis, cheilocandidosis, juxtavermillion candidosis, mucocutaneous candidosis, hyperplastic candidosis, oropharyngeal candidosis, and rare suppurative candidosis. The prognosis is usually favorable, but treatment failure or recurrence is common due to either incorrect diagnosis, missing other pathology, inability to address underlying risk factors, or inaccurate prescription of antifungal agents. In immunocompromised patients, oropharyngeal candidosis can spread to the bloodstream or upper gastrointestinal tract, leading to potentially lethal systemic candidosis. This review therefore describes oral candidosis with regard to its pathophysiology and best practice for diagnosis, practical classification, and successful management.
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4
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Lau AF. Matrix-Assisted Laser Desorption Ionization Time-of-Flight for Fungal Identification. Clin Lab Med 2021; 41:267-283. [PMID: 34020763 DOI: 10.1016/j.cll.2021.03.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Many studies have shown successful performance of matrix-assisted laser desorption ionization time-of-flight mass spectrometry for rapid yeast and mold identification, yet few laboratories have chosen to apply this technology into their routine clinical mycology workflow. This review provides an overview of the current status of matrix-assisted laser desorption ionization time-of-flight mass spectrometry for fungal identification, including key findings in the literature, processing and database considerations, updates in technology, and exciting future prospects. Significant advances toward standardization have taken place recently; thus, accurate species-level identification of yeasts and molds should be highly attainable, achievable, and practical in most clinical laboratories.
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Affiliation(s)
- Anna F Lau
- Sterility Testing Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, 10 Center Drive, Room 2C306, Bethesda, MD 20892, USA.
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5
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Ponderand L, Pavese P, Maubon D, Giraudon E, Girard T, Landelle C, Maurin M, Caspar Y. Evaluation of Rapid Sepsityper® protocol and specific MBT-Sepsityper module (Bruker Daltonics) for the rapid diagnosis of bacteremia and fungemia by MALDI-TOF-MS. Ann Clin Microbiol Antimicrob 2020; 19:60. [PMID: 33298064 PMCID: PMC7727196 DOI: 10.1186/s12941-020-00403-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 11/28/2020] [Indexed: 12/11/2022] Open
Abstract
During bloodstream infections, rapid adaptation of empirical treatment according to the microorganism identified is essential to decrease mortality. The aim of the present study was to assess the microbiological performances of a new rapid version of the Sepsityper® kit (Bruker Daltonics) allowing identification of bacteria and yeast by MALDI-TOF mass spectrometry directly from positive blood cultures in 10 min and of the specific MBT-Sepsityper module for spectra analysis, designed to increase identification performance. Identification rates were determined prospectively on 350 bacterial and 29 fungal positive blood cultures, and compared to conventional diagnostic method. Our rapid diagnosis strategy (Rapid Sepsityper® protocol: one spot with and one without formic acid extraction step) combined to MBT-Sepsityper module provided 65.4%, 78.9% and 62% reliable identification to the species level of monomicrobial positive blood cultures growing respectively Gram-positive, Gram-negative bacteria or yeast. Importantly, identification rates of Gram-positive bacteria were higher in anaerobic than in aerobic bottles (77.8% vs 22.2%; p = 0.004), if formic acid extraction step was performed (60.8% vs 39.2%; p = 1.8e−6) and if specific MBT-Sepsityper module was used (76.2% vs 61.9%, p = 0.041) while no significant differences were observed for Gram-negative bacteria. For yeasts identification, formic acid extraction step improved rapid identification rate by 37.9% while the specific MBT-Sepsityper module increased overall performances by 38%, providing up to 89.7% reliable identification if associated with the standard Sepsityper® protocol. These performances, associated with a reduce turnaround time, may help to implement a rapid identification strategy of bloodstream infections in the routine workflow of microbiology laboratories.
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Affiliation(s)
- Léa Ponderand
- Laboratoire de Bactériologie-Hygiène Hospitalière, Centre Hospitalier Universitaire Grenoble Alpes, 38000, Grenoble, France.,Université Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, 38000, Grenoble, France
| | - Patricia Pavese
- Service de Médecine Infectieuse et Tropicale, Centre Hospitalier Universitaire Grenoble Alpes, 38000, Grenoble, France
| | - Danièle Maubon
- Université Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, 38000, Grenoble, France.,Laboratoire de Parasitologie Mycologie, Centre Hospitalier Universitaire Grenoble Alpes, 38000, Grenoble, France
| | - Emmanuelle Giraudon
- Laboratoire de Parasitologie Mycologie, Centre Hospitalier Universitaire Grenoble Alpes, 38000, Grenoble, France
| | - Thomas Girard
- Laboratoire de Bactériologie-Hygiène Hospitalière, Centre Hospitalier Universitaire Grenoble Alpes, 38000, Grenoble, France
| | - Caroline Landelle
- Université Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, 38000, Grenoble, France.,Service d'Hygiène Hospitalière, Centre Hospitalier Universitaire Grenoble Alpes, 38000, Grenoble, France
| | - Max Maurin
- Laboratoire de Bactériologie-Hygiène Hospitalière, Centre Hospitalier Universitaire Grenoble Alpes, 38000, Grenoble, France.,Université Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, 38000, Grenoble, France
| | - Yvan Caspar
- Laboratoire de Bactériologie-Hygiène Hospitalière, Centre Hospitalier Universitaire Grenoble Alpes, 38000, Grenoble, France. .,Université Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, 38000, Grenoble, France. .,Laboratoire de Bactériologie-Hygiène Hospitalière, Institut de Biologie et Pathologie, Centre Hospitalier Universitaire Grenoble Alpes, CS10217, 38043, Grenoble Cedex 9, France.
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Camp I, Spettel K, Willinger B. Molecular Methods for the Diagnosis of Invasive Candidiasis. J Fungi (Basel) 2020; 6:E101. [PMID: 32640656 PMCID: PMC7558065 DOI: 10.3390/jof6030101] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 07/03/2020] [Accepted: 07/04/2020] [Indexed: 12/19/2022] Open
Abstract
Invasive infections caused by members of the genus Candida are on the rise. Especially patients in intensive care units, immunocompromised patients, and those recovering from abdominal surgery are at risk for the development of candidemia or deep-seated candidiasis. Rapid initiation of appropriate antifungal therapy can increase survival rates significantly. In the past, most of these infections were caused by C. albicans, a species that typically is very susceptible to antifungals. However, in recent years a shift towards infections caused by non-albicans species displaying various susceptibly patterns has been observed and the prompt diagnosis of the underlying species has become an essential factor determining the therapeutic outcome. The gold standard for diagnosing invasive candidiasis is blood culture, even though its sensitivity is low and the time required for species identification usually exceeds 48 h. To overcome these issues, blood culture can be combined with other methods, and a large number of tests have been developed for this purpose. The aim of this review was to give an overview on strengths and limitations of currently available molecular methods for the diagnosis of invasive candidiasis.
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Affiliation(s)
| | | | - Birgit Willinger
- Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria; (I.C.); (K.S.)
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7
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Bal AM, Palchaudhuri M. Candidaemia in the elderly: Epidemiology, management and adherence to the European Confederation of Medical Mycology quality indicators. Mycoses 2020; 63:892-899. [DOI: 10.1111/myc.13134] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/07/2020] [Accepted: 06/11/2020] [Indexed: 01/08/2023]
Affiliation(s)
- Abhijit M. Bal
- Department of Microbiology University Hospital Crosshouse Kilmarnock UK
| | - Mihir Palchaudhuri
- Department of Care of the Elderly University Hospital Crosshouse Kilmarnock UK
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8
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Capoor MR, Subudhi CP, Collier A, Bal AM. Antifungal stewardship with an emphasis on candidaemia. J Glob Antimicrob Resist 2019; 19:262-268. [DOI: 10.1016/j.jgar.2019.05.030] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 05/23/2019] [Accepted: 05/31/2019] [Indexed: 12/28/2022] Open
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9
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Identification of Candida Species from Clinical Samples in a Honduran Tertiary Hospital. Pathogens 2019; 8:pathogens8040237. [PMID: 31731617 PMCID: PMC6963973 DOI: 10.3390/pathogens8040237] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 10/25/2019] [Accepted: 10/27/2019] [Indexed: 12/15/2022] Open
Abstract
Candida species are one of the most important causes of human infections, especially in hospitals and among immunocompromised patients. The correct and rapid etiological identification of yeast infections is important to provide adequate therapy, reduce mortality, and control outbreaks. In this study, Candida species were identified in patients with suspected fungal infection, and phenotypic and genotypic identification methods were compared. A total of 167 axenic fungal cultures and 46 clinical samples were analyzed by HardyCHROM®, MicroScan®(Omron Microscan Systems Inc, Renton, WA, USA), and PCR-RFLP (Restriction Fragment Length Polymorphisms). The species of the C. albicans complex were the most frequent, followed by C. tropicalis and C. glabrata. Less common but clinically relevant species of Candida were also isolated. The comparison between the three methods was concordant, especially for the most common Candida species. Fungal DNA amplification was successful in all clinical samples.
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10
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Nemer S, Imtiaz T, Varikkara M, Collier A, Bal AM. Management of candidaemia with reference to the European confederation of medical mycology quality indicators. Infect Dis (Lond) 2019; 51:527-533. [DOI: 10.1080/23744235.2019.1606436] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
- Sophia Nemer
- Department of Renal Medicine, University Hospital Crosshouse, Kilmarnock, UK
| | - Toufeeq Imtiaz
- Department of Renal Medicine, University Hospital Crosshouse, Kilmarnock, UK
| | - Mohan Varikkara
- Department of Ophthalmology, University Hospital Ayr, Kilmarnock, UK
| | - Andrew Collier
- Department of Medicine, University Hospital Ayr, Kilmarnock, UK
| | - Abhijit M. Bal
- Department of Microbiology, University Hospital Crosshouse, Kilmarnock, UK
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