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Wu C, Ao K, Zheng Y, Jin Y, Liu Y, Chen Z, Li D. Formic acid sandwich method is well-suited for filamentous fungi identification and improves turn around time using Zybio EXS2600 mass spectrometry. BMC Microbiol 2024; 24:238. [PMID: 38961393 PMCID: PMC11220970 DOI: 10.1186/s12866-024-03394-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 06/20/2024] [Indexed: 07/05/2024] Open
Abstract
OBJECTIVES Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is extensively employed for the identification of filamentous fungi on MALDI Biotyper (Bruker Daltonics) and Vitek MS (biomerieux), but the performance of fungi identification on new EXS2600 (Zybio) is still unknow. Our study aims to evaluate the new EXS2600 system's (Zybio) ability to rapidly identify filamentous fungi and determine its effect on turnaround time (TAT) in our laboratory. METHODS We tested 117 filamentous fungi using two pretreatment methods: the formic acid sandwich (FA-sandwich) and a commercial mold extraction kit (MEK, Zybio). All isolates were confirmed via sequence analysis. Laboratory data were extracted from our laboratory information system over two 9-month periods: pre-EXS (April to December 2022) and post-EXS (April to December 2023), respectively. RESULTS The total correct identification (at the species, genus, or complex/group level) rate of fungi was high, FA-sandwich (95.73%, 112/117), followed by MEK (94.02%, 110/117). Excluding 6 isolates not in the database, species-level identification accuracy was 92.79% (103/111) for FA-sandwich and 91.89% (102/111) for MEK; genus-level accuracy was 97.29% (108/111) and 96.39% (107/111), respectively. Both methods attained a 100% correct identification rate for Aspergillus, Lichtheimia, Rhizopus Mucor and Talaromyces species, and were able to differentiate between Fusarium verticillioides and Fusarium proliferatum within the Fusarium fujikuroi species complex. Notably, high confidence was observed in the species-level identification of uncommon fungi such as Trichothecium roseum and Geotrichum candidum. The TAT for all positive cultures decreased from pre EXS2600 to post (108.379 VS 102.438, P < 0.05), and the TAT for tissue decreased most (451.538 VS 222.304, P < 0.001). CONCLUSIONS The FA-sandwich method is more efficient and accurate for identifying filamentous fungi with EXS2600 than the MEK. Our study firstly evaluated the performance of fungi identification on EXS2600 and showed it is suitable for clinical microbiology laboratories use.
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Affiliation(s)
- Chongyang Wu
- Department of Laboratory Medicine, West China Hospital of Sichuan University, Sichuan Province, Chengdu, 610041, P.R. China
| | - Keping Ao
- Department of Laboratory Medicine, West China Hospital of Sichuan University, Sichuan Province, Chengdu, 610041, P.R. China
| | - Yue Zheng
- Department of Laboratory Medicine, Yaan People's Hospital, Yaan, 625000, China
| | - Ying Jin
- Department of Laboratory Medicine, LuZhou Longmatan TCM Hospital, LuZhou, 646000, China
| | - Ya Liu
- Department of Laboratory Medicine, West China Hospital of Sichuan University, Sichuan Province, Chengdu, 610041, P.R. China
| | - Zhixing Chen
- Department of Laboratory Medicine, West China Hospital of Sichuan University, Sichuan Province, Chengdu, 610041, P.R. China
| | - Dongdong Li
- Department of Laboratory Medicine, West China Hospital of Sichuan University, Sichuan Province, Chengdu, 610041, P.R. China.
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Jiang X, Xiao D, Yu H, Sun A, Liu Q, Liu T. Evaluation of pretreatment methods for filamentous fungal detection. Sci Rep 2024; 14:10899. [PMID: 38740854 DOI: 10.1038/s41598-024-61517-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 05/07/2024] [Indexed: 05/16/2024] Open
Abstract
In order to obtain the best mass spectrometry identification results for using the most appropriate methods in clinical practice, we explore the optimal pretreatment methods for different species and morphologies of filamentous fungi. 98 fungal strains were treated with formic acid sandwich method, dispersion method, extraction method, and other methods using a medium element mass spectrometer (EXS3000) as a platform. Each strain had three targets, and the identification rates and confidence differences under different pre-treatment methods were compared to evaluate the identification effects of these methods. The mass spectrometry identification rates of 98 filamentous fungi obtained after pre-treatment with formic acid sandwich method, dispersion method, and extraction method were 85.71%, 82.65%, and 75.51%, respectively. The identification rate of the formic acid sandwich method was significantly higher than the other two methods (P < 0 005) has the best identification ability and the obtained confidence is also higher than the other two methods. The use of formic acid sandwich method for mass spectrometry identification of filamentous fungi can achieve ideal identification results, which is suitable for mass spectrometry identification of filamentous fungi in conventional laboratories.
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Affiliation(s)
- Xiaoli Jiang
- Department of Experimental Medicine, The People's Hospital of Jianyang City, Chengdu, 641400, China.
| | - Daiwen Xiao
- Department of Laboratory Medicine and Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, China
| | - Hua Yu
- Department of Laboratory Medicine and Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, China
| | - Anhua Sun
- Department of Experimental Medicine, The People's Hospital of Jianyang City, Chengdu, 641400, China
| | - Qin Liu
- Department of Experimental Medicine, The People's Hospital of Jianyang City, Chengdu, 641400, China
| | - Tao Liu
- Department of Experimental Medicine, The People's Hospital of Jianyang City, Chengdu, 641400, China
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Kabtani J, Boulanouar F, Militello M, Cassagne C, Ranque S. Candida massiliensis sp. nov. Isolated from a Clinical Sample. Mycopathologia 2023; 188:957-971. [PMID: 37728680 DOI: 10.1007/s11046-023-00792-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 08/28/2023] [Indexed: 09/21/2023]
Abstract
The majority of Candida species are known as non-pathogenic yeasts and rarely involved in human diseases. However, recently case reports of human infections caused by non-albicans Candida species have increased, mostly in immunocompromised hosts. Our study aimed to describe and characterize as thoroughly as possible, a new species of the Metschnikowia clade, named here Candida massiliensis (PMML0037), isolated from a clinical sample of human sputum. We targeted four discriminant genetic regions: "Internal Transcribed Spacers" of rRNA, D1/D2 domains (28S large subunit rRNA) and part of the genes encoding Translation Elongation Factor 1-α and β-tubulin2. The genetic data were compared to morphological characters, from scanning electron microscopy (TM 4000 Plus, SU5000), physiological, including the results of oxidation and assimilation tests of different carbon sources by the Biolog system, and chemical mapping by Energy-Dispersive X-ray Spectroscopy. Lastly, the in vitro antifungal susceptibility profile was performed using the E-test™ exponential gradient method. The multilocus analysis supported the genetic position of Candida massiliensis (PMML0037) as a new species of the Metschnikowia clade, and the phenotypic analysis highlighted its unique morphological and chemical profile when compared to the other Candida/Metschnikowia species included in the study.
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Affiliation(s)
| | | | - Muriel Militello
- IHU Méditerranée Infection, 13005, Marseille, France
- AP-HM, IRD, SSA, MEPHI, Aix-Marseille Université, 13005, Marseille, France
| | - Carole Cassagne
- IHU Méditerranée Infection, 13005, Marseille, France
- AP-HM, IRD, SSA, VITROME, Aix-Marseille Université, 13005, Marseille, France
| | - Stéphane Ranque
- IHU Méditerranée Infection, 13005, Marseille, France.
- AP-HM, IRD, SSA, VITROME, Aix-Marseille Université, 13005, Marseille, France.
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Lee EH, Choi MH, Lee KH, Song YG, Han SH. Differences of clinical characteristics and outcome in proven invasive Trichosporon infections caused by asahii and non-asahii species. Mycoses 2023; 66:992-1002. [PMID: 37515448 DOI: 10.1111/myc.13635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/22/2023] [Accepted: 07/23/2023] [Indexed: 07/30/2023]
Abstract
BACKGROUND Trichosporon is an emerging yeast that causes invasive infections in immunocompromised patients experiencing prolonged hospitalisation, indwelling venous catheters and neutropenia. METHODS This retrospective observational cohort study analysed invasive Trichosporon infections (ITIs) occurring between January 2005 and December 2022 at three tertiary hospitals and compared the clinical characteristics and prognostic factors of ITIs caused by Trichosporon asahii and non-T. asahii spp. After evaluating 1067 clinical isolates, we identified 46 patients with proven ITIs, defined as cases in which Trichosporon was isolated from blood, cerebrospinal fluid, or sterile tissues. RESULTS The patients were separated into T. asahii and non-T. asahii groups containing 25 and 21 patients, respectively, all of which except one were immunocompromised. During this period, both the number of clinical isolates and patients with ITIs (mainly T. asahii) increased; whereas, cases involving non-T. asahii spp. decreased. Compared with the non-T. asahii group, the T. asahii group had more patients with multiple catheters (84% vs. 33%, p = .001) and those receiving renal replacement therapy (48% vs. 14%, p = .005). The all-cause 28-day mortality rate after ITI in the T. asahii group (44%) was significantly higher than in the non-T. asahii group (10%, Log-rank p = .014). The multivariate Cox regression model revealed that T. asahii (reference, non-T. asahii spp.; aHR = 4.3; 95% CI = 1.2-15.2, p = .024) and neutropenia for 5 days or more (aHR = 2.2, 95% CI = 1.5-3.6, p = .035) were independent factors in the 28-day mortality after ITI. CONCLUSION The proven ITIs due to T. asahii produced more unfavourable outcomes compared with ITIs caused by non-T. asahii spp.
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Affiliation(s)
- Eun Hwa Lee
- Division of Infectious Disease, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Min Hyuk Choi
- Department of Laboratory Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Kyoung Hwa Lee
- Division of Infectious Disease, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Young Goo Song
- Division of Infectious Disease, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Sang Hoon Han
- Division of Infectious Disease, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
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Taverna CG, Vivot ME, Arias BA, Irazu L, Canteros CE. Evaluation of the CHROMagar Candida Plus medium for presumptive identification of yeasts and MALDI-TOF MS identification. Mycoses 2023; 66:977-983. [PMID: 37518770 DOI: 10.1111/myc.13633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 07/12/2023] [Accepted: 07/15/2023] [Indexed: 08/01/2023]
Abstract
Rapid and accurate yeasts species identification in clinical laboratories is important for appropriate and timely antifungal treatment. We evaluate the performance of the new medium CHROMagar™ Candida Plus for presumptive identification of yeasts species and MALDI-TOF identification. We identify 303 strains belonging to 60 clinically relevant yeasts species by using the new medium. Presumptive identification was correct at the Candida albicans complex, Candida tropicalis and Pichia kudriavzevii (Candida krusei) species. However, although this medium was able to identify all Candida auris and Candida glabrata strains, other species were misidentified as C. auris or C. glabrata. A total of 215 strains were identified by using MALDI-TOF and evaluated two incubation temperatures (30°C and 37°C) and two incubation times (24 h and 72 h). Most strains (94%; 202/215) were correctly identified at the species (n:190) or complex level (n:12) at both temperatures and incubation times. However, we observed that the time of incubation (24 h vs. 72 h) affects the score values when yeasts are incubated at 37°C, but does not affect score values when yeasts are incubated at 30°C. In conclusion, the new medium has a good performance in the presumptive identification of the C. albicans complex, C. tropicalis and P. kudriavzevii (C. krusei). In addition, this medium is useful for the screening of C. auris and C. glabrata isolates, but identification should be confirmed by other more specific techniques, like MALDI-TOF.
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Affiliation(s)
- Constanza Giselle Taverna
- Departamento Micología, Instituto Nacional de Enfermedades Infecciosas "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Matías Ezequiel Vivot
- Departamento Micología, Instituto Nacional de Enfermedades Infecciosas "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Bárbara Abigail Arias
- Departamento Micología, Instituto Nacional de Enfermedades Infecciosas "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Lucia Irazu
- Departamento de Parasitología, Instituto Nacional de Enfermedades Infecciosas "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Cristina Elena Canteros
- Departamento Micología, Instituto Nacional de Enfermedades Infecciosas "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
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Jeraldine DVM, Wim L, Ellen VE. A comparative study for optimization of MALDI-TOF MS identification of filamentous fungi. Eur J Clin Microbiol Infect Dis 2023; 42:1153-1161. [PMID: 37592107 DOI: 10.1007/s10096-023-04652-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 08/07/2023] [Indexed: 08/19/2023]
Abstract
PURPOSE To evaluate and compare the performance of three commercial culture media, two filamentous fungi libraries, and two different protein extraction procedures in MALDI-TOF MS fungal identification. METHODS A total of 21 quality control samples were cultured on Sabouraud dextrose agar (SDA), ID fungi plate medium (IDFP), and Sabouraud gentamicin chloramphenicol 2 agar (SGC2). For four consecutive days, fungal growths were inoculated on a MALDI target plate both by using a direct transfer technique (DT) and by using a formic acid-ethanol protein extraction procedure (EEP). The MALDI-TOF MS-generated spectra were identified by the MBT Bruker library and the MSI database. RESULTS Selective culture media (IDFP and SGC2) significantly outperformed the non-selective SDA medium. IDFP was superior to the SGC2 medium for dermatophyte identification. The EEP only demonstrated a benefit over DT in the underperforming SDA medium. The MBT Bruker library outperformed the MSI database in Aspergillus identification while the MSI database outperformed the MBT library in dermatophyte identification. For non-Aspergillus fungi, the libraries performed comparably. CONCLUSION The results of our study show the necessity of using selective culture media (IDFP and SGC2) for fungal identification with MALDI-TOF MS and demonstrate no significant benefit of the formic acid-ethanol protein extraction technique in these media. Given the relative strengths and weaknesses of the MBT library and the MSI database, it might currently be beneficial to consider these libraries as complementary and employ both databases to achieve optimal fungal identification.
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Affiliation(s)
| | - Laffut Wim
- Heilig Hart Algemeen Ziekenhuis Lier, Mechelsestraat 24, 2500, Lier, Belgium
| | - Van Even Ellen
- Heilig Hart Algemeen Ziekenhuis Lier, Mechelsestraat 24, 2500, Lier, Belgium
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Moreira FM, Pereira PDA, Miranda RVDSLD, Reis CMFD, Braga LMPDS, de Andrade JM, do Nascimento LG, Mattoso JMV, Forsythe SJ, da Costa LV, Brandão MLL. Evaluation of MALDI-TOF MS, sequencing of D2 LSU rRNA and internal transcribed spacer regions (ITS) for the identification of filamentous fungi isolated from a pharmaceutical facility. J Pharm Biomed Anal 2023; 234:115531. [PMID: 37354630 DOI: 10.1016/j.jpba.2023.115531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 06/12/2023] [Accepted: 06/12/2023] [Indexed: 06/26/2023]
Abstract
The identification of filamentous fungi through culture characterization may be hampered by phenotypic variability. Information obtained from the identification of microorganisms are important for investigation of sources of contamination of a product or process. The aim of this study was to identify filamentous fungal strains (n = 50) isolated from a pharmaceutical facility by using Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS), as well as D2 domain of the large-subunit (LSU) ribosomal RNA gene and internal transcribed spacer regions (ITS) sequencing. MALDI-TOF MS system only identified five strains at the species level, while 45 were not identified. The analysis through GenBank allowed the identification of up to 19 strains at the species level, while MycoBank allowed the identification of up to nine strains at the species level. The databases identified up to 11 genera: Penicillium, Aspergillus, Cladosporium, Chaetomium, Coniochaeta, Curvularia, Diaporthe, Fusarium, Trichoderma, Rhizopus and Microdochium. MALDI-TOF MS showed an insufficient database to identify the species of fungi. DNA sequencing was the best methodology to identify to the genus level but was unable to differentiate between closely related species. Therefore further methods for the identification of filamentous fungi from pharmaceutical areas at species level need to be developed.
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Guimarães ML, Júnior MAB, de Almeida VM, Pereira WVS. MALDI-TOF as a tool for microbiological monitoring in areas considered aseptic. Braz J Microbiol 2023; 54:761-768. [PMID: 37160839 PMCID: PMC10235220 DOI: 10.1007/s42770-023-00987-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 04/25/2023] [Indexed: 05/11/2023] Open
Abstract
To maintain asepsis in production environments, contamination must be constantly controlled. To this end, microbiological monitoring is constantly used with the objective of evaluating the incidence of microorganisms prevalent in the sampling of air, surface, and people, in the area of an environment considered aseptic, isolated, and identified using the rapid and automated phenotypic microbiological methodology, highlighting the MALDI-TOF mass spectrometry analysis technique (MS), being identified at the level of genus and/or species. For that purpose, microbiological control of environmental monitoring of environments considered aseptic in a pharmaceutical industry was conducted for 12 months. The isolated microorganisms were identified using the mass spectrometry identification method (MALDI-TOF). In area classification A, the most prevalent microorganisms were bacteria in the sampling person. The microbial population was composed of bacteria of the genus Micrococcus sp. and Staphylococcus sp. Based on the results, it is possible to observe that in an environment where the process requires human operations, possible microbial contamination is inevitable and requires the identification of microorganisms at least at the level of species and/or genus. The microorganisms identified and found in the sampling of the aseptic environment must be evaluated with frequency to ensure that the productive environment guarantees the quality of the product produced.
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Affiliation(s)
- Marlu Lopes Guimarães
- Programa de Pós-Graduação Em Microbiologia, Centro Universitário Funorte, Montes Claros, Minas Gerais, Brazil
| | | | - Vitor Martins de Almeida
- Instituto de Pesquisas de Produtos Naturais Walter Mors - Universidade Federal Do Rio de Janeiro, Rio de Janeiro, Brazil
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Hankins JD, Amerson-Brown MH, Brown CA, Riegler AN, Muldrew KL, Dunn JJ. Comparison of Bruker Biotyper ® and Vitek ® MS matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry platforms for the identification of filamentous fungi. Future Microbiol 2023; 18:553-561. [PMID: 37317856 DOI: 10.2217/fmb-2023-0084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023] Open
Abstract
Aims: To evaluate the performance of two matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry platforms to identify molds isolated from clinical specimens. Methods: Fifty mold isolates were analyzed on Bruker Biotyper® and Vitek® MS platforms. Two Bruker Biotyper extraction protocols were assessed alongside the US FDA-approved extraction protocol for Vitek MS. Results: The Bruker Biotyper modified NIH-developed extraction protocol correctly identified more isolates than Bruker's protocol (56 vs 33%). For species in the manufacturers' databases, Vitek MS correctly identified 85% of isolates, with 8% misidentifications. The Bruker Biotyper identified 64%, with no misidentifications. For isolates not in the databases, the Bruker Biotyper did not misidentify any, and Vitek MS misidentified 36%. Conclusion: Both the Vitek MS and Bruker Biotyper accurately identified the fungal isolates, however Vitek MS was more likely to misidentify isolates than the Bruker Biotyper.
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Affiliation(s)
- Julia D Hankins
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Pathology, Texas Children's Hospital, Houston, TX 77030, USA
| | - Megan H Amerson-Brown
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Pathology, Texas Children's Hospital, Houston, TX 77030, USA
- Department of Pathology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Cameron A Brown
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Pathology, Harris Health Ben Taub Hospital, Houston, TX 77030, USA
| | - Ashleigh N Riegler
- Department of Pathology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Kenneth L Muldrew
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Pathology, Harris Health Ben Taub Hospital, Houston, TX 77030, USA
- Department of Internal Medicine, Infectious Diseases, Baylor College of Medicine, Houston, TX 77030, USA
| | - James J Dunn
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Pathology, Texas Children's Hospital, Houston, TX 77030, USA
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Dubler S, Etringer M, Weigand MA, Brenner T, Zimmermann S, Schnitzler P, Budeus B, Rengier F, Kalinowska P, Hoo YL, Lichtenstern C. Impact of Invasive Pulmonary Aspergillosis in Critically Ill Surgical Patients with or without Solid Organ Transplantation. J Clin Med 2023; 12:jcm12093282. [PMID: 37176722 PMCID: PMC10179688 DOI: 10.3390/jcm12093282] [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: 02/25/2023] [Revised: 04/21/2023] [Accepted: 05/03/2023] [Indexed: 05/15/2023] Open
Abstract
BACKGROUND Critically ill patients, especially those who have undergone solid organ transplantation (SOT), are at risk of invasive pulmonary aspergillosis (IPA). The outcome relevance of adequately treated putative IPA (pIPA) is a matter of debate. The aim of this study is to assess the outcome relevance of pIPA in a cohort of critically ill patients with and without SOT. METHODS Data from 121 surgical critically ill patients with pIPA (n = 30) or non-pIPA (n = 91) were included. Cox regression analysis was used to identify risk factors for mortality and unfavourable outcomes after 28 and 90 days. RESULTS Mortality rates at 28 days were similar across the whole cohort of patients (pIPA: 31% vs. non-pIPA: 27%) and did not differ in the subgroup of patients after SOT (pIPA: 17% vs. non-pIPA: 22%). A higher Sequential Organ Failure Assessment (SOFA) score and evidence of bacteraemia were identified as risk factors for mortality and unfavourable outcome, whereas pIPA itself was not identified as an independent predictor for poor outcomes. CONCLUSIONS Adequately treated pIPA did not increase the risk of death or an unfavourable outcome in this mixed cohort of critically ill patients with or without SOT, whereas higher disease severity and bacteraemia negatively affected the outcome.
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Affiliation(s)
- Simon Dubler
- Department of Anaesthesiology, Heidelberg University Hospital, D-69120 Heidelberg, Germany
- Department of Anesthesiology and Intensive Care Medicine, University Hospital Essen, University Duisburg-Essen, D-45147 Essen, Germany
| | - Michael Etringer
- Department of Anaesthesiology, Heidelberg University Hospital, D-69120 Heidelberg, Germany
| | - Markus A Weigand
- Department of Anaesthesiology, Heidelberg University Hospital, D-69120 Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), University of Heidelberg, D-69120 Heidelberg, Germany
| | - Thorsten Brenner
- Department of Anesthesiology and Intensive Care Medicine, University Hospital Essen, University Duisburg-Essen, D-45147 Essen, Germany
| | - Stefan Zimmermann
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Division Bacteriology, Heidelberg University Hospital, D-69120 Heidelberg, Germany
| | - Paul Schnitzler
- Department of Infectious Diseases, Virology, Heidelberg University Hospital, D-69120 Heidelberg, Germany
| | - Bettina Budeus
- Institute of Cell Biology (Cancer Research), University of Duisburg-Essen, D-45147 Essen, Germany
| | - Fabian Rengier
- Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), University of Heidelberg, D-69120 Heidelberg, Germany
- Clinic for Diagnostic and Interventional Radiology, Heidelberg University Hospital, D-69120 Heidelberg, Germany
| | - Paulina Kalinowska
- Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), University of Heidelberg, D-69120 Heidelberg, Germany
- Clinic for Diagnostic and Interventional Radiology, Heidelberg University Hospital, D-69120 Heidelberg, Germany
| | - Yuan Lih Hoo
- Department of Anaesthesiology, Heidelberg University Hospital, D-69120 Heidelberg, Germany
| | - Christoph Lichtenstern
- Department of Anaesthesiology, Heidelberg University Hospital, D-69120 Heidelberg, Germany
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Ziuzia P, Janiec Z, Wróbel-Kwiatkowska M, Lazar Z, Rakicka-Pustułka M. Honey's Yeast-New Source of Valuable Species for Industrial Applications. Int J Mol Sci 2023; 24:ijms24097889. [PMID: 37175595 PMCID: PMC10178026 DOI: 10.3390/ijms24097889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/21/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
Honey is a rich source of compounds with biological activity; moreover, it is a valuable source of various microorganisms. The aim of this study was to isolate and identify yeast from a sample of lime honey from Poland as well as to assess its ability to biosynthesize value-added chemicals such as kynurenic acid, erythritol, mannitol, and citric acid on common carbon sources. Fifteen yeast strains belonging to the species Yarrowia lipolytica, Candida magnolia, and Starmerella magnoliae were isolated. In shake-flask screening, the best value-added compound producers were chosen. In the last step, scaling up of the culture in the bioreactor was performed. A newly isolated strain of Y. lipolytica No. 12 produced 3.9 mg/L of kynurenic acid growing on fructose. Strain Y. lipolytica No. 9 synthesized 32.6 g/L of erythritol on technical glycerol with a low concentration of byproducts. Strain Y. lipolytica No. 5 produced 15.1 g/L of mannitol on technical glycerol, and strain No. 3 produced a very high amount of citric acid (76.6 g/L) on technical glycerol. In conclusion, to the best of our knowledge this is the first study to report the use of yeast isolates from honey to produce valuable chemicals. This study proves that natural products such as lime honey can be an excellent source of wild-type yeasts with valuable production properties.
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Affiliation(s)
- Patrycja Ziuzia
- Department of Biochemistry and Molecular Biology, Wroclaw University of Environmental and Life Sciences, 31 Norwida St., 50-375 Wroclaw, Poland
| | - Zuzanna Janiec
- Department of Biotechnology and Food Microbiology, Wroclaw University of Environmental and Life Sciences, 37 Chełmońskiego St., 51-630 Wroclaw, Poland
| | - Magdalena Wróbel-Kwiatkowska
- Department of Biotechnology and Food Microbiology, Wroclaw University of Environmental and Life Sciences, 37 Chełmońskiego St., 51-630 Wroclaw, Poland
| | - Zbigniew Lazar
- Department of Biotechnology and Food Microbiology, Wroclaw University of Environmental and Life Sciences, 37 Chełmońskiego St., 51-630 Wroclaw, Poland
| | - Magdalena Rakicka-Pustułka
- Department of Biotechnology and Food Microbiology, Wroclaw University of Environmental and Life Sciences, 37 Chełmońskiego St., 51-630 Wroclaw, Poland
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12
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Stemler J, Többen C, Lass-Flörl C, Steinmann J, Ackermann K, Rath PM, Simon M, Cornely OA, Koehler P. Diagnosis and Treatment of Invasive Aspergillosis Caused by Non- fumigatus Aspergillus spp. J Fungi (Basel) 2023; 9:jof9040500. [PMID: 37108955 PMCID: PMC10141595 DOI: 10.3390/jof9040500] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 03/27/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
With increasing frequency, clinical and laboratory-based mycologists are consulted on invasive fungal diseases caused by rare fungal species. This review aims to give an overview of the management of invasive aspergillosis (IA) caused by non-fumigatus Aspergillus spp.-namely A. flavus, A. terreus, A. niger and A. nidulans-including diagnostic and therapeutic differences and similarities to A. fumigatus. A. flavus is the second most common Aspergillus spp. isolated in patients with IA and the predominant species in subtropical regions. Treatment is complicated by its intrinsic resistance against amphotericin B (AmB) and high minimum inhibitory concentrations (MIC) for voriconazole. A. nidulans has been frequently isolated in patients with long-term immunosuppression, mostly in patients with primary immunodeficiencies such as chronic granulomatous disease. It has been reported to disseminate more often than other Aspergillus spp. Innate resistance against AmB has been suggested but not yet proven, while MICs seem to be elevated. A. niger is more frequently reported in less severe infections such as otomycosis. Triazoles exhibit varying MICs and are therefore not strictly recommended as first-line treatment for IA caused by A. niger, while patient outcome seems to be more favorable when compared to IA due to other Aspergillus species. A. terreus-related infections have been reported increasingly as the cause of acute and chronic aspergillosis. A recent prospective international multicenter surveillance study showed Spain, Austria, and Israel to be the countries with the highest density of A. terreus species complex isolates collected. This species complex seems to cause dissemination more often and is intrinsically resistant to AmB. Non-fumigatus aspergillosis is difficult to manage due to complex patient histories, varying infection sites and potential intrinsic resistances to antifungals. Future investigational efforts should aim at amplifying the knowledge on specific diagnostic measures and their on-site availability, as well as defining optimal treatment strategies and outcomes of non-fumigatus aspergillosis.
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Affiliation(s)
- Jannik Stemler
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD), European Diamond Excellence Center for Medical Mycology (ECMM), Faculty of Medicine, University Hospital of Cologne, University of Cologne, 50937 Cologne, Germany
- Institute of Translational Research, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50923 Cologne, Germany
- German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, 50923 Cologne, Germany
| | - Christina Többen
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD), European Diamond Excellence Center for Medical Mycology (ECMM), Faculty of Medicine, University Hospital of Cologne, University of Cologne, 50937 Cologne, Germany
- Institute of Translational Research, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50923 Cologne, Germany
- German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, 50923 Cologne, Germany
| | - Cornelia Lass-Flörl
- Institute of Hygiene and Medical Microbiology, European Diamond Excellence Center for Medical Mycology (ECMM), Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Jörg Steinmann
- Institute of Clinical Hygiene, Medical Microbiology and Infectiology, Paracelsus Medical University, Klinikum Nürnberg, 90419 Nuremberg, Germany
- Institute of Medical Microbiology, University Hospital Essen, European Diamond Excellence Center for Medical Mycology (ECMM), 45147 Essen, Germany
| | - Katharina Ackermann
- Institute of Clinical Hygiene, Medical Microbiology and Infectiology, Paracelsus Medical University, Klinikum Nürnberg, 90419 Nuremberg, Germany
| | - Peter-Michael Rath
- Institute of Medical Microbiology, University Hospital Essen, European Diamond Excellence Center for Medical Mycology (ECMM), 45147 Essen, Germany
| | - Michaela Simon
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine, University Hospital of Cologne, University of Cologne, 50937 Cologne, Germany
| | - Oliver Andreas Cornely
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD), European Diamond Excellence Center for Medical Mycology (ECMM), Faculty of Medicine, University Hospital of Cologne, University of Cologne, 50937 Cologne, Germany
- Institute of Translational Research, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50923 Cologne, Germany
- German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, 50923 Cologne, Germany
- Clinical Trials Centre Cologne (ZKS Köln), University of Cologne, 50935 Cologne, Germany
| | - Philipp Koehler
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD), European Diamond Excellence Center for Medical Mycology (ECMM), Faculty of Medicine, University Hospital of Cologne, University of Cologne, 50937 Cologne, Germany
- Institute of Translational Research, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50923 Cologne, Germany
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13
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Zvezdanova ME, de Aledo MG, López-Mirones JI, Ortega J, Canut A, Castro C, Gomez C, Hernáez S, Oviaño M, Ercibengoa M, Alkorta M, Muñoz P, Rodriguez-Temporal D, Rodríguez-Sánchez B. Validation of an expanded, in-house library and an optimized preparation method for the identification of fungal isolates using MALDI-TOF mass spectrometry. Med Mycol 2023; 61:myad038. [PMID: 37102224 DOI: 10.1093/mmy/myad038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 03/17/2023] [Accepted: 04/25/2023] [Indexed: 04/28/2023] Open
Abstract
The goal of this study was to validate an optimized sample preparation method for filamentous fungal isolates coupled with the use of an in-house library for the identification of moulds using Matrix Assisted Laser Desorption/Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) in a multicenter context. For that purpose, three Spanish microbiology laboratories participated in the identification of 97 fungal isolates using MALDI-TOF MS coupled with the Filamentous Fungi library 3.0 (Bruker Daltonics) and an in-house library containing 314 unique fungal references. The isolates analyzed belonged to 25 species from the genus Aspergillus, Fusarium, Scedosporium/Lomentospora, the Mucorales order and the Dermatophytes group. MALDI-TOF MS identification was carried out from hyphae resuspended in water and ethanol. After a high-speed centrifugation step, the supernatant was discarded and the pellet submitted to a standard protein extraction step. The protein extract was analyzed with the MBT Smart MALDI Biotyper system (Bruker Daltonics). The rate of accurate, species-level identification obtained ranged between 84.5% and 94.8% and the score values were 1.8 for 72.2-94.9% of the cases. Two laboratories failed to identify only one isolate of Syncephalastrum sp. and Trichophyton rubrum, respectively and three isolates could not be identified in the third center (F. proliferatum, n = 1; T.interdigitale, n = 2). In conclusion, the availability of an effective sample preparation method and an extended database allowed high rates of correct identification of fungal species using MALDI-TOF MS. Some species, such as Trichophyton spp. are still difficult to identify. Although further improvements are still required, the developed methodology allowed the reliable identification of most fungal species.
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Affiliation(s)
- Margarita Estreya Zvezdanova
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Madrid 28007, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón -IiSGM-, Madrid 28007, Spain
| | - Manuel González de Aledo
- Clinical Microbiology Department, Complejo Hospitalario Universitario de A Coruña, A Coruña 15006, Spain
| | | | - Jesús Ortega
- Clinical Microbiology Department, Hospital Universitario Virgen de Valme, Seville 41014, Spain
| | - Andrés Canut
- Clinical Microbiology Department, Hospital Universitario de Álava, Vitoria-Gasteiz 01009, Spain
| | - Carmen Castro
- Clinical Microbiology Department, Hospital Universitario Virgen de Valme, Seville 41014, Spain
| | - Carmen Gomez
- Clinical Microbiology Department, Hospital Universitario de Álava, Vitoria-Gasteiz 01009, Spain
| | - Silvia Hernáez
- Clinical Microbiology Department, Hospital Universitario de Álava, Vitoria-Gasteiz 01009, Spain
| | - Marina Oviaño
- Clinical Microbiology Department, Complejo Hospitalario Universitario de A Coruña, A Coruña 15006, Spain
| | - María Ercibengoa
- Biodonostia Institute, Department of respiratory diseases and antimicrobial resistance, San Sebastián 20014, Spain
| | - Miriam Alkorta
- Biodonostia Institute, Department of diseases preventable by vaccination, San Sebastián 20014, Spain
- Clinical Microbiology Department, Hospital Universitario Donostia, San Sebastian 20014, Spain
- Microbiology Department, Faculty of Medicine, Universidad del País Vasco/ EHU-Donostia, San Sebastian 20014, Spain
| | - Patricia Muñoz
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Madrid 28007, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón -IiSGM-, Madrid 28007, Spain
- CIBER de Enfermedades Respiratorias (CIBERES CB06/06/0058), Madrid 28007, Spain
- Medicine Department, Faculty of Medicine, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - David Rodriguez-Temporal
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Madrid 28007, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón -IiSGM-, Madrid 28007, Spain
| | - Belén Rodríguez-Sánchez
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Madrid 28007, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón -IiSGM-, Madrid 28007, Spain
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14
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Maldonado I, Relloso S, Guelfand L, Fox B, Azula N, Romano V, Cantore A, Barrios R, Carnovale S, Nuske E, Minervini P. Evaluation of the MALDI-TOF mass spectrometry technique for the identification of dermatophytes: Use of an extended database. Rev Iberoam Micol 2023; 40:19-25. [PMID: 37951827 DOI: 10.1016/j.riam.2021.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 11/23/2020] [Accepted: 01/26/2021] [Indexed: 11/14/2023] Open
Abstract
BACKGROUND Identification of dermatophytes is usually performed through morphological analyses. However, it may be hindered due to the discovery of new species and complexes and, with some isolates, by the absence of fructification. Matrix-assisted laser desorption/ionisation-time-of-flight mass spectrometry (MALDI-TOF MS) seems to be an option for improving identification. AIMS To develop a database (DB) for the identification of dermatophytes with MALDI-TOF MS, including 32 isolates from the Red de Micología de la Ciudad Autónoma de Buenos Aires [Mycology Network of the Autonomous City of Buenos Aires] (RMCABA) and one reference isolate (RMCABA DB), and evaluate its performance when added to the DB from the supplier, Bruker (Bruker DB). METHODS All the isolates in the RMCABA DB were identified based on morphology and sequencing. To evaluate the performance of the extended DB (Bruker DB plus RMCABA DB), 136 clinical isolates were included. RESULTS The percentages of identification at the species level increased from 45% to 88%, but the identification at the genus level decreased from 23% to 7%. CONCLUSIONS MALDI-TOF MS yielded better performance in the identification of dermatophytes after including the RMCABA DB, which encompassed local isolates.
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Affiliation(s)
| | - Silvia Relloso
- Centro de Educación Médica e Investigaciones Clínicas Norberto Quirno [Norberto Quirno Centre for Medical Education and Clinical Research] (CEMIC), Argentina
| | - Liliana Guelfand
- Hospital General de Agudos J. A. Fernández Buenos Aires [JA Fernández Acute Care General Hospital of Buenos Aires], Argentina
| | - Bárbara Fox
- Hospital Alemán [German Hospital], Argentina
| | - Natalia Azula
- Centro de Educación Médica e Investigaciones Clínicas Norberto Quirno [Norberto Quirno Centre for Medical Education and Clinical Research] (CEMIC), Argentina
| | - Vanesa Romano
- Centro de Educación Médica e Investigaciones Clínicas Norberto Quirno [Norberto Quirno Centre for Medical Education and Clinical Research] (CEMIC), Argentina
| | - Agostina Cantore
- Hospital General de Agudos J. A. Fernández Buenos Aires [JA Fernández Acute Care General Hospital of Buenos Aires], Argentina
| | | | - Susana Carnovale
- Faculty of Medicine of the Universidad de Buenos Aires [University of Buenos Aires] (UBA), Argentina
| | - Ezequiel Nuske
- Instituto de Investigaciones en Bacteriología y Virología Molecular [Bacteriology and Molecular Virology Research Institute] of the UBA, Argentina
| | - Patricia Minervini
- Hospital de Oftalmología Santa Lucia [Santa Lucia Ophthalmology Hospital], Argentina
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15
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Zhang S, Page-Zoerkler N, Genevaz A, Roubaty C, Pollien P, Bordeaux M, Mestdagh F, Moccand C. Unlocking the Aromatic Potential of Native Coffee Yeasts: From Isolation to a Biovolatile Platform. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:4665-4674. [PMID: 36916533 PMCID: PMC10037330 DOI: 10.1021/acs.jafc.2c08263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 02/28/2023] [Accepted: 03/01/2023] [Indexed: 06/18/2023]
Abstract
Postharvest processing of coffee has been shown to impact cup quality. Yeasts are known to modulate the sensory traits of the final cup of coffee after controlled fermentation at the farm. Here, we enumerated native coffee yeasts in a Nicaraguan farm during dry and semidry postharvest processing of Arabica and Robusta beans. Subsequently, 90 endogenous yeast strains were selected from the collected endogenous isolates, identified, and subjected to high-throughput fermentation and biovolatile generation in a model system mimicking postharvesting conditions. Untargeted volatile analysis by SPME-GC-MS enabled the identification of key aroma compounds generated by the yeast pool and demonstrated differences among strains. Several genera, including Pichia, Candida, and Hanseniaspora, showed both strain- and species-level variability in volatile generation and profiles. This fermentation platform and biovolatile database could represent a versatile opportunity to accelerate the development of yeast starter cultures for generating specific and desired sensory attributes in the final cup of coffee.
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Affiliation(s)
| | | | - Aliénor Genevaz
- Nestlé
Research, Vers-Chez-Les-Blanc, 1000 Lausanne 26, Switzerland
| | - Claudia Roubaty
- Nestlé
Research, Vers-Chez-Les-Blanc, 1000 Lausanne 26, Switzerland
| | - Philippe Pollien
- Nestlé
Research, Vers-Chez-Les-Blanc, 1000 Lausanne 26, Switzerland
| | | | - Frederic Mestdagh
- Nestlé
Nespresso S.A., Route
de Lausanne 2, 1680 Romont, Switzerland
| | - Cyril Moccand
- Nestlé
Research, Vers-Chez-Les-Blanc, 1000 Lausanne 26, Switzerland
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16
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Hleba L, Hlebova M, Kovacik A, Petrova J, Maskova Z, Cubon J, Massanyi P. Use of MALDI-TOF MS to Discriminate between Aflatoxin B1-Producing and Non-Producing Strains of Aspergillus flavus. Molecules 2022; 27:molecules27227861. [PMID: 36431961 PMCID: PMC9692738 DOI: 10.3390/molecules27227861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022] Open
Abstract
Aflatoxin B1 (AFB1) is one of the most toxic mycotoxins. One of the producers of AFB1 is Aspergillus flavus. Therefore, its rapid identification plays a key role in various sectors of the food and feed industry. MALDI-TOF mass spectrometry is one of the fastest and most accurate methods today. Therefore, the aim of this research was to develop the rapid identification of producing and non-producing strains of A. flavus based on the entire mass spectrum. To accomplish the main goal a different confirmatory MALDI-TOF MS and TLC procedures such as direct AFB1 identification by scraping from TLC plates, A. flavus mycelium, nutrient media around A. flavus growth, and finally direct AFB1 identification from infected wheat and barley grains had to be conducted. In this experiment, MALDI-TOF mass spectrometry with various modifications was the main supporting technology. All confirmatory methods confirmed the presence of AFB1 in the samples of aflatoxin-producing strains of A. flavus and vice versa; AFB1 was not detected in the case of non-producing strains. Entire mass spectra (from 2 to 20 kDa) of aflatoxin-producing and non-producing A. flavus strains were collected, statistically analyzed and clustered. An in-depth analysis of the obtained entire mass spectra showed differences between AFB1-producing and non-producing strains of A. flavus. Statistical and cluster analysis divided AFB1-producing and non-producing strains of A. flavus into two monasteries. The results indicate that it is possible to distinguish between AFB1 producers and non-producers by comparing the entire mass spectra using MALDI-TOF MS. Finally, we demonstrated that if there are established local AFB1-producing and non-producing strains of A. flavus, the entire mass spectrum database identification of aflatoxigenic A. flavus strains can be even faster and cheaper, without the need to identify the toxin itself.
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Affiliation(s)
- Lukas Hleba
- Faculty of Biotechnology and Food Sciences, Institute of Biotechnology, Slovak University of Agriculture in Nitra, Tr. Andreja Hlinku 2, 949 76 Nitra, Slovakia
- Correspondence:
| | - Miroslava Hlebova
- Department of Biology, Faculty of Natural Sciences, University of Ss. Cyril and Methodius, Nám. J. Herdu 2, 917 01 Trnava, Slovakia
| | - Anton Kovacik
- Faculty of Biotechnology and Food Sciences, Institute of Applied Biology, Slovak University of Agriculture in Nitra, Tr. Andreja Hlinku 2, 949 76 Nitra, Slovakia
| | - Jana Petrova
- Faculty of Biotechnology and Food Sciences, Institute of Biotechnology, Slovak University of Agriculture in Nitra, Tr. Andreja Hlinku 2, 949 76 Nitra, Slovakia
| | - Zuzana Maskova
- Faculty of Biotechnology and Food Sciences, Institute of Biotechnology, Slovak University of Agriculture in Nitra, Tr. Andreja Hlinku 2, 949 76 Nitra, Slovakia
| | - Juraj Cubon
- Faculty of Biotechnology and Food Sciences, Institute of Food Sciences, Slovak University of Agriculture in Nitra, Tr. Andreja Hlinku 2, 949 76 Nitra, Slovakia
| | - Peter Massanyi
- Faculty of Biotechnology and Food Sciences, Institute of Applied Biology, Slovak University of Agriculture in Nitra, Tr. Andreja Hlinku 2, 949 76 Nitra, Slovakia
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17
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Vitte J, Michel M, Malinovschi A, Caminati M, Odebode A, Annesi-Maesano I, Caimmi DP, Cassagne C, Demoly P, Heffler E, Menu E, Nwaru BI, Sereme Y, Ranque S, Raulf M, Feleszko W, Janson C, Galán C. Fungal exposome, human health, and unmet needs: A 2022 update with special focus on allergy. Allergy 2022; 77:3199-3216. [PMID: 35976185 DOI: 10.1111/all.15483] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 08/01/2022] [Accepted: 08/13/2022] [Indexed: 01/28/2023]
Abstract
Humans inhale, ingest, and touch thousands of fungi each day. The ubiquity and diversity of the fungal kingdom, reflected by its complex taxonomy, are in sharp contrast with our scarce knowledge about its distribution, pathogenic effects, and effective interventions at the environmental and individual levels. Here, we present an overview of salient features of fungi as permanent players of the human exposome and key determinants of human health, through the lens of fungal allergy and other fungal hypersensitivity reactions. Improved understanding of the fungal exposome sheds new light on the epidemiology of fungal-related hypersensitivity diseases, their immunological substratum, the currently available methods, and biomarkers for environmental and medical fungi. Unmet needs are described and potential approaches are highlighted as perspectives.
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Affiliation(s)
- Joana Vitte
- IDESP, University of Montpellier and INSERM, Montpellier, France.,MEPHI, IHU Méditerranée Infection, IRD, APHM, Aix-Marseille Univ, Marseille, France
| | - Moïse Michel
- IDESP, University of Montpellier and INSERM, Montpellier, France.,MEPHI, IHU Méditerranée Infection, IRD, APHM, Aix-Marseille Univ, Marseille, France.,Immunology Laboratory, University Hospital Nîmes, Nîmes, France
| | - Andrei Malinovschi
- Department of Medical Sciences Clinical Physiology, Uppsala University, Uppsala, Sweden
| | - Marco Caminati
- Asthma, Allergy and Clinical Immunology Section, Department of Medicine, University of Verona, Verona, Italy
| | - Adeyinka Odebode
- Department of Basic Science, Kampala International University, Kampala, Uganda
| | | | - Davide Paolo Caimmi
- IDESP, University of Montpellier and INSERM, Montpellier, France.,Departement of Pneumology, University Hospital of Montpellier, Montpellier, France
| | - Carole Cassagne
- VITROME, IHU Méditerranée Infection, IRD, APHM, Aix-Marseille Univ, Marseille, France
| | - Pascal Demoly
- IDESP, University of Montpellier and INSERM, Montpellier, France.,Departement of Pneumology, University Hospital of Montpellier, Montpellier, France
| | - Enrico Heffler
- Personalized Medicine, Asthma and Allergy Humanitas Clinical and Research Center IRCCS Rozzano, Rozzano, Italy.,Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Italy
| | - Estelle Menu
- VITROME, IHU Méditerranée Infection, IRD, APHM, Aix-Marseille Univ, Marseille, France
| | - Bright I Nwaru
- Krefting Research Centre, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Youssouf Sereme
- MEPHI, IHU Méditerranée Infection, IRD, APHM, Aix-Marseille Univ, Marseille, France.,Department of Immunology, Infectiology and Hematology, Institut Necker-Enfants Malades (INEM), INSERM U1151, CNRS UMR 8253, Université Paris Descartes, Paris, France
| | - Stéphane Ranque
- VITROME, IHU Méditerranée Infection, IRD, APHM, Aix-Marseille Univ, Marseille, France
| | - Monika Raulf
- Department of Allergology and Immunology, Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr-Universität Bochum (IPA), Bochum, Germany
| | - Wojciech Feleszko
- Department of Pediatric Pulmonology and Allergy, Medical University of Warsaw, Warsaw, Poland
| | - Christer Janson
- Department of Medical Sciences Respiratory, Allergy and Sleep Research, Uppsala University, Uppsala, Sweden
| | - Carmen Galán
- International Campus of Excellence on Agrifood (ceiA3), University of Cordoba, Córdoba, Spain.,Andalusian Inter-University Institute for Earth System Research (IISTA), University of Cordoba, Córdoba, Spain
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18
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Nissan S, Boelens J, Lagrou K, Roels D. Pyrenocheata unguis-hominis: A new cause of fungal keratitis in a contact lens wearer. Am J Ophthalmol Case Rep 2022; 28:101731. [PMCID: PMC9614820 DOI: 10.1016/j.ajoc.2022.101731] [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: 07/06/2022] [Revised: 10/12/2022] [Accepted: 10/18/2022] [Indexed: 11/16/2022] Open
Abstract
Purpose Observations Conclusions
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Affiliation(s)
- Sima Nissan
- Department of Ophthalmology, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium,Corresponding author.
| | - Jerina Boelens
- Department of Clinical Biology, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - Katrien Lagrou
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Herestraat 49, 3000, Leuven, Belgium,National Reference Centre for Mycosis, Department of Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Dimitri Roels
- Department of Ophthalmology, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium
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19
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Filamentous Fungal Keratitis in Greece: A 16-Year Nationwide Multicenter Survey. Mycopathologia 2022; 187:439-453. [PMID: 36178544 DOI: 10.1007/s11046-022-00666-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 09/01/2022] [Indexed: 10/14/2022]
Abstract
In a multicenter, prospective study of filamentous fungal keratitis in Greece, predisposing factors, etiology, treatment practices, and outcome, were determined. Corneal scrapings were collected from patients with clinical suspicion of fungal keratitis, and demographic and clinical data were recorded. Fungal identification was based on morphology, molecular methods, and matrix assisted laser desorption ionization time-of-flight mass-spectrometry. A total of 35 cases were identified in a 16-year study period. Female to male ratio was 1:1.7 and median age 48 years. Corneal injury by plant material, and soft contact lens use were the main risk factors (42.8% and 31.4%, respectively). Trauma was the leading risk factor for men (68.1%), contact lens use (61.5%) for women. Fusarium species were isolated more frequently (n = 21, 61.8%). F. solani was mostly associated with trauma, F. verticillioides and F. proliferatum with soft contact lens use. Other fungi were: Purpureocillium lilacinum (14.7%), Alternaria (11.8%), Aspergillus (8.8%), and Phoma foliaceiphila, Beauveria bassiana and Curvularia spicifera, one case each. Amphotericin B and voriconazole MIC50s against Fusarium were 2 mg/L and 4 mg/L respectively. Antifungal therapy consisted mainly of voriconazole locally or both locally and systemically, alone or in combination with liposomal AmB. Cure/improvement rate with antifungal therapy alone was 52%, keratoplasty was required in 40% of cases, and enucleation in 8%. In conclusion, filamentous fungal keratitis in Greece is rare, but with considerable morbidity. A large proportion of cases resulted in keratoplasty despite appropriate antifungal treatment.Kindly confirm the given name and family name are correctly identified for all authros.ConfirmedJournal instruction requires a city and country for affiliations; however, these are missing in affiliations 1, 3, 4, 5, 6, 13. Please verify if the provided city and country are correct and amend if necessary.All provided cities and countries are correct.
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Kabtani J, Militello M, Ranque S. Coniochaeta massiliensis sp. nov. Isolated from a Clinical Sampl28. J Fungi (Basel) 2022; 8:jof8100999. [PMID: 36294564 PMCID: PMC9605391 DOI: 10.3390/jof8100999] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 09/14/2022] [Accepted: 09/15/2022] [Indexed: 11/30/2022] Open
Abstract
The genus Coniochaeta belongs to the class Ascomycota and the family Coniochaetaceae. Some of the Coniochaeta species are plant and animal pathogens, while others are known to be primarily involved in human diseases. In the last few decades, case reports of human infections with Coniochaeta have increased, mainly in immunocompromised hosts. We have described and characterised a new species in the genus Coniochaeta, here named Coniochaeta massiliensis (PMML0158), which was isolated from a clinical sample. Species identification and thorough description were based on apposite and reliable phylogenetic and phenotypic approaches. The phylogenetic methods included multilocus phylogenetic analyses of four genomic regions: ITS (rRNA Internal Transcribed Spacers 1 and 2), TEF-1α (Translation Elongation Factor-1alpha), B-tub2 (β-tubulin2), and D1/D2 domains (28S large subunit rRNA). The phenotypic characterisation consisted, first, of a physiological analysis using both EDX (energy-dispersive X-ray spectroscopy) and BiologTM advanced phenotypic technology for fixing the chemical mapping and carbon-source oxidation/assimilation profiles. Afterwards, morphological characteristics were highlighted by optical microscopy and scanning electron microscopy. The in vitro antifungal susceptibility profile was characterised using the E-testTM exponential gradient method. The molecular analysis revealed the genetic distance between the novel species Coniochaeta massiliensis (PMML0158) and other known taxa, and the phenotypic analysis confirmed its unique chemical and physiological profile when compared with all other species of this genus.
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Affiliation(s)
- Jihane Kabtani
- Institut Hospitalo-Universitaire Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Muriel Militello
- Institut Hospitalo-Universitaire Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
- Faculty of Medical and Paramedical Sciences, Aix-Marseille Université, AP-HM, IRD, SSA, MEPHI, 13005 Marseille, France
| | - Stéphane Ranque
- Institut Hospitalo-Universitaire Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
- Department of Mycology and Parasitology, Aix-Marseille Université, AP-HM, IRD, SSA, VITROME, 13005 Marseille, France
- Correspondence:
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Jackson JS, Sandak MD, McCluskey L. Ankle Fusion After Prolonged Scedosporium boydii ( Pseudallescheria boydii) Infection Following Open Trimalleolar Fracture. FOOT & ANKLE ORTHOPAEDICS 2022; 7:24730114221112934. [PMID: 35898794 PMCID: PMC9310438 DOI: 10.1177/24730114221112934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Affiliation(s)
- James Scully Jackson
- St Francis-Emory Healthcare, Mercer University School of Medicine, Macon, GA, USA
| | - Michael David Sandak
- St Francis-Emory Healthcare, Mercer University School of Medicine, Macon, GA, USA
| | - Leland McCluskey
- St Francis-Emory Healthcare, Mercer University School of Medicine, Macon, GA, USA
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22
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Gupta AK, Hall DC, Cooper EA, Ghannoum MA. Diagnosing Onychomycosis: What’s New? J Fungi (Basel) 2022; 8:jof8050464. [PMID: 35628720 PMCID: PMC9146047 DOI: 10.3390/jof8050464] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 04/26/2022] [Accepted: 04/27/2022] [Indexed: 02/05/2023] Open
Abstract
An overview of the long-established methods of diagnosing onychomycosis (potassium hydroxide testing, fungal culture, and histopathological examination) is provided followed by an outline of other diagnostic methods currently in use or under development. These methods generally use one of two diagnostic techniques: visual identification of infection (fungal elements or onychomycosis signs) or organism identification (typing of fungal genus/species). Visual diagnosis (dermoscopy, optical coherence tomography, confocal microscopy, UV fluorescence excitation) provides clinical evidence of infection, but may be limited by lack of organism information when treatment decisions are needed. The organism identification methods (lateral flow techniques, polymerase chain reaction, MALDI-TOF mass spectroscopy and Raman spectroscopy) seek to provide faster and more reliable identification than standard fungal culture methods. Additionally, artificial intelligence methods are being applied to assist with visual identification, with good success. Despite being considered the ‘gold standard’ for diagnosis, clinicians are generally well aware that the established methods have many limitations for diagnosis. The new techniques seek to augment established methods, but also have advantages and disadvantages relative to their diagnostic use. It remains to be seen which of the newer methods will become more widely used for diagnosis of onychomycosis. Clinicians need to be aware of the limitations of diagnostic utility calculations as well, and look beyond the numbers to assess which techniques will provide the best options for patient assessment and management.
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Affiliation(s)
- Aditya K. Gupta
- Department of Medicine, Division of Dermatology, University of Toronto School of Medicine, Toronto, ON M5S 3H2, Canada
- Mediprobe Research Inc., London, ON N5X 2P1, Canada; (D.C.H.); (E.A.C.)
- Correspondence: ; Tel.: +1-519-851-9715; Fax: +1-519-657-4233
| | - Deanna C. Hall
- Mediprobe Research Inc., London, ON N5X 2P1, Canada; (D.C.H.); (E.A.C.)
| | | | - Mahmoud A. Ghannoum
- Center for Medical Mycology, Department of Dermatology, Case Western Reserve University, Cleveland, OH 44106, USA;
- Department of Dermatology, University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
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Bhambri A, Srivastava M, Mahale VG, Mahale S, Karn SK. Mushrooms as Potential Sources of Active Metabolites and Medicines. Front Microbiol 2022; 13:837266. [PMID: 35558110 PMCID: PMC9090473 DOI: 10.3389/fmicb.2022.837266] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/15/2022] [Indexed: 12/12/2022] Open
Abstract
Background Mushrooms exist as an integral and vital component of the ecosystem and are very precious fungi. Mushrooms have been traditionally used in herbal medicines for many centuries. Scope and Approach There are a variety of medicinal mushrooms mentioned in the current work such as Agaricus, Amanita, Calocybe, Cantharellus, Cordyceps, Coprinus, Cortinarius, Ganoderma, Grifola, Huitlacoche, Hydnum, Lentinus, Morchella, Pleurotus, Rigidoporus, Tremella, Trametes sp., etc., which play a vital role in various diseases because of several metabolic components and nutritional values. Medicinal mushrooms can be identified morphologically on the basis of their size, color (white, black, yellow, brown, cream, pink and purple-brown, etc.), chemical reactions, consistency of the stalk and cap, mode of attachment of the gills to the stalk, and spore color and mass, and further identified at a molecular level by Internal Transcribed Spacer (ITS) regions of gene sequencing. There are also other methods that have recently begun to be used for the identification of mushrooms such as high-pressure liquid chromatography (HPLC), nuclear magnetic resonance spectroscopy (NMR), microscopy, thin-layer chromatography (TLC), DNA sequencing, gas chromatography-mass spectrometry (GC-MS), chemical finger printing, ultra-performance liquid chromatography (UPLC), fourier transform infrared spectroscopy (FTIR), liquid chromatography quadrupole time-of-flight mass spectrometry (LCMS-TOF) and high-performance thin-layer chromatography (HPTLC). Lately, the matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) technique is also used for the identification of fungi. Key Finding and Conclusion Medicinal mushrooms possess various biological activities like anti-oxidant, anti-cancer, anti-inflammatory, anti-aging, anti-tumor, anti-viral, anti-parasitic, anti-microbial, hepatoprotective, anti-HIV, anti-diabetic, and many others that will be mentioned in this article. This manuscript will provide future direction, action mechanisms, applications, and the recent collective information of medicinal mushrooms. In addition to many unknown metabolites and patented active metabolites are also included.
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Affiliation(s)
- Anne Bhambri
- Department of Biochemistry and Biotechnology, Sardar Bhagwan Singh University, Dehradun, India
| | | | | | | | - Santosh Kumar Karn
- Department of Biochemistry and Biotechnology, Sardar Bhagwan Singh University, Dehradun, India
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Classification of Environmental Strains from Order to Genus Levels Using Lipid and Protein MALDI-ToF Fingerprintings and Chemotaxonomic Network Analysis. Microorganisms 2022; 10:microorganisms10040831. [PMID: 35456880 PMCID: PMC9032901 DOI: 10.3390/microorganisms10040831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/30/2022] [Accepted: 04/13/2022] [Indexed: 11/16/2022] Open
Abstract
During the last two decades, MALDI-ToF mass spectrometry has become an efficient and widely-used tool for identifying clinical isolates. However, its use for classification and identification of environmental microorganisms remains limited by the lack of reference spectra in current databases. In addition, the interpretation of the classical dendrogram-based data representation is more difficult when the quantity of taxa or chemotaxa is larger, which implies problems of reproducibility between users. Here, we propose a workflow including a concurrent standardized protein and lipid extraction protocol as well as an analysis methodology using the reliable spectra comparison algorithm available in MetGem software. We first validated our method by comparing protein fingerprints of highly pathogenic bacteria from the Robert Koch Institute (RKI) open database and then implemented protein fingerprints of environmental isolates from French Guiana. We then applied our workflow for the classification of a set of protein and lipid fingerprints from environmental microorganisms and compared our results to classical genetic identifications using 16S and ITS region sequencing for bacteria and fungi, respectively. We demonstrated that our protocol allowed general classification at the order and genus level for bacteria whereas only the Botryosphaeriales order can be finely classified for fungi.
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Honsig C, Selitsch B, Hollenstein M, Vossen MG, Spettel K, Willinger B. Identification of Filamentous Fungi by MALDI-TOF Mass Spectrometry: Evaluation of Three Different Sample Preparation Methods and Validation of an In-House Species Cutoff. J Fungi (Basel) 2022; 8:jof8040383. [PMID: 35448614 PMCID: PMC9025689 DOI: 10.3390/jof8040383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 04/06/2022] [Accepted: 04/07/2022] [Indexed: 12/04/2022] Open
Abstract
Invasive infections caused by filamentous fungi constitute a leading cause of morbidity and mortality in immunocompromised patients. Rapid and reliable identification of filamentous fungi is essential for the early initiation of appropriate treatment. In the present study, 230 filamentous fungi isolates identified by conventional methods were investigated using MALDI-TOF MS (Bruker Daltonics, Bremen, Germany) in combination with the Filamentous Fungi Library 3.0 provided by the manufacturer. Three different sample preparation methods were applied as recommended by the manufacturer and identification rates were compared using the criteria provided by the manufacturer. Application of the more time-consuming sample preparation methods clearly improved identification at the species level. Thus, the identification rate increased from 48.9% using the simplest method to 76.1% with the most laborious procedure. Misidentifications did not occur. Furthermore, the reliability of an in-house threshold for species identification was investigated. The reduced threshold increased the rate of isolates correctly identified at the species level by up to 86.4%. As no misidentification was made at the genus level and only one misidentification of minor significance occurred at the species level, this threshold could be validated for routine use in our laboratory. In conclusion, regarding the high identification rates achieved, this commercial platform proved suitable for implementation in routine diagnosis.
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Affiliation(s)
- Claudia Honsig
- Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria; (C.H.); (B.S.); (K.S.)
| | - Brigitte Selitsch
- Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria; (C.H.); (B.S.); (K.S.)
| | - Marlene Hollenstein
- Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria;
| | - Matthias G. Vossen
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine I, Medical University of Vienna, 1090 Vienna, Austria;
| | - Kathrin Spettel
- Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria; (C.H.); (B.S.); (K.S.)
| | - Birgit Willinger
- Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria; (C.H.); (B.S.); (K.S.)
- Correspondence: ; Tel.: +43-1-40400-51560
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Lazari LC, Zerbinati RM, Rosa-Fernandes L, Santiago VF, Rosa KF, Angeli CB, Schwab G, Palmieri M, Sarmento DJS, Marinho CRF, Almeida JD, To K, Giannecchini S, Wrenger C, Sabino EC, Martinho H, Lindoso JAL, Durigon EL, Braz-Silva PH, Palmisano G. MALDI-TOF mass spectrometry of saliva samples as a prognostic tool for COVID-19. J Oral Microbiol 2022; 14:2043651. [PMID: 35251522 PMCID: PMC8890567 DOI: 10.1080/20002297.2022.2043651] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Background Methods Results Conclusion
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Affiliation(s)
- Lucas C. Lazari
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil
| | - Rodrigo M. Zerbinati
- Laboratory of Virology (LIM-52-HC-FMUSP), Institute of Tropical Medicine of São Paulo, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Livia Rosa-Fernandes
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil
- Laboratory of Experimental Immunoparasitology, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil
| | - Veronica Feijoli Santiago
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil
| | - Klaise F. Rosa
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil
| | - Claudia B. Angeli
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil
| | - Gabriela Schwab
- Laboratory of Virology (LIM-52-HC-FMUSP), Institute of Tropical Medicine of São Paulo, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Michelle Palmieri
- Department of Stomatology, School of Dentistry, University of São Paulo, São Paulo, Brazil
| | - Dmitry J. S. Sarmento
- Department of Stomatology, School of Dentistry, University of São Paulo, São Paulo, Brazil
| | - Claudio R. F. Marinho
- Laboratory of Experimental Immunoparasitology, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil
| | - Janete Dias Almeida
- Department of Biosciences and Oral Diagnosis, Institute of Science and Technology, São Paulo State University, São José dos Campos, Brazil
| | - Kelvin To
- State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, Carol Yu Centre for Infection, Li KaShing Faculty of Medicine of the University of Hong Kong, Hong Kong, Special Administrative Region, China
| | - Simone Giannecchini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Carsten Wrenger
- Unit for Drug Discovery, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil
| | - Ester C. Sabino
- Institute of Tropical Medicine of São Paulo, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Herculano Martinho
- Centro de Ciencias Naturais e Humanas, Universidade Federal do ABC, Santo André, Brazil
| | - José A. L. Lindoso
- Institute of Infectious Diseases Emílio Ribas, São Paulo, Brazil
- Laboratory of Protozoology (LIM-49-HC-FMUSP), Institute of Tropical Medicine of São Paulo, School of Medicine, University of São Paulo, São Paulo, Brazil
- Department of Infectious Diseases, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Edison L. Durigon
- Laboratory of Clinical and Molecular Virology, Department of Microbiology, ICB, University of São Paulo, São Paulo, Brazil
| | - Paulo H. Braz-Silva
- Laboratory of Virology (LIM-52-HC-FMUSP), Institute of Tropical Medicine of São Paulo, School of Medicine, University of São Paulo, São Paulo, Brazil
- Department of Stomatology, School of Dentistry, University of São Paulo, São Paulo, Brazil
| | - Giuseppe Palmisano
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil
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Shao J, Wang Q, Wei L, Wan Z, Li R, Yu J. Limitations of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for the identification of Aspergillus species. Med Mycol 2022; 60:6511566. [PMID: 35044460 DOI: 10.1093/mmy/myab084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 11/17/2021] [Indexed: 11/12/2022] Open
Abstract
This study aimed to detect the identification limitations for Aspergillus species from patients or the environment based on MALDI-TOF MS analysis. A total of 209 Aspergillus isolates were selected in this study. One hundred and sixty-eight of the strains were selected as challenge strains for MALDI-TOF MS analysis, while the remaining 41 strains were used to construct a supplementary database. The 168 challenge strains were identified by the Bruker Filamentous Fungi Library v1.0 (the Bruker Library) and identified again using the Bruker Library combined with the supplementary database (the combined database). The sensitivity of MALDI-TOF MS with the Bruker Library alone and with the combined database in identifying the challenge strains at the species level was 64.3% and 85.7%, respectively. With the combined database, the sensitivity of MALDI-TOF MS in identifying strains in Aspergillus sections Fumigati, Flavi, Nigri, Terrei, and Nidulantes was 100%, 86.5%, 76.1%, 100%, and 80%, respectively, and the sensitivity in identifying strains of other Aspergillus species was 71.4%. The specificity of MALDI-TOF MS in identifying strains in all Aspergillus sections at the species level was 100%. Even when using the combined database, MALDI-TOF MS analysis showed some misidentification for the species A. niger, A. welwitschiae, A. luchuensis, A. flavus and A. sydowii. In conclusion, with the combined database, MALDI-TOF MS showed good performance in identifying the species in Aspergillus sections Fumigati and Terrei but limited performance in distinguishing some closely related species in sections Nigri, Flavi and Nidulantes.
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Affiliation(s)
- Jin Shao
- Department of Dermatology and Venereology, Peking University First Hospital; Research Center for Medical Mycology, Peking University; Beijing Key Laboratory of Molecular Diagnosis of Dermatoses, Peking University First Hospital; National Clinical Research Center for Skin and Immune Diseases, Beijing 100034, China
| | - Qiqi Wang
- Department of Dermatology and Venereology, Peking University First Hospital; Research Center for Medical Mycology, Peking University; Beijing Key Laboratory of Molecular Diagnosis of Dermatoses, Peking University First Hospital; National Clinical Research Center for Skin and Immune Diseases, Beijing 100034, China
| | - Linwei Wei
- Department of Dermatology and Venereology, Peking University First Hospital; Research Center for Medical Mycology, Peking University; Beijing Key Laboratory of Molecular Diagnosis of Dermatoses, Peking University First Hospital; National Clinical Research Center for Skin and Immune Diseases, Beijing 100034, China
| | - Zhe Wan
- Department of Dermatology and Venereology, Peking University First Hospital; Research Center for Medical Mycology, Peking University; Beijing Key Laboratory of Molecular Diagnosis of Dermatoses, Peking University First Hospital; National Clinical Research Center for Skin and Immune Diseases, Beijing 100034, China
| | - Ruoyu Li
- Department of Dermatology and Venereology, Peking University First Hospital; Research Center for Medical Mycology, Peking University; Beijing Key Laboratory of Molecular Diagnosis of Dermatoses, Peking University First Hospital; National Clinical Research Center for Skin and Immune Diseases, Beijing 100034, China
| | - Jin Yu
- Department of Dermatology and Venereology, Peking University First Hospital; Research Center for Medical Mycology, Peking University; Beijing Key Laboratory of Molecular Diagnosis of Dermatoses, Peking University First Hospital; National Clinical Research Center for Skin and Immune Diseases, Beijing 100034, China
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Taguchi T, Ishikawa M, Ichikawa M, Tadenuma T, Hirakawa Y, Yoshino T, Maeda Y, Takeuchi H, Nojima D, Tanaami T, Matsunaga T, Tanaka T. Amplification-free detection of bacterial genes using a signaling probe-based DNA microarray. Biosens Bioelectron 2021; 194:113659. [PMID: 34571443 DOI: 10.1016/j.bios.2021.113659] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 08/31/2021] [Accepted: 09/20/2021] [Indexed: 11/29/2022]
Abstract
In this study, we developed a novel DNA microarray system that does not require fluorophore-labeling, amplification, or washing of the target nucleic acid fragments. Two types of DNA probes (so-called "signaling probes") labeled with a fluorescence dye (Cy3) and quencher molecule (BHQ2) were spotted on the DNA microarray such that fluorescent signals of Cy3 could be quenched by BHQ2 due to duplex formation between the probes. The addition of the target DNA or RNA fragments disrupted the duplex formed by the probes, resulting in the generation of fluorescence signals. We examined the assay conditions of the signaling probe-based DNA microarray, including the design of the probes, hybridization temperatures, and methods for fragmentation of target molecules. Since this approach does not require time-consuming processes, including labeling, amplification, and washing, the assay achieved specific detection of 16S rDNA and 16S rRNA extracted from Escherichia coli within 60 min, which was significantly rapid compared to conventional PCR-dependent DNA microarrays.
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Affiliation(s)
- Tomoyuki Taguchi
- Yokogawa Electric Corporation, 2-9-32, Naka-cho, Musashino-shi, Tokyo, 180-8750, Japan
| | - Machi Ishikawa
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Momoko Ichikawa
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Takashi Tadenuma
- Yokogawa Electric Corporation, 2-9-32, Naka-cho, Musashino-shi, Tokyo, 180-8750, Japan
| | - Yuko Hirakawa
- Yokogawa Electric Corporation, 2-9-32, Naka-cho, Musashino-shi, Tokyo, 180-8750, Japan; Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Tomoko Yoshino
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Yoshiaki Maeda
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Hiyori Takeuchi
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Daisuke Nojima
- Yokogawa Electric Corporation, 2-9-32, Naka-cho, Musashino-shi, Tokyo, 180-8750, Japan
| | - Takeo Tanaami
- Yokogawa Electric Corporation, 2-9-32, Naka-cho, Musashino-shi, Tokyo, 180-8750, Japan
| | - Tadashi Matsunaga
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo, 184-8588, Japan; Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15, Natsushima-cho, Yokosuka, Kanagawa, 237-0061, Japan
| | - Tsuyoshi Tanaka
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo, 184-8588, Japan.
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Aguiar PADF, Menezes RP, Penatti MPA, Moreira TA, Pimenta JP, Silva NBS, Röder DVDB. Rapid detection of biofilm-producing Candida species via MALDI-TOF mass spectrometry. J Appl Microbiol 2021; 131:2049-2060. [PMID: 33694241 DOI: 10.1111/jam.15066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 03/02/2021] [Accepted: 03/07/2021] [Indexed: 12/18/2022]
Abstract
AIMS The aim of this study was to evaluate the formation of biofilm by Candida spp. isolated from the bloodstream, using traditional spectrophotometric methodologies. In addition, the goal was to compare the results with those obtained through MALDI-TOF/MS, as well as to verify its use as a potential tool for the detection of biofilm-forming strains. METHODS AND RESULTS Hundred and thirteen isolates of Candida spp. were studied: 41 were Candida albicans, 27 C. tropicalis, 18 C. glabrata, 17 C. parapsilosis and 10 C. krusei. Metabolic activity was determined through the tetrazolium salt (XTT) reduction assay and biomass by staining with Crystal Violet. All isolates were able to form biofilm, 94% of which were strong producers, with high biomass quantification (95%; 107/113) and high metabolic activity (99%; 112/113). Mass spectra of the biofilm-producing isolates showed differences in the intensity of mass peaks when compared with the spectra of the nonproducing strains. CONCLUSIONS It was demonstrated that MALDI-TOF/MS was able to detect specific biofilm proteins, as the mass spectra of the isolates presented differences when compared with nonproducing strains. SIGNIFICANCE AND IMPACT OF THE STUDY MALDI-TOF/MS can become a valuable tool for biofilm detection at the moment of the identification of the microorganism, thus contributing greatly to the management of patients with Candidemia.
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Affiliation(s)
- P A D F Aguiar
- Faculty of Medicine of the Federal University of Uberlândia (FAMED-UFU), Uberlândia, Brazil
| | - R P Menezes
- Technical Health School of the Federal University of Uberlândia (ESTES-UFU), Uberlândia, Brazil
| | - M P A Penatti
- Technical Health School of the Federal University of Uberlândia (ESTES-UFU), Uberlândia, Brazil
| | - T A Moreira
- Clinical Analysis Laboratory of the Clinical Hospital of Uberlândia (HCU-UFU), Uberlândia, Brazil
| | - J P Pimenta
- Check-Up Medicina Laboratorial (Uberlândia), Uberlândia, Brazil
| | - N B S Silva
- Institute of Biomedical Sciences, Federal University of Uberlândia (ICBIM-UFU), Uberlândia, Brazil
| | - D V D B Röder
- Institute of Biomedical Sciences, Federal University of Uberlândia (ICBIM-UFU), Uberlândia, Brazil
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Huseynov RM, Javadov SS, Osmanov A, Khasiyev S, Valiyeva SR, Almammadova E, Denning DW. The burden of serious fungal infections in Azerbaijan. Ther Adv Infect Dis 2021; 8:20499361211043969. [PMID: 34497715 PMCID: PMC8419541 DOI: 10.1177/20499361211043969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 08/17/2021] [Indexed: 11/16/2022] Open
Abstract
Background: Azerbaijan is an upper middle-income country in South Caucasus with an area of 86,600 km2 and a total population of 10 million people and gross domestic product of US $4480 per capita. The aim of this research is to estimate fungal infection burden and highlight the problem at national and international levels. Methods: Fungal infection burden was estimated using data from epidemiological papers and population at risk and LIFE (Leading International Fungal Education) modelling. Results: The number of people living with human immunodeficiency virus (PLHIV) in 2018 was 6193, 29% of them not receiving antiretroviral therapy. Based on 90% and 20% rates of oral and oesophageal candidiasis in patients with CD4 cell count <200 µl–1 we estimate 808 and 579 patients with oral and oesophageal candidiasis, respectively. The annual incidences of cryptococcal meningitis and Pneumocystis pneumonia are 5 and 55 cases, respectively. We estimated 2307 cases of chronic pulmonary aspergillosis (CPA), 4927 patients with allergic bronchopulmonary aspergillosis (ABPA), and 6504 with severe asthma with fungal sensitization (SAFS). Using data on chronic obstructive pulmonary diseases (COPD), lung cancer, acute myeloid leukaemia rates, and number of transplantations, we estimated 693 cases of invasive aspergillosis following these conditions. Using a low-European rate for invasive candidiasis, we estimated 499 and 75 patients with candidemia and intra-abdominal candidiasis respectively. The number of adult women (15–55 years) in Azerbaijan is ~2,658,000, so it was estimated that 159,490 women suffer from recurrent vulvovaginal candidiasis (rVVC). Discussion: In total, the estimated number of people suffering from fungal diseases in Azerbaijan is 225,974 (2.3% of the population). However, the fungal rate is underestimated due to lack of epidemiological data. The most imminent need is improvement in diagnostic capabilities. This aim should be achieved via establishing a reference laboratory and equipping major clinical centers with essential diagnostics assays.
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Affiliation(s)
- Ravil M Huseynov
- The Department of Medical Microbiology and Immunology, Azerbaijan Medical University, Mardanov Qardashlari 98, Baku, Azerbaijan
| | - Samir S Javadov
- The Department of Medical Microbiology and Immunology, Azerbaijan Medical University, Baku, Azerbaijan
| | - Ali Osmanov
- Global Action Fund for Fungal Infections, Geneva, Switzerland
| | - Shahin Khasiyev
- The Department of Informatics and Statistics, Ministry of Health of Azerbaijan Republic, Baku, Azerbaijan
| | - Samira R Valiyeva
- Republican Centre for Combating AIDS, Ministry of Health of Azerbaijan Republic, Baku, Azerbaijan
| | - Esmira Almammadova
- Republican Centre for Combating AIDS, Ministry of Health of Azerbaijan Republic, Baku, Azerbaijan
| | - David W Denning
- Global Action Fund for Fungal Infections, Geneva, Switzerland
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31
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Výrostková J, Regecová I, Dudriková E, Marcinčák S, Vargová M, Kováčová M, Maľová J. Antimicrobial Resistance of Enterococcus sp. Isolated from Sheep and Goat Cheeses. Foods 2021; 10:foods10081844. [PMID: 34441623 PMCID: PMC8391679 DOI: 10.3390/foods10081844] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/29/2021] [Accepted: 08/02/2021] [Indexed: 01/13/2023] Open
Abstract
This study aimed to calculate the proportion of antibiotic resistance profiles of Enterococcus faecium, E. faecalis, and E. durans isolated from traditional sheep and goat cheeses obtained from a selected border area of Slovakia with Hungary (region Slanské vrchy). A total of 110 Enterococcus sp. were isolated from cheese samples, of which 52 strains (E. faecium (12), E. faecalis (28), E. durans (12)) were represented. After isolation and identification by polymerase chain reaction and matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry, the enterococci (E. faecium, E. faecalis, and E. durans) were submitted to susceptibility tests against nine antimicrobial agents. In general, strains of E. faecalis were more resistant than E. durans and E. faecium. A high percentage of resistance was noted in E. faecalis to rifampicin (100%), vancomycin (85.7%), teicoplanin (71.4%), erythromycin (71.4%), minocycline (57.1%), nitrofurantoin (57.1%), ciprofloxacin (14.3%), and levofloxacin (14.3%). E. durans showed resistance to rifampicin (100%), teicoplanin (100%), vancomycin (66.7%), erythromycin (66.7%), nitrofurantoin (66.7%), and minocycline (33.3%), and E. faecium showed resistance to vancomycin, teicoplanin, and erythromycin (100%). Multidrug-resistant strains were confirmed in 80% of the 52 strains in this study. Continuous identification of Enterococcus sp. and monitoring of their incidence and emerging antibiotic resistance is important in order to prevent a potential risk to public health caused by the contamination of milk and other dairy products, such as cheeses, made on farm level.
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Affiliation(s)
- Jana Výrostková
- Department of Food Hygiene Technology and Safety, University of Veterinary Medicine and Pharmacy in Košice, Komenského 73, 041 81 Košice, Slovakia; (J.V.); (E.D.); (S.M.); (M.K.); (J.M.)
| | - Ivana Regecová
- Department of Food Hygiene Technology and Safety, University of Veterinary Medicine and Pharmacy in Košice, Komenského 73, 041 81 Košice, Slovakia; (J.V.); (E.D.); (S.M.); (M.K.); (J.M.)
- Correspondence: ; Tel.: +421-907-185-658
| | - Eva Dudriková
- Department of Food Hygiene Technology and Safety, University of Veterinary Medicine and Pharmacy in Košice, Komenského 73, 041 81 Košice, Slovakia; (J.V.); (E.D.); (S.M.); (M.K.); (J.M.)
| | - Slavomír Marcinčák
- Department of Food Hygiene Technology and Safety, University of Veterinary Medicine and Pharmacy in Košice, Komenského 73, 041 81 Košice, Slovakia; (J.V.); (E.D.); (S.M.); (M.K.); (J.M.)
| | - Mária Vargová
- Department of Public Veterinary Medicine and Animal Welfare, University of Veterinary Medicine and Pharmacy in Košice, Komenského 73, 041 81 Košice, Slovakia;
| | - Mariana Kováčová
- Department of Food Hygiene Technology and Safety, University of Veterinary Medicine and Pharmacy in Košice, Komenského 73, 041 81 Košice, Slovakia; (J.V.); (E.D.); (S.M.); (M.K.); (J.M.)
| | - Jana Maľová
- Department of Food Hygiene Technology and Safety, University of Veterinary Medicine and Pharmacy in Košice, Komenského 73, 041 81 Košice, Slovakia; (J.V.); (E.D.); (S.M.); (M.K.); (J.M.)
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32
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Sun Y, Guo J, Chen R, Hu L, Xia Q, Wu W, Wang J, Hu F. Multicenter evaluation of three different MALDI-TOF MS systems for identification of clinically relevant filamentous fungi. Med Mycol 2021; 59:81-86. [PMID: 32437532 DOI: 10.1093/mmy/myaa037] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 04/09/2020] [Accepted: 04/23/2020] [Indexed: 12/18/2022] Open
Abstract
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) holds promise as a potential tool for clinical identification of filamentous fungi. However, due to the lack of an appropriate extraction protocol and the difficulty of database building, the identification power of each system differs. In this study, we selected 126 clinical mould isolates comprising 28 species identified using internal transcribed spacer (ITS) sequencing as the reference method to evaluate three MALDI-TOF MS systems. When using cultures and sample preparation as recommended by the respective vendors, of the 126 strains tested, VITEK MS identified 121 (96.0%) to species-level and 124 (98.4%) to genus-level; Biotyper identified 53 (42.1%) to species-level and 54 (42.9%) to genus-level; Autof identified 74 (58.7%) to species-level and 76 (60.3%) to genus-level. For the Autof system, the tube extraction method recommended by the vendor performed better (59%) than the on-plate lysis (51%). Our study demonstrates that MALDI-TOF MS systems can successfully identify most clinically relevant fungi, while performance is still highly dependent on the database and sample preparation protocol.
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Affiliation(s)
- Yue Sun
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China.,Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
| | - Jian Guo
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Rong Chen
- Department of Clinical Microbiology Laboratory, Shanghai Center for Clinical Laboratory, Shanghai, China
| | - Liang Hu
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Qihang Xia
- Department of Clinical Microbiology Laboratory, Shanghai Center for Clinical Laboratory, Shanghai, China
| | - Wenjuan Wu
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jinghua Wang
- Department of Clinical Microbiology Laboratory, Shanghai Center for Clinical Laboratory, Shanghai, China
| | - Fupin Hu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China.,Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
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Ning YT, Yang WH, Zhang W, Xiao M, Wang Y, Zhang JJ, Zhang G, Duan SM, Dong AY, Guo DW, Zou GL, Wen HN, Guo YY, Chen LP, Chai M, He JD, Duan Q, Zhang LX, Zhang L, Xu YC. Developing Two Rapid Protein Extraction Methods Using Focused-Ultrasonication and Zirconia-Silica Beads for Filamentous Fungi Identification by MALDI-TOF MS. Front Cell Infect Microbiol 2021; 11:687240. [PMID: 34295837 PMCID: PMC8290857 DOI: 10.3389/fcimb.2021.687240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 06/14/2021] [Indexed: 11/23/2022] Open
Abstract
Filamentous fungi identification by Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been challenging due to the lack of simple and rapid protein extraction methods and insufficient species coverage in the database. In this study, we created two rapid protein extraction methods for filamentous fungi: a one-step zirconia-silica beads method (ZSB) and a focused-ultrasonication method (FUS). The identification accuracy of two methods were evaluated with the VITEK MS, as well as number of spectra peaks and signal-to-noise ratio (S/N) with M-Discover 100 MALDI-TOF MS compared to the routine method. The better method was applied to build a filamentous fungi in-house spectra library for the M-Discover 100 MS, and then another one and routine method were performed in parallel to verify the accuracy and commonality of the in-house library. Using the two optimized methods, the dedicated operating time before MALDI-TOF MS analysis was reduced from 30 min to 7 (ZSB) or 5 (FUS) min per sample, with only a few seconds added for each additional strain. And both two methods identified isolates from most mold types equal to or better than the routine method, and the total correct identification rate using VITEK MS was 79.67, 76.42, and 76.42%, respectively. On the other hand, the two rapid methods generally achieved higher maximum and minimum S/N ratios with these isolates tested as compared to the routine method. Besides, the ZSB method produced overall mean of maximum and minimum S/N ratio higher than that by FUS. An in-house library of M-Discover MS was successfully built from 135 isolates from 42 species belonging to 18 genera using the ZSB method. Analysis of 467 isolates resulted in 97.22% correctly identified isolates to the species level by the ZSB method versus 95.50% by the routine method. The two novel methods are time- and cost-effective and allow efficient identification of filamentous fungi while providing a simplified procedure to build an in-house library. Thus, more clinical laboratories may consider adopting MALDI-TOF MS for filamentous fungi identification in the future.
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Affiliation(s)
- Ya-Ting Ning
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Graduate School, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Wen-Hang Yang
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Graduate School, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Wei Zhang
- Graduate School, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Clinical Microbiology Laboratory, The First Affiliated Hospital of Hebei North University, Zhangjiakou, China
| | - Meng Xiao
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Graduate School, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Yao Wang
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Jing-Jia Zhang
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Ge Zhang
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Si-Meng Duan
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Ai-Ying Dong
- Department of Clinical Laboratory, North China University of Science and Technology Affiliated Hospital, Tangshan, China
| | - Da-Wen Guo
- Department of Clinical Laboratory, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Gui-Ling Zou
- Department of Clinical Laboratory, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Hai-Nan Wen
- Department of Laboratory, The Affiliated Hospital of Chengde Medical University, Chengde, China
| | - Yan-Yan Guo
- Department of Clinical Laboratory, Tangshan Worker's Hospital, Tangshan, China
| | - Li-Ping Chen
- Department of Laboratory Medicine, Mudanjiang First People's Hospital, Heilongjiang, China
| | - Miao Chai
- Department of Clinical Laboratory, The First Hospital of Harbin, Harbin, China
| | - Jing-Dong He
- Department of Clinical Laboratory, Tianjin Chest Hospital, Tianjin, China
| | - Qiong Duan
- Department of Clinical Laboratory, Jinling Province People's Hospital, Jinling, China
| | - Li-Xia Zhang
- Department of Clinical Laboratory, Shanxi Provincial People's Hospital, Taiyuan, China
| | - Li Zhang
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Ying-Chun Xu
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
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Sulaiman IM, Tang K, Segars K, Miranda N, Sulaiman N, Simpson S. Application of MALDI-TOF mass spectrometry, and DNA sequencing-based SLST and MLST analysis for the identification of Cronobacter spp. isolated from environmental surveillance samples. Arch Microbiol 2021; 203:4813-4820. [PMID: 34196749 DOI: 10.1007/s00203-021-02465-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 06/10/2021] [Accepted: 06/26/2021] [Indexed: 11/27/2022]
Abstract
Cronobacter spp. are emerging infectious foodborne bacteria that can cause acute meningitis and necrotizing enterocolitis in neonates and immunocompromised individuals. Although, little is known about its reservoirs or transmission routes, it has been linked to powdered infant formula worldwide. Three Cronobacter spp. (C. sakazakii, C. malonaticus, and C. turicensis) have been described as more virulent, and isolated frequently from infant meningitis cases. The estimated mortality rates are as high as 80% in infants. Thus, surveillance and typing of Cronobacter spp. isolated from food and environmental samples is essential to prevent contamination and spread of this pathogen. In this study, we have characterized 83 Cronobacter isolates recovered from various environmental samples by conventional microbiologic protocols. Species identification was accomplished by VITEK 2 system and real-time PCR analysis. Subsequently, these isolates were analyzed using VITEK MS system. Single locus sequence typing (SLST) was achieved by characterizing the regions of 16S rRNA and rpoB genes. Multilocus sequence typing (MLST) was performed by sequence characterization of seven housekeeping genes (atpD, fusA, glnS, gltB, gyrB, infB, and pps) using ABI 3500XL Genetic Analyzer. VITEK MS system identified, the majority of isolates as Cronobacter sakazakii with a high confidence value (99.9%). MLST analysis ascertained 12 distinct clonal complexes (CC1, CC4, CC8, CC13, CC17, CC21, CC31, CC40, CC52, CC64, CC73, and CC83) for the recovered C. sakazakii isolates. The results suggest that the MALDI-TOF MS is a reliable diagnostic tool for rapid species identification whereas 7-loci MLST is a powerful technique to discriminate and differentiate Cronobacter spp. isolates.
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Affiliation(s)
- Irshad M Sulaiman
- Microbiological Sciences Branch, Southeast Food and Feed Laboratory, Office of Regulatory Science, Office of Regulatory Affairs, U.S. Food and Drug Administration, 60, Eighth Street NE, Atlanta, GA, 30309, USA.
| | - Kevin Tang
- Biotechnology Core Facility Branch, Division of Scientific Resources, National Center for Emerging and Zoonotic Infectious Diseases, U.S. Centers for Disease Control and Prevention, 1600 Clifton Road, NE, Atlanta, GA, 30329, USA
| | - Katharine Segars
- Microbiological Sciences Branch, Southeast Food and Feed Laboratory, Office of Regulatory Science, Office of Regulatory Affairs, U.S. Food and Drug Administration, 60, Eighth Street NE, Atlanta, GA, 30309, USA
| | - Nancy Miranda
- Microbiological Sciences Branch, Southeast Food and Feed Laboratory, Office of Regulatory Science, Office of Regulatory Affairs, U.S. Food and Drug Administration, 60, Eighth Street NE, Atlanta, GA, 30309, USA
| | - Nikhat Sulaiman
- Biotechnology Core Facility Branch, Division of Scientific Resources, National Center for Emerging and Zoonotic Infectious Diseases, U.S. Centers for Disease Control and Prevention, 1600 Clifton Road, NE, Atlanta, GA, 30329, USA
| | - Steven Simpson
- Microbiological Sciences Branch, Southeast Food and Feed Laboratory, Office of Regulatory Science, Office of Regulatory Affairs, U.S. Food and Drug Administration, 60, Eighth Street NE, Atlanta, GA, 30309, USA
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Heireman L, Patteet S, Steyaert S. Performance of the new ID-fungi plate using two types of reference libraries (Bruker and MSI) to identify fungi with the Bruker MALDI Biotyper. Med Mycol 2021; 58:946-957. [PMID: 32030423 DOI: 10.1093/mmy/myz138] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 11/24/2019] [Accepted: 12/24/2019] [Indexed: 02/01/2023] Open
Abstract
During the last decade, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has revolutionized the diagnosis of fungal infections. Recently, a new Conidia ID-fungi plate (IDFP) medium was introduced to facilitate growth and sampling of fungi. This study aimed to evaluate the IDFP for fungal MALDI-TOF MS identification by comparison with a standard fungal growth medium using two reference libraries. A total of 75 filamentous fungal isolates (including 32 dermatophytes) were inoculated on IDFP and Sabouraud-gentamicin-chloramphenicol (SGC) agar and identified by MALDI-TOF MS using formic acid/acetonitrile extraction. Both the commercially available Bruker library (version 2.0) and the public available MSI web application (version 2018) were applied. For 15% of the isolates, a faster growth was noticed on IDFP compared to SGC. IDFP enhanced the performance of fungal identification compared to SGC for both MSI (increase of 16% identifications to genus and 5% to species level) and Bruker library (increase of 22% identifications to genus and 8% to species level). In total, only 73% of the tested isolates were present in the Bruker library compared to 92% for MSI library. No significant difference (P = 0.46) in MALDI score between IDFP and SGC was observed for the MSI library, but scores were significantly (P = 0.03) higher for IDFP when using Bruker library, potentially explained by the prevention of agar contamination by using IDFP since the Bruker database was created from liquid media. IDFP is a promising alternative growth medium for MALDI-TOF MS fungal identification which would strongly benefit from optimizing the Bruker reference library.
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Affiliation(s)
- Laura Heireman
- Department of Laboratory Medicine, General Hospital Maria Middelares, Ghent, Belgium
| | - Sofie Patteet
- Department of Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Sophia Steyaert
- Department of Laboratory Medicine, General Hospital Maria Middelares, Ghent, Belgium
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36
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MALDI-TOF Mass Spectroscopy Applications in Clinical Microbiology. Adv Pharmacol Pharm Sci 2021; 2021:9928238. [PMID: 34041492 PMCID: PMC8121603 DOI: 10.1155/2021/9928238] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 04/30/2021] [Indexed: 02/07/2023] Open
Abstract
There is a range of proteomics methods to spot and analyze bacterial protein contents such as liquid chromatography-mass spectrometry (LC-MS), two-dimensional gel electrophoresis, and matrix-assisted laser desorption/ionization mass spectrometry (MALDI-TOF MS), which give comprehensive information about the microorganisms that may be helpful within the diagnosis and coverings of infections. Microorganism identification by mass spectrometry is predicted on identifying a characteristic spectrum of every species so matched with an outsized database within the instrument. MALDI-TOF MS is one of the diagnostic methods, which is a straightforward, quick, and precise technique, and is employed in microbial diagnostic laboratories these days and may replace other diagnostic methods. This method identifies various microorganisms such as bacteria, fungi, parasites, and viruses, which supply comprehensive information. One of the MALDI-TOF MS's crucial applications is bacteriology, which helps identify bacterial species, identify toxins, and study bacterial antibiotic resistance. By knowing these cases, we will act more effectively against bacterial infections.
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37
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Baumbach CM, Müller S, Reuschel M, Uhrlaß S, Nenoff P, Baums CG, Schrödl W. Identification of Zoophilic Dermatophytes Using MALDI-TOF Mass Spectrometry. Front Cell Infect Microbiol 2021; 11:631681. [PMID: 33996620 PMCID: PMC8113951 DOI: 10.3389/fcimb.2021.631681] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 04/14/2021] [Indexed: 01/24/2023] Open
Abstract
Dermatophytoses represent a major health burden in animals and man. Zoophilic dermatophytes usually show a high specificity to their original animal host but a zoonotic transmission is increasingly recorded. In humans, these infections elicit highly inflammatory skin lesions requiring prolonged therapy even in the immunocompetent patient. The correct identification of the causative agent is often crucial to initiate a targeted and effective therapy. To that end, matrix assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) represents a promising tool. The objective of this study was to evaluate the reliability of species identification of zoophilic dermatophytes using MALDI-TOF MS. The investigation of isolates from veterinary clinical samples suspicious of dermatophytoses suggests a good MALDI-TOF MS based identification of the most common zoophilic dermatophyte Microsporum canis. Trichophyton (T.) spp. usually achieved scores only around the cutoff value for secure species identification because of a small number of reference spectra. Moreover, these results need to be interpreted with caution due to the close taxonomic relationship of dermatophytes being reflected in very similar spectra. In our study, the analysis of 50 clinical samples of hedgehogs revealed no correct identification using the provided databases, nor for zoophilic neither for geophilic causative agents. After DNA sequencing, adaptation of sample processing and an individual extension of the in-house database, acceptable identification scores were achieved (T. erinacei and Arthroderma spp., respectively). A score-oriented distance dendrogram revealed clustering of geophilic isolates of four different species of the genus Arthroderma and underlined the close relationship of the important zoophilic agents T. erinacei, T. verrucosum and T. benhamiae by forming a subclade within a larger cluster including different dermatophytes. Taken together, MALDI-TOF MS proofed suitable for the identification of zoophilic dermatophytes provided fresh cultures are used and the reference library was previously extended with spectra of laboratory-relevant species. Performing independent molecular methods, such as sequencing, is strongly recommended to substantiate the findings from morphologic and MALDI-TOF MS analyses, especially for uncommon causative agents.
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Affiliation(s)
- Christina-Marie Baumbach
- Institute of Bacteriology and Mycology, Centre of Infectious Diseases, Faculty of Veterinary Medicine, Leipzig University, Leipzig, Germany
| | - Stefanie Müller
- Institute of Bacteriology and Mycology, Centre of Infectious Diseases, Faculty of Veterinary Medicine, Leipzig University, Leipzig, Germany
| | - Maximilian Reuschel
- Clinic for Small Mammals, Reptiles and Birds, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Silke Uhrlaß
- Laboratory for Medical Microbiology, Mölbis, Germany
| | - Pietro Nenoff
- Laboratory for Medical Microbiology, Mölbis, Germany
| | - Christoph Georg Baums
- Institute of Bacteriology and Mycology, Centre of Infectious Diseases, Faculty of Veterinary Medicine, Leipzig University, Leipzig, Germany
| | - Wieland Schrödl
- Institute of Bacteriology and Mycology, Centre of Infectious Diseases, Faculty of Veterinary Medicine, Leipzig University, Leipzig, Germany
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Shaw D, Ghosh AK, Paul S, Singh S, Chakrabarti A, Kaur H, Narang T, Dogra S, Rudramurthy SM. Matrix-assisted laser desorption/ionisation-time of flight mass spectrometry: Protocol standardisation, comparison and database expansion for faster and reliable identification of dermatophytes. Mycoses 2021; 64:926-935. [PMID: 33851439 DOI: 10.1111/myc.13285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 03/30/2021] [Accepted: 04/07/2021] [Indexed: 12/01/2022]
Abstract
BACKGROUND Accurate and early identification of dermatophytes enables prompt antifungal therapy. However, phenotypic and molecular identification methods are time-consuming. MALDI-TOF MS-based identification is rapid, but an optimum protocol is not available. OBJECTIVES To develop and validate an optimum protein extraction protocol for the efficient and accurate identification of dermatophytes by MALDI-TOF MS. MATERIALS/METHODS Trichophyton mentagrophytes complex (n = 4), T. rubrum (n = 4) and Microsporum gypseum (n = 4) were used for the optimisation of protein extraction protocols. Thirteen different methods were evaluated. A total of 125 DNA sequence confirmed clinical isolates of dermatophytes were used to create and expand the existing database. The accuracy of the created database was checked by visual inspection of MALDI spectra, MSP dendrogram and composite correlation index matrix analysis. The protocol was validated further using 234 isolates. RESULT Among 13 protein extraction methods, six correctly identified dermatophytes but with a low log score (≤1.0). The modified extraction protocol developed provided an elevated log score of 1.6. Significant log score difference was observed between the modified protocol and other existing protocols (T. mentagrophytes complex: 1.6 vs. 0.2-1.0, p < .001; T. rubrum: 1.6 vs. 0.4-1.0, p < .001; M. gypseum:1.6 vs. 0.2-1.0, p < .001). Expansion of the database enabled the identification of all 234 isolates (73.5% with log score ≥2.0 and 26.4% with log scores range: 1.75-1.99). The results were comparable to DNA sequence-based identification. CONCLUSION MALDI-TOF MS with an updated database and efficient protein extraction protocol developed in this study can identify dermatophytes accurately and also reduce the time for identifying them.
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Affiliation(s)
- Dipika Shaw
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Anup K Ghosh
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Saikat Paul
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Shreya Singh
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Arunaloke Chakrabarti
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Harsimran Kaur
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Tarun Narang
- Department of Dermatology, Venereology, and Leprology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Sunil Dogra
- Department of Dermatology, Venereology, and Leprology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Shivaprakash M Rudramurthy
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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Gupta AK, Summerbell RC, Venkataraman M, Quinlan EM. Nondermatophyte mould onychomycosis. J Eur Acad Dermatol Venereol 2021; 35:1628-1641. [PMID: 33763903 DOI: 10.1111/jdv.17240] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/09/2021] [Indexed: 01/21/2023]
Abstract
Nondermatophyte moulds (NDMs) onychomycosis is often difficult to diagnose as NDMs have been considered contaminants of nails. There are several diagnostic methods used to identify NDMs, however, repeated laboratory isolation is recommended to validate pathogenicity. With NDM and mixed infection (dermatophytes plus NDM) onychomycosis on the rise, accurate clinical diagnosis along with mycological tests is recommended. Systemic antifungal agents such as itraconazole and terbinafine (e.g. pulse regimen: 1 pulse = every day for one week, followed by no treatment for three weeks) have shown efficacy in treating onychomycosis caused by various NDMs such as Aspergillus spp., Fusarium spp., Scopulariopsis brevicaulis, and Onychocola canadensis. Studies investigating topical therapy and devices for NDM onychomycosis are limited. The emergence of antifungal resistance necessitates the incorporation of antifungal susceptibility testing into diagnosis when possible, for the management of recalcitrant infections. Case studies documented in the literature show newer azoles such as posaconazole and voriconazole as sometimes effective in treating resistant NDM onychomycosis. Treatment with broad-spectrum antifungal agents (e.g. itraconazole and efinaconazole) and other combination therapy (oral + oral and/or oral + topical) may be considerations in the management of NDM onychomycosis.
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Affiliation(s)
- A K Gupta
- Mediprobe Research Inc., London, ON, Canada.,Department of Dermatology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - R C Summerbell
- Sporometrics, Toronto, ON, Canada.,Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
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Faria DR, Melo RC, Arita GS, Sakita KM, Rodrigues-Vendramini FAV, Capoci IRG, Becker TCA, Bonfim-Mendonça PDS, Felipe MSS, Svidzinski TIE, Kioshima ES. Fungicidal Activity of a Safe 1,3,4-Oxadiazole Derivative Against Candida albicans. Pathogens 2021; 10:pathogens10030314. [PMID: 33800117 PMCID: PMC8001722 DOI: 10.3390/pathogens10030314] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/17/2021] [Accepted: 03/01/2021] [Indexed: 12/30/2022] Open
Abstract
Candida albicans is the most common species isolated from nosocomial bloodstream infections. Due to limited therapeutic arsenal and increase of drug resistance, there is an urgent need for new antifungals. Therefore, the antifungal activity against C. albicans and in vivo toxicity of a 1,3,4-oxadiazole compound (LMM6) was evaluated. This compound was selected by in silico approach based on chemical similarity. LMM6 was highly effective against several clinical C. albicans isolates, with minimum inhibitory concentration values ranging from 8 to 32 µg/mL. This compound also showed synergic effect with amphotericin B and caspofungin. In addition, quantitative assay showed that LMM6 exhibited a fungicidal profile and a promising anti-biofilm activity, pointing to its therapeutic potential. The evaluation of acute toxicity indicated that LMM6 is safe for preclinical trials. No mortality and no alterations in the investigated parameters were observed. In addition, no substantial alteration was found in Hippocratic screening, biochemical or hematological analyzes. LMM6 (5 mg/kg twice a day) was able to reduce both spleen and kidneys fungal burden and further, promoted the suppresses of inflammatory cytokines, resulting in infection control. These preclinical findings support future application of LMM6 as potential antifungal in the treatment of invasive candidiasis.
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Affiliation(s)
- Daniella Renata Faria
- Laboratory of Medical Mycology, Department of Clinical Analysis and Biomedicine, State University of Maringá (UEM), Maringá, Paraná 87020-900, Brazil; (D.R.F.); (R.C.M.); (G.S.A.); (K.M.S.); (F.A.V.R.-V.); (I.R.G.C.); (P.d.S.B.-M.); (T.I.E.S.)
| | - Raquel Cabral Melo
- Laboratory of Medical Mycology, Department of Clinical Analysis and Biomedicine, State University of Maringá (UEM), Maringá, Paraná 87020-900, Brazil; (D.R.F.); (R.C.M.); (G.S.A.); (K.M.S.); (F.A.V.R.-V.); (I.R.G.C.); (P.d.S.B.-M.); (T.I.E.S.)
| | - Glaucia Sayuri Arita
- Laboratory of Medical Mycology, Department of Clinical Analysis and Biomedicine, State University of Maringá (UEM), Maringá, Paraná 87020-900, Brazil; (D.R.F.); (R.C.M.); (G.S.A.); (K.M.S.); (F.A.V.R.-V.); (I.R.G.C.); (P.d.S.B.-M.); (T.I.E.S.)
| | - Karina Mayumi Sakita
- Laboratory of Medical Mycology, Department of Clinical Analysis and Biomedicine, State University of Maringá (UEM), Maringá, Paraná 87020-900, Brazil; (D.R.F.); (R.C.M.); (G.S.A.); (K.M.S.); (F.A.V.R.-V.); (I.R.G.C.); (P.d.S.B.-M.); (T.I.E.S.)
| | - Franciele Abigail Vilugron Rodrigues-Vendramini
- Laboratory of Medical Mycology, Department of Clinical Analysis and Biomedicine, State University of Maringá (UEM), Maringá, Paraná 87020-900, Brazil; (D.R.F.); (R.C.M.); (G.S.A.); (K.M.S.); (F.A.V.R.-V.); (I.R.G.C.); (P.d.S.B.-M.); (T.I.E.S.)
| | - Isis Regina Grenier Capoci
- Laboratory of Medical Mycology, Department of Clinical Analysis and Biomedicine, State University of Maringá (UEM), Maringá, Paraná 87020-900, Brazil; (D.R.F.); (R.C.M.); (G.S.A.); (K.M.S.); (F.A.V.R.-V.); (I.R.G.C.); (P.d.S.B.-M.); (T.I.E.S.)
| | - Tania Cristina Alexandrino Becker
- Laboratory of General Pathology, Department of Basic Health Sciences, State University of Maringá, Maringá (UEM), Maringá, Paraná 87020-900, Brazil;
| | - Patrícia de Souza Bonfim-Mendonça
- Laboratory of Medical Mycology, Department of Clinical Analysis and Biomedicine, State University of Maringá (UEM), Maringá, Paraná 87020-900, Brazil; (D.R.F.); (R.C.M.); (G.S.A.); (K.M.S.); (F.A.V.R.-V.); (I.R.G.C.); (P.d.S.B.-M.); (T.I.E.S.)
| | - Maria Sueli Soares Felipe
- Program of Genomic Sciences and Biotechnology, Catholic University of Brasilia, Brasília 70790-160, Brazil;
| | - Terezinha Inez Estivalet Svidzinski
- Laboratory of Medical Mycology, Department of Clinical Analysis and Biomedicine, State University of Maringá (UEM), Maringá, Paraná 87020-900, Brazil; (D.R.F.); (R.C.M.); (G.S.A.); (K.M.S.); (F.A.V.R.-V.); (I.R.G.C.); (P.d.S.B.-M.); (T.I.E.S.)
| | - Erika Seki Kioshima
- Laboratory of Medical Mycology, Department of Clinical Analysis and Biomedicine, State University of Maringá (UEM), Maringá, Paraná 87020-900, Brazil; (D.R.F.); (R.C.M.); (G.S.A.); (K.M.S.); (F.A.V.R.-V.); (I.R.G.C.); (P.d.S.B.-M.); (T.I.E.S.)
- Correspondence: or ; Tel.: +55-44-3011-4810
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Exploration of tissue distribution of ginsenoside Rg1 by LC-MS/MS and nanospray desorption electrospray ionization mass spectrometry. J Pharm Biomed Anal 2021; 198:113999. [PMID: 33706145 DOI: 10.1016/j.jpba.2021.113999] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 02/17/2021] [Accepted: 02/26/2021] [Indexed: 11/21/2022]
Abstract
Ginsenoside Rg1 (Rg1) was one of the dominent active components in several Panax medicinal species as Panax notoginseng and Panaxginseng with diversified bioactivities. However, the study on tissue distribution of Rg1 remained limited and needed to be further explored for elucidation of its spatial distribution. In the present study, a LC-MS/MS combined with nanospray desorption electrospray ionization (DESI) mass spectrometry method was developed for exploration of tissue distribution of Rg1 at different time points after intravenous administration to rats. Furthermore, a MS inlet-heat method was developed to improve the imaging efficacy of Rg1 in brain tissue. The results obtained from LC-MS/MS analysis indicated that kidney possessed the highest tissue concentration, followed by liver, lung, spleen, heart and brain. Meanwhile, the elimination of Rg1 was swift within 1 h. For the spatial distribution of Rg1 by DESI-MS, Rg1 mainly accumulated in the pelvis section of kidney. Meanwhile, the imaging result of brain implied that Rg1 might be distributed in the pons and medulla oblongata region of brain at 15 min after intravenous administration. It is anticipated that the data on tissue distribution of Rg1 could provide references for further probing its efficacy and drug development.
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Yi Q, Xiao M, Fan X, Zhang G, Yang Y, Zhang JJ, Duan SM, Cheng JW, Li Y, Zhou ML, Yu SY, Huang JJ, Chen XF, Hou X, Kong F, Kudinha T, Xu YC. Evaluation of Autof MS 1000 and Vitek MS MALDI-TOF MS System in Identification of Closely-Related Yeasts Causing Invasive Fungal Diseases. Front Cell Infect Microbiol 2021; 11:628828. [PMID: 33680993 PMCID: PMC7930211 DOI: 10.3389/fcimb.2021.628828] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 01/04/2021] [Indexed: 11/13/2022] Open
Abstract
Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has been accepted as a rapid, accurate, and less labor-intensive method in the identification of microorganisms in clinical laboratories. However, there is limited data on systematic evaluation of its effectiveness in the identification of phylogenetically closely-related yeast species. In this study, we evaluated two commercially available MALDI-TOF systems, Autof MS 1000 and Vitek MS, for the identification of yeasts within closely-related species complexes. A total of 1,228 yeast isolates, representing 14 different species of five species complexes, including 479 of Candida parapsilosis complex, 323 of Candida albicans complex, 95 of Candida glabrata complex, 16 of Candida haemulonii complex (including two Candida auris), and 315 of Cryptococcus neoformans complex, collected under the National China Hospital Invasive Fungal Surveillance Net (CHIF-NET) program, were studied. Autof MS 1000 and Vitek MS systems correctly identified 99.2% and 89.2% of the isolates, with major error rate of 0.4% versus 1.6%, and minor error rate of 0.1% versus 3.5%, respectively. The proportion of isolates accurately identified by Autof MS 1000 and Vitek MS per each yeast complex, respectively, was as follows; C. albicans complex, 99.4% vs 96.3%; C. parapsilosis complex, 99.0% vs 79.1%; C glabrata complex, 98.9% vs 94.7%; C. haemulonii complex, 100% vs 93.8%; and C. neoformans, 99.4% vs 95.2%. Overall, Autof MS 1000 exhibited good capacity in yeast identification while Vitek MS had lower identification accuracy, especially in the identification of less common species within phylogenetically closely-related species complexes.
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Affiliation(s)
- Qiaolian Yi
- Department of Laboratory Medicine, and Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Meng Xiao
- Department of Laboratory Medicine, and Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.,Graduate School, Peking Union Medical College, Beijing, China
| | - Xin Fan
- Department of Infectious Diseases and Clinical Microbiology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Ge Zhang
- Department of Laboratory Medicine, and Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Yang Yang
- Department of Laboratory Medicine, and Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Jing-Jia Zhang
- Department of Laboratory Medicine, and Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Si-Meng Duan
- Department of Laboratory Medicine, and Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Jing-Wei Cheng
- Department of Laboratory Medicine, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Ying Li
- Department of Laboratory Medicine, and Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Meng-Lan Zhou
- Department of Laboratory Medicine, and Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Shu-Ying Yu
- Department of Laboratory Medicine, and Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Jing-Jing Huang
- Department of Laboratory Medicine, and Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Xin-Fei Chen
- Department of Laboratory Medicine, and Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Xin Hou
- Department of Laboratory Medicine, and Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Fanrong Kong
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead Hospital, The University of Sydney, Westmead, NSW, Australia
| | - Timothy Kudinha
- Department of Clinical Laboratory, Charles Sturt University, Orange, NSW, Australia.,New South Wales Health Pathology, Regional and Rural, Orange Hospital, NSW, Australia
| | - Ying-Chun Xu
- Department of Laboratory Medicine, and Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
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Investigation of skin microbiota reveals Mycobacterium ulcerans-Aspergillus sp. trans-kingdom communication. Sci Rep 2021; 11:3777. [PMID: 33580189 PMCID: PMC7881091 DOI: 10.1038/s41598-021-83236-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 01/07/2021] [Indexed: 11/24/2022] Open
Abstract
Mycobacterium ulcerans secrete a series of non-ribosomal-encoded toxins known as mycolactones that are responsible for causing a disabling ulceration of the skin and subcutaneous tissues named Buruli ulcer. The disease is the sole non-contagion among the three most common mycobacterial diseases in humans. Direct contact with contaminated wetlands is a risk factor for Buruli ulcer, responsible for M. ulcerans skin carriage before transcutaneous inoculation with this opportunistic pathogen. In this study, we analysed the bacterial and fungal skin microbiota in individuals exposed to M. ulcerans in Burkina Faso. We showed that M. ulcerans-specific DNA sequences were detected on the unbreached skin of 6/52 (11.5%) asymptomatic farmers living in Sindou versus 0/52 (0%) of those living in the non-endemic region of Tenkodogo. Then, we cultured the skin microbiota of asymptomatic M. ulcerans carriers and negative control individuals, all living in the region of Sindou. A total of 84 different bacterial and fungal species were isolated, 21 from M. ulcerans-negative skin samples, 31 from M. ulcerans-positive samples and 32 from both. More specifically, Actinobacteria, Aspergillus niger and Aspergillus flavus were significantly associated with M. ulcerans skin carriage. We further observed that in vitro, mycolactones induced spore germination of A. flavus, attracting the fungal network. These unprecedented observations suggest that interactions with fungi may modulate the outcome of M. ulcerans skin carriage, opening new venues to the understanding of Buruli ulcer pathology, prophylaxis and treatment of this still neglected tropical infection.
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Hu S, Kang H, Gu F, Wang C, Cheng S, Gong W, Wang L, Gu B, Yang Y. Rapid Detection Method for Pathogenic Candida Captured by Magnetic Nanoparticles and Identified Using SERS via AgNPs . Int J Nanomedicine 2021; 16:941-950. [PMID: 33603361 PMCID: PMC7884937 DOI: 10.2147/ijn.s285339] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 01/19/2021] [Indexed: 01/21/2023] Open
Abstract
Purpose Candidemia infection is common in the clinic and has a high mortality rate. Candida albicans, Candida tropicalis, and Candida krusei are very important and common pathogenic species. Candida is difficult to isolate from clinical samples and culture, and immunological detection cannot distinguish these related strains. Furthermore, Candida has a complex cell wall, which causes difficulties in the extraction of DNA for nucleic acid detection. The purpose of this study was to establish a protocol for the direct identification of Candida from serum. Materials and Methods We synthesized Fe3O4@PEI (where PEI stands for polyethylenimine) magnetic nanoparticles to capture Candida and prepared positively charged silver nanoparticles (AgNPs+) as the substrate for surface-enhanced Raman scattering (SERS). Candida was directly identified from serum by SERS detection. Results Orthogonal partial least squares discriminant analysis (OPLS-DA) was used as the multivariate analysis tool. Principal component analysis confirmed that this method can clearly distinguish common Candida. After 10-fold cross-validation, the accuracy of training data in this model was 100% and the accuracy of test data was 99.8%, indicating that the model has good classification ability. Conclusion The detection could be completed within 40 minutes using Fe3O4@PEI and AgNPs+ prepared in advance. This is the first time that Fe3O4@PEI was used in the detection of Candida by SERS. We report the first rapid method to identify fungi directly from serum without breaking the cell wall to extract DNA from the fungi.
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Affiliation(s)
- Shan Hu
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing Key Laboratory of New Molecular Diagnosis Technologies for Infectious Diseases, Beijing, 100850, People's Republic of China.,Department of Laboratory Medicine, Xuzhou Tumor Hospital, Xuzhou, 221005, People's Republic of China.,Xuzhou Key Laboratory of Laboratory Diagnostics, Medical Technology School of Xuzhou Medical University, Xuzhou, 221004, People's Republic of China
| | - Haiquan Kang
- Department of Laboratory Medicine, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221006, People's Republic of China
| | - Feng Gu
- Department of Laboratory Medicine, Xuzhou Tumor Hospital, Xuzhou, 221005, People's Republic of China
| | - Chongwen Wang
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing Key Laboratory of New Molecular Diagnosis Technologies for Infectious Diseases, Beijing, 100850, People's Republic of China.,College of Life Sciences, Anhui Agricultural University, Hefei, 230036, People's Republic of China
| | - Siyun Cheng
- Xuzhou Key Laboratory of Laboratory Diagnostics, Medical Technology School of Xuzhou Medical University, Xuzhou, 221004, People's Republic of China
| | - Wenjing Gong
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing Key Laboratory of New Molecular Diagnosis Technologies for Infectious Diseases, Beijing, 100850, People's Republic of China
| | - Liping Wang
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing Key Laboratory of New Molecular Diagnosis Technologies for Infectious Diseases, Beijing, 100850, People's Republic of China
| | - Bing Gu
- Xuzhou Key Laboratory of Laboratory Diagnostics, Medical Technology School of Xuzhou Medical University, Xuzhou, 221004, People's Republic of China.,Department of Laboratory Medicine, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221006, People's Republic of China
| | - Ying Yang
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing Key Laboratory of New Molecular Diagnosis Technologies for Infectious Diseases, Beijing, 100850, People's Republic of China
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Wang J, Wang H, Cai K, Yu P, Liu Y, Zhao G, Chen R, Xu R, Yu M. Evaluation of three sample preparation methods for the identification of clinical strains by using two MALDI-TOF MS systems. JOURNAL OF MASS SPECTROMETRY : JMS 2021; 56:e4696. [PMID: 33421261 PMCID: PMC7900945 DOI: 10.1002/jms.4696] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 11/16/2020] [Accepted: 12/09/2020] [Indexed: 05/07/2023]
Abstract
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has revolutionized the microbial identification, especially in the clinical microbiology laboratories. However, although numerous studies on the identification of microorganisms by MALDI-TOF MS have been reported previously, few studies focused on the effect of pretreatment on identification. Due to the sensitivity of MALDI-TOF MS, different preparation methods will lead to changes in microbial protein fingerprints. In this study, for evaluating a more appropriate preparation method for the clinical microbiology identification, we analyzed the performance of three sample preparation methods on two different MALDI-TOF MS systems. A total of 321 clinical isolates, 127 species, were employed in the comparative study of three different sample preparation methods including the direct colony transfer method (DCTM), the on-target extraction method (OTEM), and the in-tube extraction method (ITEM) compatible with MALDI-TOF MS. All isolates were tested on the Microflex LT and Autof ms1000 devices. The spectra were analyzed using the Bruker biotyper and the Autof ms1000 systems. The results were confirmed by 16/18S rRNA sequencing. Results reveal that the accuracies of isolates identification by Bruker biotyper successfully identified 83.8%, 96.0%, and 95.3% after performing the DCTM, OTEM, and ITEM, respectively, while the Autof ms1000 identified 97.5%, 100%, and 99.7%. These data suggested that the identification rates are comparable among the three preparation methods using the Autof ms1000 and Bruker microflex LT systems but the OTEM is more suitable and necessary for clinical application, owing to its key advantages of simplicity and accuracy.
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Affiliation(s)
- Jinghua Wang
- Department of Clinical Microbiology LaboratoryShanghai Center for Clinical LaboratoryShanghaiChina
| | - Hualiang Wang
- Department of Clinical Microbiology LaboratoryShanghai Center for Clinical LaboratoryShanghaiChina
| | - Keya Cai
- Diagnostics DepartmentAutobio Diagnostics Co., Ltd.ZhengzhouChina
| | - Peijuan Yu
- Department of Clinical LaboratorySecond Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Yajuan Liu
- Diagnostics DepartmentAutobio Diagnostics Co., Ltd.ZhengzhouChina
| | - Gaoling Zhao
- Diagnostics DepartmentAutobio Diagnostics Co., Ltd.ZhengzhouChina
| | - Rong Chen
- Department of Clinical Microbiology LaboratoryShanghai Center for Clinical LaboratoryShanghaiChina
| | - Rong Xu
- Department of Clinical Microbiology LaboratoryShanghai Center for Clinical LaboratoryShanghaiChina
| | - Maowen Yu
- Department of Clinical LaboratoryJintang First People's HospitalChengduChina
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Lu JJ, Lo HJ, Lee CH, Chen MJ, Lin CC, Chen YZ, Tsai MH, Wang SH. The Use of MALDI-TOF Mass Spectrometry to Analyze Commensal Oral Yeasts in Nursing Home Residents. Microorganisms 2021; 9:microorganisms9010142. [PMID: 33435490 PMCID: PMC7828027 DOI: 10.3390/microorganisms9010142] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/17/2020] [Accepted: 01/06/2021] [Indexed: 12/20/2022] Open
Abstract
Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a rapid and accurate method to identify microorganisms in clinical laboratories. This study isolates yeast-like microorganisms in the oral washes that are collected from non-bedridden nursing home residents, using CHROMagar Candida plates, and identifies them using Bruker MALDI-TOF MS. The ribosomal DNA sequences of the isolates are then examined. Three hundred and twenty yeast isolates are isolated from the oral washes. Candida species form the majority (78.1%), followed by Trichosporon/Cutaneotrichosporon species (8.8%). Bruker MALDI-TOF MS gives a high-level confidence, with a log(score) value of ≥1.8, and identifies 96.9% of the isolates. There are six inconclusive results (1.9%), and those sequences are verified as rare clinical species, including Candida ethanolica, Cutaneotrichosporon jirovecii, Exophiala dermatitidis, and Fereydounia khargensis. Almost all of the isolates have a regular color on the CHROMagar Candida plates. If the colonies are grouped by color on the plates, a specific dominant yeast species is present in each color group, except for purple or orange isolates. In conclusion, MALDI-TOF MS is verified as a fast, accurate and practical method to analyze oral yeasts in elderly subjects.
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Affiliation(s)
- Jang-Jih Lu
- Department of Laboratory Medicine, Chang-Gung Memorial Hospital Linkou, Taoyuan City 333, Taiwan; (J.-J.L.); (C.-H.L.); (M.-J.C.)
- Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan City 333, Taiwan
- Department of Medicine, College of Medicine, Chang Gung University, Taoyuan City 333, Taiwan
| | - Hsiu-Jung Lo
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli County 350, Taiwan; (H.-J.L.); (C.-C.L.); (Y.-Z.C.)
- School of Dentistry, China Medical University, Taichung City 404, Taiwan
| | - Chih-Hua Lee
- Department of Laboratory Medicine, Chang-Gung Memorial Hospital Linkou, Taoyuan City 333, Taiwan; (J.-J.L.); (C.-H.L.); (M.-J.C.)
| | - Mei-Jun Chen
- Department of Laboratory Medicine, Chang-Gung Memorial Hospital Linkou, Taoyuan City 333, Taiwan; (J.-J.L.); (C.-H.L.); (M.-J.C.)
- Division of Neonatology and Pediatric Hematology/Oncology, Department of Pediatrics, Chang Gung Memorial Hospital, Yunlin County 638, Taiwan;
| | - Chih-Chao Lin
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli County 350, Taiwan; (H.-J.L.); (C.-C.L.); (Y.-Z.C.)
| | - Yin-Zhi Chen
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli County 350, Taiwan; (H.-J.L.); (C.-C.L.); (Y.-Z.C.)
| | - Ming-Horng Tsai
- Division of Neonatology and Pediatric Hematology/Oncology, Department of Pediatrics, Chang Gung Memorial Hospital, Yunlin County 638, Taiwan;
| | - Shao-Hung Wang
- Department of Microbiology, Immunology and Biopharmaceuticals, National Chiayi University, Chiayi City 600, Taiwan
- Correspondence: ; Tel.: +886-5-2717225; Fax: +886-5-2717831
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47
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Korem M, Cohen MJ, Michael-Gayego A, Castiel D, Assous MV, Amit S. Misidentification of Candida dubliniensis isolates with the VITEK MS. J Mycol Med 2021; 31:101107. [PMID: 33388671 DOI: 10.1016/j.mycmed.2020.101107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 12/08/2020] [Accepted: 12/18/2020] [Indexed: 11/18/2022]
Abstract
The phylogenetic relatedness of Candida dubliniensis and C. albicans may lead to misidentification of C. dubliniensis and underestimation of its clinical significance. We evaluated the performance of VITEK-MS in identifying C. dubliniensis isolates following growth on different culture media. Correct identification was documented in 98% of the isolates grown on blood agar media whereas only 44% were correctly identified from SDA or CHROMagar. The use of non-manufacturer validated media for identifying C. dubliniensis with VITEK-MS, may result in misidentification of these isolates as C. albicans. This finding calls for reassessing the accuracy of fungal isolates identification in local workflows using non-validated culture media.
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Affiliation(s)
- Maya Korem
- Faculty of Medicine, Hebrew University of Jerusalem Department of Clinical Microbiology and Infectious Diseases, Hadassah Medical Center, Jerusalem, Israel.
| | - Matan Joel Cohen
- Clalit Health Services, Jerusalem District, affiliated with the Hebrew University Hadassah Medical School, Jerusalem, Israel
| | - Ayelet Michael-Gayego
- Faculty of Medicine, Hebrew University of Jerusalem Department of Clinical Microbiology and Infectious Diseases, Hadassah Medical Center, Jerusalem, Israel
| | - Dafna Castiel
- Faculty of Medicine, Hebrew University of Jerusalem Department of Clinical Microbiology and Infectious Diseases, Hadassah Medical Center, Jerusalem, Israel
| | - Marc V Assous
- Clinical Microbiology laboratory, Shaare Zedek Medical Center, Affiliated with the Hebrew University Hadassah Medical School, Jerusalem, Israel
| | - Sharon Amit
- Clinical Microbiology laboratory, The Chaim Sheba Medical Center, Ramat Gan, Israel
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48
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Aboul-Ella H, Hamed R, Abo-Elyazeed H. Recent trends in rapid diagnostic techniques for dermatophytosis. Int J Vet Sci Med 2020; 8:115-123. [PMID: 33426048 PMCID: PMC7751388 DOI: 10.1080/23144599.2020.1850204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 10/24/2020] [Accepted: 11/09/2020] [Indexed: 11/04/2022] Open
Abstract
Dermatophytosis is a common contagious disease of both humans and animals. It is caused by a group of filamentous fungi known as dermatophytes, including several genera and various species. An accurate diagnosis of dermatophytes as a causative agent of a skin lesion requires up to one month of conventional laboratory diagnostics. The conventional gold standard diagnostic method is a direct microscopic examination followed by 3 to 4 weeks of Sabouraud's dextrose agar (SDA) culturing, and it may require further post-culturing identification through biochemical tests or microculture technique application. The laborious, exhaustive, and time-consuming gold standard method was a real challenge facing all dermatologists to achieve a rapid, accurate dermatophytosis diagnosis. Various studies developed more rapid, accurate, reliable, sensitive, and specific diagnostic tools. All developed techniques showed more rapidity than the classical method but variable specificities and sensitivities. An extensive bibliography is included and discussed through this review, showing recent variable dermatophytes diagnostic categories with an illustration of weaknesses, strengths, and prospects.
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Affiliation(s)
- Hassan Aboul-Ella
- Department of Microbiology, Faculty of Veterinary Medicine, Cairo University, GizaEgypt
| | - Rafik Hamed
- Bacteriology Biotechnology Diagnostics Department, Institute for Evaluation of Veterinary Biologics (CLEVB), Agricultural Research Center (ARC), Cairo, Egypt
| | - Heidy Abo-Elyazeed
- Department of Microbiology, Faculty of Veterinary Medicine, Cairo University, GizaEgypt
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49
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Update on Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry Identification of Filamentous Fungi. J Clin Microbiol 2020; 58:JCM.01263-20. [PMID: 32938733 DOI: 10.1128/jcm.01263-20] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)-based species identification has found its place in many clinical routine diagnostic laboratories over the past years, allowing significantly reduced turnaround times and high-precision results. With regard to MALDI-TOF MS for filamentous fungi, here, we discuss different approaches for sample processing and growth conditions before analysis. In particular, we review the performances of different commercially available databases as well as the potential of complementary (self-constructed) in-house databases.
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50
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Nabet C, Imbert S, Normand AC, Blanchet D, Chanlin R, Becker P, Demar M, Piarroux R. Unexpected mould diversity in clinical isolates from French Guiana and associated identification difficulties. Med Mycol 2020; 59:myaa091. [PMID: 33111143 DOI: 10.1093/mmy/myaa091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/05/2020] [Accepted: 10/12/2020] [Indexed: 12/14/2022] Open
Abstract
New mold species are increasingly reported in invasive fungal infections. However, these fungi are often misdiagnosed or undiagnosed due to the use of inappropriate laboratory diagnostic tools. Tropical countries, such as French Guiana, harbor a vast diversity of environmental fungi representing a potential source of emerging pathogens. To assess the impact of this diversity on the accuracy of mold-infection diagnoses, we identified mold clinical isolates in French Guiana during a five-month follow-up using both microscopy and matrix-assisted laser desorption ionization time-of-flight mass spectrometry. In total, 38.8% of the 98 obtained molds isolates could not be identified and required a DNA-based identification. Fungal diversity was high, including 46 species, 26 genera, and 13 orders. Fungal ecology was unusual, as Aspergillus species accounted for only 27% of all isolates, and the Nigri section was the most abundant out of the six detected Aspergillus sections. Macromycetes (orders Agaricales, Polyporales, and Russulales) and endophytic fungi accounted for respectively 11% and 14% of all isolates. Thus, in tropical areas with high fungal diversity, such as French Guiana, routine mold identification tools are inadequate. Molecular identifications, as well as morphological descriptions, are necessary for the construction of region-specific mass spectrum databases. These advances will improve the diagnosis and clinical management of new fungal infections. LAY SUMMARY In French Guiana, environmental fungal diversity may be a source of emerging pathogens. We evaluated microscopy and mass spectrometry to identify mold clinical isolates. With 39% of unidentified isolates, a region-specific mass spectrum database would improve the diagnosis of new fungal infections.
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Affiliation(s)
- C Nabet
- Sorbonne Université, INSERM, Institut Pierre-Louis d'Epidémiologie et de Santé Publique, AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Service de Parasitologie-Mycologie, Paris, France
| | - S Imbert
- Sorbonne Université, INSERM, CNRS, Centre d'Immunologie et des Maladies Infectieuses, Cimi-Paris, AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Service de Parasitologie-Mycologie, Paris, France
| | - A C Normand
- Sorbonne Université, INSERM, Institut Pierre-Louis d'Epidémiologie et de Santé Publique, AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Service de Parasitologie-Mycologie, Paris, France
| | - D Blanchet
- Department of Parasitology-Mycology, Hôpital Andrée Rosemon, Cayenne, French Guiana
| | - R Chanlin
- Department of Parasitology-Mycology, Hôpital Andrée Rosemon, Cayenne, French Guiana
| | - P Becker
- Sciensano, BCCM/IHEM collection, Mycology and Aerobiology Unit, Brussels, Belgium
| | - M Demar
- Department of Parasitology-Mycology, Hôpital Andrée Rosemon, Cayenne, French Guiana
- EA 3593, Ecosystèmes Amazoniens et Pathologies Tropicales, Université de Guyane, Cayenne, French Guiana
| | - R Piarroux
- Sorbonne Université, INSERM, Institut Pierre-Louis d'Epidémiologie et de Santé Publique, AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Service de Parasitologie-Mycologie, Paris, France
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