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Birhanu AG. Mass spectrometry-based proteomics as an emerging tool in clinical laboratories. Clin Proteomics 2023; 20:32. [PMID: 37633929 PMCID: PMC10464495 DOI: 10.1186/s12014-023-09424-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 08/03/2023] [Indexed: 08/28/2023] Open
Abstract
Mass spectrometry (MS)-based proteomics have been increasingly implemented in various disciplines of laboratory medicine to identify and quantify biomolecules in a variety of biological specimens. MS-based proteomics is continuously expanding and widely applied in biomarker discovery for early detection, prognosis and markers for treatment response prediction and monitoring. Furthermore, making these advanced tests more accessible and affordable will have the greatest healthcare benefit.This review article highlights the new paradigms MS-based clinical proteomics has created in microbiology laboratories, cancer research and diagnosis of metabolic disorders. The technique is preferred over conventional methods in disease detection and therapy monitoring for its combined advantages in multiplexing capacity, remarkable analytical specificity and sensitivity and low turnaround time.Despite the achievements in the development and adoption of a number of MS-based clinical proteomics practices, more are expected to undergo transition from bench to bedside in the near future. The review provides insights from early trials and recent progresses (mainly covering literature from the NCBI database) in the application of proteomics in clinical laboratories.
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Abed AB, Hürkan K, Ünal A, Aydın B, Korcan SE. Phenotypic and molecular genetics study of Geotrichum candidumLink (1809) and Geotrichum silvicola Pimenta (2005) cultivated on mitis salivarius agar. Mol Biol Rep 2023:10.1007/s11033-023-08443-z. [PMID: 37294469 DOI: 10.1007/s11033-023-08443-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 04/11/2023] [Indexed: 06/10/2023]
Abstract
BACKGROUND Geotrichum is a genus of fungi found in different habitats throughout the world. Although Geotrichum and its related species have been extensively reclassified and taxonomically revised, it is still the target for many researches. METHODS AND RESULTS In this study, phenotypic and molecular genetics comparisons were performed between Geotrichum candidum and Geotrichum silvicola. Mitis Salivarius Agar was used as the growing medium for the phenotypic comparison study, which was carried out at two temperatures (20-25 and 37 °C). For genotypic comparison, we compared the 18 S, ITS, and 28 S sequences of universal DNA barcode regions of both species. Important findings on the new culture media for fungal isolation were revealed by the results. The phenotypic variation between the two species' colonies, including their shapes, sizes, textures and growth rates, were strikingly different. DNA sequences of both species showed that pairwise identities of the species were 99.9% for 18 S, 100% for ITS and 99.6% for 28 S regions. CONCLUSIONS Contrary to what is commonly seen, the results showed that 18 S, ITS and 28 S failed to discriminate the species. The first investigation into the performance of Mitis Salivarius Agar as a fungus culture medium is reported in this work, and proved its efficiency. Additionally, this is the first study to compare G. candidum with G. silvicola by means of both phenotypic and genotypic analysis.
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Affiliation(s)
- Ahmed Badri Abed
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Uşak University, Uşak, 64200, Turkey.
| | - Kaan Hürkan
- Faculty of Agriculture, Department of Agricultural Biotechnology, Iğdır University, Iğdır, Turkey
| | - Arzu Ünal
- Faculty of Agriculture, Department of Agricultural Biotechnology, Iğdır University, Iğdır, Turkey
| | - Büşra Aydın
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Uşak University, Uşak, 64200, Turkey
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Candida Genus Maximum Incidence in Boar Semen Even after Preservation, Is It Not a Risk for AI though? Molecules 2022; 27:molecules27217539. [PMID: 36364363 PMCID: PMC9656137 DOI: 10.3390/molecules27217539] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/24/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022] Open
Abstract
There is little information in the literature about the fungal contamination of boar semen and its persistence during storage. The challenge of this study was to perform a mycological screening to identify the yeast in the raw semen at 12/24 h after dilution. The research was done in pig farms in the N-E area of Romania, with maximum biosecurity and state-of-the-art technology. All the examined ejaculates (101) were considered to be normal for each spermogram parameter, with microbiological determinations in T0 at the time of ejaculate collection, T1 at the time of dilution, and T2 at 24 h of storage. Microbiological determinations (mycological spermogram) were performed for quantitative (LogCFU/mL) and qualitative (typification of fungal genera) identification. Bacterial burden (×103 LogCFU/mL) after dilution (T1) decreased drastically (p < 0.0001) compared to the one in the raw semen (T0). After 24 h of storage at 17 °C, the mean value of the bacteriospermia remained constant at an average value of 0.44. Mycospermia had a constant trend at T0 (raw) and T1 (0.149 vs. 0.140) and was slightly higher at T2 (0.236). The difference between T1 vs. T2 (p = 0.0419) was close to the statistical reference value (p = 0.05). Of the total genera identified (24), the fungi had a proportion of 37.4% (9/15) and a ratio of 1:1.6. Regarding the total species (34), the fungi had a frequency of 29.42% (10/24) with a ratio between the fungi and bacteria of 1:2.4. A fertility rate of 86% was observed in the L1 group (50 AI sows with doses and mycospermia from T1), and an 82% rate was observed in the L2 group (50 AI sows with doses and mycospermia from T2). The litter size of L1 was 9.63 piglets and 9.56 for L2. Regarding the total number of piglets obtained between the two groups, there was a slight decrease of 22 piglets in group L2, without statistical differences (p > 0.05). The predominant genera persisted after dilution during a 12 h storage at 17 °C, where yeasts, such as Candida parapsilosis and C. sake were identified in more than 92% of AI doses.
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Faster and accurate identification of clinically important Trichosporon using MALDI TOF MS. Indian J Med Microbiol 2022; 40:359-364. [PMID: 35738950 DOI: 10.1016/j.ijmmb.2022.05.014] [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: 11/28/2021] [Revised: 04/11/2022] [Accepted: 05/28/2022] [Indexed: 11/22/2022]
Abstract
PURPOSE Trichosporon species are emerging human pathogens, accounting for the second most common cause of non-candidal mycosis. Rapid and reliable identification of these agents allows a better understanding of their epidemiology and therapeutic management. The Matrix-Assisted Laser Desorption Ionization-Time-of-Flight Mass Spectrometry (MALDI-TOF MS) technique has the potential to be precise, fast and cost-effective. However, the precision of identification totally depends upon the type of protein extraction method used and embedded database in the system. Our objectives were to standardize the protein extraction technique and expand the present Bruker database by creating an in-house database and validating it with diverse clinical Trichosporon species of Indian origin. METHODS Two different protein extraction protocols (on-plate and off-plate) were evaluated. The off-plate protocol was finalized for the identification. MALDI TOF MS with the existing Bruker database was evaluated for its ability to identify a total of 79 intergenic spacer 1 (IGS1) gene sequence confirmed clinical isolates of 5 different Trichosporon species. RESULTS As outcome, off plate protocol yielded higher accuracy (73% on the species level and 95% on the genus level) than on-plate (25% on the genus level) in terms of log scores. The existing database for Trichosporon species was enriched with 28 sequence confirmed isolates, which improved accuracy from 73% to 100% and were identified up to species level with a log score >2.3. CONCLUSIONS Used with standardized protein-extraction protocol along with an expanded database, MALDI-TOF MS could be a rapid and reliable approach to identify clinical Trichosporon species routinely in the laboratory.
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Sarvestani HK, Ramandi A, Getso MI, Razavyoon T, Javidnia J, Golrizi MB, Saboor-Yaraghi AA, Ansari S. Mass spectrometry in research laboratories and clinical diagnostic: a new era in medical mycology. Braz J Microbiol 2022; 53:689-707. [PMID: 35344203 PMCID: PMC9151960 DOI: 10.1007/s42770-022-00715-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 02/14/2022] [Indexed: 02/01/2023] Open
Abstract
Diagnosis by clinical mycology laboratory plays a critical role in patient care by providing definitive knowledge of the cause of infection and antimicrobial susceptibility data to physicians. Rapid diagnostic methods are likely to improve patient. Aggressive resuscitation bundles, adequate source control, and appropriate antibiotic therapy are cornerstones for success in the treatment of patients. Routine methods for identifying clinical specimen fungal pathogen are based on the cultivation on different media with the subsequent examination of its phenotypic characteristics comprising a combination of microscopic and colony morphologies. As some fungi cannot be readily identified using these methods, molecular diagnostic methods may be required. These methods are fast, but it can cost a lot. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is suitable for high-throughput and rapid diagnostics at low costs. It can be considered an alternative for conventional biochemical and molecular identification systems in a microbiological laboratory. The reliability and accuracy of this method have been scrutinized in many surveys and have been compared with several methods including sequencing and molecular methods. According to these findings, the reliability and accuracy of this method are very high and can be trusted. With all the benefits of this technique, the libraries of MALDI-TOF MS need to be strengthened to enhance its performance. This review provides an overview of the most recent research literature that has investigated the applications and usage of MT-MS to the identification of microorganisms, mycotoxins, antifungal susceptibility examination, and mycobiome research.
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Affiliation(s)
- Hasti Kamali Sarvestani
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Alireza Ramandi
- Students' Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Muhammad Ibrahim Getso
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
- Department of Medical Microbiology and Parasitology, College of Health Sciences, Bayero University, PMB, Kano, 3011, Nigeria
| | - Taraneh Razavyoon
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Javad Javidnia
- Student Research Committee, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
- Department of Medical Mycology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Miaad Banay Golrizi
- Student Research Committee, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Ali-Akbar Saboor-Yaraghi
- Department of Nutrition and Biochemistry, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
- Department of Medical Parasitology and Mycology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Saham Ansari
- Department of Medical Parasitology and Mycology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Dogra S, Arora A, Aggarwal A, Passi G, Sharma A, Singh G, Barnwal RP. Mucormycosis Amid COVID-19 Crisis: Pathogenesis, Diagnosis, and Novel Treatment Strategies to Combat the Spread. Front Microbiol 2022; 12:794176. [PMID: 35058909 PMCID: PMC8763841 DOI: 10.3389/fmicb.2021.794176] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 11/30/2021] [Indexed: 01/01/2023] Open
Abstract
The havoc unleashed by COVID-19 pandemic has paved way for secondary ominous fungal infections like Mucormycosis. It is caused by a class of opportunistic pathogens from the order Mucorales. Fatality rates due to this contagious infection are extremely high. Numerous clinical manifestations result in damage to multiple organs subject to the patient's underlying condition. Lack of a proper detection method and reliable treatment has made the management of this infection troublesome. Several reports studying the behavior pattern of Mucorales inside the host by modulation of its defense mechanisms have helped in understanding the pathogenesis of this angio-invasive infection. Many recent advances in diagnosis and treatment of this fungal infection have not been much beneficial. Therefore, there is a need to foster more viable strategies. This article summarizes current and imminent approaches that could aid effective management of these secondary infections in these times of global pandemic. It is foreseen that the development of newer antifungal drugs, antimicrobial peptides, and nanotechnology-based approaches for drug delivery would help combat this infection and curb its spread.
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Affiliation(s)
- Shreya Dogra
- Department of Biophysics, Panjab University, Chandigarh, India
| | - Akanksha Arora
- Department of Biophysics, Panjab University, Chandigarh, India
| | - Aashni Aggarwal
- Department of Biophysics, Panjab University, Chandigarh, India
| | - Gautam Passi
- Department of Biophysics, Panjab University, Chandigarh, India
| | - Akanksha Sharma
- Department of Biophysics, Panjab University, Chandigarh, India
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, India
| | - Gurpal Singh
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, India
| | - Ravi P. Barnwal
- Department of Biophysics, Panjab University, Chandigarh, India
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7
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New Tools in Laboratory Diagnosis of Invasive Fungal Infections. Fungal Biol 2022. [DOI: 10.1007/978-3-030-89664-5_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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A Pilot Clinical Study on Post-Operative Recurrence Provides Biological Clues for a Role of Candida Yeasts and Fluconazole in Crohn's Disease. J Fungi (Basel) 2021; 7:jof7050324. [PMID: 33922391 PMCID: PMC8146386 DOI: 10.3390/jof7050324] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/15/2021] [Accepted: 04/16/2021] [Indexed: 02/06/2023] Open
Abstract
Background and aims: This study prompted by growing evidence of the relationship between the yeast Candida albicans and Crohn’s disease (CD) was intended to assess the effect of a 6-month course of the antifungal fluconazole (FCZ) on post-operative recurrence of CD. Methods: Mycological samples (mouth swabs and stools) and serum samples were collected from 28 CD patients randomized to receive either FCZ (n = 14) or placebo (n = 14) before surgical resection. Serological analysis focused on levels of calprotectin, anti-glycan antibodies, and antibody markers of C. albicans pathogenic transition. Levels of galectin-3 and mannose binding lectin (MBL) involved in C. albicans sensing and inflammation were also measured. Results: 1, 2, 3, and 6 months after surgery, endoscopy revealed recurrence in 5/12 (41.7%) patients in the FCZ group and 5/9 (55.6%) in the placebo group, the small cohort preventing any clinical conclusions. In both groups, surgery was followed by a marked decrease in C. albicans colonization and biomarkers of C. albicans pathogenic transition decreased to non-significant levels. Anti-glycan antibodies also decreased but remained significant for CD. Galectin-3 and calprotectin also decreased. Conversely, MBL levels, which inversely correlated with anti-C. albicans antibodies before surgery, remained stable. Building biostatistical multivariate models to analyze he changes in antibody and lectin levels revealed a significant relationship between C. albicans and CD. Conclusion: Several combinations of biomarkers of adaptive and innate immunity targeting C. albicans were predictive of CD recurrence after surgery, with area under the curves (AUCs) as high as 0.86. FCZ had a positive effect on biomarkers evolution. ClinicalTrials.gov ID: NCT02997059, 19 December 2016. University Hospital Lille, Ministry of Health, France. Effect of Fluconazole on the Levels of Anti-Saccharomyces cerevisiae Antibodies (ASCA) After Surgical Resection for Crohn’s Disease. Multicenter, Randomized, and Controlled in Two Parallel Groups Versus Placebo.
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Komatsu K, Yamaguchi S, Yasumura R, Takahashi K. Cutaneous abscess due to
Candida dubliniensis
: A case report. J Dermatol 2020; 47:e253-e254. [DOI: 10.1111/1346-8138.15373] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Kotaro Komatsu
- Department of Dermatology University of the Ryukyus Graduate School of Medicine Nishihara Japan
| | - Sayaka Yamaguchi
- Department of Dermatology University of the Ryukyus Graduate School of Medicine Nishihara Japan
| | - Ryo Yasumura
- Department of Dermatology University of the Ryukyus Graduate School of Medicine Nishihara Japan
| | - Kenzo Takahashi
- Department of Dermatology University of the Ryukyus Graduate School of Medicine Nishihara Japan
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Pote ST, Sonawane MS, Rahi P, Shah SR, Shouche YS, Patole MS, Thakar MR, Sharma R. Distribution of Pathogenic Yeasts in Different Clinical Samples: Their Identification, Antifungal Susceptibility Pattern, and Cell Invasion Assays. Infect Drug Resist 2020; 13:1133-1145. [PMID: 32368104 PMCID: PMC7182453 DOI: 10.2147/idr.s238002] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 02/25/2020] [Indexed: 12/27/2022] Open
Abstract
Introduction Species of genus Candida are part of the common microbiota of humans; however, some of the Candida species are known opportunistic pathogens. Formation of biofilms, resistance to antifungal drugs, and increase in asymptomatic infections demands more studies on isolation, identification and characterization of Candida from clinical samples. Methods The present manuscript deals with assessment of authentic yeast identification by three methods viz., DNA sequencing of 28S rRNA gene, protein profiles using MALDI-TOF MS, and colony coloration on chromogenic media. Antifungal susceptibility and in vitro cell invasion assays were performed to further characterize these isolates. Results Comparison of three methods showed that DNA sequence analysis correctly identified more than 99.4% of the isolates up to species level as compared to 89% by MALDI-TOF MS. In this study, we isolated a total of 176 yeasts from clinical samples and preliminary morphological characters indicated that these yeast isolates belong to the genus Candida. The species distribution of isolates was as follows: 75 isolates of Candida albicans (42.61%), 50 of C. tropicalis (28.40%), 22 of C. glabrata (12.5%), 14 of C. parapsilosis (7.95%) and 4 of Clavispora lusitaniae (2.27%). Other species like Cyberlindnera fabianii, Issatchenkia orientalis, Kluyveromyces marxianus, Kodamaea ohmeri, Lodderomyces sp., and Trichosporon asahii were less than 2%. Antifungal susceptibility assay performed with 157 isolates showed that most of the isolates were resistant to the four azoles viz., clotrimazole, fluconazole, itraconazole, and ketoconazole, and the frequency of resistance was more in non-albicans Candida isolates. The susceptibility to azole drugs ranged from 7% to 48%, while 75% of the tested yeasts were susceptible to nystatin. Moreover, 88 isolates were also tested for their capacity to invade human cells using HeLa cells. In vitro invasion assay showed that most of the C. albicans isolates showed epithelial cell invasion as compared to isolates belonging to C. glabrata, C. parapsilosis and C. tropicalis. Discussion The identification of yeasts of clinical origin by sequencing of 28S rRNA gene performed better than MALDI-TOF MS. The present study reiterates the world scenario wherein there is a shift from Candida strains to emerging opportunistic pathogens which were earlier regarded as environmental strains. The present study enlightens the current understanding of identification methods for clinical yeast isolates, increased antifungal drug resistance, epithelial cell invasion as a virulence factor, and diversity of yeasts in Indian clinical samples.
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Affiliation(s)
- Satish T Pote
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science, NCCS Complex, S.P. Pune University, Pune 411 007, Maharashtra, India.,National AIDS Research Institute, Pune 411026, Maharashtra, India
| | - Mahesh S Sonawane
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science, NCCS Complex, S.P. Pune University, Pune 411 007, Maharashtra, India
| | - Praveen Rahi
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science, NCCS Complex, S.P. Pune University, Pune 411 007, Maharashtra, India
| | - Sunil R Shah
- Bharati Vidyapeeth Deemed University Medical College, Bharati Vidyapeeth, Pune 411043, Maharashtra, India
| | - Yogesh S Shouche
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science, NCCS Complex, S.P. Pune University, Pune 411 007, Maharashtra, India
| | - Milind S Patole
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science, NCCS Complex, S.P. Pune University, Pune 411 007, Maharashtra, India
| | - Madhuri R Thakar
- National AIDS Research Institute, Pune 411026, Maharashtra, India
| | - Rohit Sharma
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science, NCCS Complex, S.P. Pune University, Pune 411 007, Maharashtra, India
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Poissy J, Damonti L, Bignon A, Khanna N, Von Kietzell M, Boggian K, Neofytos D, Vuotto F, Coiteux V, Artru F, Zimmerli S, Pagani JL, Calandra T, Sendid B, Poulain D, van Delden C, Lamoth F, Marchetti O, Bochud PY. Risk factors for candidemia: a prospective matched case-control study. CRITICAL CARE : THE OFFICIAL JOURNAL OF THE CRITICAL CARE FORUM 2020; 24:109. [PMID: 32188500 PMCID: PMC7081522 DOI: 10.1186/s13054-020-2766-1] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 02/07/2020] [Indexed: 12/29/2022]
Abstract
Background Candidemia is an opportunistic infection associated with high morbidity and mortality in patients hospitalized both inside and outside intensive care units (ICUs). Identification of patients at risk is crucial to ensure prompt antifungal therapy. We sought to assess risk factors for candidemia and death, both outside and inside ICUs. Methods This prospective multicenter matched case-control study involved six teaching hospitals in Switzerland and France. Cases were defined by positive blood cultures for Candida sp. Controls were matched to cases using the following criteria: age, hospitalization ward, hospitalization duration, and, when applicable, type of surgery. One to three controls were enrolled by case. Risk factors were analyzed by univariate and multivariate conditional regression models, as a basis for a new scoring system to predict candidemia. Results One hundred ninety-two candidemic patients and 411 matched controls were included. Forty-four percent of included patients were hospitalized in ICUs, and 56% were hospitalized outside ICUs. Independent risk factors for candidemia in the ICU population included total parenteral nutrition, acute kidney injury, heart disease, prior septic shock, and exposure to aminoglycoside antibiotics. Independent risk factors for candidemia in the non-ICU population included central venous catheter, total parenteral nutrition, and exposure to glycopeptides and nitroimidazoles. The accuracy of the scores based on these risk factors is better in the ICU than in the non-ICU population. Independent risk factors for death in candidemic patients included septic shock, acute kidney injury, and the number of antibiotics to which patients were exposed before candidemia. Discussion While this study shows a role for known and novel risk factors for candidemia, it specifically highlights important differences in their distribution according to the hospital setting (ICU versus non-ICU). Conclusion This study provides novel risk scores for candidemia accounting for the hospital setting and recent progress in patients’ management strategies and fungal epidemiology.
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Affiliation(s)
- Julien Poissy
- Current affiliation : Univ. Lille, Inserm U1285, CHU Lille, Pôle de réanimation, NRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000, Lille, France.,Inserm, U995-2 "Fungal Associated Invasive and Inflammatory Diseases", F-59000, Lille, France.,Infectious Diseases Service, Department of Medicine, Lausanne University Hospital and University of Lausanne, rue du Bugnon 46, CH-1011, Lausanne, Switzerland
| | - Lauro Damonti
- Infectious Diseases Service, Department of Medicine, Lausanne University Hospital and University of Lausanne, rue du Bugnon 46, CH-1011, Lausanne, Switzerland.,Department of Infectious Diseases Department, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Anne Bignon
- Surgical Intensive Care Unit, University Hospital of Lille, F-59000, Lille, France
| | - Nina Khanna
- Division of Infectious Diseases and Hospital Epidemiology, University and University Hospital of Basel, Basel, Switzerland
| | - Matthias Von Kietzell
- Infectious Diseases Department, Cantonal Hospital of Saint Gallen, St. Gallen, Switzerland
| | - Katia Boggian
- Infectious Diseases Department, Cantonal Hospital of Saint Gallen, St. Gallen, Switzerland
| | - Dionysios Neofytos
- Transplant Infectious Diseases Unit, University Hospitals of Geneva, Geneva, Switzerland
| | - Fanny Vuotto
- Infectious Diseases Department, University Hospital of Lille, F-59000, Lille, France
| | - Valérie Coiteux
- Hematological Disorders Department, University Hospital and University of Lille, F-59000, Lille, France
| | - Florent Artru
- Digestive Intensive Care Department, University Hospital and University of Lille, F-59000, Lille, France
| | - Stephan Zimmerli
- Department of Infectious Diseases Department, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Jean-Luc Pagani
- Adult Intensive Care Service, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Thierry Calandra
- Infectious Diseases Service, Department of Medicine, Lausanne University Hospital and University of Lausanne, rue du Bugnon 46, CH-1011, Lausanne, Switzerland
| | - Boualem Sendid
- Inserm, U995-2 "Fungal Associated Invasive and Inflammatory Diseases", F-59000, Lille, France.,Laboratory of Mycology and Parasitology, Hospital and University of Lille, F-59000, Lille, France
| | - Daniel Poulain
- Inserm, U995-2 "Fungal Associated Invasive and Inflammatory Diseases", F-59000, Lille, France.,Laboratory of Mycology and Parasitology, Hospital and University of Lille, F-59000, Lille, France
| | - Christian van Delden
- Transplant Infectious Diseases Unit, University Hospitals of Geneva, Geneva, Switzerland
| | - Frédéric Lamoth
- Infectious Diseases Service, Department of Medicine, Lausanne University Hospital and University of Lausanne, rue du Bugnon 46, CH-1011, Lausanne, Switzerland.,Microbiology Institute, Lausanne University Hospital and University of Lausanne, CH-1010, Lausanne, Switzerland
| | - Oscar Marchetti
- Infectious Diseases Service, Department of Medicine, Lausanne University Hospital and University of Lausanne, rue du Bugnon 46, CH-1011, Lausanne, Switzerland.,Department of Medicine, Ensemble Hospitalier de la Côte, CH-1110, Morges, Switzerland
| | - Pierre-Yves Bochud
- Infectious Diseases Service, Department of Medicine, Lausanne University Hospital and University of Lausanne, rue du Bugnon 46, CH-1011, Lausanne, Switzerland.
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Arastehfar A, Daneshnia F, Kord M, Roudbary M, Zarrinfar H, Fang W, Hashemi SJ, Najafzadeh MJ, Khodavaisy S, Pan W, Liao W, Badali H, Rezaie S, Zomorodian K, Hagen F, Boekhout T. Comparison of 21-Plex PCR and API 20C AUX, MALDI-TOF MS, and rDNA Sequencing for a Wide Range of Clinically Isolated Yeast Species: Improved Identification by Combining 21-Plex PCR and API 20C AUX as an Alternative Strategy for Developing Countries. Front Cell Infect Microbiol 2019; 9:21. [PMID: 30828570 PMCID: PMC6385604 DOI: 10.3389/fcimb.2019.00021] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 01/22/2019] [Indexed: 12/31/2022] Open
Abstract
Occurrence of non-Candida albicans Candida (NCAC) species that are associated with elevated MIC values and therapeutic failures are increasing. As a result, timely and accurate means of identification to the species level is becoming an essential part of diagnostic practices in clinical settings. In this study, 301 clinically isolated yeast strains recovered from various anatomical sites [Blood (n = 145), other sites (n = 156)] were used to assess the accuracy and practicality of API 20C AUX and 21-plex PCR compared to MALDI-TOF MS and large subunit rDNA (LSU rDNA). MALDI-TOF MS correctly identified 98.33% of yeast isolates, 100% of top five Candida species, 95.7% of rare yeast species, while 1.3% of isolates were misidentified. API 20C AUX correctly identified 83.7% of yeast isolates, 97.2% of top five Candida species, 61.8% of rare yeast species, while 16.2% of yeast isolates were misidentified. The 21-plex PCR, accurately identified 87.3% of yeast isolates, 100% of top five Candida species, 72% of rare yeast species, but it misidentified 1.3% of rare yeast species while 9.9% of whole yeast isolates were not identified. The combination of rapidity of 21-plex PCR and comprehensiveness of API 20C AUX, led to correct identification of 92% of included yeast isolates. Due to expensiveness of MALDI-TOF MS and sequencing, this combination strategy could be the most accurate and inexpensive alternative identification strategy for developing countries. Moreover, by the advent and development of cost-effective, reliable, and rapid PCR machines that cost 130 US dollars, 21-plex could be integrated in routine laboratories of developing and resource-limited countries to specifically identify 95% causative agents of yeast-related infections in human. Databases of MALDI-TOF MS, API 20C AUX, and the number of target species identified by 21-plex require further improvement to keep up with the diverse spectrum of yeast species.
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Affiliation(s)
- Amir Arastehfar
- Yeast Biodiversity Department, Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands
| | - Farnaz Daneshnia
- Yeast Biodiversity Department, Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands
| | - Mohammad Kord
- Department of Medical Parasitology and Mycology, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Roudbary
- Department of Medical Mycology and Parasitology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Hossein Zarrinfar
- Allergy Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Wenjie Fang
- Shanghai Key Laboratory of Molecular Medical Mycology, Department of Dermatology, Shanghai Institute of Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Sayed Jamal Hashemi
- Department of Medical Parasitology and Mycology, Tehran University of Medical Sciences, Tehran, Iran.,Food Microbiology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Javad Najafzadeh
- Department of Parasitology and Mycology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Sadegh Khodavaisy
- Department of Medical Parasitology and Mycology, Tehran University of Medical Sciences, Tehran, Iran.,Zoonoses Research Center, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Weihua Pan
- Shanghai Key Laboratory of Molecular Medical Mycology, Department of Dermatology, Shanghai Institute of Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Wanqing Liao
- Shanghai Key Laboratory of Molecular Medical Mycology, Department of Dermatology, Shanghai Institute of Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Hamid Badali
- Department of Medical Mycology, Invasive Fungi Research Center, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Sassan Rezaie
- Department of Medical Parasitology and Mycology, Tehran University of Medical Sciences, Tehran, Iran
| | - Kamiar Zomorodian
- Department of Medical Mycology and Parasitology, Basic Sciences in Infectious Diseases Research Center, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ferry Hagen
- Yeast Biodiversity Department, Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands
| | - Teun Boekhout
- Yeast Biodiversity Department, Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands.,Shanghai Key Laboratory of Molecular Medical Mycology, Department of Dermatology, Shanghai Institute of Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China.,Yeast Biodiversity Department, Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
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13
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A Moldy Application of MALDI: MALDI-ToF Mass Spectrometry for Fungal Identification. J Fungi (Basel) 2019; 5:jof5010004. [PMID: 30609833 PMCID: PMC6463175 DOI: 10.3390/jof5010004] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 12/07/2018] [Accepted: 12/25/2018] [Indexed: 12/20/2022] Open
Abstract
As a result of its being inexpensive, easy to perform, fast and accurate, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-ToF MS) is quickly becoming the standard means of bacterial identification from cultures in clinical microbiology laboratories. Its adoption for routine identification of yeasts and even dimorphic and filamentous fungi in cultures, while slower, is now being realized, with many of the same benefits as have been recognized on the bacterial side. In this review, the use of MALDI-ToF MS for identification of yeasts, and dimorphic and filamentous fungi grown in culture will be reviewed, with strengths and limitations addressed.
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14
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Hu Z, Zhang J, Chen Z, Jin Z, Leng P, Zhou J, Xie X. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometric identification and antifungal susceptibility analysis of Candida species isolated from patients with invasive yeast infections in five university hospitals. Braz J Microbiol 2018; 50:99-105. [PMID: 30637643 DOI: 10.1007/s42770-018-0027-0] [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: 07/25/2018] [Accepted: 10/15/2018] [Indexed: 11/29/2022] Open
Abstract
In this multicenter study, we compared the performance of the Bruker Biotyper MS system and VITEK 2 YST systems for invasive yeast identification, investigated the distribution of isolated species, and evaluated the antifungal susceptibility profiles of Candida albicans, Candida parapsilosis, and Candida tropicalis. In cases of discrepant results lack of identification with either method, molecular identification techniques were employed. We tested 216 clinical isolates, and concordance between the two methods was observed for 192/216 isolates (88.9%). For five unidentified strains (2.3%), an internal transcribed spacer (ITS) sequencing approach was used. In brief, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-ToF MS) provided short turnaround times and more reliable results than those of Vitek 2 YST. In Wuhan, C. albicans, C. parapsilosis, Candida glabrata, and C. tropicalis were the most common pathogens (93.0%) in patients with candidemia. Cryptococcus neoformans was mainly detected in cerebrospinal fluid samples (88.9%). Trichosporon asahii were all isolated from drainage fluids in the Surgery. Candida albicans was clearly susceptible to azoles, while C. parapsilosis and C. tropicalis displayed differences in susceptibility to azoles. Our findings provide a basis for the practical application of MALDI-ToF MS for identification and for the use of ATB FUNGUS 3 to characterize the susceptibility of Candida spp., thereby providing significant data for therapeutic decisions.
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Affiliation(s)
- Zhimin Hu
- Department of Clinical Microbiology Laboratory, Wuhan No. 1 Hospital of Tongji Medical College, Huazhong University of Science and Technology, No. 215 Zhongshan Ave., Wuhan, 430022, China.
| | - Juling Zhang
- Department of Clinical Laboratory, PLA 302 Hospital, No. 100 West Fourth Ring Road, Peking, 100166, China
| | - Zhongju Chen
- Department of Clinical Microbiology Laboratory, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, No. 1095 Liberation Ave., Wuhan, 430030, China
| | - Zhengjiang Jin
- Department of Clinical Microbiology Laboratory, Hubei Women and Children's Hospital, No. 745 Wuluo Road, Wuhan, 430070, China
| | - Pei Leng
- Department of Clinical Laboratory, Wuhan Women and Children Medical Care Center, No. 100 Xianggang Road, Wuhan, 430015, China
| | - Junying Zhou
- Department of Clinical Microbiology Laboratory, Zhongnan Hospital of Wuhan University, No. 169 Donghu Road, Wuhan, 430071, China
| | - Xiaofang Xie
- Department of Clinical Microbiology Laboratory, The First Affiliated Hospital of Soochow University, No. 188 Shizi Street, Soochow, 215006, China
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15
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Arastehfar A, Fang W, Pan W, Liao W, Yan L, Boekhout T. Identification of nine cryptic species of Candida albicans, C. glabrata, and C. parapsilosis complexes using one-step multiplex PCR. BMC Infect Dis 2018; 18:480. [PMID: 30253748 PMCID: PMC6156947 DOI: 10.1186/s12879-018-3381-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 09/13/2018] [Indexed: 01/24/2023] Open
Abstract
Background Candida albicans, Candida glabrata, and Candida parapsilosis are three prevalent causes of candidiasis, worldwide. These species are considered as nine medically important complex species. Limited knowledge about these newly recognized species prompted us to develop a one-step, multiplex PCR to detect and identify them in clinical settings. Methods Primers targeting Hyphal Wall Protein I gene for the C. albicans, C. dubliniensis, C. africana, Intergenic Spacer for the C. glabrata, C. nivariensis, C. bracarensis, and Intein and ITS rDNA for the C. parapsilosis, C. orthopsilosis, and C. metapsilosis were designed. Using 168 CBS reference strains and 280 clinical isolates, the specificity and reproducibility of the developed assay were evaluated. Results Our developed assay successfully identified and distinguished all the nine species. No cross-reaction with closely- and distantly-related yeast species, Aspergillus species and human DNA was observed, resulting in 100% specificity. The ambiguous results obtained by MALDI-TOF for C. albicans and C. africana were corrected by our 9-plex PCR assay. This assay identified all the cryptic complex species from two test sets from Iran and China, correctly. Conclusions Our developed multiplex assay is accurate, specific, cost/time-saving, and works without the tedious DNA extraction steps. It could be integrated into routine clinical laboratories and as a reliable identification tool and has the potential to be implemented into epidemiological studies to broaden the limited knowledge of cryptic species complexes. Electronic supplementary material The online version of this article (10.1186/s12879-018-3381-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Amir Arastehfar
- Westerdijk Fungal Biodiversity Institute, Utrecht, 3584, the Netherlands
| | - Wenjie Fang
- Westerdijk Fungal Biodiversity Institute, Utrecht, 3584, the Netherlands.,Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, 200003, China
| | - Weihua Pan
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, 200003, China.
| | - Wanqing Liao
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, 200003, China
| | - Liang Yan
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, 200003, China
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, 3584, the Netherlands. .,Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, 200003, China. .,Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, 1012 WX, the Netherlands.
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16
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Ruiz de Alegría Puig C, Agüero-Balbín J, Fernández-Mazarrasa C, Martínez-Martínez L. Evaluation of the Vitek-MS™ system in the identification of Candida isolates from bloodstream infections. Rev Iberoam Micol 2018; 35:130-133. [DOI: 10.1016/j.riam.2018.02.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 01/17/2018] [Accepted: 02/26/2018] [Indexed: 01/13/2023] Open
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17
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Honnavar P, Ghosh AK, Paul S, Shankarnarayan SA, Singh P, Dogra S, Chakrabarti A, Rudramurthy SM. Identification of Malassezia species by MALDI-TOF MS after expansion of database. Diagn Microbiol Infect Dis 2018; 92:118-123. [PMID: 30025965 DOI: 10.1016/j.diagmicrobio.2018.05.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 05/10/2018] [Accepted: 05/22/2018] [Indexed: 11/18/2022]
Abstract
The taxonomy of Malassezia species is evolving with introduction of molecular techniques, and difficulty is faced to identify the species by phenotypic methods. Among 15 known Malassezia species, the present Bruker database could identify only 2 species. The present study was aimed to improve Matrix -assisted laser desorption ionization time-flight mass spectrometry (MALDI-TOF MS) based identification of Malassezia species. A total of 88 isolates (DNA sequencing confirmed) for database preparation and, for the validation of database, 190 isolates confirmed by polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) were used. The main spectrum profile dendrogram showed the sufficient discrimination between all the species by MALDI-TOF MS. The updated Malassezia database could identify 94.7% and 5.3% strains to the species and genus level, respectively. MALDI-TOF MS is a significantly reliable technique, and results were comparable with PCR-RFLP with kappa value 0.9. In conclusion, MALDI-TOF MS could be a possible alternative tool to other molecular methods for rapid and accurate identification of Malassezia species.
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Affiliation(s)
- P Honnavar
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - A K Ghosh
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - S Paul
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - S A Shankarnarayan
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - P Singh
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - S Dogra
- Department of Dermatology, Venerology and Leprology, Postgraduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - A Chakrabarti
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - S M Rudramurthy
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, 160012, India.
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18
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Chang EY, Fatima S, Balan S, Bhyravabhotla K, Erickson M, Chan A, Ivonye C, Bradley C. Candida dubliniensis abscess: A clinical case and a review of the literature. Med Mycol Case Rep 2018; 21:41-43. [PMID: 30090694 PMCID: PMC6077146 DOI: 10.1016/j.mmcr.2018.04.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Revised: 03/16/2018] [Accepted: 04/16/2018] [Indexed: 11/29/2022] Open
Abstract
Candida dubliniensis infections are rare in the absence of prolonged immunocompromised status or intravenous drug abuse. We present a case of a C. dubliniensis soft tissue abscess in a patient with uncontrolled diabetes as his only immunocompromising risk factor, treated with surgical drainage and medical management.
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Affiliation(s)
- Eric Y Chang
- Department of Internal Medicine, Morehouse School of Medicine, 720 Westview Dr. S.W., Atlanta, GA 30310, USA
| | - Shaheen Fatima
- Department of Internal Medicine, Morehouse School of Medicine, 720 Westview Dr. S.W., Atlanta, GA 30310, USA
| | - Shuba Balan
- Department of Internal Medicine, Morehouse School of Medicine, 720 Westview Dr. S.W., Atlanta, GA 30310, USA
| | - Kshama Bhyravabhotla
- Department of Internal Medicine, Morehouse School of Medicine, 720 Westview Dr. S.W., Atlanta, GA 30310, USA
| | - Marc Erickson
- Department of Internal Medicine, Morehouse School of Medicine, 720 Westview Dr. S.W., Atlanta, GA 30310, USA
| | - Austin Chan
- Department of Internal Medicine, Morehouse School of Medicine, 720 Westview Dr. S.W., Atlanta, GA 30310, USA.,Division of Infectious Diseases, Department of Internal Medicine, Morehouse School of Medicine, 720 Westview Dr. S.W., Atlanta, GA 30310, USA
| | - Chinedu Ivonye
- Department of Internal Medicine, Morehouse School of Medicine, 720 Westview Dr. S.W., Atlanta, GA 30310, USA
| | - Cinnamon Bradley
- Department of Internal Medicine, Morehouse School of Medicine, 720 Westview Dr. S.W., Atlanta, GA 30310, USA
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19
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Shao J, Wan Z, Li R, Yu J. Species Identification and Delineation of Pathogenic Mucorales by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry. J Clin Microbiol 2018; 56:e01886-17. [PMID: 29436422 PMCID: PMC5869826 DOI: 10.1128/jcm.01886-17] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 01/29/2018] [Indexed: 11/20/2022] Open
Abstract
This study aimed to validate the effectiveness of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)-based identification of filamentous fungi of the order Mucorales. A total of 111 isolates covering six genera preserved at the Research Center for Medical Mycology of Peking University were selected for MALDI-TOF MS analysis. We emphasized the study of 23 strains of Mucor irregularis predominantly isolated from patients in China. We first used the Bruker Filamentous Fungi library (v1.0) to identify all 111 isolates. To increase the identification rate, we created a compensatory in-house database, the Beijing Medical University (BMU) database, using 13 reference strains covering 6 species, including M. irregularis, Mucor hiemalis, Mucor racemosus, Cunninghamella bertholletiae, Cunninghamella phaeospora, and Cunninghamella echinulata All 111 isolates were then identified by MALDI-TOF MS using a combination of the Bruker library and BMU database. MALDI-TOF MS identified 55 (49.5%) and 74 (66.7%) isolates at the species and genus levels, respectively, using the Bruker Filamentous Fungi library v1.0 alone. A combination of the Bruker library and BMU database allowed MALDI-TOF MS to identify 90 (81.1%) and 111 (100%) isolates at the species and genus levels, respectively, with a significantly increased accuracy rate. MALDI-TOF MS poorly identified Mucorales when the Bruker library was used alone due to its lack of some fungal species. In contrast, this technique perfectly identified M. irregularis after main spectrum profiles (MSPs) of relevant reference strains were added to the Bruker library. With an expanded Bruker library, MALDI-TOF MS is an effective tool for the identification of pathogenic Mucorales.
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Affiliation(s)
- Jin Shao
- Department of Dermatology, Peking University First Hospital, Beijing, China
- Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China
- Research Center for Medical Mycology, Peking University, Beijing, China
| | - Zhe Wan
- Department of Dermatology, Peking University First Hospital, Beijing, China
- Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China
- Research Center for Medical Mycology, Peking University, Beijing, China
| | - Ruoyu Li
- Department of Dermatology, Peking University First Hospital, Beijing, China
- Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China
- Research Center for Medical Mycology, Peking University, Beijing, China
| | - Jin Yu
- Department of Dermatology, Peking University First Hospital, Beijing, China
- Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China
- Research Center for Medical Mycology, Peking University, Beijing, China
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20
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Li MC, Chang TC, Chen HM, Wu CJ, Su SL, Lee SSJ, Chen PL, Lee NY, Lee CC, Li CW, Syue LS, Ko WC. Oligonucleotide Array and VITEK Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry in Species Identification of Blood Yeast Isolates. Front Microbiol 2018; 9:51. [PMID: 29434578 PMCID: PMC5790773 DOI: 10.3389/fmicb.2018.00051] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 01/10/2018] [Indexed: 01/03/2023] Open
Abstract
We evaluated matrix-assisted laser desorption ionization time-of-flight mass spectrometry using VITEK MS (IVD database) and an oligonucleotide array based on the internal transcribed spacer-1 (ITS-1) and ITS-2 sequences of rRNA genes for the identification of Candida spp. from blood cultures. Five-hundred and twelve consecutive bloodstream yeast isolates were collected daily and initially identified by the phenotypic automated method (VITEK YBC or VITEK2 YST card). Inconsistent results were confirmed by D1-D2 region of 28S rRNA genes and ITSs. Excluding two unidentified yeast isolates, the oligonucleotide array and VITEK MS correctly identified 99.6% (508) and 96.9% (494) of 510 yeast isolates, respectively. The oligonucleotide array and VITEK MS demonstrated high correct identification rates for four major Candida species (C. albicans 100%, 98.4%; C. glabrata 100%, 100%; C. parapsilosis 100%, 93.3%; C. tropicalis 100%, 97.3%), but lower correct identification rates for other Candida species (91.7 and 87.5%, respectively). In conclusion, the identification performance of the oligonucleotide array is comparable to that of VITEK MS, and can serve as a supplemental tool for the identification of Candida species.
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Affiliation(s)
- Ming-Chi Li
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Center for Infection Control, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Tsung C Chang
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Hung-Mo Chen
- Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chi-Jung Wu
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Tainan, Taiwan
| | - Shu-Li Su
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Susan S-J Lee
- Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan.,Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Po-Lin Chen
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Center for Infection Control, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Department of Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Nan-Yao Lee
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Center for Infection Control, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Department of Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ching-Chi Lee
- Department of Internal Medicine, Madou Sin-Lau Hospital, Tainan, Taiwan
| | - Chia-Wen Li
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Center for Infection Control, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ling-Shan Syue
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Center for Infection Control, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Wen-Chien Ko
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Center for Infection Control, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Department of Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
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21
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Aslani N, Janbabaei G, Abastabar M, Meis JF, Babaeian M, Khodavaisy S, Boekhout T, Badali H. Identification of uncommon oral yeasts from cancer patients by MALDI-TOF mass spectrometry. BMC Infect Dis 2018; 18:24. [PMID: 29310582 PMCID: PMC5759378 DOI: 10.1186/s12879-017-2916-5] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 12/13/2017] [Indexed: 11/29/2022] Open
Abstract
Background Opportunistic infections due to Candida species occur frequently in cancer patients because of their inherent immunosuppression. The aim of the present study was to investigate the epidemiology of yeast species from the oral cavity of patients during treatment for oncological and haematological malignancies. Methods MALDI-TOF was performed to identify yeasts isolated from the oral cavity of 350 cancer patients. Moreover, antifungal susceptibility testing was performed in according to CLSI guidelines (M27-A3). Results Among 162 yeasts and yeast-like fungi isolated from the oral cavity of cancer patients, Candida albicans was the most common species (50.6%), followed by Candida glabrata (24.7%), Pichia kudriavzevii (Candida krusei (9.9%)), Candida tropicalis (4.3%), Candida dubliniensis (3.7%), Kluyveromyces marxianus (Candida kefyr (3.7%)) and Candida parapsilosis (1%). In addition, uncommon yeast species i.e., Saprochaete capitata, Saccharomyces cerevisiae, Clavispora lusitaniae (C. lusitaniae) and Pichia kluyveri (C. eremophila) were recovered from oral lesions. Oral colonization by C. albicans, non-albicans Candida species and uncommon yeasts were as follow; 55%, 44% and 1%, whereas oral infection due to C. albicans was 33.3%, non-albicans Candida species 60.6%, and uncommon yeasts 6.1%. Poor oral hygiene and xerostomia were identified as independent risk factors associated with oral yeast colonization. The overall resistance to fluconazole was 11.7% (19/162). Low MIC values were observed for anidulafungin for all Candida and uncommon yeast species. Conclusions This current study provides insight into the prevalence and susceptibility profiles of Candida species, including emerging Candida species and uncommon yeasts, isolated from the oral cavity of Iranian cancer patients. The incidence of oral candidiasis was higher amongst patients with hematological malignancies. The majority of oral infections were caused by non-albicans Candida species which were often more resistant to anti-fungal agents. Our findings suggest that anidulafungin should be used as antifungal of choice for prophylaxis in clinically high-risk patients with documented oral colonization or infection.
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Affiliation(s)
- Narges Aslani
- Student Research Committee, Mazandaran University of Medical Sciences, Sari, Iran.,Department of Medical Mycology and Parasitology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Ghasem Janbabaei
- Gastrointestinal Cancer Research Center, Mazandaran University of Medical Sciences, Sari, Iran
| | - Mahdi Abastabar
- Department of Medical Mycology and Parasitology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Jacques F Meis
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital (CWZ), Nijmegen, The Netherlands.,Center of Expertise in Mycology Radboudumc/CWZ, Nijmegen, The Netherlands
| | - Mahasti Babaeian
- Gastrointestinal Cancer Research Center, Mazandaran University of Medical Sciences, Sari, Iran
| | - Sadegh Khodavaisy
- Department of Medical Mycology and Parasitology, Tehran University of Medical Sciences, Tehran, Iran
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Hamid Badali
- Department of Medical Mycology and Parasitology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran. .,Invasive Fungi Research Center (IFRC), School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran.
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22
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Alizadeh M, Kolecka A, Boekhout T, Zarrinfar H, Ghanbari Nahzag MA, Badiee P, Rezaei-Matehkolaei A, Fata A, Dolatabadi S, Najafzadeh MJ. Identification of Candida species isolated from vulvovaginitis using matrix assisted laser desorption ionization-time of flight mass spectrometry. Curr Med Mycol 2017; 3:21-25. [PMID: 29707675 PMCID: PMC5917097 DOI: 10.29252/cmm.3.4.21] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Background and Purpose: Vulvovaginal candidiasis (VVC) is a common problem in women. The purpose of this study was to identify Candida isolates by matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) from women with vulvovaginitis that were referred to Ghaem Hospital, Mashhad, Iran. Materials and Methods: This study was conducted on 65 clinical samples isolated from women that were referred to Ghaem Hospital. All specimens were identified using phenotyping techniques, such as microscopy and culture on Sabouraud dextrose agar and corn meal agar. In addition, all isolates were processed for MALDI-TOF MS identification. Results: Out of the 65 analyzed isolates, 61 (94%) samples were recognized by MALDI-TOF MS. However, the remaining four isolates (6%) had no reliable identification. According to the results, C. albicans (58.5%) was the most frequently isolated species, followed by C. tropicalis (16.9%), C. glabrata (7.7%), C. parapsilosis (7.7%), and guilliermondii (3.1%). Conclusion: As the findings indicated, MALDI TOF MS was successful in the identification of clinical Candida species. C. albicans was identified as the most common Candida species isolated from the women with VVC. Moreover, C. tropicalis was the most common species among the non-albicans Candida species.
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Affiliation(s)
- Majid Alizadeh
- Department of Parasitology and Mycology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Anna Kolecka
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Hossein Zarrinfar
- Allergy Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohamad A Ghanbari Nahzag
- Department of Parasitology and Mycology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Parisa Badiee
- Alborzi Clinical Microbiology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ali Rezaei-Matehkolaei
- Department of Medical Mycology, School of Medicine, Health Research Institute, Infectious and Tropical Diseases Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Abdolmajid Fata
- Department of Parasitology and Mycology, Research Center for Cutaneous Leishmaniasis, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Somayeh Dolatabadi
- Faculty of Engineering, Sabzevar University of New Technologies, Sabzevar, Iran
| | - Mohammad J Najafzadeh
- Department of Parasitology and Mycology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Cancer Molecular Pathology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
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23
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Cassagne C, Normand AC, L'Ollivier C, Ranque S, Piarroux R. Performance of MALDI-TOF MS platforms for fungal identification. Mycoses 2016; 59:678-690. [DOI: 10.1111/myc.12506] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 03/04/2016] [Accepted: 03/12/2016] [Indexed: 01/03/2023]
Affiliation(s)
- Carole Cassagne
- Parasitology and Mycology; Assistance Publique-Hôpitaux de Marseille; CHU Timone-Adultes; Marseilles CEDEX 5 France
- Aix-Marseille University; UMR MD3 IP-TPT; Marseilles France
| | - Anne-Cécile Normand
- Parasitology and Mycology; Assistance Publique-Hôpitaux de Marseille; CHU Timone-Adultes; Marseilles CEDEX 5 France
| | - Coralie L'Ollivier
- Parasitology and Mycology; Assistance Publique-Hôpitaux de Marseille; CHU Timone-Adultes; Marseilles CEDEX 5 France
- Aix-Marseille University; UMR MD3 IP-TPT; Marseilles France
| | - Stéphane Ranque
- Parasitology and Mycology; Assistance Publique-Hôpitaux de Marseille; CHU Timone-Adultes; Marseilles CEDEX 5 France
- Aix-Marseille University; UMR MD3 IP-TPT; Marseilles France
| | - Renaud Piarroux
- Parasitology and Mycology; Assistance Publique-Hôpitaux de Marseille; CHU Timone-Adultes; Marseilles CEDEX 5 France
- Aix-Marseille University; UMR MD3 IP-TPT; Marseilles France
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24
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Soler L, Labas V, Thélie A, Grasseau I, Teixeira-Gomes AP, Blesbois E. Intact Cell MALDI-TOF MS on Sperm: A Molecular Test For Male Fertility Diagnosis. Mol Cell Proteomics 2016; 15:1998-2010. [PMID: 27044871 PMCID: PMC5083112 DOI: 10.1074/mcp.m116.058289] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 04/01/2016] [Indexed: 11/06/2022] Open
Abstract
Currently, evaluation of sperm quality is primarily based on in vitro measures of sperm function such as motility, viability and/or acrosome reaction. However, results are often poorly correlated with fertility, and alternative diagnostic tools are therefore needed both in veterinary and human medicine. In a recent pilot study, we demonstrated that MS profiles from intact chicken sperm using MALDI-TOF profiles could detect significant differences between fertile/subfertile spermatozoa showing that such profiles could be useful for in vitro male fertility testing. In the present study, we performed larger standardized experimental procedures designed for the development of fertility- predictive mathematical models based on sperm cell MALDI-TOF MS profiles acquired through a fast, automated method. This intact cell MALDI-TOF MS-based method showed high diagnostic accuracy in identifying fertile/subfertile males in a large male population of known fertility from two distinct genetic lineages (meat and egg laying lines). We additionally identified 40% of the m/z peaks observed in sperm MS profiles through a top-down high-resolution protein identification analysis. This revealed that the MALDI-TOF MS spectra obtained from intact sperm cells contained a large proportion of protein degradation products, many implicated in important functional pathways in sperm such as energy metabolism, structure and movement. Proteins identified by our predictive model included diverse and important functional classes providing new insights into sperm function as it relates to fertility differences in this experimental system. Thus, in addition to the chicken model system developed here, with the use of appropriate models these methods should effectively translate to other animal taxa where similar tests for fertility are warranted.
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Affiliation(s)
- Laura Soler
- From the ‡INRA, UMR85 Physiologie de la Reproduction et des Comportements, F-37380 Nouzilly, France; §CNRS, UMR7247, F-37380 Nouzilly, France; ¶Université François Rabelais de Tours, F-37000 Tours, France
| | - Valérie Labas
- From the ‡INRA, UMR85 Physiologie de la Reproduction et des Comportements, F-37380 Nouzilly, France; §CNRS, UMR7247, F-37380 Nouzilly, France; ¶Université François Rabelais de Tours, F-37000 Tours, France; ‖IFCE, F-37380 Nouzilly, France;
| | - Aurore Thélie
- From the ‡INRA, UMR85 Physiologie de la Reproduction et des Comportements, F-37380 Nouzilly, France; §CNRS, UMR7247, F-37380 Nouzilly, France; ¶Université François Rabelais de Tours, F-37000 Tours, France; ‖IFCE, F-37380 Nouzilly, France
| | - Isabelle Grasseau
- From the ‡INRA, UMR85 Physiologie de la Reproduction et des Comportements, F-37380 Nouzilly, France; §CNRS, UMR7247, F-37380 Nouzilly, France; ¶Université François Rabelais de Tours, F-37000 Tours, France; ‖IFCE, F-37380 Nouzilly, France
| | - Ana-Paula Teixeira-Gomes
- **INRA, Plateforme d'Analyse Intégrative des Biomolécules, Laboratoire de Spectrométrie de Masse, F-37380 Nouzilly, France; ‡‡INRA, UMR1282 Infectiologie et Santé Publique, F-37380 Nouzilly, France; §§Université François Rabelais de Tours, UMR1282 Infectiologie et Santé Publique, F-37000 Tours, France
| | - Elisabeth Blesbois
- From the ‡INRA, UMR85 Physiologie de la Reproduction et des Comportements, F-37380 Nouzilly, France; §CNRS, UMR7247, F-37380 Nouzilly, France; ¶Université François Rabelais de Tours, F-37000 Tours, France; ‖IFCE, F-37380 Nouzilly, France
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25
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Cassagne C, Normand AC, Bonzon L, L'Ollivier C, Gautier M, Jeddi F, Ranque S, Piarroux R. Routine identification and mixed species detection in 6,192 clinical yeast isolates. Med Mycol 2015; 54:256-65. [DOI: 10.1093/mmy/myv095] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 10/04/2015] [Indexed: 11/14/2022] Open
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26
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García-Agudo L, Galán F, García-Martos P, Carranza R, Rodríguez-Iglesias M. [Utility of mass spectrometry in the microbiological diagnosis of candiduria]. Rev Iberoam Micol 2015; 33:58-9. [PMID: 26561412 DOI: 10.1016/j.riam.2015.02.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2014] [Revised: 01/10/2015] [Accepted: 02/25/2015] [Indexed: 11/17/2022] Open
Affiliation(s)
- Lidia García-Agudo
- Helse Møre og Romsdal, Molde sykehus, Laboratorium for medisinsk mikrobiologi, Noruega.
| | - Fátima Galán
- Servicio de Microbiología, Hospital Puerta del Mar, Cádiz, España
| | | | - Rafael Carranza
- Servicio de Análisis Clínicos, Hospital General La Mancha-Centro, Alcázar de San Juan, Ciudad Real, España
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27
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Suh SO, Houseknecht JL, Grosso KM, Carrion ME. Characterization of the medically important yeast Trichosporon mucoides and its close sister Trichosporon dermatis by traditional and advanced technologies. J Med Microbiol 2015; 64:1135-1143. [DOI: 10.1099/jmm.0.000134] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Sung-Oui Suh
- ATCC, 10801 University Blvd., Manassas, VA 20110, USA
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28
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Flandrois JP, Perrière G, Gouy M. leBIBIQBPP: a set of databases and a webtool for automatic phylogenetic analysis of prokaryotic sequences. BMC Bioinformatics 2015; 16:251. [PMID: 26264559 PMCID: PMC4531848 DOI: 10.1186/s12859-015-0692-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 07/31/2015] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Estimating the phylogenetic position of bacterial and archaeal organisms by genetic sequence comparisons is considered as the gold-standard in taxonomy. This is also a way to identify the species of origin of the sequence. The quality of the reference database used in such analyses is crucial: the database must reflect the up-to-date bacterial nomenclature and accurately indicate the species of origin of its sequences. DESCRIPTION leBIBI(QBPP) is a web tool taking as input a series of nucleotide sequences belonging to one of a set of reference markers (e.g., SSU rRNA, rpoB, groEL2) and automatically retrieving closely related sequences, aligning them, and performing phylogenetic reconstruction using an approximate maximum likelihood approach. The system returns a set of quality parameters and, if possible, a suggested taxonomic assigment for the input sequences. The reference databases are extracted from GenBank and present four degrees of stringency, from the "superstringent" degree (one type strain per species) to the loosely parsed degree ("lax" database). A set of one hundred to more than a thousand sequences may be analyzed at a time. The speed of the process has been optimized through careful hardware selection and database design. CONCLUSION leBIBI(QBPP) is a powerful tool helping biologists to position bacterial or archaeal sequence commonly used markers in a phylogeny. It is a diagnostic tool for clinical, industrial and environmental microbiology laboratory, as well as an exploratory tool for more specialized laboratories. Its main advantages, relatively to comparable systems are: i) the use of a broad set of databases covering diverse markers with various degrees of stringency; ii) the use of an approximate Maximum Likelihood approach for phylogenetic reconstruction; iii) a speed compatible with on-line usage; and iv) providing fully documented results to help the user in decision making.
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Affiliation(s)
- Jean-Pierre Flandrois
- Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Claude Bernard - Lyon 1, 43 bd. du 11 Novembre 1918, Villeurbanne, 69622, France.
| | - Guy Perrière
- Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Claude Bernard - Lyon 1, 43 bd. du 11 Novembre 1918, Villeurbanne, 69622, France.
| | - Manolo Gouy
- Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Claude Bernard - Lyon 1, 43 bd. du 11 Novembre 1918, Villeurbanne, 69622, France.
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29
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Singhal N, Kumar M, Kanaujia PK, Virdi JS. MALDI-TOF mass spectrometry: an emerging technology for microbial identification and diagnosis. Front Microbiol 2015; 6:791. [PMID: 26300860 PMCID: PMC4525378 DOI: 10.3389/fmicb.2015.00791] [Citation(s) in RCA: 800] [Impact Index Per Article: 88.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 07/21/2015] [Indexed: 01/13/2023] Open
Abstract
Currently microorganisms are best identified using 16S rRNA and 18S rRNA gene sequencing. However, in recent years matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has emerged as a potential tool for microbial identification and diagnosis. During the MALDI-TOF MS process, microbes are identified using either intact cells or cell extracts. The process is rapid, sensitive, and economical in terms of both labor and costs involved. The technology has been readily imbibed by microbiologists who have reported usage of MALDI-TOF MS for a number of purposes like, microbial identification and strain typing, epidemiological studies, detection of biological warfare agents, detection of water- and food-borne pathogens, detection of antibiotic resistance and detection of blood and urinary tract pathogens etc. The limitation of the technology is that identification of new isolates is possible only if the spectral database contains peptide mass fingerprints of the type strains of specific genera/species/subspecies/strains. This review provides an overview of the status and recent applications of mass spectrometry for microbial identification. It also explores the usefulness of this exciting new technology for diagnosis of diseases caused by bacteria, viruses, and fungi.
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Affiliation(s)
- Neelja Singhal
- Department of Microbiology, University of Delhi New Delhi, India
| | - Manish Kumar
- Department of Biophysics, University of Delhi New Delhi, India
| | - Pawan K Kanaujia
- Department of Microbiology, University of Delhi New Delhi, India
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30
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Saracli M. MALDI-TOF MS: A Rapid and New Approach in Fungal Diagnosis and Susceptibility Testing. Med Mycol 2015. [DOI: 10.1201/b18707-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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31
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Galán F, García-Agudo L, Guerrero I, Marín P, García-Tapia A, García-Martos P, Rodríguez-Iglesias M. Evaluación de la espectrometría de masas en la identificación de levaduras de interés clínico. Enferm Infecc Microbiol Clin 2015; 33:372-8. [DOI: 10.1016/j.eimc.2014.10.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 07/29/2014] [Accepted: 10/01/2014] [Indexed: 10/24/2022]
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32
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Becker PT, Stubbe D, Claessens J, Roesems S, Bastin Y, Planard C, Cassagne C, Piarroux R, Hendrickx M. Quality control in culture collections: Confirming identity of filamentous fungi by MALDI-TOF MS. MYCOSCIENCE 2015. [DOI: 10.1016/j.myc.2014.08.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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33
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Relloso MS, Nievas J, Fares Taie S, Farquharson V, Mujica MT, Romano V, Zarate MS, Smayevsky J. Evaluación de la espectrometría de masas: MALDI-TOF MS para la identificación rápida y confiable de levaduras. Rev Argent Microbiol 2015; 47:103-7. [DOI: 10.1016/j.ram.2015.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 02/03/2015] [Accepted: 02/04/2015] [Indexed: 11/29/2022] Open
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34
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Kelly MS, Benjamin DK, Smith PB. The epidemiology and diagnosis of invasive candidiasis among premature infants. Clin Perinatol 2015; 42:105-17, viii-ix. [PMID: 25677999 PMCID: PMC4328135 DOI: 10.1016/j.clp.2014.10.008] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Invasive candidiasis is a leading infectious cause of morbidity and mortality in premature infants. Improved recognition of modifiable risk factors and antifungal prophylaxis has contributed to the recent decline in the incidence of this infection among infants. Invasive candidiasis typically occurs in the first 6 weeks of life and presents with nonspecific signs of sepsis. Definitive diagnosis relies on the growth of Candida in blood culture or cultures from other normally sterile sites, but this may identify fewer than half of cases. Improved diagnostics are needed to guide the initiation of antifungal therapy in premature infants.
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Affiliation(s)
- Matthew S. Kelly
- Duke Clinical Research Institute, Durham, North Carolina
- Department of Pediatrics, Duke University, Durham, North Carolina
| | - Daniel K. Benjamin
- Duke Clinical Research Institute, Durham, North Carolina
- Department of Pediatrics, Duke University, Durham, North Carolina
| | - P. Brian Smith
- Duke Clinical Research Institute, Durham, North Carolina
- Department of Pediatrics, Duke University, Durham, North Carolina
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35
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Karimi L, Mirhendi H, Khodadadi H, Mohammadi R. Molecular identification of uncommon clinical yeast species in Iran. Curr Med Mycol 2015; 1:1-6. [PMID: 28680981 PMCID: PMC5490306 DOI: 10.18869/acadpub.cmm.1.2.1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Background and Purpose: By using advanced detection/identification methods, the list of emerging uncommon opportunistic yeast infections is rapidly expanding worldwide. Our aim in the present study was sequence-based species delineation of previously unidentified yeasts obtained from a clinically yeast collection. Materials and Methods: A total of twenty three out of the 855 (5.7%) yeast isolates which formerly remained unidentified by PCR-RFLP method, were subjected to sequence analysis of the entire internal transcribed spacers (ITS) regions of rDNA. The precise species recognition was performed by the comparison of the sequences with the reliable GenBank database. Results: Sequencing analysis of the ITS region of the strains revealed several uncommon yeasts that were not reported previously in Iran. The species include Hanseniaspora uvarum, Saccharomyces cerevisiae, Sporidiobolus salmonicolor, Pichia fabianii, Pichia fermentans, Candida famata, Candida inconspicua, Candida maqnoliae, Candida guilliermondii, Candida kefyr, Candida rugosa, Candida lusitaniae, Candida orthopsilosis, and Candida viswanathii. Conclusion: We identified several rare clinical isolates selected from a big collection at the species level by ITS-sequencing. As the list of yeast species as opportunistic human fungal infections is increasing dramatically, and many isolates remain unidentified using conventional methods, more sensitive and specific advanced approaches help us to clarify the aspects of microbial epidemiology of the yeast infections.
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Affiliation(s)
- L Karimi
- Dr. Beheshti Hospital, Social Security Organization, Shiraz, Iran
| | - H Mirhendi
- Department of Medical Parasitology and Mycology, School of Public Health, National Institute of Health Research, Tehran University of Medical Sciences, Tehran, Iran
| | - H Khodadadi
- Department of Medical Parasitology and Mycology, School of Medicine; Shiraz University of Medical Sciences, Shiraz, Iran
| | - R Mohammadi
- Department of Medical Parasitology and Mycology, School of Medicine; Isfahan University of Medical Sciences
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36
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Becker PT, de Bel A, Martiny D, Ranque S, Piarroux R, Cassagne C, Detandt M, Hendrickx M. Identification of filamentous fungi isolates by MALDI-TOF mass spectrometry: clinical evaluation of an extended reference spectra library. Med Mycol 2014; 52:826-34. [DOI: 10.1093/mmy/myu064] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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37
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Chao QT, Lee TF, Teng SH, Peng LY, Chen PH, Teng LJ, Hsueh PR. Comparison of the accuracy of two conventional phenotypic methods and two MALDI-TOF MS systems with that of DNA sequencing analysis for correctly identifying clinically encountered yeasts. PLoS One 2014; 9:e109376. [PMID: 25330370 PMCID: PMC4199611 DOI: 10.1371/journal.pone.0109376] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 09/03/2014] [Indexed: 01/21/2023] Open
Abstract
We assessed the accuracy of species-level identification of two commercially available matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) systems (Bruker Biotyper and Vitek MS) and two conventional phenotypic methods (Phoenix 100 YBC and Vitek 2 Yeast ID) with that of rDNA gene sequencing analysis among 200 clinical isolates of commonly encountered yeasts. The correct identification rates of the 200 yeast isolates to species or complex (Candida parapsilosis complex, C. guilliermondii complex and C. rugosa complex) levels by the Bruker Biotyper, Vitek MS (using in vitro devices [IVD] database), Phoenix 100 YBC and Vitek 2 Yeast ID (Sabouraud's dextrose agar) systems were 92.5%, 79.5%, 89%, and 74%, respectively. An additional 72 isolates of C. parapsilosis complex and 18 from the above 200 isolates (30 in each of C. parapsilosis, C. metapsilosis, and C. orthopsilosis) were also evaluated separately. Bruker Biotyper system could accurately identify all C. parapsilosis complex to species level. Using Vitek 2 MS (IVD) system, all C. parapsilosis but none of C. metapsilosis, or C. orthopsilosis could be accurately identified. Among the 89 yeasts misidentified by the Vitek 2 MS (IVD) system, 39 (43.8%), including 27 C. orthopsilosis isolates, could be correctly identified Using the Vitek MS Plus SARAMIS database for research use only. This resulted in an increase in the rate of correct identification of all yeast isolates (87.5%) by Vitek 2 MS. The two species in C. guilliermondii complex (C. guilliermondii and C. fermentati) isolates were correctly identified by cluster analysis of spectra generated by the Bruker Biotyper system. Based on the results obtained in the current study, MALDI-TOF MS systems present a promising alternative for the routine identification of yeast species, including clinically commonly and rarely encountered yeast species and several species belonging to C. parapsilosis complex, C. guilliermondii complex, and C. rugosa complex.
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Affiliation(s)
- Qiao-Ting Chao
- Departments of Laboratory Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Tai-Fen Lee
- Departments of Laboratory Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan; Department and Graduate Institute of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Shih-Hua Teng
- Department of Graduate Institute of Biomedical Sciences, Chang Gung University, Tao-Yuan, Taiwan; Bruker Taiwan Co., Ltd., Taipei, Taiwan
| | - Li-Yun Peng
- Departments of Laboratory Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Ping-Hung Chen
- Departments of Laboratory Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Lee-Jene Teng
- Departments of Laboratory Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan; Department and Graduate Institute of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Po-Ren Hsueh
- Departments of Laboratory Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan; Departments of and Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
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38
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Sanata B, Salam OA, Ibrahim S, Adama Z, Mamoudou C, Simplice KD, Jacques S, Robert GT, Christophe H. Digestive fungal flora in asymptomatic subjects in Bobo-Dioulasso, Burkina Faso. Asian Pac J Trop Biomed 2014; 4:659-62. [PMID: 25183337 DOI: 10.12980/apjtb.4.201414b27] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Accepted: 07/15/2014] [Indexed: 10/24/2022] Open
Abstract
OBJECTIVE To identify Candida species in asymptomatic subjects in Bobo-Dioulasso (Burkina Faso) by the matrix-assisted laser desorption ionization-time of flight mass spectrometry. METHODS A cross-sectional study was conducted from January to February 2013 in Bobo-Dioulasso to collect fecal and urine specimens from voluntary donors. Fungal strains were isolated on Sabouraud dextrose agar and analyzed using matrix-assisted laser desorption ionisation-time-of-flight mass spectrometry. RESULTS A total of 135 samples including stools (78.5%, 106/135) and urine (21.5%, 29/135) were analyzed. The results revealed that fecal specimens contained mainly Candida krusei (C. krusei) (42.5%) followed by Candida albicans (29.3%), Candida glabrata (18.0%) and Candida tropicalis (C. tropicalis) (4.7%). C. krusei (34.6%) was also found to be the most frequently identified in urine samples followed by Candida albicans (27.0%), C. tropicalis (15.4%) and Candida parapsilosis. However, uncommon species such as Candida nivariensis, Candida kefyr, Candida norvegensis, Candida parapsilosis, Candida lusitaniae and Candida robusta were also identified from fecal and urines samples. CONCLUSIONS This study noted the emergence of species such as C. krusei, Candida glabrata, Candida parapsiolosis, C. tropicalis, Candida nivariensis, Candida norvegensis, and others. It is an imperative to take into account the existence of these species in the therapeutic management of patients in Bobo-Dioulasso.
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Affiliation(s)
- Bamba Sanata
- Department of Parasitology-Mycology, University Hospital Sanou Souro, Bobo-Dioulasso, Burkina Faso ; Department of Parasitology-Mycology, Higher Institute of Health Sciences, Polytechnic University of Bobo-Dioulasso, Burkina Faso
| | - Ouédraogo Abdoul Salam
- Department of Bacteriology-Virology, Higher Institute of Health Sciences, Polytechnic University of Bobo-Dioulasso, Burkina Faso
| | - Sangaré Ibrahim
- Department of Parasitology-Mycology, University Hospital Sanou Souro, Bobo-Dioulasso, Burkina Faso ; Department of Parasitology-Mycology, Higher Institute of Health Sciences, Polytechnic University of Bobo-Dioulasso, Burkina Faso
| | - Zida Adama
- Faculty of Health Sciences, University of Ouagadougou, Burkina Faso
| | - Cissé Mamoudou
- Department of Parasitology-Mycology, Higher Institute of Health Sciences, Polytechnic University of Bobo-Dioulasso, Burkina Faso
| | - Karou D Simplice
- Biomolecular Research Center Pietro Annigoni (CERBA/LABIOGENE), Ouagadougou, Burkina Faso
| | - Simpore Jacques
- Biomolecular Research Center Pietro Annigoni (CERBA/LABIOGENE), Ouagadougou, Burkina Faso
| | - Guiguemdé T Robert
- Department of Parasitology-Mycology, Higher Institute of Health Sciences, Polytechnic University of Bobo-Dioulasso, Burkina Faso
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Genetic diversity among Candida albicans isolates associated with vertical transmission in preterm triplets. Mycopathologia 2014; 178:285-90. [PMID: 25151365 DOI: 10.1007/s11046-014-9803-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 08/13/2014] [Indexed: 01/11/2023]
Abstract
We report a case of congenital candidiasis in triplets, in the context of premature labor at 25 weeks gestation, without symptomatic vaginitis or chorioamnionitis. All three infants died as a result of prematurity, aggravated by systemic candidiasis. Multi-locus sequence typing confirmed vertical transmission of Candida albicans from the mother to the triplets and revealed a slight diversity among the strains isolated from the neonates.
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40
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Jamal WY, Ahmad S, Khan ZU, Rotimi VO. Comparative evaluation of two matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) systems for the identification of clinically significant yeasts. Int J Infect Dis 2014; 26:167-70. [PMID: 25080355 DOI: 10.1016/j.ijid.2014.05.031] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 05/30/2014] [Indexed: 01/08/2023] Open
Abstract
OBJECTIVES To prospectively evaluate the performance of two matrix-assisted laser desorption/ionization time-of-flight mass spectrometry systems (MALDI-TOF MS) for the identification of clinically significant yeast isolates compared to the VITEK 2 system. METHODS One hundred and eighty-eight consecutive yeast isolates were analyzed by Bruker Biotyper and VITEK MS. The results were compared with the conventional VITEK 2 yeast identification system. Discrepant results were resolved by direct sequencing of rDNA. RESULTS Accurate identification by VITEK 2, VITEK MS, and Bruker Biotyper MS was 94.1% (177/188), 93.0% (175/188), and 92.6% (174/188), respectively. Three isolates were not identified by VITEK MS, while nine Candida orthopsilosis were misidentified as Candida parapsilosis, as this species is not present in its database. Eleven isolates were not identified or were wrongly identified by Bruker Biotyper and although another 14 were correctly identified, the score was unreliable at <1.7. CONCLUSION The overall accuracy of rapid MALDI-TOF MS systems was essentially comparable to that of the conventional VITEK 2 yeast identification system. However, future expansion of the databases may further improve the outcome and accuracy of identification of yeast species.
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Affiliation(s)
- W Y Jamal
- Department of Microbiology, Faculty of Medicine, Kuwait University, PO Box 24923, Safat 13110, Kuwait; Microbiology Unit, Mubarak Al Kabir Hospital, Jabriya, Kuwait.
| | - S Ahmad
- Department of Microbiology, Faculty of Medicine, Kuwait University, PO Box 24923, Safat 13110, Kuwait; Microbiology Unit, Mubarak Al Kabir Hospital, Jabriya, Kuwait
| | - Z U Khan
- Department of Microbiology, Faculty of Medicine, Kuwait University, PO Box 24923, Safat 13110, Kuwait; Microbiology Unit, Mubarak Al Kabir Hospital, Jabriya, Kuwait
| | - V O Rotimi
- Department of Microbiology, Faculty of Medicine, Kuwait University, PO Box 24923, Safat 13110, Kuwait; Microbiology Unit, Mubarak Al Kabir Hospital, Jabriya, Kuwait
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Microbial typing by matrix-assisted laser desorption ionization-time of flight mass spectrometry: do we need guidance for data interpretation? J Clin Microbiol 2014; 53:760-5. [PMID: 25056329 DOI: 10.1128/jcm.01635-14] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The integration of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) in clinical microbiology has revolutionized species identification of bacteria, yeasts, and molds. However, beyond straightforward identification, the method has also been suggested to have the potential for subspecies-level or even type-level epidemiological analyses. This minireview explores MALDI-TOF MS-based typing, which has already been performed on many clinically relevant species. We discuss the limits of the method's resolution and we suggest interpretative criteria allowing valid comparison of strain-specific data. We conclude that guidelines for MALDI-TOF MS-based typing can be developed along the same lines as those used for the interpretation of data from pulsed-field gel electrophoresis (PFGE).
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42
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Fast and accurate identification of dermatophytes by matrix-assisted laser desorption ionization-time of flight mass spectrometry: validation in the clinical laboratory. J Clin Microbiol 2014; 52:3440-3. [PMID: 25031434 DOI: 10.1128/jcm.01428-14] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The performance of a matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) workflow using an extensive reference database for dermatophyte identification was evaluated on 176 clinical strains. Using a direct-deposit procedure after 3 incubation days yielded 40% correct identification. Both increasing incubation time and using an extraction procedure resulted in 100% correct identification.
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Accuracy of matrix-assisted laser desorption ionization-time of flight mass spectrometry for identification of clinical pathogenic fungi: a meta-analysis. J Clin Microbiol 2014; 52:2573-82. [PMID: 24829234 DOI: 10.1128/jcm.00700-14] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Fungal infections in the clinic have become increasingly serious. In many cases, the identification of clinically relevant fungi remains time-consuming and may also be unreliable. Matrix-assisted laser desorption ionization-time of flight mass spectroscopy (MALDI-TOF MS) is a newly developed diagnostic tool that is increasingly being employed to rapidly and accurately identify clinical pathogenic microorganisms. The present meta-analysis aimed to systematically evaluate the accuracy of MALDI-TOF MS for the identification of clinical pathogenic fungi. After a rigorous selection process, 33 articles, involving 38 trials and a total of 9,977 fungal isolates, were included in the meta-analysis. The random-effects pooled identification accuracy of MALDI-TOF MS increased from 0.955 (95% confidence interval [CI], 0.939 to 0.969) at the species level to 0.977 (95% CI, 0.955 to 0.993) at the genus level (P < 0.001; χ(2) = 15.452). Subgroup analyses were performed at the species level for several categories, including strain, source of strain, system, system database, and modified outcomes, to calculate the accuracy and to investigate heterogeneity. These analyses revealed significant differences between the overall meta-analysis and some of the subanalyses. In parallel, significant differences in heterogeneity among different systems and among different methods for calculating the identification ratios were found by multivariate metaregression, but none of the factors, except for the moderator of outcome, was significantly associated with heterogeneity by univariate metaregression. In summary, the MALDI-TOF MS method is highly accurate for the identification of clinically pathogenic fungi; future studies should analyze the comprehensive capability of this technology for clinical diagnostic microbiology.
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Lackner M, Caramalho R, Lass-Flörl C. Laboratory diagnosis of mucormycosis: current status and future perspectives. Future Microbiol 2014; 9:683-95. [DOI: 10.2217/fmb.14.23] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
ABSTRACT: Fungal infections caused by members of the Mucorales order are rapidly progressing and fatal. The importance of mucormycosis has grown in recent years as the number of patients with predisposing factors has increased dramatically. Clinical symptoms are elusive and conventional techniques are often insensitive and unspecific; in particular, cultures are often negative even though direct microscopy is positive. For early diagnosis of the causative agent of disease and subsequently guiding therapy to improving patients’ outcome, molecular assays are promising add-ons. This article provides an overview on current laboratory methods for diagnosing mucormycosis with a special focus on new molecular-based tools. We aim to highlight the pros and cons of various techniques at hand. Given the increase in number and the severity of these infections, molecular approaches for improved diagnosis are highly warranted.
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Affiliation(s)
- Michaela Lackner
- Division of Hygiene and Medical Microbiology, Innsbruck Medical University, Schöpfstrasse 41, 6020 Innsbruck, Austria
| | - Rita Caramalho
- Division of Hygiene and Medical Microbiology, Innsbruck Medical University, Schöpfstrasse 41, 6020 Innsbruck, Austria
| | - Cornelia Lass-Flörl
- Division of Hygiene and Medical Microbiology, Innsbruck Medical University, Schöpfstrasse 41, 6020 Innsbruck, Austria
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Duran-Valle MT, Sanz-Rodriguez N, Munoz-Paraiso C, Almagro-Molto M, Gomez-Garces JL. Identification of clinical yeasts by Vitek MS system compared with API ID 32 C. Med Mycol 2014; 52:342-9. [DOI: 10.1093/mmy/myt036] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Development and validation of an in-house database for matrix-assisted laser desorption ionization-time of flight mass spectrometry-based yeast identification using a fast protein extraction procedure. J Clin Microbiol 2014; 52:1453-8. [PMID: 24554755 DOI: 10.1128/jcm.03355-13] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
In recent studies evaluating the usefulness of the matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)-based identification of yeasts for the routine diagnosis of fungal infections, preanalytical sample processing has emerged as a critical step for reliable MALDI-TOF MS outcomes, especially when the Bruker Daltonics Biotyper software was used. In addition, inadequate results often occurred due to discrepancies between the methods used for clinical testing and database construction. Therefore, we created an in-house MALDI-TOF MS library using the spectra from 156 reference and clinical yeast isolates (48 species in 11 genera), which were generated with a fast sample preparation procedure. After a retrospective validation study, our database was evaluated on 4,232 yeasts routinely isolated during a 6-month period and fast prepared for MALDI-TOF MS analysis. Thus, 4,209 (99.5%) of the isolates were successfully identified to the species level (with scores of ≥2.0), with 1,676 (39.6%) having scores of >2.3. For the remaining 23 (0.5%) isolates, no reliable identification (with scores of <1.7) was obtained. Interestingly, these isolates were almost always from species uniquely represented or not included in the database. As the MALDI-TOF MS results were, except for 23 isolates, validated without additional phenotypic or molecular tests, our proposed strategy can enhance the rapidity and accuracy of MALDI-TOF MS in identifying medically important yeast species. However, while continuous updating of our database will be necessary to enrich it with more strains/species of new and emerging yeasts, the present in-house MALDI-TOF MS library can be made publicly available for future multicenter studies.
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Kolecka A, Khayhan K, Arabatzis M, Velegraki A, Kostrzewa M, Andersson A, Scheynius A, Cafarchia C, Iatta R, Montagna M, Youngchim S, Cabañes F, Hoopman P, Kraak B, Groenewald M, Boekhout T. Efficient identification ofMalasseziayeasts by matrix‐assisted laser desorption ionization‐time of flight mass spectrometry (MALDI‐TOF MS). Br J Dermatol 2014; 170:332-41. [DOI: 10.1111/bjd.12680] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/05/2013] [Indexed: 12/15/2022]
Affiliation(s)
- A. Kolecka
- Department of Yeast and Basidiomycete Research CBS‐KNAW Fungal Biodiversity Centre Uppsalalaan 8 3584CT Utrecht the Netherlands
| | - K. Khayhan
- Department of Yeast and Basidiomycete Research CBS‐KNAW Fungal Biodiversity Centre Uppsalalaan 8 3584CT Utrecht the Netherlands
- Department of Microbiology and Parasitology Faculty of Medical Sciences University of Phayao Phayao Thailand
| | - M. Arabatzis
- Research Mycology Laboratory (K.A. 70/3/6915) Microbiology Department Medical School of University of Athens Athens Greece
| | - A. Velegraki
- Research Mycology Laboratory (K.A. 70/3/6915) Microbiology Department Medical School of University of Athens Athens Greece
| | - M. Kostrzewa
- Bioanalytical Development Bruker Daltonics GmbH Bremen Germany
| | - A. Andersson
- Translational Immunology Unit Department of Medicine Solna Karolinska Institutet Stockholm Sweden
| | - A. Scheynius
- Translational Immunology Unit Department of Medicine Solna Karolinska Institutet Stockholm Sweden
| | - C. Cafarchia
- Department of Veterinary Medicine Aldo Moro University of Bari Bari Italy
| | - R. Iatta
- Department of Veterinary Medicine Aldo Moro University of Bari Bari Italy
| | - M.T. Montagna
- Department of Biomedical Science and Human Oncology Section of Hygiene Aldo Moro University of Bari Bari Italy
| | - S. Youngchim
- Department of Microbiology Faculty of Medicine Chiang Mai University Chiang Mai Thailand
| | - F.J. Cabañes
- Department of Animal Health and Anatomy Universitat Autònoma de Barcelona Bellaterra Barcelona Spain
| | - P. Hoopman
- Department of Yeast and Basidiomycete Research CBS‐KNAW Fungal Biodiversity Centre Uppsalalaan 8 3584CT Utrecht the Netherlands
| | - B. Kraak
- Department of Yeast and Basidiomycete Research CBS‐KNAW Fungal Biodiversity Centre Uppsalalaan 8 3584CT Utrecht the Netherlands
| | - M. Groenewald
- Department of Yeast and Basidiomycete Research CBS‐KNAW Fungal Biodiversity Centre Uppsalalaan 8 3584CT Utrecht the Netherlands
| | - T. Boekhout
- Department of Yeast and Basidiomycete Research CBS‐KNAW Fungal Biodiversity Centre Uppsalalaan 8 3584CT Utrecht the Netherlands
- Department of Internal Medicine and Infectious Diseases University Medical Center Utrecht the Netherlands
- Department of Dermatology Shanghai Key Laboratory of Molecular Medical Mycology Second Military Medical University Changzheng Hospital Institute of Dermatology and Medical Mycology Shanghai China
- Institute of Microbiology Chinese Academy of Sciences Beijing China
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Lacroix C, Gicquel A, Sendid B, Meyer J, Accoceberry I, François N, Morio F, Desoubeaux G, Chandenier J, Kauffmann-Lacroix C, Hennequin C, Guitard J, Nassif X, Bougnoux ME. Evaluation of two matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) systems for the identification of Candida species. Clin Microbiol Infect 2014; 20:153-8. [DOI: 10.1111/1469-0691.12210] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 01/27/2013] [Accepted: 02/24/2013] [Indexed: 01/01/2023]
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50
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Evaluation of a short, on-plate formic acid extraction method for matrix-assisted laser desorption ionization-time of flight mass spectrometry-based identification of clinically relevant yeast isolates. J Clin Microbiol 2014; 52:1253-5. [PMID: 24478407 DOI: 10.1128/jcm.03489-13] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
This report describes a short, on-plate formic acid (FA) extraction method for the identification of clinical yeast isolates using matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS). A total of 41.1% (78/190) and 63.7% (121/190) of yeasts were identified using species log score thresholds of >2.0 and >1.9, respectively. Overall, 97.4% (185/190) of yeasts were identified in combination with conventional FA extraction.
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