1
|
Won EJ, Park SJ, Jo U, Sung H, Choi EJ, Kim MN. Phaeohyphomycosis due to Pleurostomophora richardsiae in a Patient with a Hematological Malignancy. MYCOBIOLOGY 2023; 51:468-470. [PMID: 38179113 PMCID: PMC10763908 DOI: 10.1080/12298093.2023.2275500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 10/20/2023] [Indexed: 01/06/2024]
Affiliation(s)
- Eun Jeong Won
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Sook-Ja Park
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Uiree Jo
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Heungsup Sung
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Eun-Ji Choi
- Department of Hematology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Mi-Na Kim
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| |
Collapse
|
2
|
Lecerf P, De Paepe R, Jazaeri Y, Normand AC, Martiny D, Packeu A. Evaluation of a Liquid Media MALDI-TOF MS Protocol for the Identification of Dermatophytes Isolated from Tinea capitis Infections. J Fungi (Basel) 2022; 8:jof8121248. [PMID: 36547581 PMCID: PMC9783569 DOI: 10.3390/jof8121248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 11/15/2022] [Accepted: 11/18/2022] [Indexed: 11/29/2022] Open
Abstract
One of the most common types of tinea is the superficial infection of the hair and scalp area known as tinea capitis. It is responsible for frequent outbreaks in nurseries and schools and represents a global health problem. Correct identification of the infection agent is essential in the determination of the infection source, epidemiological course, and treatment initiation. The conventional identification methods (direct exam, culture, DNA sequencing) are time-consuming, require experienced staff, are time-consuming, and the latter is expensive for routine identifications. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is gaining new ground for routine identification of filamentous fungi. The main advantages of MALDI-TOF MS are its rapid and accurate identification capability, relatively low cost, and easy integration into the laboratory routine. Its accuracy heavily depends on the quality of the reference spectra database. Identification of clinical isolates with MALDI-TOF MS protocol requires a sub-culturing step to ensure reliable identification. It can take days to weeks before fungal growth appears on solid medium. In this study, a unique MALDI-TOF MS protocol using liquid cultures of dermatophyte species was developed in order to shorten the turnaround time for the culture and identification of clinical isolates. Material and Method A standard MALDI-TOF MS protocol was adapted for liquid instead of solid cultures. Three different databases were tested. Results Using the liquid media MALDI-TOF MS protocol, a global rate of 62% correct identification (RCI) was obtained, compared with 87% for the protocol based on solid cultures. Trichophyton tonsurans was not correctly identified in all isolates using liquid cultures, with 88% of the isolates misidentified as Trichophyton interdigitale. The turnaround time for primary isolates for the solid and liquid protocols were respectively 11.7 and 11.6 days (no significant difference between both methods (p = 0.96)). Conclusions The newly designed liquid MALDI-TOF MS protocol did not lead to a significantly shorter turnaround time for the identification of dermatophytes isolated from tinea capitis infections. The turnaround time for the method with primary isolates was not significantly lower, and the rate of correct identification decreased remarkably, which emphasizes the need for a sub-culturing step. Using different database did not lead to improvement in turnaround time or rate of correct identification. This study highlights the importance of the medium and the reference database when performing MALDI-TOF MS.
Collapse
Affiliation(s)
- Pauline Lecerf
- Dermatology Department, University Hospital Brugmann & Saint-Pierre, Université Libre de Bruxelles, 1020 Brussels, Belgium
- Correspondence:
| | - Roelke De Paepe
- Mycology and Aerobiology Department, Sciensano, 1050 Brussels, Belgium
| | - Yasaman Jazaeri
- Dermatology Department, University Hospital Brugmann & Saint-Pierre, Université Libre de Bruxelles, 1020 Brussels, Belgium
| | - Anne-Cécile Normand
- Parasitology/Mycology Department AP-HP, Hôpitaux de Paris, 75013 Paris, France
| | - Delphine Martiny
- Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles Universitair Laboratorium Brussel (LHUB-ULB), Université Libre de Bruxelles (ULB), 1000 Brussels, Belgium
- Faculty of Medicine and Franco, University of Mons (UMONS), 7000 Mons, Belgium
| | - Ann Packeu
- Mycology and Aerobiology Department, Sciensano, 1050 Brussels, Belgium
- BCCM/IHEM Fungal Collection, Sciensano, Mycology and Aerobiology Section, 1050 Brussels, Belgium
| |
Collapse
|
3
|
Production of Satratoxin G and H Is Tightly Linked to Sporulation in Stachybotrys chartarum. Toxins (Basel) 2022; 14:toxins14080515. [PMID: 36006177 PMCID: PMC9413001 DOI: 10.3390/toxins14080515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 07/22/2022] [Accepted: 07/26/2022] [Indexed: 12/10/2022] Open
Abstract
Stachybotrys chartarum is a toxigenic fungus that is frequently isolated from damp building materials or improperly stored forage. Macrocyclic trichothecenes and in particular satratoxins are the most potent mycotoxins known to be produced by this fungus. Exposure of humans or animals to these secondary metabolites can be associated with severe health problems. To assess the pathogenic potential of S. chartarum isolates, it is essential to cultivate them under conditions that reliably promote toxin production. Potato dextrose agar (PDA) was reported to be the optimal nutrition medium for satratoxin production. In this study, the growth of S. chartarum genotype S strains on PDA from two manufacturers led to divergent results, namely, well-grown and sporulating cultures with high satratoxin concentrations (20.8 ± 0.4 µg/cm2) versus cultures with sparse sporulation and low satratoxin production (0.3 ± 0.1 µg/cm2). This finding is important for any attempt to identify toxigenic S. chartarum isolates. Further experiments performed with the two media provided strong evidence for a link between satratoxin production and sporulation. A comparison of three-point and one-point cultures grown on the two types of PDA, furthermore, demonstrated an inter-colony communication that influences both sporulation and mycotoxin production of S. chartarum genotype S strains.
Collapse
|
4
|
Sarvestani HK, Ramandi A, Getso MI, Razavyoon T, Javidnia J, Golrizi MB, Saboor-Yaraghi AA, Ansari S. Mass spectrometry in research laboratories and clinical diagnostic: a new era in medical mycology. Braz J Microbiol 2022; 53:689-707. [PMID: 35344203 PMCID: PMC9151960 DOI: 10.1007/s42770-022-00715-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 02/14/2022] [Indexed: 02/01/2023] Open
Abstract
Diagnosis by clinical mycology laboratory plays a critical role in patient care by providing definitive knowledge of the cause of infection and antimicrobial susceptibility data to physicians. Rapid diagnostic methods are likely to improve patient. Aggressive resuscitation bundles, adequate source control, and appropriate antibiotic therapy are cornerstones for success in the treatment of patients. Routine methods for identifying clinical specimen fungal pathogen are based on the cultivation on different media with the subsequent examination of its phenotypic characteristics comprising a combination of microscopic and colony morphologies. As some fungi cannot be readily identified using these methods, molecular diagnostic methods may be required. These methods are fast, but it can cost a lot. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is suitable for high-throughput and rapid diagnostics at low costs. It can be considered an alternative for conventional biochemical and molecular identification systems in a microbiological laboratory. The reliability and accuracy of this method have been scrutinized in many surveys and have been compared with several methods including sequencing and molecular methods. According to these findings, the reliability and accuracy of this method are very high and can be trusted. With all the benefits of this technique, the libraries of MALDI-TOF MS need to be strengthened to enhance its performance. This review provides an overview of the most recent research literature that has investigated the applications and usage of MT-MS to the identification of microorganisms, mycotoxins, antifungal susceptibility examination, and mycobiome research.
Collapse
Affiliation(s)
- Hasti Kamali Sarvestani
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Alireza Ramandi
- Students' Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Muhammad Ibrahim Getso
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
- Department of Medical Microbiology and Parasitology, College of Health Sciences, Bayero University, PMB, Kano, 3011, Nigeria
| | - Taraneh Razavyoon
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Javad Javidnia
- Student Research Committee, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
- Department of Medical Mycology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Miaad Banay Golrizi
- Student Research Committee, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Ali-Akbar Saboor-Yaraghi
- Department of Nutrition and Biochemistry, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
- Department of Medical Parasitology and Mycology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Saham Ansari
- Department of Medical Parasitology and Mycology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| |
Collapse
|
5
|
Evaluation of Nanopore Sequencing as a Diagnostic Tool for the Rapid Identification of Mycoplasma bovis from Individual and Pooled Respiratory Tract Samples. J Clin Microbiol 2021; 59:e0111021. [PMID: 34550807 DOI: 10.1128/jcm.01110-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Rapid identification of Mycoplasma bovis infections in cattle is a key factor to guide antimicrobial therapy and biosecurity measures. Recently, Nanopore sequencing became an affordable diagnostic tool for both clinically relevant viruses and bacteria, but the diagnostic accuracy for M. bovis identification is undocumented. Therefore, in this study Nanopore sequencing was compared to rapid identification of M. bovis with matrix-assisted laser desorption ionization-time of flight mass spectrometry (RIMM) and a triplex real-time PCR assay in a Bayesian latent class model (BLCM) for M. bovis in bronchoalveolar lavage fluid (BALf) samples obtained from calves. In practice, pooling of samples is often used to save money, but the influence on diagnostic accuracy has not been described for M. bovis. Therefore, a convenience sample of 17 pooled samples containing 5 individual BALf samples per farm was analyzed as well. The results for the pooled samples were compared with those for the individual samples to determine sensitivity and specificity. The BLCM showed good sensitivity (77.3% [95% credible interval, 57.8 to 92.8%]) and high specificity (97.4% [91.5 to 99.7%]) for Nanopore sequencing, compared to RIMM (sensitivity, 93.0% [76.8 to 99.5%]; specificity, 91.3% [82.5 to 97.0%]) and real-time PCR (sensitivity, 94.6% [89.7 to 97.7%]; specificity, 86.0% [76.1 to 93.6%]). Sensitivity and specificity of pooled analysis for M. bovis were 85.7% (95% confidence interval, 59.8 to 111.6%) and 90.0% (71.4 to 108.6%%), respectively, for Nanopore sequencing and 100% (100% to 100%) and 88.9% (68.4 to 109.4%) for RIMM. In conclusion, Nanopore sequencing is a rapid, reliable tool for the identification of M. bovis. To reduce costs and increase the chance of M. bovis identification, pooling of 5 samples for Nanopore sequencing and RIMM is possible.
Collapse
|
6
|
MALDI-TOF MS: Foundations and a Practical Approach to the Clinically Relevant Filamentous Fungi Identification. CURRENT FUNGAL INFECTION REPORTS 2021. [DOI: 10.1007/s12281-021-00423-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
|
7
|
Szultka-Młyńska M, Janiszewska D, Pomastowski P, Złoch M, Kupczyk W, Buszewski B. Identification of Bacteria Associated with Post-Operative Wounds of Patients with the Use of Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry Approach. Molecules 2021; 26:5007. [PMID: 34443592 PMCID: PMC8402041 DOI: 10.3390/molecules26165007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/13/2021] [Accepted: 08/16/2021] [Indexed: 11/25/2022] Open
Abstract
The bacterial infection of post-operative wounds is a common health problem. Therefore, it is important to investigate fast and accurate methods of identifying bacteria in clinical samples. The aim of the study was to analyse the use of the MALDI-TOF MS technique to identify microorganism wounds that are difficult to heal. The most common bacteria are Escherichia coli, Staphylococcus spp., and Enterococcus spp. We also demonstrate the effect of culture conditions, such as the used growth medium (solid: Brain Heart Infusion Agar, Mueller Hilton Agar, Glucose Bromocresol Purple Agar, and Vancomycin Resistance Enterococci Agar Base and liquid: Tryptic Soy Broth and BACTEC Lytic/10 Anaerobic/F), the incubation time (4, 6, and 24h), and the method of the preparation of bacterial protein extracts (the standard method based on the Bruker guideline, the Sepsityper method) to identify factors and the quality of the obtained mass spectra. By comparing the protein profiles of bacteria from patients not treated with antibiotics to those treated with antibiotics based on the presence/absence of specific signals and using the UniProt platform, it was possible to predict the probable mechanism of the action of the antibiotic used and the mechanism of drug resistance.
Collapse
Affiliation(s)
- Małgorzata Szultka-Młyńska
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, Gagarin 7, 87-100 Torun, Poland; (D.J.); (B.B.)
| | - Daria Janiszewska
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, Gagarin 7, 87-100 Torun, Poland; (D.J.); (B.B.)
| | - Paweł Pomastowski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wilenska 4, 87-100 Torun, Poland; (P.P.); (M.Z.)
| | - Michał Złoch
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wilenska 4, 87-100 Torun, Poland; (P.P.); (M.Z.)
| | - Wojciech Kupczyk
- Department of General, Gastroenterological and Oncological Surgery, Collegium Medicum, Nicolaus Copernicus University, 87-100 Torun, Poland;
| | - Bogusław Buszewski
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, Gagarin 7, 87-100 Torun, Poland; (D.J.); (B.B.)
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wilenska 4, 87-100 Torun, Poland; (P.P.); (M.Z.)
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
Muggia L, Ametrano CG, Sterflinger K, Tesei D. An Overview of Genomics, Phylogenomics and Proteomics Approaches in Ascomycota. Life (Basel) 2020; 10:E356. [PMID: 33348904 PMCID: PMC7765829 DOI: 10.3390/life10120356] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/10/2020] [Accepted: 12/12/2020] [Indexed: 12/26/2022] Open
Abstract
Fungi are among the most successful eukaryotes on Earth: they have evolved strategies to survive in the most diverse environments and stressful conditions and have been selected and exploited for multiple aims by humans. The characteristic features intrinsic of Fungi have required evolutionary changes and adaptations at deep molecular levels. Omics approaches, nowadays including genomics, metagenomics, phylogenomics, transcriptomics, metabolomics, and proteomics have enormously advanced the way to understand fungal diversity at diverse taxonomic levels, under changeable conditions and in still under-investigated environments. These approaches can be applied both on environmental communities and on individual organisms, either in nature or in axenic culture and have led the traditional morphology-based fungal systematic to increasingly implement molecular-based approaches. The advent of next-generation sequencing technologies was key to boost advances in fungal genomics and proteomics research. Much effort has also been directed towards the development of methodologies for optimal genomic DNA and protein extraction and separation. To date, the amount of proteomics investigations in Ascomycetes exceeds those carried out in any other fungal group. This is primarily due to the preponderance of their involvement in plant and animal diseases and multiple industrial applications, and therefore the need to understand the biological basis of the infectious process to develop mechanisms for biologic control, as well as to detect key proteins with roles in stress survival. Here we chose to present an overview as much comprehensive as possible of the major advances, mainly of the past decade, in the fields of genomics (including phylogenomics) and proteomics of Ascomycota, focusing particularly on those reporting on opportunistic pathogenic, extremophilic, polyextremotolerant and lichenized fungi. We also present a review of the mostly used genome sequencing technologies and methods for DNA sequence and protein analyses applied so far for fungi.
Collapse
Affiliation(s)
- Lucia Muggia
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
| | - Claudio G. Ametrano
- Grainger Bioinformatics Center, Department of Science and Education, The Field Museum, Chicago, IL 60605, USA;
| | - Katja Sterflinger
- Academy of Fine Arts Vienna, Institute of Natual Sciences and Technology in the Arts, 1090 Vienna, Austria;
| | - Donatella Tesei
- Department of Biotechnology, University of Natural Resources and Life Sciences, 1190 Vienna, Austria;
| |
Collapse
|
10
|
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.
Collapse
|
11
|
Development and Validation of an In-House Library for Filamentous Fungi Identification by MALDI-TOF MS in a Clinical Laboratory in Medellin (Colombia). Microorganisms 2020; 8:microorganisms8091362. [PMID: 32899976 PMCID: PMC7563289 DOI: 10.3390/microorganisms8091362] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 08/30/2020] [Accepted: 09/04/2020] [Indexed: 12/15/2022] Open
Abstract
Identification of filamentous fungi by conventional phenotypic methods are time-consuming, and a correct identification at the species level is prone to errors. Therefore, a more accurate and faster time-to-results, and cost-effective technique, is required, such as the Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS). In this study, we describe the development of an in-house spectra library for the identification of filamentous fungi frequently isolated from patients with infections. An in-house spectra library was constructed using 14 reference strains grown in solid medium. Clinical isolates were identified either by the in-house spectra library or the Biotyper commercial library from Bruker Daltonics. Fungal identification was carried following the Biotyper’s established scores: ≤1.699: not reliably identified (NRI); 1.700–1.999: genus-level; ≥2.000: species-level. Clinical isolates were identified, with the in-house library, at species- and genus-level at 88.70% (55) and 3.22% (2), respectively. While 4.80% (3) was NRI and 3.22% (2) was discrepant concerning sequencing. On the contrary, identification up to species and genus-level with the commercial library was 44.44% (16) and 22.22% (8), respectively. NRI and the discrepancy was 30.55% (11) and 2.77% (1), respectively. For the reaming 26 isolates, 16 from Neoscytalidium dimidiatum and 10 from Sporothrix spp., respectively, the absence of spectrum and the specific spectra within the Sporothrix complex in the commercial library resulted in the inability to obtain an identification. In conclusion, the current results advocate the importance that each clinical microbiological laboratory needs to develop an ad hoc library associated with the MALDI-TOF MS fungal identification to overcome the limitations of the available commercial libraries.
Collapse
|
12
|
Rapid Identification of Mycoplasma bovis Strains from Bovine Bronchoalveolar Lavage Fluid with Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry after Enrichment Procedure. J Clin Microbiol 2020; 58:JCM.00004-20. [PMID: 32229599 DOI: 10.1128/jcm.00004-20] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 03/23/2020] [Indexed: 12/11/2022] Open
Abstract
Mycoplasma bovis is a leading cause of pneumonia in modern calf rearing. Fast identification is essential to ensure appropriate antimicrobial therapy. Therefore, the objective of this study was to develop a protocol to identify M. bovis from bronchoalveolar lavage fluid (BALf) with matrix-assisted laser desorption ionization-time of flight mass spectrometry MALDI-TOF MS and to determine the diagnostic accuracy in comparison with other techniques. BALf was obtained from 104 cattle, and the presence of M. bovis was determined in the following three ways: (i) rapid identification of M. bovis with MALDI-TOF MS (RIMM) (BALf was enriched and after 24, 48, and 72 h of incubation and was analyzed using MALDI-TOF MS), (ii) triplex real-time PCR for M. bovis, Mycoplasma bovirhinis, and Mycoplasma dispar, and (iii) 10-day incubation on selective-indicative agar. The diagnostic accuracy of the three tests was determined with Bayesian latent class modeling (BLCM). After 24 h of enrichment, M. bovis was identified with MALDI-TOF MS in 3 out of 104 BALf samples. After 48 and 72 h of enrichment, 32/104 and 38/100 samples, respectively, were M. bovis positive. Lipase-positive Mycoplasma-like colonies were seen in 28 of 104 samples. Real-time PCR resulted in 28/104 positive and 12/104 doubtful results for M. bovis The BLCM showed a sensitivity (Se) and specificity (Sp) of 86.6% (95% credible interval [CI], 69.4% to 97.6%) and 86.4% (CI, 76.1 to 93.8) for RIMM. For real-time PCR, Se was 94.8% (CI, 89.9 to 97.9) and Sp was 88.9% (CI, 78.0 to 97.4). For selective-indicative agar, Se and Sp were 70.5% (CI, 52.1 to 87.1) and 93.9% (CI, 85.9 to 98.4), respectively. These results suggest that rapid identification of M. bovis with MALDI-TOF MS after an enrichment procedure is a promising test for routine diagnostics in veterinary laboratories.
Collapse
|
13
|
Zhang F, Lyon CJ, Walls RJ, Ning B, Fan J, Hu TY. Cathepsin B Dependent Cleavage Product of Serum Amyloid A1 Identifies Patients with Chemotherapy-Related Cardiotoxicity. ACS Pharmacol Transl Sci 2019; 2:333-341. [PMID: 32259067 DOI: 10.1021/acsptsci.9b00035] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Indexed: 02/08/2023]
Abstract
Improvements in long-term cancer survival rates have resulted in an increase in the prevalence of chemotherapy-linked cardiac failure, but treatment-induced cardiac injuries may not be detected until long after therapy. Monitoring cardiac function is recommended; however, cardiovascular injury in cancer patients differs from those with primary cardiac dysfunction, which limits the utility of traditional cardiac biomarkers. Here we examined plasma levels of peptides produced by cathepsin B, which is released during chemotherapy-induced cardiac injury. We applied nanotrap fractionation to enrich plasma peptides from cancer patients treated with or without chemotherapy. Peptides associated with chemotherapy-induced cardiotoxicity, but not other cardiac injury, were identified by mass spectrometry, and their dependence on cathepsin B activity was determined using enzyme inhibition experiments. We found that a peptide (SAA-1525) derived from serum amyloid A1 was significantly increased in cardiotoxicity patients, and its production was inhibited when plasma samples were pretreated with cathepsin B specific inhibitors. Plasma SAA-1525 also correlated with other markers of cardiac injury. Analysis of plasma SAA-1525 levels may hold potential as a rapid and minimally invasive method to monitor subclinical injury, thereby allowing timely intervention to mitigate further cardiac damage and avoid more severe clinical presentation.
Collapse
Affiliation(s)
- Fangfang Zhang
- Department of Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China.,Virginia G. Piper Biodesign Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Christopher J Lyon
- Virginia G. Piper Biodesign Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Robert J Walls
- Virginia G. Piper Biodesign Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Bo Ning
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Jia Fan
- Virginia G. Piper Biodesign Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Tony Y Hu
- Department of Biochemistry and Molecular Biology, School of Medicine, Tulane University, New Orleans, Louisiana 70112, United States
| |
Collapse
|
14
|
Pinheiro D, Monteiro C, Faria MA, Pinto E. Vitek ® MS v3.0 System in the Identification of Filamentous Fungi. Mycopathologia 2019; 184:645-651. [PMID: 31506883 DOI: 10.1007/s11046-019-00377-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 08/21/2019] [Indexed: 12/19/2022]
Abstract
Infections caused by filamentous fungi are rising in incidence and became a serious health concern. Their rapid and reliable identification in the clinical laboratory is essential for an early and accurate diagnosis to guide timely therapy. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been reported as a rapid and reliable method for identification of bacteria and yeasts isolated from clinical samples. However, it has less used for molds identification. The aim of this study was to evaluate Vitek® MS (a MALDI-TOF MS system) ability to identify molds and differentiate species within a complex. A collection of 90 filamentous fungi, 70 clinical and 20 environmental isolates, was studied by morphological and molecular methods and by Vitek® MS. Seventy-four isolates (82.2%) were identified using Vitek® MS v3.0 at Genus/Complex/Species group level; within these, 47/74 (63.5%) were correctly identified at species level and only one was misidentified. In contrast, 16/90 isolates (17.8%) were not identified, of which 13 were not present in the database. Results here expressed favor Vitek® MS v3.0 as a very useful system for identification of most common clinical isolates of filamentous fungi. Accordingly, it may be an important tool for clinical microbiology laboratories in their task to answer to clinicians, adequately and rapidly, helping in proper patient's management.
Collapse
Affiliation(s)
- Dolores Pinheiro
- Laboratory of Microbiology, Service of Clinical Pathology, Centro Hospitalar Universitário de S. João, Alameda Prof. Hernâni Monteiro, 4200-319, Porto, Portugal.
| | - Carolina Monteiro
- Laboratory of Microbiology, Biological Sciences Department, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Miguel A Faria
- LAQV-REQUIMTE, Laboratory of Bromatology and Hydrology, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313, Porto, Portugal
| | - Eugénia Pinto
- Laboratory of Microbiology, Biological Sciences Department, Faculty of Pharmacy, University of Porto, Porto, Portugal.,Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Edifício do Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal
| |
Collapse
|
15
|
ITS rDNA Gene Analysis Versus MALDI-TOF MS For Identification of Neoscytalidium dimidiatum Isolated from Onychomycosis and Dermatomycosis Cases in Medellin (Colombia). Microorganisms 2019; 7:microorganisms7090306. [PMID: 31480602 PMCID: PMC6780217 DOI: 10.3390/microorganisms7090306] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 08/27/2019] [Accepted: 08/30/2019] [Indexed: 12/30/2022] Open
Abstract
Within the Neoscytalidium genus, N. dimidiatum, N. oculus, N. orchidacearum, and N. novaehollandiae have been recognized. Although these species are frequently found in soil, N. dimidiatum has been identified as an etiologic agent of onychomycosis or dermatomycosis, and N. oculus has been identified as an etiologic agent of an ocular lesion. All these species can be cultured in vitro, but their morphological identification by macroscopic and microscopic traits is difficult and imprecise due to their similarity. In this study, 34 isolates of Neoscytalidium spp. from 32 onychomycosis and two dermatomycosis cases in Medellin (Colombia) were identified at the species level using sequencing of the ITS1+5.8S+ITS2 nuclear rDNA region and MALDI-TOF mass spectrometry (MS). Neoscytalidium dimidiatum strain MUM 17.21 was used to construct the reference spectrum in the in-house library to identify the clinical isolates by MALDI-TOF MS. Additionally, N. dimidiatum PPC-216 and PLAB-055 strains were used to validate the in-house constructed reference spectra. Although four groups were observed in the dendrogram obtained from the proteins of each isolate profile, MALDI-TOF MS and sequencing results are in accordance, since all isolates were identified as N. dimidiatum.
Collapse
|
16
|
Chan WK, Wildeboer D, Garelick H, Purchase D. Competition of As and other Group 15 elements for surface binding sites of an extremophilic Acidomyces acidophilus isolated from a historical tin mining site. Extremophiles 2018; 22:795-809. [PMID: 30039469 DOI: 10.1007/s00792-018-1039-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Accepted: 07/09/2018] [Indexed: 11/30/2022]
Abstract
An arsenic-resistant fungal strain, designated WKC-1, was isolated from a waste roaster pile in a historical tin mine in Cornwall, UK and successfully identified to be Acidomyces acidophilus using matrix-assisted laser desorption/ionization time-of-flight/time-of-flight tandem mass spectrometry (MALDI-TOF/TOF MS) proteomic-based biotyping approach. WKC-1 showed considerable resistance to As5+ and Sb5+ where the minimal inhibitory concentration (MIC) were 22500 and 100 mg L-1, respectively, on Czapex-Dox Agar (CDA) medium; it was substantially more resistant to As5+ than the reference strains CBS 335.97 and CCF 4251. In a modified CDA medium containing 0.02 mg L-1 phosphate, WKC-1 was able to remove 70.30% of As5+ (100 mg L-1). Sorption experiment showed that the maximum capacity of As5+ uptake was 170.82 mg g-1 dry biomass as predicted by the Langmuir model. The presence of Sb5+ reduced the As5+ uptake by nearly 40%. Based on the Fourier-transform infrared spectroscopy (FT-IR) analysis, we propose that Sb is competing with As for these sorption sites: OH, NH, CH, SO3 and PO4 on the fungal cell surface. To our knowledge, this is the first report on the impact of other Group 15 elements on the biosorption of As5+ in Acidomyces acidophilus.
Collapse
Affiliation(s)
- Wai Kit Chan
- Department of Natural Science, Faculty of Science and Technology, Middlesex University, The Burroughs, London, NW4 4BT, UK
| | - Dirk Wildeboer
- Department of Natural Science, Faculty of Science and Technology, Middlesex University, The Burroughs, London, NW4 4BT, UK
| | - Hemda Garelick
- Department of Natural Science, Faculty of Science and Technology, Middlesex University, The Burroughs, London, NW4 4BT, UK
| | - Diane Purchase
- Department of Natural Science, Faculty of Science and Technology, Middlesex University, The Burroughs, London, NW4 4BT, UK.
| |
Collapse
|
17
|
Quéro L, Girard V, Pawtowski A, Tréguer S, Weill A, Arend S, Cellière B, Polsinelli S, Monnin V, van Belkum A, Vasseur V, Nodet P, Mounier J. Development and application of MALDI-TOF MS for identification of food spoilage fungi. Food Microbiol 2018; 81:76-88. [PMID: 30910090 DOI: 10.1016/j.fm.2018.05.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 03/30/2018] [Accepted: 05/01/2018] [Indexed: 01/20/2023]
Abstract
Filamentous fungi are frequently involved in food spoilage and cause important food losses and substantial economic damage. Their rapid and accurate identification is a key step to better manage food safety and quality. In recent years, MALDI-TOF MS has emerged as a powerful tool to identify microorganisms and has successfully been applied to the identification of filamentous fungi especially in the clinical context. The aim of this study was to implement a spectral database representative of food spoilage molds. To this end, after application of a standardized extraction protocol, 6477 spectra were acquired from 618 fungal strains belonging to 136 species and integrated in the VITEK MS database. The performances of this database were then evaluated by cross-validation and ∼95% of correct identification to the species level was achieved, independently of the cultivation medium and incubation time. The database was also challenged with external isolates belonging to 52 species claimed in the database and 90% were correctly identified to the species level. To our best knowledge, this is the most comprehensive database of food-relevant filamentous fungi developed to date. This study demonstrates that MALDI-TOF MS could be an alternative to conventional techniques for the rapid and reliable identification of spoilage fungi in food and industrial environments.
Collapse
Affiliation(s)
- Laura Quéro
- Université de Brest, EA 3882, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, IBSAM, ESIAB, Technopôle Brest-Iroise, 29280 Plouzané, France; BioMérieux, R&D Microbiologie, Route de Port Michaud, 38390 La Balme les Grottes, France.
| | - Victoria Girard
- BioMérieux, R&D Microbiologie, Route de Port Michaud, 38390 La Balme les Grottes, France.
| | - Audrey Pawtowski
- Université de Brest, EA 3882, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, IBSAM, ESIAB, Technopôle Brest-Iroise, 29280 Plouzané, France.
| | - Sylvie Tréguer
- Université de Brest, EA 3882, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, IBSAM, ESIAB, Technopôle Brest-Iroise, 29280 Plouzané, France.
| | - Amélie Weill
- Université de Brest, EA 3882, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, IBSAM, ESIAB, Technopôle Brest-Iroise, 29280 Plouzané, France; Université de Bretagne Occidentale Culture Collection, Université de Brest, ESIAB, Technopôle Brest-Iroise, 29280 Plouzané, France.
| | - Sandrine Arend
- BioMérieux, R&D Microbiologie, Route de Port Michaud, 38390 La Balme les Grottes, France.
| | - Béatrice Cellière
- BioMérieux, R&D Microbiologie, Route de Port Michaud, 38390 La Balme les Grottes, France.
| | - Sophie Polsinelli
- BioMérieux, R&D Microbiologie, Route de Port Michaud, 38390 La Balme les Grottes, France.
| | - Valérie Monnin
- BioMérieux, R&D Microbiologie, Route de Port Michaud, 38390 La Balme les Grottes, France.
| | - Alex van Belkum
- BioMérieux, R&D Microbiologie, Route de Port Michaud, 38390 La Balme les Grottes, France.
| | - Valérie Vasseur
- Université de Brest, EA 3882, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, IBSAM, ESIAB, Technopôle Brest-Iroise, 29280 Plouzané, France.
| | - Patrice Nodet
- Université de Brest, EA 3882, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, IBSAM, ESIAB, Technopôle Brest-Iroise, 29280 Plouzané, France.
| | - Jérôme Mounier
- Université de Brest, EA 3882, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, IBSAM, ESIAB, Technopôle Brest-Iroise, 29280 Plouzané, France.
| |
Collapse
|
18
|
Shao J, Wan Z, Li R, Yu J. Species Identification and Delineation of Pathogenic Mucorales by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry. J Clin Microbiol 2018; 56:e01886-17. [PMID: 29436422 PMCID: PMC5869826 DOI: 10.1128/jcm.01886-17] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 01/29/2018] [Indexed: 11/20/2022] Open
Abstract
This study aimed to validate the effectiveness of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)-based identification of filamentous fungi of the order Mucorales. A total of 111 isolates covering six genera preserved at the Research Center for Medical Mycology of Peking University were selected for MALDI-TOF MS analysis. We emphasized the study of 23 strains of Mucor irregularis predominantly isolated from patients in China. We first used the Bruker Filamentous Fungi library (v1.0) to identify all 111 isolates. To increase the identification rate, we created a compensatory in-house database, the Beijing Medical University (BMU) database, using 13 reference strains covering 6 species, including M. irregularis, Mucor hiemalis, Mucor racemosus, Cunninghamella bertholletiae, Cunninghamella phaeospora, and Cunninghamella echinulata All 111 isolates were then identified by MALDI-TOF MS using a combination of the Bruker library and BMU database. MALDI-TOF MS identified 55 (49.5%) and 74 (66.7%) isolates at the species and genus levels, respectively, using the Bruker Filamentous Fungi library v1.0 alone. A combination of the Bruker library and BMU database allowed MALDI-TOF MS to identify 90 (81.1%) and 111 (100%) isolates at the species and genus levels, respectively, with a significantly increased accuracy rate. MALDI-TOF MS poorly identified Mucorales when the Bruker library was used alone due to its lack of some fungal species. In contrast, this technique perfectly identified M. irregularis after main spectrum profiles (MSPs) of relevant reference strains were added to the Bruker library. With an expanded Bruker library, MALDI-TOF MS is an effective tool for the identification of pathogenic Mucorales.
Collapse
Affiliation(s)
- Jin Shao
- Department of Dermatology, Peking University First Hospital, Beijing, China
- Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China
- Research Center for Medical Mycology, Peking University, Beijing, China
| | - Zhe Wan
- Department of Dermatology, Peking University First Hospital, Beijing, China
- Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China
- Research Center for Medical Mycology, Peking University, Beijing, China
| | - Ruoyu Li
- Department of Dermatology, Peking University First Hospital, Beijing, China
- Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China
- Research Center for Medical Mycology, Peking University, Beijing, China
| | - Jin Yu
- Department of Dermatology, Peking University First Hospital, Beijing, China
- Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China
- Research Center for Medical Mycology, Peking University, Beijing, China
| |
Collapse
|
19
|
Kamali Sarwestani Z, Hashemi SJ, Rezaie S, Gerami Shoar M, Mahmoudi S, Elahi M, Bahardoost M, Tajdini A, Abutalebian S, Daie Ghazvini R. Species identification and in vitro antifungal susceptibility testing of Aspergillus section Nigri strains isolated from otomycosis patients. J Mycol Med 2018. [PMID: 29540288 DOI: 10.1016/j.mycmed.2018.02.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
INTRODUCTION Aspergillus niger is the most commonly reported etiology of otomycosis based on morphological characteristics. This fungus is a member of Aspergillus section Nigri, a set of morphologically indistinguishable species that can harbor various antifungal susceptibility patterns. The aim of this study was to accurately identify and determine the susceptibility pattern of a set of black aspergilli isolated from otomycosis patients. METHODS Forty-three black Aspergillus isolates from otomycosis patients were identified by using the PCR-sequencing of the β-tubulin gene. Furthermore, the susceptibility of isolates to three antifungal drugs, including fluconazole (FLU), clotrimazole (CLT) and nystatin (NS), were tested according to CLSI M38-A2. The data were analyzed using the SPSS software (version 15). RESULTS The majority of isolates were identified as A. tubingensis (32/43, 74.42%) followed by A. niger (11/43, 25.58%). The lowest minimum inhibitory concentration (MIC) values were observed for NS with geometric means (GM) of 4.65μg/mL and 4.83μg/mL against A. tubingensis and A. niger isolates, respectively. CLT showed wide MIC ranges and a statistically significant inter-species difference was observed between A. tubingensis and A. niger isolates (P<0.05). FLU was inactive against both species with GMs>64μg/mL. CONCLUSION Species other than A. niger can be more frequent as observed in our study. In addition, considering the low and variable activity of tested antifungal drugs, empirical treatment can result in treatment failure. Accurate identification and antifungal susceptibility testing of isolates is, however, recommended.
Collapse
Affiliation(s)
- Z Kamali Sarwestani
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Pour Sina st., Keshavarz Blvd., Tehran, Iran
| | - S J Hashemi
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Pour Sina st., Keshavarz Blvd., Tehran, Iran
| | - S Rezaie
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Pour Sina st., Keshavarz Blvd., Tehran, Iran
| | - M Gerami Shoar
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Pour Sina st., Keshavarz Blvd., Tehran, Iran
| | - S Mahmoudi
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Pour Sina st., Keshavarz Blvd., Tehran, Iran; Students' Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - M Elahi
- Department of Head and Neck surgery, AmirAlam Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - M Bahardoost
- Colorectal research center, Iran University of Medical Sciences, Tehran, Iran; Department of Epidemiology and Biostatistics, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - A Tajdini
- Department of Head and Neck surgery, AmirAlam Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - S Abutalebian
- Department of Medical Parasitology and Mycology, School of Medicine, Isfahan University of Medical Science, Isfahan, Iran
| | - R Daie Ghazvini
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Pour Sina st., Keshavarz Blvd., Tehran, Iran.
| |
Collapse
|
20
|
Multicenter Evaluation of the Vitek MS v3.0 System for the Identification of Filamentous Fungi. J Clin Microbiol 2018; 56:JCM.01353-17. [PMID: 29142047 DOI: 10.1128/jcm.01353-17] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 11/03/2017] [Indexed: 12/21/2022] Open
Abstract
Invasive fungal infections are an important cause of morbidity and mortality affecting primarily immunocompromised patients. While fungal identification to the species level is critical to providing appropriate therapy, it can be slow and laborious and often relies on subjective morphological criteria. The use of matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry has the potential to speed up and improve the accuracy of identification. In this multicenter study, we evaluated the accuracy of the Vitek MS v3.0 system in identifying 1,601 clinical mold isolates compared to identification by DNA sequence analysis and supported by morphological and phenotypic testing. Among the 1,519 isolates representing organisms in the v3.0 database, 91% (n = 1,387) were correctly identified to the species level. An additional 27 isolates (2%) were correctly identified to the genus level. Fifteen isolates were incorrectly identified, due to either a single incorrect identification (n = 13) or multiple identifications from different genera (n = 2). In those cases, when a single identification was provided that was not correct, the misidentification was within the same genus. The Vitek MS v3.0 was unable to identify 91 (6%) isolates, despite repeat testing. These isolates were distributed among all the genera. When considering all isolates tested, even those that were not represented in the database, the Vitek MS v3.0 provided a single correct identification 98% of the time. These findings demonstrate that the Vitek MS v3.0 system is highly accurate for the identification of common molds encountered in the clinical mycology laboratory.
Collapse
|
21
|
Fernández AL, Andres PO, Veciño CH, Nagel CB, Mujica MT. Subcutaneous infection by Graphium basitruncatum in a heart transplant patient. Braz J Infect Dis 2017; 21:670-674. [PMID: 28923505 PMCID: PMC9425465 DOI: 10.1016/j.bjid.2017.08.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 08/03/2017] [Accepted: 08/14/2017] [Indexed: 11/18/2022] Open
Abstract
Graphium basitruncatum, a synanamorph of Pseudoallescheria has been rarely reported in human infections. We report a case of subcutaneous phaeohyphomycosis caused by this fungus in a heart transplant recipient. We also describe the phenotypic, molecular methods and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) used to achieve isolate identification.
Collapse
Affiliation(s)
- Analía L Fernández
- Hospital Universitario Fundación Favaloro, Laboratorio Central Servicio de Microbiología, Buenos Aires, Argentina; Universidad de Buenos Aires, Facultad de Medicina, Departamento de Microbiología y Parasitología Médica, Buenos Aires, Argentina
| | - Patricia O Andres
- Hospital Universitario Fundación Favaloro, Laboratorio Central Servicio de Microbiología, Buenos Aires, Argentina
| | - Cecilia H Veciño
- Universidad de Buenos Aires, Facultad de Medicina, Departamento de Microbiología y Parasitología Médica, Buenos Aires, Argentina
| | - Claudia B Nagel
- Hospital Universitario Fundación Favaloro, División Infectología, Buenos Aires, Argentina
| | - María Teresa Mujica
- Universidad de Buenos Aires, Facultad de Medicina, Departamento de Microbiología y Parasitología Médica, Buenos Aires, Argentina.
| |
Collapse
|
22
|
Vithanage NR, Bhongir J, Jadhav SR, Ranadheera CS, Palombo EA, Yeager TR, Datta N. Species-Level Discrimination of Psychrotrophic Pathogenic and Spoilage Gram-Negative Raw Milk Isolates Using a Combined MALDI-TOF MS Proteomics–Bioinformatics-based Approach. J Proteome Res 2017; 16:2188-2203. [DOI: 10.1021/acs.jproteome.6b01046] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Nuwan R. Vithanage
- College
of Health and Biomedicine, Victoria University, Werribee, Victoria 3030, Australia
- Advanced
Food Systems, Victoria University, Werribee, Victoria 3030, Australia
| | - Jeevana Bhongir
- College
of Health and Biomedicine, Victoria University, Werribee, Victoria 3030, Australia
| | - Snehal R. Jadhav
- Faculty
of Science, Engineering and Technology, Swinburne University of Technology, Hawthorn, Victoria 3122, Australia
| | - Chaminda S. Ranadheera
- College
of Health and Biomedicine, Victoria University, Werribee, Victoria 3030, Australia
- Advanced
Food Systems, Victoria University, Werribee, Victoria 3030, Australia
| | - Enzo A. Palombo
- Faculty
of Science, Engineering and Technology, Swinburne University of Technology, Hawthorn, Victoria 3122, Australia
| | - Thomas R. Yeager
- College
of Engineering and Science, Victoria University, Melbourne, Victoria 8001, Australia
- Institute
for Sustainability and Innovation, Victoria University, Werribee, Victoria 3030, Australia
- Advanced
Food Systems, Victoria University, Werribee, Victoria 3030, Australia
| | - Nivedita Datta
- College
of Health and Biomedicine, Victoria University, Werribee, Victoria 3030, Australia
- Institute
for Sustainability and Innovation, Victoria University, Werribee, Victoria 3030, Australia
- Advanced
Food Systems, Victoria University, Werribee, Victoria 3030, Australia
| |
Collapse
|
23
|
Identification of microorganisms grown on chromogenic media by MALDI-TOF MS. J Microbiol Methods 2017; 136:17-20. [DOI: 10.1016/j.mimet.2017.03.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 03/01/2017] [Accepted: 03/02/2017] [Indexed: 11/22/2022]
|
24
|
Kumaran S, Abdelhamid HN, Wu HF. Quantification analysis of protein and mycelium contents upon inhibition of melanin for Aspergillus niger: a study of matrix assisted laser desorption/ionization mass spectrometry (MALDI-MS). RSC Adv 2017. [DOI: 10.1039/c7ra03741d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Mass spectrometry (MS) provides a simple discrimination method for microorganisms.
Collapse
Affiliation(s)
- Sekar Kumaran
- Department of Chemistry and Center for Nanoscience and Nanotechnology
- National Sun Yat-Sen University
- Kaohsiung
- Taiwan
- School of Pharmacy
| | - Hani Nasser Abdelhamid
- Department of Chemistry and Center for Nanoscience and Nanotechnology
- National Sun Yat-Sen University
- Kaohsiung
- Taiwan
- School of Pharmacy
| | - Hui-Fen Wu
- Department of Chemistry and Center for Nanoscience and Nanotechnology
- National Sun Yat-Sen University
- Kaohsiung
- Taiwan
- School of Pharmacy
| |
Collapse
|
25
|
Maldonado I, García Ramírez D, Striebeck P, Lafage M, Fernández Canigia L. Espectrometría de masas MALDI-TOF: evaluación de la etapa preanalítica para la identificación de hongos miceliales. Rev Argent Microbiol 2017; 49:7-14. [DOI: 10.1016/j.ram.2016.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 09/06/2016] [Accepted: 10/06/2016] [Indexed: 11/26/2022] Open
|
26
|
Abstract
MALDI-TOF MS has become the standard method for routine identification of most microbial organisms in clinical laboratories and has largely replaced biochemical assays. Classification relies on extensive well curated databases, ideally covering the full spectrum of microorganisms encountered in the specimens at hands. The protocols for harvesting cells and procuring material suitable for downstream MALDI-TOF MS analyses vary in specific details between the different groups of organisms, e.g., gram-positive or -negative bacteria, mycobacteria, or fungi. With respect to fungi, methods further vary between yeasts and moulds; and even among different mould genera if they do not lyse in a similar fashion. Purification of microbial materials from clinical specimen allows the direct identification of bacteria; however this is not yet fully adapted to fungi. In this chapter, I look into the differences between the underlying methods for yeast and moulds, and for production of samples suitable for MALDI-TOF MS species identification from cultures and different clinical materials.
Collapse
Affiliation(s)
- Oliver Bader
- Institute for Medical Microbiology, University Medical Center Göttingen, Kreuzbergring 57, Göttingen, D-37075, Germany.
| |
Collapse
|
27
|
Emerging and Future Applications of Matrix-Assisted Laser Desorption Ionization Time-of-Flight (MALDI-TOF) Mass Spectrometry in the Clinical Microbiology Laboratory. J Mol Diagn 2016; 18:789-802. [DOI: 10.1016/j.jmoldx.2016.07.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 06/29/2016] [Accepted: 07/21/2016] [Indexed: 12/17/2022] Open
|
28
|
Rahi P, Prakash O, Shouche YS. Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass-Spectrometry (MALDI-TOF MS) Based Microbial Identifications: Challenges and Scopes for Microbial Ecologists. Front Microbiol 2016; 7:1359. [PMID: 27625644 PMCID: PMC5003876 DOI: 10.3389/fmicb.2016.01359] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 08/17/2016] [Indexed: 12/29/2022] Open
Abstract
Matrix-assisted laser desorption/ionization time-of-flight mass-spectrometry (MALDI-TOF MS) based biotyping is an emerging technique for high-throughput and rapid microbial identification. Due to its relatively higher accuracy, comprehensive database of clinically important microorganisms and low-cost compared to other microbial identification methods, MALDI-TOF MS has started replacing existing practices prevalent in clinical diagnosis. However, applicability of MALDI-TOF MS in the area of microbial ecology research is still limited mainly due to the lack of data on non-clinical microorganisms. Intense research activities on cultivation of microbial diversity by conventional as well as by innovative and high-throughput methods has substantially increased the number of microbial species known today. This important area of research is in urgent need of rapid and reliable method(s) for characterization and de-replication of microorganisms from various ecosystems. MALDI-TOF MS based characterization, in our opinion, appears to be the most suitable technique for such studies. Reliability of MALDI-TOF MS based identification method depends mainly on accuracy and width of reference databases, which need continuous expansion and improvement. In this review, we propose a common strategy to generate MALDI-TOF MS spectral database and advocated its sharing, and also discuss the role of MALDI-TOF MS based high-throughput microbial identification in microbial ecology studies.
Collapse
Affiliation(s)
- Praveen Rahi
- Microbial Culture Collection, National Centre for Cell Science Pune, India
| | - Om Prakash
- Microbial Culture Collection, National Centre for Cell Science Pune, India
| | - Yogesh S Shouche
- Microbial Culture Collection, National Centre for Cell Science Pune, India
| |
Collapse
|
29
|
Ulrich S, Biermaier B, Bader O, Wolf G, Straubinger RK, Didier A, Sperner B, Schwaiger K, Gareis M, Gottschalk C. Identification of Stachybotrys spp. by MALDI-TOF mass spectrometry. Anal Bioanal Chem 2016; 408:7565-7581. [PMID: 27475444 DOI: 10.1007/s00216-016-9800-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 07/01/2016] [Accepted: 07/14/2016] [Indexed: 11/26/2022]
Abstract
Stachybotrys (S.) spp. are omnipresent cellulolytic molds. Some species are highly toxic owing to their ability to synthesize various secondary metabolites such as macrocyclic trichothecenes or hemolysins. The reliable identification of Stachybotrys at species level is currently limited to genome-based identification. This study aimed to establish a fast and reliable MALDI-TOF MS identification method by optimizing the pre-analytical steps for protein extraction for subsequent generation of high-quality fingerprint mass spectra. Eight reference strains of the American Type Culture Collection and the Technical University of Denmark were cultivated in triplicate (biological repetitions) for 2 days in malt extract broth. The mycelia (1.5 ml) were first washed with 75 % ethanol and an additional washing step with dimethyl sulfoxide (10 %) was added to remove unspecific low weight masses. Furthermore, mycelia were broken with roughened glass beads in formic acid (70 %) and acetonitrile. The method was successfully applied to a total of 45 isolates of Stachybotrys originating from three different habitats (indoor, feed, and food samples; n = 15 each): Twenty-seven isolates of S. chartarum and 18 isolates of S. chlorohalonata could be identified by MALDI-TOF MS. The data obtained exactly matched those obtained by genome-based identification. The mean score values for S. chartarum ranged from 2.509 to 2.739 and from 2.148 to 2.622 for S. chlorohalonata with a very good reproducibility: the relative standard deviations were between 0.3 % and 6.8 %. Thus, MALDI-TOF MS proved to be a fast and reliable alternative to identification of Stachybotrys spp. by nucleotide amplification and sequencing.
Collapse
Affiliation(s)
- Sebastian Ulrich
- Chair of Food Safety, Department of Veterinary Sciences, LMU Munich, Schoenleutnerstr. 8, 85764, Oberschleissheim, Germany.
| | - Barbara Biermaier
- Chair of Food Safety, Department of Veterinary Sciences, LMU Munich, Schoenleutnerstr. 8, 85764, Oberschleissheim, Germany
| | - Oliver Bader
- Institute for Medical Microbiology, University Medical Center Goettingen, Kreuzbergring 57, 37075, Goettingen, Germany
| | - Georg Wolf
- Chair of Microbiology and Mycology, Department of Veterinary Sciences, LMU Munich, Veterinaerstr. 13, 80539, Munich, Germany
| | - Reinhard K Straubinger
- Chair of Microbiology and Mycology, Department of Veterinary Sciences, LMU Munich, Veterinaerstr. 13, 80539, Munich, Germany
| | - Andrea Didier
- Chair for Hygiene and Technology of Milk, Department of Veterinary Sciences, LMU Munich, Schoenleutnerstr. 8, 85764, Oberschleissheim, Germany
| | - Brigitte Sperner
- Chair of Food Safety, Department of Veterinary Sciences, LMU Munich, Schoenleutnerstr. 8, 85764, Oberschleissheim, Germany
| | - Karin Schwaiger
- Chair of Food Safety, Department of Veterinary Sciences, LMU Munich, Schoenleutnerstr. 8, 85764, Oberschleissheim, Germany
| | - Manfred Gareis
- Chair of Food Safety, Department of Veterinary Sciences, LMU Munich, Schoenleutnerstr. 8, 85764, Oberschleissheim, Germany
| | - Christoph Gottschalk
- Chair of Food Safety, Department of Veterinary Sciences, LMU Munich, Schoenleutnerstr. 8, 85764, Oberschleissheim, Germany
| |
Collapse
|
30
|
Ergin Ç, Gök Y, Bayğu Y, Gümral R, Özhak-Baysan B, Döğen A, Öğünç D, Ilkit M, Seyedmousavi S. ATR-FTIR Spectroscopy Highlights the Problem of Distinguishing Between Exophiala dermatitidis and E. phaeomuriformis Using MALDI-TOF MS. MICROBIAL ECOLOGY 2016; 71:339-346. [PMID: 26373644 DOI: 10.1007/s00248-015-0670-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 08/28/2015] [Indexed: 06/05/2023]
Abstract
The present study compared two chemical-based methods, namely, matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS) and attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy, to understand the misidentification of Exophiala dermatitidis and Exophiala phaeomuriformis. The study utilized 44 E. dermatitidis and 26 E. phaeomuriformis strains, which were partially treated with strong acids and bases for further evaluation. MALDI-TOF MS and ATR-FTIR spectroscopy data of the two Exophiala species were compared. Data groupings were observed for the chromic acid- and nitric acid-treated species when the black yeast sources were categorized as creosoted-oak sleepers, concrete sleepers, or dishwasher isolates. The MALDI-TOF MS data for the metalloenzyme-containing regions were consistent with the ATR-FTIR spectroscopy data. These results indicated that environmental isolates might contain metals not found in human isolates and might interfere with chemical-based identification methods. Therefore, MALDI-TOF MS reference libraries should be created for clinical strains and should exclude petroleum-associated environmental isolates.
Collapse
Affiliation(s)
- Çağrı Ergin
- Department of Microbiology, Faculty of Medicine, Pamukkale University, Denizli, Turkey.
| | - Yaşar Gök
- Chemistry Department, Faculty of Science and Arts, Pamukkale University, Denizli, Turkey
| | - Yasemin Bayğu
- Chemistry Department, Faculty of Science and Arts, Pamukkale University, Denizli, Turkey
| | - Ramazan Gümral
- Department of Microbiology, Gülhane Military Medical Academy, Ankara, Turkey
| | - Betil Özhak-Baysan
- Department of Microbiology, Faculty of Medicine, University of Akdeniz, Antalya, Turkey
| | - Aylin Döğen
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Mersin, Mersin, Turkey
| | - Dilara Öğünç
- Department of Microbiology, Faculty of Medicine, University of Akdeniz, Antalya, Turkey
| | - Macit Ilkit
- Division of Mycology, Department of Microbiology, Faculty of Medicine, University of Çukurova, Adana, Turkey
| | - Seyedmojtaba Seyedmousavi
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands
- Invasive Fungi Research Center, Mazandaran University Medical Center, Sari, Iran
| |
Collapse
|
31
|
Pushing the Limits of MALDI-TOF Mass Spectrometry: Beyond Fungal Species Identification. J Fungi (Basel) 2015; 1:367-383. [PMID: 29376916 PMCID: PMC5753130 DOI: 10.3390/jof1030367] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 10/05/2015] [Accepted: 10/07/2015] [Indexed: 12/12/2022] Open
Abstract
Matrix assisted laser desorption ionization time of flight (MALDI-TOF) is a powerful analytical tool that has revolutionized microbial identification. Routinely used for bacterial identification, MALDI-TOF has recently been applied to both yeast and filamentous fungi, confirming its pivotal role in the rapid and reliable diagnosis of infections. Subspecies-level identification holds an important role in epidemiological investigations aimed at tracing virulent or drug resistant clones. This review focuses on present and future applications of this versatile tool in the clinical mycology laboratory.
Collapse
|
32
|
van Diepeningen AD, Brankovics B, Iltes J, van der Lee TAJ, Waalwijk C. Diagnosis of Fusarium Infections: Approaches to Identification by the Clinical Mycology Laboratory. CURRENT FUNGAL INFECTION REPORTS 2015; 9:135-143. [PMID: 26301000 PMCID: PMC4537702 DOI: 10.1007/s12281-015-0225-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Infections caused by the genus Fusarium have emerged over the past decades and range from onychomycosis and keratitis in healthy individuals to deep and disseminated infections with high mortality rates in immune-compromised patients. As antifungal susceptibility can differ between the different Fusarium species, identification at species level is recommended. Several clinical observations as hyaline hyphae in tissue, necrotic lesions in the skin and positive blood tests with fungal growth or presence of fungal cell wall components may be the first hints for fusariosis. Many laboratories rely on morphological identification, but especially multi-locus sequencing proves better to discriminate among members of the species complexes involved in human infection. DNA-based diagnostic tools have best discriminatory power when based on translation elongation factor 1-α or the RNA polymerase II second largest subunit. However, assays based on the detection of other fusarial cell compounds such as peptides and cell wall components may also be used for identification. The purpose of this review is to provide an overview and a comparison of the different tools currently available for the diagnosis of fusariosis.
Collapse
Affiliation(s)
| | - Balázs Brankovics
- />CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- />Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Jearidienne Iltes
- />CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Theo A. J. van der Lee
- />Plant Research International Wageningen UR, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Cees Waalwijk
- />Plant Research International Wageningen UR, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| |
Collapse
|
33
|
Saracli M. MALDI-TOF MS: A Rapid and New Approach in Fungal Diagnosis and Susceptibility Testing. Med Mycol 2015. [DOI: 10.1201/b18707-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
|
34
|
Gruenwald M, Rabenstein A, Remesch M, Kuever J. MALDI-TOF mass spectrometry fingerprinting: A diagnostic tool to differentiate dematiaceous fungi Stachybotrys chartarum and Stachybotrys chlorohalonata. J Microbiol Methods 2015; 115:83-8. [PMID: 26036596 DOI: 10.1016/j.mimet.2015.05.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 05/27/2015] [Accepted: 05/29/2015] [Indexed: 11/17/2022]
Abstract
Stachybotrys chartarum and Stachybotrys chlorohalonata are two closely related species. Unambiguous identification of these two species is a challenging task if relying solely on morphological criteria and therefore smarter and less labor-intensive approaches are needed. Here we show that even such closely related species of fungi as S. chartarum and S. chlorohalonata are unequivocally discriminated by their highly reproducible MALDI-TOF-MS fingerprints (matrix assisted laser desorption/ionization time-of-flight mass spectrometry fingerprints). We examined 19 Stachybotrys and one Aspergillus isolate by MALDI-TOF-MS. All but one isolate produced melanin containing conidia on malt extract agar. Mass spectra were obtained in good quality from the analysis of hyaline and darkly pigmented conidia by circumventing the property of melanin which causes signal suppression. MALDI-TOF fingerprint analysis clearly discriminated not only the two morphologically similar species S. chartarum and S. chlorohalonata from each other but separated them precisely from Stachybotrys bisbyi and Aspergillus versicolor isolates. Furthermore, even S. chartarum chemotypes A and S could be differentiated into two distinct groups by their MALDI-TOF fingerprints. The chemotypes of S. chartarum isolates were identified by trichodiene synthase 5 (tri5) sequences prior to mass spectra analysis. Additionally, species identities of all isolates were verified by their 18S rRNA and tri5 gene sequences.
Collapse
Affiliation(s)
- Maike Gruenwald
- Bremen Institute for Materials Testing, Microbiology Department, Paul-Feller-Straße 1, 28199 Bremen, Germany.
| | - Andreas Rabenstein
- Bremen Institute for Materials Testing, Microbiology Department, Paul-Feller-Straße 1, 28199 Bremen, Germany.
| | - Markko Remesch
- Bremen Institute for Materials Testing, Microbiology Department, Paul-Feller-Straße 1, 28199 Bremen, Germany.
| | - Jan Kuever
- Bremen Institute for Materials Testing, Microbiology Department, Paul-Feller-Straße 1, 28199 Bremen, Germany.
| |
Collapse
|
35
|
Becker PT, Stubbe D, Claessens J, Roesems S, Bastin Y, Planard C, Cassagne C, Piarroux R, Hendrickx M. Quality control in culture collections: Confirming identity of filamentous fungi by MALDI-TOF MS. MYCOSCIENCE 2015. [DOI: 10.1016/j.myc.2014.08.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
36
|
Bourassa L, Butler-Wu SM. MALDI-TOF Mass Spectrometry for Microorganism Identification. METHODS IN MICROBIOLOGY 2015. [DOI: 10.1016/bs.mim.2015.07.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
37
|
Kondori N, Erhard M, Welinder-Olsson C, Groenewald M, Verkley G, Moore ERB. Analyses of black fungi by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS): species-level identification of clinical isolates of Exophiala dermatitidis. FEMS Microbiol Lett 2014; 362:1-6. [PMID: 25790495 DOI: 10.1093/femsle/fnu016] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Conventional mycological identifications based on the recognition of morphological characteristics can be problematic. A relatively new methodology applicable for the identification of microorganisms is based on the exploitation of taxon- specific mass patterns recorded from abundant cell proteins directly from whole-cell preparations, using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). This study reports the application of MALDI-TOF MS for the differentiation and identifications of black yeasts, isolated from the respiratory tracts of patients with cystic fibrosis (CF). Initial phenotypic and DNA sequence-based analyses identified these isolates to be Exophiala dermatitidis. The type strains of E. dermatitidis (CBS 207.35(T)) and other species of Exophiala were included in the MALDI-TOF MS analyses to establish the references for comparing the mass spectra of the clinical isolates of Exophiala. MALDI-TOF MS analyses exhibited extremely close relationships among the clinical isolates and with the spectra generated from the type strain of E. dermatitidis. The relationships observed between the E. dermatitidis strains from the MALDI-TOF MS profiling analyses were supported by DNA sequence-based analyses of the rRNA ITS1 and ITS2 regions. These data demonstrated the applicability of MALDI-TOF MS as a reliable, rapid and cost-effective method for the identification of isolates of E. dermatitidis and other clinically relevant fungi and yeasts that typically are difficult to identify by conventional methods.
Collapse
Affiliation(s)
- Nahid Kondori
- Department of Infectious Diseases, Sahlgrenska Academy of the University of Gothenburg, SE-40234 Gothenburg, Sweden
| | | | - Christina Welinder-Olsson
- Department of Infectious Diseases, Sahlgrenska Academy of the University of Gothenburg, SE-40234 Gothenburg, Sweden
| | - Marizeth Groenewald
- Centraalbureau voor Schimmelcultures (CBS), CBS-KNAW Fungal Biodiversity Centre, 3584 CT Utrecht, Netherlands
| | - Gerard Verkley
- Centraalbureau voor Schimmelcultures (CBS), CBS-KNAW Fungal Biodiversity Centre, 3584 CT Utrecht, Netherlands
| | - Edward R B Moore
- Department of Infectious Diseases, Sahlgrenska Academy of the University of Gothenburg, SE-40234 Gothenburg, Sweden Culture Collection University of Gothenburg, Sahlgrenska Academy of the University of Gothenburg, SE-40234 Gothenburg, Sweden
| |
Collapse
|
38
|
Becker PT, de Bel A, Martiny D, Ranque S, Piarroux R, Cassagne C, Detandt M, Hendrickx M. Identification of filamentous fungi isolates by MALDI-TOF mass spectrometry: clinical evaluation of an extended reference spectra library. Med Mycol 2014; 52:826-34. [DOI: 10.1093/mmy/myu064] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
|
39
|
The Genus Scedosporium and Pseudallescheria: Current Challenges in Laboratory Diagnosis. CURRENT CLINICAL MICROBIOLOGY REPORTS 2014. [DOI: 10.1007/s40588-014-0001-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
|
40
|
Current Status in Diagnosis of Scedosporium Infections: What Is the Impact of New Molecular Methods? CURRENT FUNGAL INFECTION REPORTS 2014. [DOI: 10.1007/s12281-014-0193-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
41
|
Use of the Bruker MALDI Biotyper for identification of molds in the clinical mycology laboratory. J Clin Microbiol 2014; 52:2797-803. [PMID: 24850347 DOI: 10.1128/jcm.00049-14] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is increasingly used for the identification of bacteria and fungi in the diagnostic laboratory. We evaluated the mold database of Bruker Daltonik (Bremen, Germany), the Filamentous Fungi Library 1.0. First, we studied 83 phenotypically and molecularly well-characterized, nondermatophyte, nondematiaceous molds from a clinical strain collection. Using the manufacturer-recommended interpretation criteria, genus and species identification rates were 78.3% and 54.2%, respectively. Reducing the species cutoff from 2.0 to 1.7 significantly increased species identification to 71.1% without increasing misidentifications. In a subsequent prospective study, 200 consecutive clinical mold isolates were identified by the MALDI Biotyper and our conventional identification algorithm. Discrepancies were resolved by ribosomal DNA (rDNA) internal transcribed spacer region sequence analysis. For the MALDI Biotyper, genus and species identification rates were 83.5% and 79.0%, respectively, when using a species cutoff of 1.7. Not identified were 16.5% of the isolates. Concordant genus and species assignments of MALDI-TOF MS and the conventional identification algorithm were observed for 98.2% and 64.2% of the isolates, respectively. Four erroneous species assignments were observed using the MALDI Biotyper. The MALDI Biotyper seems highly reliable for the identification of molds when using the Filamentous Fungi Library 1.0 and a species cutoff of 1.7. However, expansion of the database is required to reduce the number of nonidentified isolates.
Collapse
|
42
|
Buskirk AD, Templeton SP, Nayak AP, Hettick JM, Law BF, Green BJ, Beezhold DH. Pulmonary immune responses to Aspergillus fumigatus in an immunocompetent mouse model of repeated exposures. J Immunotoxicol 2014; 11:180-9. [PMID: 23919459 PMCID: PMC4604601 DOI: 10.3109/1547691x.2013.819054] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Aspergillus fumigatus is a filamentous fungus that produces abundant pigmented conidia. Several fungal components have been identified as virulence factors, including melanin; however, the impact of these factors in a repeated exposure model resembling natural environmental exposures remains unknown. This study examined the role of fungal melanin in the stimulation of pulmonary immune responses using immunocompetent BALB/c mice in a multiple exposure model. It compared conidia from wild-type A. fumigatus to two melanin mutants of the same strain, Δarp2 (tan) or Δalb1 (white). Mass spectrometry-based analysis of conidial extracts demonstrated that there was little difference in the protein fingerprint profiles between the three strains. Field emission scanning electron microscopy demonstrated that the immunologically inert Rodlet A layer remained intact in melanin-deficient conidia. Thus, the primary difference between the strains was the extent of melanization. Histopathology indicated that each A. fumigatus strain induced lung inflammation, regardless of the extent of melanization. In mice exposed to Δalb1 conidia, an increase in airway eosinophils and a decrease in neutrophils and CD8(+) IL-17(+) (Tc17) cells were observed. Additionally, it was shown that melanin mutant conidia were more rapidly cleared from the lungs than wild-type conidia. These data suggest that the presence of fungal melanin may modulate the pulmonary immune response in a mouse model of repeated exposures to A. fumigatus conidia.
Collapse
Affiliation(s)
- Amanda D. Buskirk
- Allergy and Clinical Immunology Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA
- Department of Microbiology, Immunology and Cell Biology, West Virginia University, Morgantown, WV, USA
| | - Steven P. Templeton
- Allergy and Clinical Immunology Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA
- Department of Microbiology and Immunology, Indiana University School of Medicine, Terre Haute, IN, USA
| | - Ajay P. Nayak
- Allergy and Clinical Immunology Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA
| | - Justin M. Hettick
- Allergy and Clinical Immunology Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA
| | - Brandon F. Law
- Allergy and Clinical Immunology Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA
| | - Brett J. Green
- Allergy and Clinical Immunology Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA
| | - Donald H. Beezhold
- Allergy and Clinical Immunology Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA
| |
Collapse
|
43
|
Szcepanowska H, Mathia TG, Belin P. Morphology of fungal stains on paper characterized with multi-scale and multi-sensory surface metrology. SCANNING 2014; 36:76-85. [PMID: 23630072 DOI: 10.1002/sca.21095] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2012] [Accepted: 03/16/2013] [Indexed: 06/02/2023]
Abstract
Pigmentation of paper induced by fungi is one of the most complex phenomenons because it involves living organisms growing on a heterogeneous paper substrate. A novel approach to the study of interfaces of fungi and paper in black stains produced by pigmented Dematiaceous fungi with meristematic growth was undertaken applying surface metrology techniques: confocal laser scanning microscope (CLSM) white-light, confocal chromatic aberration profilometer (LCA) and scanning electron microscope in variable pressure (SEM-VP); fungal morphology was examined with transmitted light microscopy (TLM). The role of paper topography and surface morphology in fungi-induced biodeterioration was investigated elucidating some of the dynamic interactions of fungi with paper, spatial distribution of biological deposits, inclusions in paper matrix, and patterns of fungal growth on paper thus contributing to a better understanding of biodeterioration of paper-based cultural heritage. So far, to the authors' knowledge, there are no published reports on the investigation of interfaces of bio-stains and paper utilizing surface metrology techniques.
Collapse
|
44
|
Discrimination of Aspergillus lentulus from Aspergillus fumigatus by Raman spectroscopy and MALDI-TOF MS. Eur J Clin Microbiol Infect Dis 2013; 33:245-51. [DOI: 10.1007/s10096-013-1951-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2013] [Accepted: 08/06/2013] [Indexed: 10/26/2022]
|
45
|
State-of-the-Art Procedures and Quality Management in Diagnostic Medical Mycology. CURRENT FUNGAL INFECTION REPORTS 2013. [DOI: 10.1007/s12281-013-0145-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
|
46
|
Zampieri D, Santos VG, Braga PAC, Ferreira CR, Ballottin D, Tasic L, Basso AC, Sanches BV, Pontes JHF, da Silva BP, Garboggini FF, Eberlin MN, Tata A. Microorganisms in cryopreserved semen and culture media used in the in vitro production (IVP) of bovine embryos identified by matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS). Theriogenology 2013; 80:337-45. [PMID: 23756041 DOI: 10.1016/j.theriogenology.2013.04.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 04/15/2013] [Accepted: 04/22/2013] [Indexed: 01/04/2023]
Abstract
Commercial cattle breeders produce their own herd offspring for the dairy and beef market using artificial insemination. The procedure involves sanitary risks associated with the collection and commercialization of the germplasm, and the in vitro production and transfer of the bovine embryos must be monitored by strict health surveillance. To avoid the spreading of infectious diseases, one must rely on using controlled and monitored germplasm, media, and reagents that are guaranteed free of pathogens. In this article, we investigated the use of a new mass spectrometric approach for fast and accurate identification of bacteria and fungi in bovine semen and in culture media employed in the embryo in vitro production process. The microorganisms isolated from samples obtained in a commercial bovine embryo IVP setting were identified in a few minutes by their conserved peptide/protein profile, obtained applying matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS), matched against a commercial database. The successful microorganisms MS identification has been confirmed by DNA amplification and sequencing. Therefore, the MS technique seems to offer a powerful tool for rapid and accurate microorganism identification in semen and culture media samples.
Collapse
Affiliation(s)
- Dávila Zampieri
- ThoMSon Mass Spectrometry Laboratory, Institute of Chemistry, University of Campinas, Campinas, Sao Paulo, Brazil
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
47
|
Bader O. MALDI-TOF-MS-based species identification and typing approaches in medical mycology. Proteomics 2013; 13:788-99. [DOI: 10.1002/pmic.201200468] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2012] [Revised: 11/17/2012] [Accepted: 11/24/2012] [Indexed: 12/26/2022]
Affiliation(s)
- Oliver Bader
- Institute for Medical Microbiology and German National Reference Center for Systemic Mycoses; University Medical Center Göttingen; Göttingen Germany
| |
Collapse
|
48
|
Braga PAC, Tata A, Gonçalves dos Santos V, Barreiro JR, Schwab NV, Veiga dos Santos M, Eberlin MN, Ferreira CR. Bacterial identification: from the agar plate to the mass spectrometer. RSC Adv 2013. [DOI: 10.1039/c2ra22063f] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|
49
|
Vermeulen E, Verhaegen J, Indevuyst C, Lagrou K. Update on the Evolving Role of MALDI-TOF MS for Laboratory Diagnosis of Fungal Infections. CURRENT FUNGAL INFECTION REPORTS 2012. [DOI: 10.1007/s12281-012-0093-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
50
|
Successful identification of clinical dermatophyte and Neoscytalidium species by matrix-assisted laser desorption ionization-time of flight mass spectrometry. J Clin Microbiol 2012; 50:2277-81. [PMID: 22535981 DOI: 10.1128/jcm.06634-11] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Dermatophytes are keratinolytic fungi responsible for a wide variety of diseases of glabrous skin, nails, and hair. Their identification, currently based on morphological criteria, is hindered by intraspecies morphological variability and the atypical morphology of some clinical isolates. The aim of this study was to evaluate matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) as a routine tool for identifying dermatophyte and Neoscytalidium species, both of which cause dermatomycoses. We first developed a spectral database of 12 different species of common and unusual dermatophytes and two molds responsible for dermatomycoses (Neoscytalidium dimidiatum and N. dimidiatum var. hyalinum). We then prospectively tested the performance of the database on 381 clinical dermatophyte and Neoscytalidium isolates. Correct identification of the species was obtained for 331/360 dermatophytes (91.9%) and 18/21 Neoscytalidium isolates (85.7%). The results of MALDI-TOF MS and standard identification disagreed for only 2 isolates. These results suggest that MALDI-TOF MS could be a useful tool for routine and fast identification of dermatophytes and Neoscytalidium spp. in clinical mycology laboratories.
Collapse
|