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Saiman L, Waters V, LiPuma JJ, Hoffman LR, Alby K, Zhang SX, Yau YC, Downey DG, Sermet-Gaudelus I, Bouchara JP, Kidd TJ, Bell SC, Brown AW. Practical Guidance for Clinical Microbiology Laboratories: Updated guidance for processing respiratory tract samples from people with cystic fibrosis. Clin Microbiol Rev 2024:e0021521. [PMID: 39158301 DOI: 10.1128/cmr.00215-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/20/2024] Open
Abstract
SUMMARYThis guidance presents recommendations for clinical microbiology laboratories for processing respiratory samples from people with cystic fibrosis (pwCF). Appropriate processing of respiratory samples is crucial to detect bacterial and fungal pathogens, guide treatment, monitor the epidemiology of cystic fibrosis (CF) pathogens, and assess therapeutic interventions. Thanks to CF transmembrane conductance regulator modulator therapy, the health of pwCF has improved, but as a result, fewer pwCF spontaneously expectorate sputum. Thus, the collection of sputum samples has decreased, while the collection of other types of respiratory samples such as oropharyngeal and bronchoalveolar lavage samples has increased. To optimize the detection of microorganisms, including Pseudomonas aeruginosa, Staphylococcus aureus, Haemophilus influenzae, and Burkholderia cepacia complex; other less common non-lactose fermenting Gram-negative bacilli, e.g., Stenotrophomonas maltopholia, Inquilinus, Achromobacter, Ralstonia, and Pandoraea species; and yeasts and filamentous fungi, non-selective and selective culture media are recommended for all types of respiratory samples, including samples obtained from pwCF after lung transplantation. There are no consensus recommendations for laboratory practices to detect, characterize, and report small colony variants (SCVs) of S. aureus, although studies are ongoing to address the potential clinical impact of SCVs. Accurate identification of less common Gram-negative bacilli, e.g., S. maltopholia, Inquilinus, Achromobacter, Ralstonia, and Pandoraea species, as well as yeasts and filamentous fungi, is recommended to understand their epidemiology and clinical import.
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Affiliation(s)
- Lisa Saiman
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
- Department of Infection Prevention and Control, NewYork-Presbyterian Hospital, New York, New York, USA
| | - Valerie Waters
- Division of Infectious Diseases, Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - John J LiPuma
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Lucas R Hoffman
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Kevin Alby
- Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Sean X Zhang
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Yvonne C Yau
- Division of Microbiology, Department of Paediatric Laboratory Medicine, Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Damian G Downey
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University, Belfast, Ireland
| | | | - Jean-Philippe Bouchara
- University of Angers-University of Brest, Infections Respiratoires Fongiques, Angers, France
| | - Timothy J Kidd
- Microbiology Division, Pathology Queensland Central Laboratory, The University of Queensland, Brisbane, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Scott C Bell
- The Prince Charles Hospital, Faculty of Medicine, The University of Queensland, Brisbane, Australia
- The Translational Research Institute, Brisbane, Australia
| | - A Whitney Brown
- Cystic Fibrosis Foundation, Bethesda, Maryland, USA
- Inova Advanced Lung Disease and Transplant Program, Inova Fairfax Hospital, Falls Church, Virginia, USA
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Ghanouni A, Avila SA, de la Garza AG, Sharfi D, Singiser H, Stampfer SD, Lyon GM, Babiker A. Cladophialophora bantiana orbital cellulitis after penetrating injury. Orbit 2024; 43:495-500. [PMID: 36847499 DOI: 10.1080/01676830.2023.2181976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 02/12/2023] [Indexed: 03/01/2023]
Abstract
A 75-year-old immunocompetent male presented with a right orbital cellulitis after a foreign body penetrating injury. He was taken for orbitotomy with foreign body removal and started on broad-spectrum antibiotics. Intra-operative cultures were positive for Cladophialophora bantiana, a mold known for causing brain abscesses with no prior reports of orbital invasion in the literature. Following culture results, the patient was managed with voriconazole and required multiple orbitotomies and washouts for infection control.
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Affiliation(s)
- Arian Ghanouni
- Department of Surgery, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Sarah A Avila
- Department of Ophthalmology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Adam G de la Garza
- Department of Ophthalmology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Duaa Sharfi
- Department of Ophthalmology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Heather Singiser
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Samuel D Stampfer
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - George Marshall Lyon
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Ahmed Babiker
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
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Ebsa G, Gizaw B, Admassie M, Desalegn A, Alemu T. Screening, characterization and optimization of potential dichlorodiphenyl trichloroethane (DDT) degrading fungi. Heliyon 2024; 10:e33289. [PMID: 39022069 PMCID: PMC11253139 DOI: 10.1016/j.heliyon.2024.e33289] [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: 10/20/2023] [Revised: 05/21/2024] [Accepted: 06/18/2024] [Indexed: 07/20/2024] Open
Abstract
Dichlorodiphenyltrichloroethane is an organo-chlorine insecticide used for malaria and agricultural pest control, but it is the most persistent pollutant, endangering both human and environmental health. The primary aim of the research is to screen, characterize, and assess putative fungi that degrade DDT for mycoremediation. Samples of soil and wastewater were gathered from Addis Ababa, Koka, and Ziway. Fungi were isolated and purified using potato dextrose media. Matrix-Assisted Laser Desorption, Ionization, and Flight Duration The technique of mass spectrometry was employed to identify fungi. It was found that the finally selected isolate, AS1, was Aspergillus niger. Based on growth factor optimization at DDT concentrations (0, 3500, and 7000 ppm), temperatures (25, 30, and 35 °C), and pH levels (4, 7, and 10), the potential DDT-tolerant fungal isolates were investigated. A Box-Behnken experimental design was used to analyze and optimize fungal biomass and sporulation. The highest biomass (0.981 ± 0.22 g) and spore count (5.60 ± 0.32 log/mL) of A. niger were found through optimization assessment, and this fungus was chosen as a potential DDT-degrader. For DDT degradation investigations by A. niger in DDT-amended liquid media, gas chromatograph-electron capture detector technology was employed. DDT and its main metabolites, DDE and DDD, were eliminated from both media to the tune of 96-99 % at initial DDT concentrations of 1750, 3500, 5250, and 7000 ppm. In conclusion, it is a promising candidate for detoxifying and/or removing DDT and its breakdown products from contaminated environments.
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Affiliation(s)
- Girma Ebsa
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, P. O. Box: 1176, Addis Ababa, Ethiopia
| | - Birhanu Gizaw
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, P. O. Box: 1176, Addis Ababa, Ethiopia
| | - Mesele Admassie
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, P. O. Box: 1176, Addis Ababa, Ethiopia
| | - Asnake Desalegn
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, P. O. Box: 1176, Addis Ababa, Ethiopia
| | - Tesfaye Alemu
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, P. O. Box: 1176, Addis Ababa, Ethiopia
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Gruszecka J, Filip R. Epidemiological Study of Pathogens in Spontaneous Bacterial Peritonitis in 2017-2024-A Preliminary Report of the University Hospital in South-Eastern Poland. Microorganisms 2024; 12:1008. [PMID: 38792837 PMCID: PMC11123777 DOI: 10.3390/microorganisms12051008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/13/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
Spontaneous Bacterial Peritonitis (SBP) is a serious complication and a common cause of death in patients with liver cirrhosis. Between January 2017 and March 2024, a retrospective study was conducted involving 302 patients (>18 years old) with ascites treated at a tertiary referral center in south-eastern Poland. Microbiological analysis of the ascitic fluids was performed in all patients. The presence of microorganisms was found in samples from 17 patients, and 21 pathogens were isolated, including 15 Gram-positive bacteria and 6 Gram-negative bacteria. Staphylococcus epidermidis, MRCNS (methicillin-resistant coagulase-negative staphylococci, resistant to all beta-lactam antibiotics: penicillins, penicillins with beta-lactamase inhibitor, cephalosporins and carbapenems) was the main pathogen detected (19.05%, 4/21), followed by Enterococcus faecalis (9.52%, 2/21), Enterococcus faecium (9.52%, 2/21), Staphylococcus haemolyticus, MRCNS (4.76%, 1/21), Streptococcus mitis (9.52%, 2/21), Streptococcus parasanguinis (9.52%, 2/21), Micrococcus luteus (4.76%, 1/21) and Bacillus spp. (4.76%, 1/21). The following Gram-negative bacteria were also found in the specimens examined: Escherichia coli, ESBL (extended-spectrum β-lactamase producing E. coli) (4.76%, 1/21), Escherichia coli (4.76%, 1/21), Pseudomonas aeruginosa (4.76%, 1/21), Klebsiella oxytoca (9.52%, 2/21) and Sphingomonas paucimobilis (4.76%, 1/21). Gram-positive bacteria caused nosocomial infections in nine patients with SBP, Gram-negative bacteria caused nosocomial infections in two patients. In six patients with SBP, community-acquired infections caused by Gram-negative bacteria were found in three cases, Gram-positive bacteria in two cases, and in one case, community-acquired infection was caused by mixed Gram-positive and Gram-negative. Bacteria isolated from patients with hospital-acquired SBP showed higher drug resistance than those found in patients with non-hospital SBP. Bacterial infections in cirrhotic patients with complications may be responsible for their deteriorating health. Prompt intervention is critical to reducing mortality.
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Affiliation(s)
- Jolanta Gruszecka
- Institute of Health Sciences, Medical College of Rzeszow University, 35-310 Rzeszow, Poland;
- Department of Clinical Microbiology, Clinical Hospital No. 2, 35-301 Rzeszow, Poland
| | - Rafał Filip
- Faculty of Medicine, Medical College of Rzeszow University, 35-959 Rzeszow, Poland
- IBD Unit, Department of Gastroenterology, Clinical Hospital No. 2, 35-301 Rzeszow, Poland
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Abstract
Invasive fusariosis is a serious invasive fungal disease, affecting immunocompetent and, more frequently, immunocompromised patients. Localized disease is the typical clinical form in immunocompetent patients. Immunocompromised hosts at elevated risk of developing invasive fusariosis are patients with acute leukemia receiving chemotherapeutic regimens for remission induction, and those undergoing allogeneic hematopoietic cell transplant. In this setting, the infection is usually disseminated with positive blood cultures, multiple painful metastatic skin lesions, and lung involvement. Currently available antifungal agents have poor in vitro activity against Fusarium species, but a clear-cut correlation between in vitro activity and clinical effectiveness does not exist. The outcome of invasive fusariosis is largely dependent on the resolution of immunosuppression, especially neutrophil recovery in neutropenic patients.
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Affiliation(s)
- Marcio Nucci
- University Hospital, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Grupo Oncoclínicas, Rio de Janeiro, Brazil
| | - Elias Anaissie
- CTI Clinical Trial and Consulting, Cincinnati, Ohio, USA
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Jeraldine DVM, Wim L, Ellen VE. A comparative study for optimization of MALDI-TOF MS identification of filamentous fungi. Eur J Clin Microbiol Infect Dis 2023; 42:1153-1161. [PMID: 37592107 DOI: 10.1007/s10096-023-04652-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 08/07/2023] [Indexed: 08/19/2023]
Abstract
PURPOSE To evaluate and compare the performance of three commercial culture media, two filamentous fungi libraries, and two different protein extraction procedures in MALDI-TOF MS fungal identification. METHODS A total of 21 quality control samples were cultured on Sabouraud dextrose agar (SDA), ID fungi plate medium (IDFP), and Sabouraud gentamicin chloramphenicol 2 agar (SGC2). For four consecutive days, fungal growths were inoculated on a MALDI target plate both by using a direct transfer technique (DT) and by using a formic acid-ethanol protein extraction procedure (EEP). The MALDI-TOF MS-generated spectra were identified by the MBT Bruker library and the MSI database. RESULTS Selective culture media (IDFP and SGC2) significantly outperformed the non-selective SDA medium. IDFP was superior to the SGC2 medium for dermatophyte identification. The EEP only demonstrated a benefit over DT in the underperforming SDA medium. The MBT Bruker library outperformed the MSI database in Aspergillus identification while the MSI database outperformed the MBT library in dermatophyte identification. For non-Aspergillus fungi, the libraries performed comparably. CONCLUSION The results of our study show the necessity of using selective culture media (IDFP and SGC2) for fungal identification with MALDI-TOF MS and demonstrate no significant benefit of the formic acid-ethanol protein extraction technique in these media. Given the relative strengths and weaknesses of the MBT library and the MSI database, it might currently be beneficial to consider these libraries as complementary and employ both databases to achieve optimal fungal identification.
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Affiliation(s)
| | - Laffut Wim
- Heilig Hart Algemeen Ziekenhuis Lier, Mechelsestraat 24, 2500, Lier, Belgium
| | - Van Even Ellen
- Heilig Hart Algemeen Ziekenhuis Lier, Mechelsestraat 24, 2500, Lier, Belgium
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Bagga B, Das S, Tawde Y, Singh S, Shaw T, Sharma S, Ghosh A. Fusarium Keratitis From a Comprehensive Eye Health Care Facility in South India: Molecular Characterization by MALDI-TOF Versus PCR Sequencing, Species Complex Distribution, and Clinical Correlation. Cornea 2023; Publish Ahead of Print:00003226-990000000-00304. [PMID: 37267470 DOI: 10.1097/ico.0000000000003315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 04/20/2023] [Indexed: 06/04/2023]
Abstract
PURPOSE Fusarium keratitis possesses significant diagnostic and therapeutic challenges. Medically relevant Fusaria belong to various species complexes and show prominent differences in their antifungal susceptibility profile which may influence the clinical outcome. Rapid diagnostic methods are warranted for precise identification of species complexes for prompt initiation of correct antifungals. The aim of the study was to compare between matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) and PCR sequencing for correct species-level identification and to analyze the clinical outcome among different Fusarium species complexes. METHODS Twenty-nine culture-proven Fusarium keratitis cases were included in this study. A phylogenetic tree was constructed after TEF1α gene sequencing and isolates were subjected to MALDI-TOF MS, followed by database expansion and identification. Clinical outcome and risk association among species complexes were analyzed retrospectively. RESULTS Maximum likelihood phylogeny categorized 68.9% isolates as Fusarium solani species complex (FSSC), 17.2% as Fusarium dimerum species complex (FDSC), followed by 13.7% as Fusarium fujikuroi species complex (FFSC). With extended database, MALDI-TOF MS could correctly speciate 96.5% (28/29) isolates. Previous antibiotic usage (P = 0.034) and preoperative antifungal treatment with natamycin, voriconazole, or ketoconazole (P = 0.025) were significantly higher in the FSSC group. The patients in the FFSC group had a significantly longer duration of symptoms at the time of clinical presentation to the clinic (15 days vs. 5 days, P = 0.030). Among 11 patients with a clinically poor outcome, 9 (31%) had FSSC infection. CONCLUSIONS Patients infected with the FSSC had more aggressive infection with poor prognosis. MALDI-TOF MS can serve as the best alternative method to conventional molecular identification with reduced turnaround time, which may help the ophthalmologists to consider the appropriate antifungals or early surgical intervention for improved outcome.
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Affiliation(s)
- Bhupesh Bagga
- Department of Cornea and Anterior Segment, L. V. Prasad Eye Institute, Hyderabad, Telangana, India
| | - Sourav Das
- Department of Medical Microbiology (Mycology Division), Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Yamini Tawde
- Department of Medical Microbiology (Mycology Division), Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Shreya Singh
- Department of Microbiology, Dr B. R. Ambedkar Institute of Medical Sciences (AIMS Mohali), Chandigarh, India
| | - Tushar Shaw
- Department of Life and Allied Health Sciences, Ramaiah University of Applied Sciences, Bangalore, Karnataka, India; and
| | - Savitri Sharma
- Jhaveri Microbiology Centre, L V Prasad Eye Institute, Hyderabad, Telangana, India
| | - Anup Ghosh
- Department of Medical Microbiology (Mycology Division), Post Graduate Institute of Medical Education and Research, Chandigarh, India
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Zvezdanova ME, de Aledo MG, López-Mirones JI, Ortega J, Canut A, Castro C, Gomez C, Hernáez S, Oviaño M, Ercibengoa M, Alkorta M, Muñoz P, Rodriguez-Temporal D, Rodríguez-Sánchez B. Validation of an expanded, in-house library and an optimized preparation method for the identification of fungal isolates using MALDI-TOF mass spectrometry. Med Mycol 2023; 61:myad038. [PMID: 37102224 DOI: 10.1093/mmy/myad038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 03/17/2023] [Accepted: 04/25/2023] [Indexed: 04/28/2023] Open
Abstract
The goal of this study was to validate an optimized sample preparation method for filamentous fungal isolates coupled with the use of an in-house library for the identification of moulds using Matrix Assisted Laser Desorption/Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) in a multicenter context. For that purpose, three Spanish microbiology laboratories participated in the identification of 97 fungal isolates using MALDI-TOF MS coupled with the Filamentous Fungi library 3.0 (Bruker Daltonics) and an in-house library containing 314 unique fungal references. The isolates analyzed belonged to 25 species from the genus Aspergillus, Fusarium, Scedosporium/Lomentospora, the Mucorales order and the Dermatophytes group. MALDI-TOF MS identification was carried out from hyphae resuspended in water and ethanol. After a high-speed centrifugation step, the supernatant was discarded and the pellet submitted to a standard protein extraction step. The protein extract was analyzed with the MBT Smart MALDI Biotyper system (Bruker Daltonics). The rate of accurate, species-level identification obtained ranged between 84.5% and 94.8% and the score values were 1.8 for 72.2-94.9% of the cases. Two laboratories failed to identify only one isolate of Syncephalastrum sp. and Trichophyton rubrum, respectively and three isolates could not be identified in the third center (F. proliferatum, n = 1; T.interdigitale, n = 2). In conclusion, the availability of an effective sample preparation method and an extended database allowed high rates of correct identification of fungal species using MALDI-TOF MS. Some species, such as Trichophyton spp. are still difficult to identify. Although further improvements are still required, the developed methodology allowed the reliable identification of most fungal species.
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Affiliation(s)
- Margarita Estreya Zvezdanova
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Madrid 28007, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón -IiSGM-, Madrid 28007, Spain
| | - Manuel González de Aledo
- Clinical Microbiology Department, Complejo Hospitalario Universitario de A Coruña, A Coruña 15006, Spain
| | | | - Jesús Ortega
- Clinical Microbiology Department, Hospital Universitario Virgen de Valme, Seville 41014, Spain
| | - Andrés Canut
- Clinical Microbiology Department, Hospital Universitario de Álava, Vitoria-Gasteiz 01009, Spain
| | - Carmen Castro
- Clinical Microbiology Department, Hospital Universitario Virgen de Valme, Seville 41014, Spain
| | - Carmen Gomez
- Clinical Microbiology Department, Hospital Universitario de Álava, Vitoria-Gasteiz 01009, Spain
| | - Silvia Hernáez
- Clinical Microbiology Department, Hospital Universitario de Álava, Vitoria-Gasteiz 01009, Spain
| | - Marina Oviaño
- Clinical Microbiology Department, Complejo Hospitalario Universitario de A Coruña, A Coruña 15006, Spain
| | - María Ercibengoa
- Biodonostia Institute, Department of respiratory diseases and antimicrobial resistance, San Sebastián 20014, Spain
| | - Miriam Alkorta
- Biodonostia Institute, Department of diseases preventable by vaccination, San Sebastián 20014, Spain
- Clinical Microbiology Department, Hospital Universitario Donostia, San Sebastian 20014, Spain
- Microbiology Department, Faculty of Medicine, Universidad del País Vasco/ EHU-Donostia, San Sebastian 20014, Spain
| | - Patricia Muñoz
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Madrid 28007, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón -IiSGM-, Madrid 28007, Spain
- CIBER de Enfermedades Respiratorias (CIBERES CB06/06/0058), Madrid 28007, Spain
- Medicine Department, Faculty of Medicine, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - David Rodriguez-Temporal
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Madrid 28007, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón -IiSGM-, Madrid 28007, Spain
| | - Belén Rodríguez-Sánchez
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Madrid 28007, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón -IiSGM-, Madrid 28007, Spain
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Tsuchida S, Yamashita K, Murata S, Miyabe A, Satoh M, Matsushita K, Nakayama T, Nomura F, Umemura H. Evaluation of a novel sample preparation method for identifying Aspergillus fumigatus using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry: Combining Yatalase and silica beads treatment. J Microbiol Methods 2023; 207:106706. [PMID: 36925050 DOI: 10.1016/j.mimet.2023.106706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 03/12/2023] [Accepted: 03/13/2023] [Indexed: 03/15/2023]
Abstract
Aspergillus spp. belong to filamentous fungi and sometimes cause invasive aspergillosis which has high mortality. Filamentous fungi are generally identified morphologically. However, morphologic identification is time consuming and requires advanced skills. It is difficult to train technicians and ensure a high level of quality. Therefore, an identification technique that is both accurate and relatively easy to learn is needed. In the present study, we focused on the effects of Yatalase and silica beads, which enable the efficient extraction of proteins via cell wall disruption of Aspergillus spp., and aimed to establish a novel sample preparation method using Yatalase and silica beads to enhance the efficiency of Aspergillus spp. identification with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The sample preparation method using the combination of Yatalase and silica beads showed higher accuracy for the identification of Aspergillus spp. compared with Yatalase or silica beads alone. The Yatalase/silica beads method also resulted in significantly higher identification scores compared with the conventional method for the identification of Aspergillus fumigatus (n = 33). These findings indicate that our novel Yatalase/silica beads method provides more reliable identification of A. fumigatus than does the conventional method.
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Affiliation(s)
- Sachio Tsuchida
- Division of Laboratory Medicine, Department of Pathology and Microbiology, Nihon University School of Medicine, 30-1 Oyaguchikamicho, Itabashi-ku, Tokyo 173-8610, Japan; Division of Clinical Mass Spectrometry, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | - Koji Yamashita
- Department of Clinical Laboratory, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan; Division of Clinical Research, Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | - Syota Murata
- Department of Clinical Laboratory, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | - Akiko Miyabe
- Department of Clinical Laboratory, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | - Mamoru Satoh
- Division of Clinical Mass Spectrometry, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | - Kazuyuki Matsushita
- Department of Clinical Laboratory, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | - Tomohiro Nakayama
- Division of Laboratory Medicine, Department of Pathology and Microbiology, Nihon University School of Medicine, 30-1 Oyaguchikamicho, Itabashi-ku, Tokyo 173-8610, Japan
| | - Fumio Nomura
- Division of Clinical Mass Spectrometry, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | - Hiroshi Umemura
- Division of Laboratory Medicine, Department of Pathology and Microbiology, Nihon University School of Medicine, 30-1 Oyaguchikamicho, Itabashi-ku, Tokyo 173-8610, Japan; Division of Clinical Mass Spectrometry, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan.
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10
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Tomar K, Roy ID, Natarajan MR, Singh AK, Ramanujam V. Surgical Challenges in the Management of Post COVID-19 Midface Mucormycosis (PCoMM): An Institutional Protocol. J Craniofac Surg 2023; 34:e46-e52. [PMID: 36008879 PMCID: PMC9793999 DOI: 10.1097/scs.0000000000008963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/20/2022] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND The coronavirus disease 2019 (COVID-19) pandemic has posed another serious threat, mucormycosis infection, affecting the maxilla and orbitocerebral region. This condition has not spared world population from its merciless claws. This article addresses the challenges faced by the maxillofacial surgeons in setting the protocols from preoperative diagnosis, surgical management to postoperative care, including short-term and long-term rehabilitation. To manage this relentlessly progressing condition, a multispecialty team approach is to be activated in diagnosing, managing, and rehabilitating the patients. PURPOSE The purpose of this clinical study is to document and analyze the clinical and demographic data, presentation of the lesion, the diagnostic methods followed for early clinical detection, and management of post COVID-19 midface mucormycosis. The article also discusses postoperative medical management and prosthetic rehabilitation. RESULTS Most of the mucormycosis cases reporting to our center were treated and recovered patients of Severe Acute Respiratory Syndrome Coronavirus 2 infection. Thirty-four (n=34) case were operated for post COVID-19 midface mucormycosis between October 2020 and December 2021. Male to Female ratio is 1:42. The average age of the patients was 57.5 years. Maximum patients were in fifth and sixth decade of life. Maxilla was the involved bone. Treatment was primarily surgical debridement to extended or radical maxillectomy. All patients were treated with Liposomal Amphotericin B and tab posaconazole for 3 to 4 weeks depending upon the age, weight, and physiological state of the patients to attain an optimal cumulative load. Three patients succumbed to illness postoperatively (n=3, 1.02%). Average duration of hospital stay was 47 days. The average review period was 5.1 months.
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A Practical Workflow for the Identification of Aspergillus, Fusarium, Mucorales by MALDI-TOF MS: Database, Medium, and Incubation Optimization. J Clin Microbiol 2022; 60:e0103222. [PMID: 36326257 PMCID: PMC9769873 DOI: 10.1128/jcm.01032-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
There is an increasing body of literature on the utility of MALDI-TOF MS in the identification of filamentous fungi. However, the process still lacks standardization. In this study, we attempted to establish a practical workflow for the identification of three clinically important molds: Aspergillus, Fusarium, and Mucorales using MALDI-TOF MS. We evaluated the performance of Bruker Filamentous Fungi database v3.0 for the identification of these fungi, highlighting when there would be a benefit of using an additional database, the MSI-2 for further identification. We also examined two other variables, namely, medium effect and incubation time on the accuracy of fungal identification. The Bruker database achieved correct species level identification in 85.7% of Aspergillus and 90% of Mucorales, and correct species-complex level in 94.4% of Fusarium. Analysis of spectra using the MSI-2 database would also offer additional value for species identification of Aspergillus species, especially when suspecting species with known identification limits within the Bruker database. This issue would only be of importance in selected cases where species-level identification would impact therapeutic options. Id-Fungi plates (IDFP) had almost equivalent performance to Sabouraud dextrose agar (SDA) for species-level identification of isolates and enabled an easier harvest of the isolates with occasional faster identification. Our study showed accurate identification at 24 h for Fusarium and Mucorales species, but not for Aspergillus species, which generally required 48 h.
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Elbehiry A, Aldubaib M, Abalkhail A, Marzouk E, ALbeloushi A, Moussa I, Ibrahem M, Albazie H, Alqarni A, Anagreyyah S, Alghamdi S, Rawway M. How MALDI-TOF Mass Spectrometry Technology Contributes to Microbial Infection Control in Healthcare Settings. Vaccines (Basel) 2022; 10:1881. [PMID: 36366389 PMCID: PMC9699604 DOI: 10.3390/vaccines10111881] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 11/01/2022] [Accepted: 11/07/2022] [Indexed: 08/01/2023] Open
Abstract
Healthcare settings have been utilizing matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) since 2010. MALDI-TOF MS has various benefits over the conventional method of biochemical identification, including ease of use, speed, accuracy, and low cost. This approach can solve many of the obstacles to identifying bacteria, fungi and viruses. As technology advanced, more and more databases kept track of spectra, allowing species with similar morphological, genotypic, and biochemical traits to be identified. Using MALDI-TOF MS for identification has become more accurate and quicker due to advances in sample preparation and database enrichment. Rapid sample detection and colony identification using MALDI-TOF MS have produced promising results. A key application of MALDI-TOF MS is quickly identifying highly virulent and drug-resistant diseases. Here, we present a review of the scientific literature assessing the effectiveness of MALDI-TOF MS for locating clinically relevant pathogenic bacteria, fungi, and viruses. MALDI-TOF MS is a useful strategy for locating clinical pathogens, however, it also has some drawbacks. A small number of spectra in the database and inherent similarities among organisms can make it difficult to distinguish between different species, which can result in misidentifications. The majority of the time additional testing may correct these problems, which happen very seldom. In conclusion, infectious illness diagnosis and clinical care are being revolutionized by the use of MALDI-TOF MS in the clinical microbiology laboratory.
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Affiliation(s)
- Ayman Elbehiry
- Department of Public Health, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah 52741, Saudi Arabia
- Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, University of Sadat City, Sadat City 32511, Egypt
| | - Musaad Aldubaib
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, Qassim University, Buraydah 52571, Saudi Arabia
| | - Adil Abalkhail
- Department of Public Health, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah 52741, Saudi Arabia
| | - Eman Marzouk
- Department of Public Health, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah 52741, Saudi Arabia
| | - Ahmad ALbeloushi
- Al Bukayriyah General Hospital, Qassim, Al Bukayriyah 52725, Saudi Arabia
| | - Ihab Moussa
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Mai Ibrahem
- Department of Public Health, College of Applied Medical Science, King Khalid University, Abha 61421, Saudi Arabia
- Department of Aquatic Animal Medicine and Management, Faculty of Veterinary Medicine, Cairo University, Cairo 12211, Egypt
| | - Hamad Albazie
- Department of Public Health, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah 52741, Saudi Arabia
| | - Abdullah Alqarni
- Department of Support Service, King Fahad Armed Hospital, Jeddah 23311, Saudi Arabia
| | - Sulaiman Anagreyyah
- Department of Preventive Medicine, King Fahad Armed Hospital, Jeddah 23311, Saudi Arabia
| | - Saleh Alghamdi
- Department of Biomedical Engineering, King Fahad Armed Hospital, Jeddah 23311, Saudi Arabia
| | - Mohammed Rawway
- Biology Department, College of Science, Jouf University, Sakaka 42421, Saudi Arabia
- Botany and Microbiology Department, Faculty of Science, AL-Azhar University, Assiut 71524, Egypt
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13
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Chen YC, Chayakulkeeree M, Chakrabarti A, Gan GG, Kwong YL, Liu WL, Tan BH, Todi S. Unmet needs and practical solutions in the management of invasive mould infections in Asia. J Antimicrob Chemother 2022; 77:2579-2585. [PMID: 35904002 DOI: 10.1093/jac/dkac251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Management of invasive mould infections (IMIs) is challenging in Asia, as awareness among medical practitioners can be low and resources are limited. Timely diagnosis and appropriate treatment of IMIs can mitigate the impact on morbidity and mortality, but diagnostic methods, as well as access to preferred antifungal medications, may vary throughout the region. Knowledge of local epidemiology and accurate diagnosis and identification of causal pathogens would facilitate optimal treatment but data in Asia are lacking. To address these unmet needs in the management of IMIs, this paper is a call for urgent action in the following areas: improving awareness of the threat of IMIs; providing education to frontline clinicians across a broad range of specialties on 'red flags' for suspicion of IMIs; prioritizing cost-effective rapid diagnostic testing; improving access to preferred antifungal medications; and closing the gaps in local epidemiological data on IMIs to inform local treatment guidelines.
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Affiliation(s)
- Yee-Chun Chen
- Division of Infectious Diseases, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Methee Chayakulkeeree
- Division of Infectious Diseases and Tropical Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Arunaloke Chakrabarti
- Department of Medical Microbiology, Postgraduate Institute of Medical Education & Research, Chandigarh, India.,Doodhadhari Burfani Hospital and Research Institute, Haridwar, India
| | - Gin Gin Gan
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Yok Lam Kwong
- Division of Haematology, Oncology and Bone Marrow Transplantation, University of Hong Kong, Pokfulam, Hong Kong
| | - Wei-Lun Liu
- School of Medicine, College of Medicine, Fu Jen Catholic University, New Taipei, Taiwan.,Division of Critical Care Medicine, Department of Emergency and Critical Care Medicine, Fu Jen Catholic University Hospital, Fu Jen Catholic University, New Taipei, Taiwan
| | - Ban Hock Tan
- Department of Infectious Diseases, Singapore General Hospital Singapore 169608, Singapore
| | - Subhash Todi
- Critical Care and Emergency Medicine, AMRI Hospitals, Kolkata, India
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14
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Development of Indirect ELISA and its evaluation in Comparison with KOH hydrolysis and Fungal culture for the immuno diagnosis of Trichophyton rubrum and Trichophyton mentagrophytes infection in Humans. Acta Trop 2022; 235:106590. [PMID: 35907501 DOI: 10.1016/j.actatropica.2022.106590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 06/25/2022] [Accepted: 07/05/2022] [Indexed: 11/24/2022]
Abstract
Trichophyton is a keratinophilic fungus that can invade keratinized tissues of humans and cause superficial mycoses called dermatophytosis. The objective of this study was to develop and evaluate indirect ELISA in comparison with gold standard methods such as direct microscopic examination of KOH mounts and fungal culture for the diagnosis of Trichophyton infection in humans. The present investigation reports the production and partial purification of T. rubrum mycelial antigens and production of specific polyclonal antibodies. It also reports the development and optimization of indirect ELISA and evaluation of its potential in comparison with gold standard methods for the diagnosis of Trichophyton infection in humans. The diagnostic sensitivity and specificity of Trichophyton indirect ELISA was 93.75% and 93.33 % respectively. The positive and negative predictive values were high as well, found to be 93.75% and 90.00% respectively indicating usefulness of the assay. In all comparisons, the correlation coefficient (r) value was >0.5 indicating strong correlation between KOH hydrolysis test, fungal culture method and indirect ELISA. A significant correlation coefficient of 0.856 (P < 0.0001) was obtained between indirect ELISA and fungal culture method. This shows a good agreement between fungal culture method and indirect ELISA. The present study clearly shows diagnostic performance of Trichophyton indirect ELISA developed in this study is efficient as fungal culture method for the diagnosis of Trichophyton infection in humans.
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15
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Fissel JA, Holdren-Serrell CK, Memon W, Zhang SX. Performance of a Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry Testing Algorithm for the Rapid Identification of Clinical Filamentous Molds. Front Cell Infect Microbiol 2022; 12:915049. [PMID: 35782139 PMCID: PMC9240618 DOI: 10.3389/fcimb.2022.915049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 05/17/2022] [Indexed: 11/28/2022] Open
Abstract
One of the most significant challenges in the treatment of fungal infections is the relatively long turnaround time (TAT) required for fungal species identification. The length of TAT to identification can impact patient clinical outcomes by delaying appropriate targeted therapy. Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) has demonstrated exceptional utility in the rapid identification of bacteria and yeasts in the clinical microbiology laboratory. The capability of MALDI-TOF MS for rapid identification of clinical isolates presents an opportunity for significant advancement in the identification of filamentous molds. In this study, we employed a diagnostic algorithm using MALDI-TOF MS for the rapid identification of filamentous molds in order to assess the impact of this technology on TATs. The majority of isolates included in this study were able to be identified by MALDI-TOF MS (78%). Further, these isolates were identified in less than three days from first detection of colony growth. This study demonstrates the utility of MALDI-TOF MS in the rapid identification of filamentous molds in the clinical mycology laboratory.
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Affiliation(s)
- John A. Fissel
- Division of Medical Microbiology, Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA, United States
| | | | - Warda Memon
- Microbiology Laboratory, The Johns Hopkins Hospital, Baltimore, MD, United States
| | - Sean X. Zhang
- Division of Medical Microbiology, Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Microbiology Laboratory, The Johns Hopkins Hospital, Baltimore, MD, United States
- *Correspondence: Sean X. Zhang,
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16
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Gupta AK, Hall DC, Cooper EA, Ghannoum MA. Diagnosing Onychomycosis: What’s New? J Fungi (Basel) 2022; 8:jof8050464. [PMID: 35628720 PMCID: PMC9146047 DOI: 10.3390/jof8050464] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 04/26/2022] [Accepted: 04/27/2022] [Indexed: 02/05/2023] Open
Abstract
An overview of the long-established methods of diagnosing onychomycosis (potassium hydroxide testing, fungal culture, and histopathological examination) is provided followed by an outline of other diagnostic methods currently in use or under development. These methods generally use one of two diagnostic techniques: visual identification of infection (fungal elements or onychomycosis signs) or organism identification (typing of fungal genus/species). Visual diagnosis (dermoscopy, optical coherence tomography, confocal microscopy, UV fluorescence excitation) provides clinical evidence of infection, but may be limited by lack of organism information when treatment decisions are needed. The organism identification methods (lateral flow techniques, polymerase chain reaction, MALDI-TOF mass spectroscopy and Raman spectroscopy) seek to provide faster and more reliable identification than standard fungal culture methods. Additionally, artificial intelligence methods are being applied to assist with visual identification, with good success. Despite being considered the ‘gold standard’ for diagnosis, clinicians are generally well aware that the established methods have many limitations for diagnosis. The new techniques seek to augment established methods, but also have advantages and disadvantages relative to their diagnostic use. It remains to be seen which of the newer methods will become more widely used for diagnosis of onychomycosis. Clinicians need to be aware of the limitations of diagnostic utility calculations as well, and look beyond the numbers to assess which techniques will provide the best options for patient assessment and management.
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Affiliation(s)
- Aditya K. Gupta
- Department of Medicine, Division of Dermatology, University of Toronto School of Medicine, Toronto, ON M5S 3H2, Canada
- Mediprobe Research Inc., London, ON N5X 2P1, Canada; (D.C.H.); (E.A.C.)
- Correspondence: ; Tel.: +1-519-851-9715; Fax: +1-519-657-4233
| | - Deanna C. Hall
- Mediprobe Research Inc., London, ON N5X 2P1, Canada; (D.C.H.); (E.A.C.)
| | | | - Mahmoud A. Ghannoum
- Center for Medical Mycology, Department of Dermatology, Case Western Reserve University, Cleveland, OH 44106, USA;
- Department of Dermatology, University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
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Honsig C, Selitsch B, Hollenstein M, Vossen MG, Spettel K, Willinger B. Identification of Filamentous Fungi by MALDI-TOF Mass Spectrometry: Evaluation of Three Different Sample Preparation Methods and Validation of an In-House Species Cutoff. J Fungi (Basel) 2022; 8:jof8040383. [PMID: 35448614 PMCID: PMC9025689 DOI: 10.3390/jof8040383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 04/06/2022] [Accepted: 04/07/2022] [Indexed: 12/04/2022] Open
Abstract
Invasive infections caused by filamentous fungi constitute a leading cause of morbidity and mortality in immunocompromised patients. Rapid and reliable identification of filamentous fungi is essential for the early initiation of appropriate treatment. In the present study, 230 filamentous fungi isolates identified by conventional methods were investigated using MALDI-TOF MS (Bruker Daltonics, Bremen, Germany) in combination with the Filamentous Fungi Library 3.0 provided by the manufacturer. Three different sample preparation methods were applied as recommended by the manufacturer and identification rates were compared using the criteria provided by the manufacturer. Application of the more time-consuming sample preparation methods clearly improved identification at the species level. Thus, the identification rate increased from 48.9% using the simplest method to 76.1% with the most laborious procedure. Misidentifications did not occur. Furthermore, the reliability of an in-house threshold for species identification was investigated. The reduced threshold increased the rate of isolates correctly identified at the species level by up to 86.4%. As no misidentification was made at the genus level and only one misidentification of minor significance occurred at the species level, this threshold could be validated for routine use in our laboratory. In conclusion, regarding the high identification rates achieved, this commercial platform proved suitable for implementation in routine diagnosis.
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Affiliation(s)
- Claudia Honsig
- Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria; (C.H.); (B.S.); (K.S.)
| | - Brigitte Selitsch
- Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria; (C.H.); (B.S.); (K.S.)
| | - Marlene Hollenstein
- Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria;
| | - Matthias G. Vossen
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine I, Medical University of Vienna, 1090 Vienna, Austria;
| | - Kathrin Spettel
- Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria; (C.H.); (B.S.); (K.S.)
| | - Birgit Willinger
- Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria; (C.H.); (B.S.); (K.S.)
- Correspondence: ; Tel.: +43-1-40400-51560
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18
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Motteu N, Goemaere B, Bladt S, Packeu A. Implementation of MALDI-TOF Mass Spectrometry to Identify Fungi From the Indoor Environment as an Added Value to the Classical Morphology-Based Identification Tool. FRONTIERS IN ALLERGY 2022; 3:826148. [PMID: 35386655 PMCID: PMC8974682 DOI: 10.3389/falgy.2022.826148] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 02/16/2022] [Indexed: 12/03/2022] Open
Abstract
Introduction During the last decades, molds in the indoor environment have raised concern regarding their potential adverse health effects. The genera Aspergillus, Cladosporium, Penicillium, Alternaria, and yeasts, the most common fungi found indoors, include species with high allergenic and toxigenic potentials. Identification of these molds is generally performed by microscopy. This method has, however, some limitations as it requires mycologists with high expertise while identification is often limited to the genus level. Therefore, it is necessary to seek for fast and accurate tools, such as Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDITOF MS), enabling an identification to the species level and guiding general practitioners in their search for the underlying cause of a health problem. Methods In this study, 149 fungal air and dust isolates from 43 dwellings in Brussels were taken in collaboration with Brussels Environment RCIB/CRIPI and identified by both microscopy and MALDI-TOF MS in Sciensano's Indoor Mycology laboratory. Spectra obtained via MALDI-TOF MS were compared with data available in an in-house created reference database containing over 1,700 strains from the BCCM/IHEM fungal collection. Results A total of 149 isolates including 18 yeasts and 131 filamentous fungi were analyzed. Microscopic analysis indicated 18 yeast species and allowed identification of 79 isolates (53%) to the genus level. Only 36 isolates (24%) could be identified to the species complex level. Fifteen molds (10%) could not be identified, and one was indicated as sterile mycelia. No isolate was identified to species level. MALDI-TOF MS analysis identified 137 (92%) of the 149 isolates with a logscore > 1.7. Of these 137 isolates, 129 (87%) were identified to the species level (logscore > 2.0). For only 8 isolates (5%), identification was limited to the genus/section level (1.7 < logscore <2.0), and 12 isolates (8%) could not be identified. Conclusion A comparison of results obtained with both methods indicates an increased precision in identifications with MALDI-TOF MS analysis for 92% of the isolates, emphasizing its highly added value to the standard microscopic analysis in routine practice. In addition, MALDI-TOF MS also enables to assess the accuracy of microscopic identifications.
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Affiliation(s)
- Natacha Motteu
- Mycology and Aerobiology, Sciensano, Brussels, Belgium
- *Correspondence: Natacha Motteu
| | | | - Sandrine Bladt
- Brussels Environment, Regional Intervention Cell for Indoor Pollution (RCIB/CRIPI), Brussels, Belgium
| | - Ann Packeu
- Mycology and Aerobiology, Sciensano, Brussels, Belgium
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Radcliffe C, Radcliffe AJ, Azar MM, Grant M. Dematiaceous fungal infections in solid organ transplantation: systematic review and bayesian meta-analysis. Transpl Infect Dis 2022; 24:e13819. [PMID: 35253959 DOI: 10.1111/tid.13819] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 02/03/2022] [Accepted: 02/19/2022] [Indexed: 12/18/2022]
Abstract
BACKGROUND Dematiaceous fungi cause a number of infectious syndromes referred to as phaeohyphomycosis among both immunocompetent and immunocompromised hosts. We performed a systematic review to characterize these infections in solid organ transplant recipients (SOTR). METHODS We searched PubMed database (last searched 1/6/2022) for English-language reports on dematiaceous fungal infections in SOTR. Included reports needed individualized demographic, treatment, and outcome data; pediatric reports were excluded. A universally applicable bias assessment was performed on reports. Models for infection type and outcome were created using the Bayesian paradigm. RESULTS We included 149 reports on 201 cases of dematiaceous fungal infections in SOTR. The mean age was 54 years, 72% were men, and kidney recipients accounted for 61% of cases. Skin and soft tissue infection (SSTI) was the most common infectious syndrome (73%). Death from infection occurred in 7% of cases (14/201), with disseminated (32%) cases having the highest mortality. Our model for infection type predicted the relative probability of central nervous system infection to be highest in liver recipients. Across all transplant types, higher relative probabilities of disseminated and pulmonary infections occur in the early post-transplant period, and the predicted probabilities for these infection types decreased after 100 months post-transplantation. DISCUSSION We identified SSTI as the most common dematiaceous fungal infections in SOTR. Disseminated infections carried the worst prognosis. The evidence in this review is limited by the heterogeneity of included cases. No funding source was used, and this review's protocol was not registered. This article is protected by copyright. All rights reserved.
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Affiliation(s)
| | | | - Marwan M Azar
- Yale University School of Medicine, New Haven, CT, USA.,Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, USA
| | - Matthew Grant
- Yale University School of Medicine, New Haven, CT, USA.,Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, USA
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De Carolis E, Posteraro B, Sanguinetti M. Old and New Insights into Sporothrix schenckii Complex Biology and Identification. Pathogens 2022; 11:pathogens11030297. [PMID: 35335621 PMCID: PMC8948913 DOI: 10.3390/pathogens11030297] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 02/04/2023] Open
Abstract
Sporothrix schenckii is a worldwide-distributed thermally dimorphic fungus, which usually causes a subacute to chronic infection through traumatic implantation or inoculation of its infectious propagules. The fungus encompasses a group of phylogenetically closely related species, thus named the S. schenckii complex, of which S. schenckii sensu stricto and S. brasiliensis are main causative species of sporotrichosis. Owing to a multifaceted molecular dynamic, the S. schenckii complex can switch between the mycelium and the yeast form. This characteristic along with a varying cell wall composition account for significant species-specific differences in the host range, virulence, and susceptibility to antifungal drugs. While culture remains the gold standard to diagnose sporotrichosis, polymerase chain reaction (PCR) or matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry-based methods have become an essential for accurate species identification in many clinical laboratories. If directly applied on tissue samples, molecular methods are helpful to improve both sensitivity of and time to the etiological diagnosis of sporotrichosis. This mini-review aims to put together the old and new knowledge on the S. schenckii complex biology and identification, with particular emphasis on the laboratory diagnosis-related aspects of disease.
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Affiliation(s)
- Elena De Carolis
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy;
- Correspondence:
| | - Brunella Posteraro
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, 00168 Rome, Italy;
| | - Maurizio Sanguinetti
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy;
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21
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Gupta P, Malhotra HS, Saxena P, Singh R, Shukla D, Hasan MS, Verma V, Banerjee G, Puri B, Dandu H. Utility of itraconazole and terbinafine in mucormycosis: a proof-of-concept analysis. J Investig Med 2022; 70:914-918. [PMID: 35078866 DOI: 10.1136/jim-2021-002179] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2022] [Indexed: 11/04/2022]
Abstract
An epidemic of mucormycosis followed the second wave of COVID 19 in the state of Uttar Pradesh, India in May 2021. This epidemic, however, had additional challenges to offer in the form of acute shortage of all forms of amphotericin B, posaconazole and isavuconazole. It was, therefore, planned to assess the trends in minimum inhibitory concentration (MIC) of antifungal agents, viz itraconazole and terbinafine, and provide a template for personalized therapy to see whether the results could be translated clinically. This is an observational, single-center study. Samples comprising nasal swab, nasal and paranasal sinus tissue, brain tissue, brain abscess and orbital content, derived from 322 patients from northern India with mucormycosis, of whom 215 were male and 107 were female, were used for analysis. Cultures were identified both by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and conventional methods of identification. Antifungal susceptibility was done for amphotericin B, posaconazole, isavuconazole, itraconazole and terbinafine as per Clinical Laboratory Standard Institute M38-A2. The outcome was identification of the species of mucormycosis and susceptibility to itraconazole and terbinafine besides other primary antifungal agents. Patients or the public were not involved in the design, or conduct, or reporting or in the dissemination plans of our research. Of 322 patients, 203 were culture-positive, of whom 173 were positive by both MALDI-TOF and conventional methods of identification. Final antifungal susceptibility testing was available for 150 patients. The most common Mucorales found to cause this epidemic was Rhizopus oryzae, followed by R. microsporus Amphotericin B, posaconazole and isavuconazole had low MIC values in 98.8% of all Mucorales identified. The MIC of itraconazole was species-dependent. 97.7% of R oryzae had MIC ≤2 µg/mL. However, only 36.5% of R microsporus had MIC ≤2 µg/mL. For terbinafine, 85.2% of R. microsporus had MIC ≤2 µg/mL. We conclude that identification at the species level is required as antifungal susceptibilities seem to be species-dependent. Assessment of the efficacy of itraconazole and terbinafine warrants further studies with clinical assessment and therapeutic drug monitoring as they seem to be potential candidates especially when the primary agents are not available.
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Affiliation(s)
- Prashant Gupta
- Microbiology, King George's Medical University, Lucknow, Uttar Pradesh, India
| | | | - Priyamvada Saxena
- Microbiology, King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Riddhi Singh
- Microbiology, King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Deeksha Shukla
- Microbiology, King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Mohd Saqib Hasan
- Microbiology, King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Veerendra Verma
- ENT, King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Gopa Banerjee
- Microbiology, King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Bipin Puri
- Department of Pediatric Surgery, King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Himanshu Dandu
- Medicine, King George's Medical University, Lucknow, Uttar Pradesh, India
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22
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OUP accepted manuscript. J AOAC Int 2022; 105:1468-1474. [DOI: 10.1093/jaoacint/qsac036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 03/02/2022] [Accepted: 03/06/2022] [Indexed: 11/13/2022]
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OUP accepted manuscript. Med Mycol 2022; 60:6561619. [DOI: 10.1093/mmy/myac027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 03/18/2022] [Accepted: 03/29/2022] [Indexed: 11/12/2022] Open
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Bupha-Intr O, Butters C, Reynolds G, Kennedy K, Meyer W, Patil S, Bryant P, Morrissey CO. Consensus guidelines for the diagnosis and management of invasive fungal disease due to moulds other than Aspergillus in the haematology/oncology setting, 2021. Intern Med J 2021; 51 Suppl 7:177-219. [PMID: 34937139 DOI: 10.1111/imj.15592] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Invasive fungal disease (IFD) due to moulds other than Aspergillus is a significant cause of mortality in patients with malignancies or post haemopoietic stem cell transplantation. The current guidelines focus on the diagnosis and management of the common non-Aspergillus moulds (NAM), such as Mucorales, Scedosporium species (spp.), Lomentospora prolificans and Fusarium spp. Rare but emerging NAM including Paecilomyces variotii, Purpureocillium lilacinum and Scopulariopsis spp. are also reviewed. Culture and histological examination of tissue biopsy specimens remain the mainstay of diagnosis, but molecular methods are increasingly being used. As NAM frequently disseminate, blood cultures and skin examination with biopsy of any suspicious lesions are critically important. Treatment requires a multidisciplinary approach with surgical debridement as a central component. Other management strategies include control of the underlying disease/predisposing factors, augmentation of the host response and the reduction of immunosuppression. Carefully selected antifungal therapy, guided by susceptibility testing, is critical to cure. We also outline novel antifungal agents still in clinical trial which offer substantial potential for improved outcomes in the future. Paediatric recommendations follow those of adults. Ongoing epidemiological research, improvement in diagnostics and the development of new antifungal agents will continue to improve the poor outcomes that have been traditionally associated with IFD due to NAM.
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Affiliation(s)
- Olivia Bupha-Intr
- Department of Infection Services, Wellington Regional Hospital, Wellington, New Zealand
| | - Coen Butters
- Department of General Paediatric and Adolescent Medicine, John Hunter Children's Hospital, Newcastle, New South Wales, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia.,Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Gemma Reynolds
- Department of Infectious Diseases, Austin Health, Melbourne, Victoria, Australia
| | - Karina Kennedy
- Department of Infectious Diseases and Microbiology, Canberra Hospital and Health Services, Canberra, Australian Capital Territory, Australia.,ANU Medical School, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Wieland Meyer
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Westmead Clinical School and Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Research and Education Network, Westmead Hospital, Sydney, New South Wales, Australia.,Westmead Institute for Medical Research, Sydney, New South Wales, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, New South Wales, Australia
| | - Sushrut Patil
- Malignant Haematology and Stem Cell Transplantation Service, Department of Clinical Haematology, The Alfred Hospital, Melbourne, Victoria, Australia
| | - Penelope Bryant
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia.,Department of Infectious Diseases, The Royal Children's Hospital, Melbourne, Victoria, Australia.,Infection and Immunity, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Catherine O Morrissey
- Department of Infectious Diseases, The Alfred Hospital, Melbourne, Victoria, Australia.,Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
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Arastehfar A, Carvalho A, Houbraken J, Lombardi L, Garcia-Rubio R, Jenks J, Rivero-Menendez O, Aljohani R, Jacobsen I, Berman J, Osherov N, Hedayati M, Ilkit M, Armstrong-James D, Gabaldón T, Meletiadis J, Kostrzewa M, Pan W, Lass-Flörl C, Perlin D, Hoenigl M. Aspergillus fumigatus and aspergillosis: From basics to clinics. Stud Mycol 2021; 100:100115. [PMID: 34035866 PMCID: PMC8131930 DOI: 10.1016/j.simyco.2021.100115] [Citation(s) in RCA: 106] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The airborne fungus Aspergillus fumigatus poses a serious health threat to humans by causing numerous invasive infections and a notable mortality in humans, especially in immunocompromised patients. Mould-active azoles are the frontline therapeutics employed to treat aspergillosis. The global emergence of azole-resistant A. fumigatus isolates in clinic and environment, however, notoriously limits the therapeutic options of mould-active antifungals and potentially can be attributed to a mortality rate reaching up to 100 %. Although specific mutations in CYP 51A are the main cause of azole resistance, there is a new wave of azole-resistant isolates with wild-type CYP 51A genotype challenging the efficacy of the current diagnostic tools. Therefore, applications of whole-genome sequencing are increasingly gaining popularity to overcome such challenges. Prominent echinocandin tolerance, as well as liver and kidney toxicity posed by amphotericin B, necessitate a continuous quest for novel antifungal drugs to combat emerging azole-resistant A. fumigatus isolates. Animal models and the tools used for genetic engineering require further refinement to facilitate a better understanding about the resistance mechanisms, virulence, and immune reactions orchestrated against A. fumigatus. This review paper comprehensively discusses the current clinical challenges caused by A. fumigatus and provides insights on how to address them.
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Affiliation(s)
- A. Arastehfar
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, 07110, USA
| | - A. Carvalho
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's - PT Government Associate Laboratory, Guimarães/Braga, Portugal
| | - J. Houbraken
- Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands
| | - L. Lombardi
- UCD Conway Institute and School of Medicine, University College Dublin, Dublin 4, Ireland
| | - R. Garcia-Rubio
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, 07110, USA
| | - J.D. Jenks
- Department of Medicine, University of California San Diego, San Diego, CA, 92103, USA
- Clinical and Translational Fungal-Working Group, University of California San Diego, La Jolla, CA, 92093, USA
| | - O. Rivero-Menendez
- Medical Mycology Reference Laboratory, National Center for Microbiology, Instituto de Salud Carlos III, Madrid, 28222, Spain
| | - R. Aljohani
- Department of Infectious Diseases, Imperial College London, London, UK
| | - I.D. Jacobsen
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology—Hans Knöll Institute, Jena, Germany
- Institute for Microbiology, Friedrich Schiller University, Jena, Germany
| | - J. Berman
- Research Group Microbial Immunology, Leibniz Institute for Natural Product Research and Infection Biology—Hans Knöll Institute, Jena, Germany
| | - N. Osherov
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine Ramat-Aviv, Tel-Aviv, 69978, Israel
| | - M.T. Hedayati
- Invasive Fungi Research Center/Department of Medical Mycology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - M. Ilkit
- Division of Mycology, Department of Microbiology, Faculty of Medicine, Çukurova University, 01330, Adana, Turkey
| | | | - T. Gabaldón
- Life Sciences Programme, Supercomputing Center (BSC-CNS), Jordi Girona, Barcelona, 08034, Spain
- Mechanisms of Disease Programme, Institute for Research in Biomedicine (IRB), Barcelona, Spain
- ICREA, Pg. Lluís Companys 23, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010, Barcelona, Spain
| | - J. Meletiadis
- Clinical Microbiology Laboratory, Attikon University Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | | | - W. Pan
- Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, 200003, China
| | - C. Lass-Flörl
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - D.S. Perlin
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, 07110, USA
| | - M. Hoenigl
- Department of Medicine, University of California San Diego, San Diego, CA, 92103, USA
- Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of Graz, 8036, Graz, Austria
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, San Diego, CA 92093, USA
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26
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Shin JH, Kim SH, Lee D, Lee SY, Chun S, Lee JH, Won EJ, Choi HJ, Choi HW, Kee SJ, Shin MG, Shin JH. Performance Evaluation of VITEK MS for the Identification of a Wide Spectrum of Clinically Relevant Filamentous Fungi Using a Korean Collection. Ann Lab Med 2021; 41:214-220. [PMID: 33063683 PMCID: PMC7591280 DOI: 10.3343/alm.2021.41.2.214] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 04/25/2020] [Accepted: 09/19/2020] [Indexed: 11/28/2022] Open
Abstract
The correct identification of filamentous fungi is challenging. We evaluated the performance of the VITEK MS v3.0 system (bioMérieux, Marcy-l’Étoile, France) for the identification of a wide spectrum of clinically relevant filamentous fungi using a Korean collection. Strains that were added to the upgraded v3.2 database were additionally identified by the VITEK MS v3.2 system. Of the 105 tested isolates, including 37 Aspergillus (nine species), 41 dermatophytes (seven species), and 27 other molds (17 species), 43 (41.0%) showed “no identification” or “multiple species identification” results at the initial VITEK MS testing; these isolates were retested using the same method. Compared with sequence-based identification, the correct identification rate using VITEK MS for Aspergillus, dermatophytes, other molds, and total mold isolates was 67.6%, 56.1%, 48.1%, and 58.1% at the initial testing and 94.6%, 78.0%, 55.6%, and 78.1% with retesting, respectively. Following retesting, 19 (18.1%) and two (1.9%) isolates showed “no identification” and “misidentification” results, respectively. VITEK MS reliably identified various filamentous fungi recovered in Korea, with a very low rate of misidentification.
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Affiliation(s)
- Ju Hyeon Shin
- Department of Laboratory Medicine, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, Hwasun, Korea
| | - Soo Hyun Kim
- Department of Laboratory Medicine, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, Hwasun, Korea.,Department of Microbiology, Chonnam National University Medical School, Hwasun, Korea
| | - Dain Lee
- Department of Laboratory Medicine, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, Hwasun, Korea
| | - Seung Yeob Lee
- Department of Laboratory Medicine, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, Hwasun, Korea
| | - Sejong Chun
- Department of Laboratory Medicine, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, Hwasun, Korea
| | - Jun Hyung Lee
- Department of Laboratory Medicine, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, Hwasun, Korea
| | - Eun Jeong Won
- Department of Laboratory Medicine, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, Hwasun, Korea.,Department of Parasitology and Tropical Medicine, Chonnam National University Medical School, Hwasun, Korea
| | - Hyun Jung Choi
- Department of Laboratory Medicine, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, Hwasun, Korea
| | - Hyun Woo Choi
- Department of Laboratory Medicine, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, Hwasun, Korea
| | - Seung Jung Kee
- Department of Laboratory Medicine, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, Hwasun, Korea
| | - Myung Geun Shin
- Department of Laboratory Medicine, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, Hwasun, Korea
| | - Jong Hee Shin
- Department of Laboratory Medicine, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, Hwasun, Korea
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COVID-19 associated mucormycosis: Staging and management recommendations (Report of a multi-disciplinary expert committee). J Oral Biol Craniofac Res 2021; 11:569-580. [PMID: 34395187 PMCID: PMC8354814 DOI: 10.1016/j.jobcr.2021.08.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 07/28/2021] [Accepted: 08/04/2021] [Indexed: 12/26/2022] Open
Abstract
Even before the onslaught of COVID-19 pandemic could settle, the unprecedented rise in cases with COVID-19 associated mucormycosis pushed the medical health to the fringe. Hyperglycaemia and corticosteroids appear to be the most consistent associations leading to the commonest manifestation of mucormycosis, Rhino-Orbito-Cerebral Mucormycosis. To address challenges right from categorisation and staging of the disease to the management of relentless progression, a multi-disciplinary expert committee was formed to handle the task in an evidence-based format to enforce best practices. The report of the committee on one hand attempts to succinctly present the currently available evidence while at the other also attempts to bridge the evidence-deficient gaps with the specialty-specific virtuosity of experts.
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28
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Cuchí-Burgos E, Rubio-Casino R, Ballestero-Téllez M, Pariente-Jiménez F, Pérez-Jové J, Blanco-Suárez A. Commercial real time PCR implementation for rapid diagnosis of onychomycosis: A new workflow in a clinical laboratory. ACTA ACUST UNITED AC 2021; 39:326-329. [PMID: 34353508 DOI: 10.1016/j.eimce.2020.05.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 05/27/2020] [Indexed: 11/26/2022]
Abstract
INTRODUCTION Onychomycosis is a frequent and underdiagnosed condition. Approximately 90% of toenail onychomycosis infections are caused by dermatophytes, but classical diagnosis based on culture and microscopy observation is slow and has low sensitivity. Both limitations can be solved incorporating molecular techniques to routine diagnosis of onychomycosis. OBJECTIVE Prospective evaluation of the utility of incorporating in the clinical laboratory workflow a commercial real time PCR (qPCR) for dermatophytes detection in nails after potassium hydroxide direct observation screening. MATERIALS AND METHODS 152 nail samples were included (34 KOH negative and 118 KOH positive) and processed by culture and qPCR. RESULTS In the negative KOH group, only one dermatophyte grew in culture and three were detected by qPCR. In the group of positive KOH, 57 dermatophytes grew in culture and 81 were detected by qPCR. In this group, 25% of diagnosed dermatophytes were detected only by qPCR. The sensitivity of qPCR compared to culture is 92.8% and time of response decreases from days to hours. CONCLUSION Based in our results, we propose a workflow algorithm for a clinical laboratory that eliminates culture for qPCR positive samples.
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Singh S, Pal N, Chander J, Sardana R, Mahajan B, Joseph N, Chakrabarti A, Rudramurthy SM, Hariprasath P, Paul S, Kaur H, Ghosh A. Mucormycosis caused by Syncephalastrum spp.: Clinical profile, molecular characterization, antifungal susceptibility and review of literature. CLINICAL INFECTION IN PRACTICE 2021. [DOI: 10.1016/j.clinpr.2021.100074] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
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30
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Song Y, Liu X, Yang Z, Meng X, Xue R, Yu J, Al-Hatmi AMS, de Hoog GS, Li R. Molecular and MALDI-ToF MS differentiation and antifungal susceptibility of prevalent clinical Fusarium species in China. Mycoses 2021; 64:1261-1271. [PMID: 34173979 DOI: 10.1111/myc.13345] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 06/19/2021] [Accepted: 06/22/2021] [Indexed: 11/28/2022]
Abstract
BACKGROUND Fusarium species are emerging causative agents of superficial and disseminated human infections. Early diagnosis and treatment contribute to better prognosis of severe infection. OBJECTIVES To detect the effectiveness of matrix-assisted laser desorption ionisation time of flight mass spectrometry (MALDI-ToF MS) for Fusarium identification, and evaluate the susceptibility profiles to clinical available antifungals. METHODS All 203 clinical Fusarium isolates and 25 environmental isolates were identified by using translation elongation factor 1-alpha (TEF1) and RNA polymerase subunit II (RPB2) sequencing and MALDI-ToF MS. Antifungal susceptibility testing was determined by a microdilution method following the CLSI approved standard M38-A3 document. RESULTS Correct identification rates at the species and genus levels were 89.04% (203/228) and 95.18% (217/228), respectively, using Bruker Filamentous Fungi Library 1.0 combined with the novel database. Seven species complexes with 19 Fusarium species were identified, including F. solani (59.21%, n = 135), F. verticillioides (17.54%, n = 40), F. proliferatum (6.58%, n = 15) and F. oxysporum (4.39%, n = 10). Four uncommon species complexes (F. incarnatum-equiseti SC, F. dimerum SC, F. redolens SC and F. sporotrichioides SC) were also identified. A high degree of antifungal resistance was observed. Fusarium isolates exhibited lower MICs to luliconazole and terbinafine compared with amphotericin B and voriconazole, which in turn were significantly more active than amorolfine, fluconazole and itraconazole. CONCLUSIONS MALDI-ToF MS showed good performance in Fusarium species with an adapted Bruker library and expanded database. Fusarium isolates exhibited lower MICs to luliconazole and terbinafine compared to amphotericin B and voriconazole.
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Affiliation(s)
- Yinggai Song
- Department of Dermatology and Venerology, Peking University First Hospital, Beijing, China.,Research Center for Medical Mycology, Peking University, Beijing, China.,National Clinical Research Center for Skin and Immune Diseases, Beijing, China.,Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China
| | - Xiao Liu
- Department of Dermatology and Venerology, Peking University First Hospital, Beijing, China.,Research Center for Medical Mycology, Peking University, Beijing, China.,National Clinical Research Center for Skin and Immune Diseases, Beijing, China.,Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China
| | - Zhining Yang
- Department of Clinical Laboratory, Shanxi Provincial People's Hospital, Shanxi, China
| | - Xingye Meng
- Department of Dermatology and Venerology, Peking University First Hospital, Beijing, China.,Research Center for Medical Mycology, Peking University, Beijing, China.,National Clinical Research Center for Skin and Immune Diseases, Beijing, China.,Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China
| | - Ruoning Xue
- Department of Dermatology and Venerology, Peking University First Hospital, Beijing, China.,Research Center for Medical Mycology, Peking University, Beijing, China.,National Clinical Research Center for Skin and Immune Diseases, Beijing, China.,Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China
| | - Jin Yu
- Department of Dermatology and Venerology, Peking University First Hospital, Beijing, China.,Research Center for Medical Mycology, Peking University, Beijing, China.,National Clinical Research Center for Skin and Immune Diseases, Beijing, China.,Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China
| | | | - G Sybren de Hoog
- Research Center for Medical Mycology, Peking University, Beijing, China.,Natural and Medical Sciences Research Center, Nizwa, Oman.,Center of Expertise in Mycology of Radboud University Medical Center/Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
| | - Ruoyu Li
- Department of Dermatology and Venerology, Peking University First Hospital, Beijing, China.,Research Center for Medical Mycology, Peking University, Beijing, China.,National Clinical Research Center for Skin and Immune Diseases, Beijing, China.,Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China
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Recognition of Diagnostic Gaps for Laboratory Diagnosis of Fungal Diseases: Expert Opinion from the Fungal Diagnostics Laboratories Consortium (FDLC). J Clin Microbiol 2021; 59:e0178420. [PMID: 33504591 DOI: 10.1128/jcm.01784-20] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Fungal infections are a rising threat to our immunocompromised patient population, as well as other nonimmunocompromised patients with various medical conditions. However, little progress has been made in the past decade to improve fungal diagnostics. To jointly address this diagnostic challenge, the Fungal Diagnostics Laboratory Consortium (FDLC) was recently created. The FDLC consists of 26 laboratories from the United States and Canada that routinely provide fungal diagnostic services for patient care. A survey of fungal diagnostic capacity among the 26 members of the FDLC was recently completed, identifying the following diagnostic gaps: lack of molecular detection of mucormycosis; lack of an optimal diagnostic algorithm incorporating fungal biomarkers and molecular tools for early and accurate diagnosis of Pneumocystis pneumonia, aspergillosis, candidemia, and endemic mycoses; lack of a standardized molecular approach to identify fungal pathogens directly in formalin-fixed paraffin-embedded tissues; lack of robust databases to enhance mold identification with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry; suboptimal diagnostic approaches for mold blood cultures, tissue culture processing for Mucorales, and fungal respiratory cultures for cystic fibrosis patients; inadequate capacity for fungal point-of-care testing to detect and identify new, emerging or underrecognized, rare, or uncommon fungal pathogens; and performance of antifungal susceptibility testing. In this commentary, the FDLC delineates the most pressing unmet diagnostic needs and provides expert opinion on how to fulfill them. Most importantly, the FDLC provides a robust laboratory network to tackle these diagnostic gaps and ultimately to improve and enhance the clinical laboratory's capability to rapidly and accurately diagnose fungal infections.
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Heireman L, Patteet S, Steyaert S. Performance of the new ID-fungi plate using two types of reference libraries (Bruker and MSI) to identify fungi with the Bruker MALDI Biotyper. Med Mycol 2021; 58:946-957. [PMID: 32030423 DOI: 10.1093/mmy/myz138] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 11/24/2019] [Accepted: 12/24/2019] [Indexed: 02/01/2023] Open
Abstract
During the last decade, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has revolutionized the diagnosis of fungal infections. Recently, a new Conidia ID-fungi plate (IDFP) medium was introduced to facilitate growth and sampling of fungi. This study aimed to evaluate the IDFP for fungal MALDI-TOF MS identification by comparison with a standard fungal growth medium using two reference libraries. A total of 75 filamentous fungal isolates (including 32 dermatophytes) were inoculated on IDFP and Sabouraud-gentamicin-chloramphenicol (SGC) agar and identified by MALDI-TOF MS using formic acid/acetonitrile extraction. Both the commercially available Bruker library (version 2.0) and the public available MSI web application (version 2018) were applied. For 15% of the isolates, a faster growth was noticed on IDFP compared to SGC. IDFP enhanced the performance of fungal identification compared to SGC for both MSI (increase of 16% identifications to genus and 5% to species level) and Bruker library (increase of 22% identifications to genus and 8% to species level). In total, only 73% of the tested isolates were present in the Bruker library compared to 92% for MSI library. No significant difference (P = 0.46) in MALDI score between IDFP and SGC was observed for the MSI library, but scores were significantly (P = 0.03) higher for IDFP when using Bruker library, potentially explained by the prevention of agar contamination by using IDFP since the Bruker database was created from liquid media. IDFP is a promising alternative growth medium for MALDI-TOF MS fungal identification which would strongly benefit from optimizing the Bruker reference library.
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Affiliation(s)
- Laura Heireman
- Department of Laboratory Medicine, General Hospital Maria Middelares, Ghent, Belgium
| | - Sofie Patteet
- Department of Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Sophia Steyaert
- Department of Laboratory Medicine, General Hospital Maria Middelares, Ghent, Belgium
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Comparative evaluation of the Bruker Biotyper and Vitek MS matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) systems for non-albicans Candida and uncommon yeast isolates. J Microbiol Methods 2021; 185:106232. [PMID: 33961963 DOI: 10.1016/j.mimet.2021.106232] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 04/24/2021] [Accepted: 05/02/2021] [Indexed: 12/16/2022]
Abstract
INTRODUCTION Rapid and accurate diagnosis is critically important in invasive and disseminated fungal infections for appropriate antifungal treatment. HYPOTHESIS MALDI-TOF MS systems are effective for fast and accurate identification of Candida species. AIM We aimed to compare two MALDI-TOF MS systems for the rapid identification of non-albicans Candida and rare clinical yeast species. METHODOLOGY This study included 157 isolates representing 23 yeast species. All isolates were identified using Bruker MALDI Biotyper and VITEK MS systems. If both MALDI-TOF MS systems yielded the same results for a certain isolate, the identification is regarded as correct. We performed internal transcribed spacer (ITS) DNA sequencing on five fungal isolates with discordant species names or that were unidentified by the two MALDI-TOF MS systems. RESULTS The yeast identification sensitivity of MALDI Biotyper was 98.7%, whereas that of VITEK MS was 96.8%. Both MALDI-TOF MS systems correctly identified all strains belonging to four prevalent species, namely, Candida parapsilosis, Candida tropicalis, Candida glabrata, and Candida krusei. For the 19 rare clinical yeast species, identification rates were 96.7% for MALDI Biotyper and 91.7% for VITEK MS. The ITS sequence analysis of five isolates yielded two Meyerozyma caribbica, two Cyberlindnera fabianii, and one Candida dubliniensis. CONCLUSIONS This study showed the high performance of both MALDI-TOF MS systems, identifying over 90% of yeast isolates in a short time. The disadvantages of these systems are that some species are not present in the databases and it cannot distinguish closely related species. The sensitivity of MALDI-TOF MS systems constantly improves with the expansion of databases in parallel with taxonomic developments for the identification of rare clinical yeast species.
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Identification and in vitro antifungal susceptibility of causative agents of onychomycosis due to Aspergillus species in Mashhad, Iran. Sci Rep 2021; 11:6808. [PMID: 33762586 PMCID: PMC7991633 DOI: 10.1038/s41598-021-86038-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 03/09/2021] [Indexed: 01/30/2023] Open
Abstract
Aspergillus species are emerging causative agents of non-dermatophyte mold onychomycosis. In this study, 48 Aspergillus isolates were obtained from patients with onychomycosis in Mashhad, Iran, during 2015–2018. The aim is to identify the Aspergillus isolates to the species level by using partial calmodulin and beta-tubulin gene sequencing and MALDI-TOF MS, and to evaluate their in vitro susceptibility to ten antifungal drugs: terbinafine, itraconazole, voriconazole, posaconazole, ravuconazole, isavuconazole, caspofungin, micafungin, anidulafungin and amphotericin B according to CLSI M38-A3. Our results indicate that A.flavus (n = 38, 79%) is the most common Aspergillus species causing onychomycosis in Mashhad, Iran. Other detected species were A. terreus (n = 3), A. tubingensis (n = 2), A. niger (n = 1), A. welwitschiae (n = 1), A. minisclerotigenes (n = 1), A. citrinoterreus (n = 1) and A. ochraceus (n = 1). Aspergillus flavus, A. terreus and A. niger isolates were correctly identified at the species level by MALDI-TOF MS, while all cryptic species were misidentified. In conclusion, A. flavus is the predominant Aspergillus species causing onychomycosis due to Aspergillus spp. in Mashhad, Iran. MALDI-TOF MS holds promise as a fast and accurate identification tool, particularly for common Aspergillus species. It is important that the current database of reference spectra, representing different Aspergillus species is expanded to increase the precision of the species-level identification. Terbinafine, posaconazole and echinocandins were in vitro most active against the studies Aspergillus isolates and terbinafine could be the first choice for treatment of onychomycosis due to Aspergillus.
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Cardot Martin E, Renaux C, Catherinot E, Limousin L, Couderc LJ, Vasse M. Rapid identification of fungi from respiratory samples by Bruker Biotyper matrix-assisted laser desorption/ionisation time-of-flight using ID-FUNGI plates. Eur J Clin Microbiol Infect Dis 2021; 40:391-395. [PMID: 32808108 DOI: 10.1007/s10096-020-04007-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 08/11/2020] [Indexed: 12/27/2022]
Abstract
Identification of moulds is crucial for the clinical management of patients. The goal of this study was to evaluate the new ID-FUNGI plate (IDFP) for the identification of moulds by MALDI Biotyper. IDFP was compared with Sabouraud with gentamicin and chloramphenicol plate (SAB) for the identification of 80 moulds from respiratory samples and eight reference strains. With the direct transfer method, species identification rose from 6% with SAB to 68% with IDFP using score cut-off 2 and from 20 to 75% using cut-off 1.7 (p < 0.001). Our study highlights that the new IDFP improves mycological diagnostic and workflow in laboratories.
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Affiliation(s)
| | - Claudine Renaux
- Department of Microbiology, Foch Hospital, 92150, Suresnes, France
| | | | - Lucie Limousin
- Department of Microbiology, Foch Hospital, 92150, Suresnes, France
| | - Louis Jean Couderc
- Department of Pneumonology, Foch Hospital, 92150, Suresnes, France
- UPRES EA 220, Department of Pneumonology, Faculty of Life Sciences Simone Veil, University Paris-Saclay, 91190, Saint-Aubin, France
| | - Marc Vasse
- Department of Microbiology, Foch Hospital, 92150, Suresnes, France
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Cultrera R, Torelli R, Sarnicola C, Segala D, Mengoli A, Chiaretto G, Perri P, Sanguinetti M. Identification and molecular characterization of Subramaniula asteroides causing human fungal keratitis: a case report. BMC Infect Dis 2021; 21:82. [PMID: 33461505 PMCID: PMC7814578 DOI: 10.1186/s12879-021-05768-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 01/05/2021] [Indexed: 11/17/2022] Open
Abstract
Background Keratitis due to by filamentous fungi are not easy to diagnose thus causing a delay in correct therapy. There are many descriptions of keratitis due to Candida, Fusarium and Aspergillus genera. Subramaniula genus has only recently been reported to cause human infections and there are few descriptions of eye infections due to this filamentous fungus. Diagnosis of fungal keratitis is usually based on microscopic and cultural techniques of samples obtained by corneal swabbing or scraping. Considering the amount of time required to obtain culture results it is wise to use other diagnostic methods, such as molecular analyses. Therapeutic options against these fungi are limited by low tissue penetration in the eye due to ocular barriers. We describe the first case of S. asteroides human keratitis treated with isavuconazole. Case presentation We describe a rare case of fungal keratitis unresponsive to antimicrobial treatment in a 65-year-old male patient without a history of diabetes or immunological diseases. He reported that the onset of symptoms occurred during a long holiday in Cape Verde Island. Initial treatment with topical antibiotics associated to steroids were ineffective, allowing a slow clinical progression of disease to corneal perforation. On admission in our Hospital, slit-lamp examination of the left eye showed conjunctival congestion and hyperemia, a large inferior corneal ulceration with brown pigment, corneal edema, about 3 mm of hypopyon and irido-lenticular synechiae. The slow clinical progression of the disease to corneal perforation and the aspect of the ulcer were consistent with a mycotic etiology. Molecular methods used on fungal colonies isolated by Sabouraud’s dextrose agar cultures allowed the identification of Subramaniula asteroids from corneal scraping. Antimicrobial test showed a good susceptibility of this filamentous fungus to voriconazole and isavuconazole. Moreover, this fungal keratitis was successfully treated with isavuconazole, without side effects, observing a progressive clinical improvement. Conclusions Molecular methods may be useful for the identification of filamentous fungal keratitis on scraping samples thus shortening the time of diagnosis. Systemic therapy by isavuconazole could be useful to treat the filamentous fungal keratitis, reducing the possible adverse effects due to the use of voriconazole by systemic administration.
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Affiliation(s)
- Rosario Cultrera
- Department of Morphology, Surgery and Experimental Medicine, Infectious Diseases Unit, University 'S. Anna' Hospital of Ferrara, Via Aldo Moro 8, 44124, Ferrara, Italy.
| | - Riccardo Torelli
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Largo Agostino Gemelli 8, 00168, Rome, Italy
| | - Caterina Sarnicola
- Department of Biomedical and Surgical Sciences, Ophthalmology Unit, 'S. Anna' University Hospital of Ferrara, Via Aldo Moro 8, 44124, Ferrara, Italy
| | - Daniela Segala
- Department of Morphology, Surgery and Experimental Medicine, Infectious Diseases Unit, University 'S. Anna' Hospital of Ferrara, Via Aldo Moro 8, 44124, Ferrara, Italy
| | - Andrea Mengoli
- Department of Biomedical and Surgical Sciences, Ophthalmology Unit, 'S. Anna' University Hospital of Ferrara, Via Aldo Moro 8, 44124, Ferrara, Italy
| | - Giuseppina Chiaretto
- Clinical Microbiology, 'S. Anna' University Hospital of Ferrara, Via Aldo Moro 8, 44124, Ferrara, Italy
| | - Paolo Perri
- Department of Biomedical and Surgical Sciences, Ophthalmology Unit, 'S. Anna' University Hospital of Ferrara, Via Aldo Moro 8, 44124, Ferrara, Italy
| | - Maurizio Sanguinetti
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Largo Agostino Gemelli 8, 00168, Rome, Italy.,Dipartimento di Scienze Biotecnologiche di base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Largo Agostino Gemelli 8, 00168, Rome, Italy
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K. Hussain K, Malavia D, M. Johnson E, Littlechild J, Winlove CP, Vollmer F, Gow NAR. Biosensors and Diagnostics for Fungal Detection. J Fungi (Basel) 2020; 6:E349. [PMID: 33302535 PMCID: PMC7770582 DOI: 10.3390/jof6040349] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/02/2020] [Accepted: 12/02/2020] [Indexed: 12/14/2022] Open
Abstract
Early detection is critical to the successful treatment of life-threatening infections caused by fungal pathogens, as late diagnosis of systemic infection almost always equates with a poor prognosis. The field of fungal diagnostics has some tests that are relatively simple, rapid to perform and are potentially suitable at the point of care. However, there are also more complex high-technology methodologies that offer new opportunities regarding the scale and precision of fungal diagnosis, but may be more limited in their portability and affordability. Future developments in this field are increasingly incorporating new technologies provided by the use of new format biosensors. This overview provides a critical review of current fungal diagnostics and the development of new biophysical technologies that are being applied for selective new sensitive fungal biosensors to augment traditional diagnostic methodologies.
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Affiliation(s)
- Khalil K. Hussain
- Medical Research Council Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK; (D.M.); (E.M.J.)
| | - Dhara Malavia
- Medical Research Council Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK; (D.M.); (E.M.J.)
| | - Elizabeth M. Johnson
- Medical Research Council Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK; (D.M.); (E.M.J.)
- UK National Mycology Reference Laboratory (MRL), Public Health England South-West, Science Quarter Southmead Hospital, Southmead, Bristol BS10 5NB, UK
| | - Jennifer Littlechild
- Biocatalysis Centre, University of Exeter, The Henry Wellcome Building for Biocatalysis, Stocker Road, Exeter EX4 4QD, UK;
| | - C. Peter Winlove
- Department of Physics and Astronomy, College of Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter EX4 4QD, UK;
| | - Frank Vollmer
- Living Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, UK;
| | - Neil A. R. Gow
- Medical Research Council Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK; (D.M.); (E.M.J.)
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Petrucelli MF, de Abreu MH, Cantelli BAM, Segura GG, Nishimura FG, Bitencourt TA, Marins M, Fachin AL. Epidemiology and Diagnostic Perspectives of Dermatophytoses. J Fungi (Basel) 2020; 6:E310. [PMID: 33238603 PMCID: PMC7712040 DOI: 10.3390/jof6040310] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 10/27/2020] [Accepted: 11/02/2020] [Indexed: 12/12/2022] Open
Abstract
Dermatophytoses affect about 25% of the world population, and the filamentous fungus Trichophyton rubrum is the main causative agent of this group of diseases. Dermatomycoses are caused by pathogenic fungi that generally trigger superficial infections and that feed on keratinized substrates such as skin, hair, and nails. However, there are an increasing number of reports describing dermatophytes that invade deep layers such as the dermis and hypodermis and that can cause deep infections in diabetic and immunocompromised patients, as well as in individuals with immunodeficiency. Despite the high incidence and importance of dermatophytes in clinical mycology, the diagnosis of this type of infection is not always accurate. The conventional methods most commonly used for mycological diagnosis are based on the identification of microbiological and biochemical features. However, in view of the limitations of these conventional methods, molecular diagnostic techniques are increasingly being used because of their higher sensitivity, specificity and rapidity and have become more accessible. The most widely used molecular techniques are conventional PCR, quantitative PCR, multiplex PCR, nested, PCR, PCR-RFLP, and PCR-ELISA. Another promising technique for the identification of microorganisms is the analysis of protein profiles by MALDI-TOF MS. Molecular techniques are promising but it is necessary to improve the quality and availability of the information in genomic and proteomic databases in order to streamline the use of bioinformatics in the identification of dermatophytes of clinical interest.
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Affiliation(s)
- Monise Fazolin Petrucelli
- Biotechnology Unit, Unaerp, Av. Costábile Romano, 2201, Ribeirão Preto SP 14096-900, Brazil; (M.F.P.); (M.H.d.A.); (B.A.M.C.); (G.G.S.); (F.G.N.); (T.A.B.); (M.M.)
| | - Mariana Heinzen de Abreu
- Biotechnology Unit, Unaerp, Av. Costábile Romano, 2201, Ribeirão Preto SP 14096-900, Brazil; (M.F.P.); (M.H.d.A.); (B.A.M.C.); (G.G.S.); (F.G.N.); (T.A.B.); (M.M.)
| | - Bruna Aline Michelotto Cantelli
- Biotechnology Unit, Unaerp, Av. Costábile Romano, 2201, Ribeirão Preto SP 14096-900, Brazil; (M.F.P.); (M.H.d.A.); (B.A.M.C.); (G.G.S.); (F.G.N.); (T.A.B.); (M.M.)
| | - Gabriela Gonzalez Segura
- Biotechnology Unit, Unaerp, Av. Costábile Romano, 2201, Ribeirão Preto SP 14096-900, Brazil; (M.F.P.); (M.H.d.A.); (B.A.M.C.); (G.G.S.); (F.G.N.); (T.A.B.); (M.M.)
| | - Felipe Garcia Nishimura
- Biotechnology Unit, Unaerp, Av. Costábile Romano, 2201, Ribeirão Preto SP 14096-900, Brazil; (M.F.P.); (M.H.d.A.); (B.A.M.C.); (G.G.S.); (F.G.N.); (T.A.B.); (M.M.)
| | - Tamires Aparecida Bitencourt
- Biotechnology Unit, Unaerp, Av. Costábile Romano, 2201, Ribeirão Preto SP 14096-900, Brazil; (M.F.P.); (M.H.d.A.); (B.A.M.C.); (G.G.S.); (F.G.N.); (T.A.B.); (M.M.)
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto SP 14049-900, Brazil
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto SP 14049-900, Brazil
| | - Mozart Marins
- Biotechnology Unit, Unaerp, Av. Costábile Romano, 2201, Ribeirão Preto SP 14096-900, Brazil; (M.F.P.); (M.H.d.A.); (B.A.M.C.); (G.G.S.); (F.G.N.); (T.A.B.); (M.M.)
| | - Ana Lúcia Fachin
- Biotechnology Unit, Unaerp, Av. Costábile Romano, 2201, Ribeirão Preto SP 14096-900, Brazil; (M.F.P.); (M.H.d.A.); (B.A.M.C.); (G.G.S.); (F.G.N.); (T.A.B.); (M.M.)
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Update on Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry Identification of Filamentous Fungi. J Clin Microbiol 2020; 58:JCM.01263-20. [PMID: 32938733 DOI: 10.1128/jcm.01263-20] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)-based species identification has found its place in many clinical routine diagnostic laboratories over the past years, allowing significantly reduced turnaround times and high-precision results. With regard to MALDI-TOF MS for filamentous fungi, here, we discuss different approaches for sample processing and growth conditions before analysis. In particular, we review the performances of different commercially available databases as well as the potential of complementary (self-constructed) in-house databases.
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Nabet C, Imbert S, Normand AC, Blanchet D, Chanlin R, Becker P, Demar M, Piarroux R. Unexpected mould diversity in clinical isolates from French Guiana and associated identification difficulties. Med Mycol 2020; 59:myaa091. [PMID: 33111143 DOI: 10.1093/mmy/myaa091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/05/2020] [Accepted: 10/12/2020] [Indexed: 12/14/2022] Open
Abstract
New mold species are increasingly reported in invasive fungal infections. However, these fungi are often misdiagnosed or undiagnosed due to the use of inappropriate laboratory diagnostic tools. Tropical countries, such as French Guiana, harbor a vast diversity of environmental fungi representing a potential source of emerging pathogens. To assess the impact of this diversity on the accuracy of mold-infection diagnoses, we identified mold clinical isolates in French Guiana during a five-month follow-up using both microscopy and matrix-assisted laser desorption ionization time-of-flight mass spectrometry. In total, 38.8% of the 98 obtained molds isolates could not be identified and required a DNA-based identification. Fungal diversity was high, including 46 species, 26 genera, and 13 orders. Fungal ecology was unusual, as Aspergillus species accounted for only 27% of all isolates, and the Nigri section was the most abundant out of the six detected Aspergillus sections. Macromycetes (orders Agaricales, Polyporales, and Russulales) and endophytic fungi accounted for respectively 11% and 14% of all isolates. Thus, in tropical areas with high fungal diversity, such as French Guiana, routine mold identification tools are inadequate. Molecular identifications, as well as morphological descriptions, are necessary for the construction of region-specific mass spectrum databases. These advances will improve the diagnosis and clinical management of new fungal infections. LAY SUMMARY In French Guiana, environmental fungal diversity may be a source of emerging pathogens. We evaluated microscopy and mass spectrometry to identify mold clinical isolates. With 39% of unidentified isolates, a region-specific mass spectrum database would improve the diagnosis of new fungal infections.
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Affiliation(s)
- C Nabet
- Sorbonne Université, INSERM, Institut Pierre-Louis d'Epidémiologie et de Santé Publique, AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Service de Parasitologie-Mycologie, Paris, France
| | - S Imbert
- Sorbonne Université, INSERM, CNRS, Centre d'Immunologie et des Maladies Infectieuses, Cimi-Paris, AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Service de Parasitologie-Mycologie, Paris, France
| | - A C Normand
- Sorbonne Université, INSERM, Institut Pierre-Louis d'Epidémiologie et de Santé Publique, AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Service de Parasitologie-Mycologie, Paris, France
| | - D Blanchet
- Department of Parasitology-Mycology, Hôpital Andrée Rosemon, Cayenne, French Guiana
| | - R Chanlin
- Department of Parasitology-Mycology, Hôpital Andrée Rosemon, Cayenne, French Guiana
| | - P Becker
- Sciensano, BCCM/IHEM collection, Mycology and Aerobiology Unit, Brussels, Belgium
| | - M Demar
- Department of Parasitology-Mycology, Hôpital Andrée Rosemon, Cayenne, French Guiana
- EA 3593, Ecosystèmes Amazoniens et Pathologies Tropicales, Université de Guyane, Cayenne, French Guiana
| | - R Piarroux
- Sorbonne Université, INSERM, Institut Pierre-Louis d'Epidémiologie et de Santé Publique, AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Service de Parasitologie-Mycologie, Paris, France
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Adhikari S, Nice EC, Deutsch EW, Lane L, Omenn GS, Pennington SR, Paik YK, Overall CM, Corrales FJ, Cristea IM, Van Eyk JE, Uhlén M, Lindskog C, Chan DW, Bairoch A, Waddington JC, Justice JL, LaBaer J, Rodriguez H, He F, Kostrzewa M, Ping P, Gundry RL, Stewart P, Srivastava S, Srivastava S, Nogueira FCS, Domont GB, Vandenbrouck Y, Lam MPY, Wennersten S, Vizcaino JA, Wilkins M, Schwenk JM, Lundberg E, Bandeira N, Marko-Varga G, Weintraub ST, Pineau C, Kusebauch U, Moritz RL, Ahn SB, Palmblad M, Snyder MP, Aebersold R, Baker MS. A high-stringency blueprint of the human proteome. Nat Commun 2020; 11:5301. [PMID: 33067450 PMCID: PMC7568584 DOI: 10.1038/s41467-020-19045-9] [Citation(s) in RCA: 131] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 09/25/2020] [Indexed: 02/07/2023] Open
Abstract
The Human Proteome Organization (HUPO) launched the Human Proteome Project (HPP) in 2010, creating an international framework for global collaboration, data sharing, quality assurance and enhancing accurate annotation of the genome-encoded proteome. During the subsequent decade, the HPP established collaborations, developed guidelines and metrics, and undertook reanalysis of previously deposited community data, continuously increasing the coverage of the human proteome. On the occasion of the HPP's tenth anniversary, we here report a 90.4% complete high-stringency human proteome blueprint. This knowledge is essential for discerning molecular processes in health and disease, as we demonstrate by highlighting potential roles the human proteome plays in our understanding, diagnosis and treatment of cancers, cardiovascular and infectious diseases.
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Affiliation(s)
- Subash Adhikari
- Faculty of Medicine, Health and Human Sciences, Department of Biomedical Sciences, Macquarie University, North Ryde, NSW, 2109, Australia
| | - Edouard C Nice
- Faculty of Medicine, Health and Human Sciences, Department of Biomedical Sciences, Macquarie University, North Ryde, NSW, 2109, Australia
- Faculty of Medicine, Nursing and Health Sciences, Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, 3800, Australia
| | - Eric W Deutsch
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA, 98109, USA
| | - Lydie Lane
- Faculty of Medicine, SIB-Swiss Institute of Bioinformatics and Department of Microbiology and Molecular Medicine, University of Geneva, CMU, Michel-Servet 1, 1211, Geneva, Switzerland
| | - Gilbert S Omenn
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109-2218, USA
| | - Stephen R Pennington
- UCD Conway Institute of Biomolecular and Biomedical Research, School of Medicine, University College Dublin, Dublin, Ireland
| | - Young-Ki Paik
- Yonsei Proteome Research Center, 50 Yonsei-ro, Sudaemoon-ku, Seoul, 120-749, South Korea
| | | | - Fernando J Corrales
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología-CSIC, Proteored-ISCIII, 28049, Madrid, Spain
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Jennifer E Van Eyk
- Cedars Sinai Medical Center, Advanced Clinical Biosystems Research Institute, The Smidt Heart Institute, Los Angeles, CA, 90048, USA
| | - Mathias Uhlén
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 17121, Solna, Sweden
| | - Cecilia Lindskog
- Rudbeck Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, 75185, Uppsala, Sweden
| | - Daniel W Chan
- Department of Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21224, USA
| | - Amos Bairoch
- Faculty of Medicine, SIB-Swiss Institute of Bioinformatics and Department of Microbiology and Molecular Medicine, University of Geneva, CMU, Michel-Servet 1, 1211, Geneva, Switzerland
| | - James C Waddington
- UCD Conway Institute of Biomolecular and Biomedical Research, School of Medicine, University College Dublin, Dublin, Ireland
| | - Joshua L Justice
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Joshua LaBaer
- Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Fuchu He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Markus Kostrzewa
- Bruker Daltonik GmbH, Microbiology and Diagnostics, Fahrenheitstrasse, 428359, Bremen, Germany
| | - Peipei Ping
- Cardiac Proteomics and Signaling Laboratory, Department of Physiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Rebekah L Gundry
- CardiOmics Program, Center for Heart and Vascular Research, Division of Cardiovascular Medicine and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Peter Stewart
- Department of Chemical Pathology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | | | - Sudhir Srivastava
- Cancer Biomarkers Research Branch, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Suite 5E136, Rockville, MD, 20852, USA
| | - Fabio C S Nogueira
- Proteomics Unit and Laboratory of Proteomics, Institute of Chemistry, Federal University of Rio de Janeiro, Av Athos da Silveria Ramos, 149, 21941-909, Rio de Janeiro, RJ, Brazil
| | - Gilberto B Domont
- Proteomics Unit and Laboratory of Proteomics, Institute of Chemistry, Federal University of Rio de Janeiro, Av Athos da Silveria Ramos, 149, 21941-909, Rio de Janeiro, RJ, Brazil
| | - Yves Vandenbrouck
- University of Grenoble Alpes, Inserm, CEA, IRIG-BGE, U1038, 38000, Grenoble, France
| | - Maggie P Y Lam
- Departments of Medicine-Cardiology and Biochemistry and Molecular Genetics, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
- Consortium for Fibrosis Research and Translation, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Sara Wennersten
- Division of Cardiology, Department of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Juan Antonio Vizcaino
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Marc Wilkins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Jochen M Schwenk
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 17121, Solna, Sweden
| | - Emma Lundberg
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 17121, Solna, Sweden
| | - Nuno Bandeira
- Department of Computer Science and Engineering, University of California, San Diego, 9500 Gilman Drive, Mail Code 0404, La Jolla, CA, 92093-0404, USA
| | | | - Susan T Weintraub
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center San Antonio, UT Health, 7703 Floyd Curl Drive, San Antonio, TX, 78229-3900, USA
| | - Charles Pineau
- University of Rennes, Inserm, EHESP, IREST, UMR_S 1085, F-35042, Rennes, France
| | - Ulrike Kusebauch
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA, 98109, USA
| | - Robert L Moritz
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA, 98109, USA
| | - Seong Beom Ahn
- Faculty of Medicine, Health and Human Sciences, Department of Biomedical Sciences, Macquarie University, North Ryde, NSW, 2109, Australia
| | - Magnus Palmblad
- Leiden University Medical Center, Leiden, 2333, The Netherlands
| | - Michael P Snyder
- Department of Genetics, Stanford School of Medicine, Stanford, CA, 94305, USA
| | - Ruedi Aebersold
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA, 98109, USA
- Faculty of Science, University of Zurich, Zurich, Switzerland
| | - Mark S Baker
- Faculty of Medicine, Health and Human Sciences, Department of Biomedical Sciences, Macquarie University, North Ryde, NSW, 2109, Australia.
- Department of Genetics, Stanford School of Medicine, Stanford, CA, 94305, USA.
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42
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M Américo F, P Machado Siqueira L, B Del Negro GM, M Favero Gimenes V, S Trindade MR, L Motta A, Santos de Freitas R, Rossi F, L Colombo A, Benard G, N de Almeida Júnior J. Evaluating VITEK MS for the identification of clinically relevant Aspergillus species. Med Mycol 2020; 58:322-327. [PMID: 31204789 DOI: 10.1093/mmy/myz066] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 05/14/2019] [Accepted: 05/24/2019] [Indexed: 12/27/2022] Open
Abstract
Aspergillus spp. identification has become more relevant in clinical practice since azole-resistant cryptic species have been related to invasive fungal infections. Conventional morphologic identification is not able to discriminate Aspergillus species, and DNA sequencing is not feasible for clinical laboratories. MALDI-TOF mass spectrometry is an emergent technology that has been explored to provide fast and accurate identification of microorganisms, including clinically relevant moulds. However, only a few studies have explored the platform VITEK MS for the identification of Aspergillus species. Hence, we provided additional data regarding the performance of the VITEK MS system for the identification of Aspergillus species, including azole-resistant ones. We also improved the RUO system by adding additional spectral profiles from well-identified Aspergillus strains belonging to different noncryptic and cryptic species. The IVD library correctly identified 91.6% of the organisms at genus and section level, and 84.7% at species level, including the azole-resistant Aspergillus lentulus and Aspergillus calidoustus. The organisms belonging to Aspergillus cryptic species had only 31.2% of correct species identification. The RUO library plus our in-house SuperSpectra correctly identified 100% of the organisms at genus and section level and 91.6% at species level. Among organisms belonging to Aspergillus cryptic species, 68.7% had correct species identification. Some closely related Aspergillus cryptic species showed similar spectral profiles and were difficult to be differentiated.
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Affiliation(s)
- Fernanda M Américo
- Laboratorio de Micologia Medica (LIM 53), Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo, Brazil
| | - Lumena P Machado Siqueira
- Laboratorio de Micologia Medica (LIM 53), Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo, Brazil
| | - Gilda Maria B Del Negro
- Laboratorio de Micologia Medica (LIM 53), Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo, Brazil
| | - Viviane M Favero Gimenes
- Laboratorio de Micologia Medica (LIM 53), Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo, Brazil
| | - Mario Roberto S Trindade
- Laboratório Especial de Micologia, Disciplina de Infectologia, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Adriana L Motta
- Laboratorio de Micologia Medica (LIM 53), Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo, Brazil
| | - Roseli Santos de Freitas
- Laboratorio de Micologia Medica (LIM 53), Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo, Brazil
| | - Flavia Rossi
- Laboratório Central (LIM 03), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Arnaldo L Colombo
- Laboratório Especial de Micologia, Disciplina de Infectologia, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Gil Benard
- Laboratorio de Micologia Medica (LIM 53), Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo, Brazil
| | - João N de Almeida Júnior
- Laboratorio de Micologia Medica (LIM 53), Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo, Brazil.,Laboratório Especial de Micologia, Disciplina de Infectologia, Universidade Federal de São Paulo, São Paulo, Brazil.,Laboratório Central (LIM 03), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
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Performance and Application of 16S rRNA Gene Cycle Sequencing for Routine Identification of Bacteria in the Clinical Microbiology Laboratory. Clin Microbiol Rev 2020; 33:33/4/e00053-19. [PMID: 32907806 DOI: 10.1128/cmr.00053-19] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
This review provides a state-of-the-art description of the performance of Sanger cycle sequencing of the 16S rRNA gene for routine identification of bacteria in the clinical microbiology laboratory. A detailed description of the technology and current methodology is outlined with a major focus on proper data analyses and interpretation of sequences. The remainder of the article is focused on a comprehensive evaluation of the application of this method for identification of bacterial pathogens based on analyses of 16S multialignment sequences. In particular, the existing limitations of similarity within 16S for genus- and species-level differentiation of clinically relevant pathogens and the lack of sequence data currently available in public databases is highlighted. A multiyear experience is described of a large regional clinical microbiology service with direct 16S broad-range PCR followed by cycle sequencing for direct detection of pathogens in appropriate clinical samples. The ability of proteomics (matrix-assisted desorption ionization-time of flight) versus 16S sequencing for bacterial identification and genotyping is compared. Finally, the potential for whole-genome analysis by next-generation sequencing (NGS) to replace 16S sequencing for routine diagnostic use is presented for several applications, including the barriers that must be overcome to fully implement newer genomic methods in clinical microbiology. A future challenge for large clinical, reference, and research laboratories, as well as for industry, will be the translation of vast amounts of accrued NGS microbial data into convenient algorithm testing schemes for various applications (i.e., microbial identification, genotyping, and metagenomics and microbiome analyses) so that clinically relevant information can be reported to physicians in a format that is understood and actionable. These challenges will not be faced by clinical microbiologists alone but by every scientist involved in a domain where natural diversity of genes and gene sequences plays a critical role in disease, health, pathogenicity, epidemiology, and other aspects of life-forms. Overcoming these challenges will require global multidisciplinary efforts across fields that do not normally interact with the clinical arena to make vast amounts of sequencing data clinically interpretable and actionable at the bedside.
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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.
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Cuchí-Burgos E, Rubio-Casino R, Ballestero-Téllez M, Pariente-Jiménez F, Pérez-Jové J, Blanco-Suárez A. Commercial real time PCR implementation for rapid diagnosis of onychomycosis: A new workflow in a clinical laboratory. Enferm Infecc Microbiol Clin 2020. [PMID: 32682562 DOI: 10.1016/j.eimc.2020.05.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
INTRODUCTION Onychomycosis is a frequent and underdiagnosed condition. Approximately 90% of toenail onychomycosis infections are caused by dermatophytes, but classical diagnosis based on culture and microscopy observation is slow and has low sensitivity. Both limitations can be solved incorporating molecular techniques to routine diagnosis of onychomycosis. OBJECTIVE Prospective evaluation of the utility of incorporating in the clinical laboratory workflow a commercial real time PCR (qPCR) for dermatophytes detection in nails after potassium hydroxide direct observation screening. MATERIALS AND METHODS 152 nail samples were included (34 KOH negative and 118 KOH positive) and processed by culture and qPCR. RESULTS In the negative KOH group, only one dermatophyte grew in culture and three were detected by qPCR. In the group of positive KOH, 57 dermatophytes grew in culture and 81 were detected by qPCR. In this group, 25% of diagnosed dermatophytes were detected only by qPCR. The sensitivity of qPCR compared to culture is 92.8% and time of response decreases from days to hours. CONCLUSION Based in our results, we propose a workflow algorithm for a clinical laboratory that eliminates culture for qPCR positive samples.
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Larkin PMK, Multani A, Beaird OE, Dayo AJ, Fishbein GA, Yang S. A Collaborative Tale of Diagnosing and Treating Chronic Pulmonary Aspergillosis, from the Perspectives of Clinical Microbiologists, Surgical Pathologists, and Infectious Disease Clinicians. J Fungi (Basel) 2020; 6:E106. [PMID: 32664547 PMCID: PMC7558816 DOI: 10.3390/jof6030106] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/08/2020] [Accepted: 07/09/2020] [Indexed: 02/06/2023] Open
Abstract
Chronic pulmonary aspergillosis (CPA) refers to a spectrum of Aspergillus-mediated disease that is associated with high morbidity and mortality, with its true prevalence vastly underestimated. The diagnosis of CPA includes characteristic radiographical findings in conjunction with persistent and systemic symptoms present for at least three months, and evidence of Aspergillus infection. Traditionally, Aspergillus infection has been confirmed through histopathology and microbiological studies, including fungal culture and serology, but these methodologies have limitations that are discussed in this review. The treatment of CPA requires an individualized approach and consideration of both medical and surgical options. Most Aspergillus species are considered susceptible to mold-active triazoles, echinocandins, and amphotericin B; however, antifungal resistance is emerging and well documented, demonstrating the need for novel therapies and antifungal susceptibility testing that correlates with clinical response. Here, we describe the clinical presentation, diagnosis, and treatment of CPA, with an emphasis on the strengths and pitfalls of diagnostic and treatment approaches, as well as future directions, including whole genome sequencing and metagenomic sequencing. The advancement of molecular technology enables rapid and precise species level identification, and the determination of molecular mechanisms of resistance, bridging the clinical infectious disease, anatomical pathology, microbiology, and molecular biology disciplines.
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Affiliation(s)
- Paige M. K. Larkin
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA; (P.M.K.L.); (A.J.D.); (G.A.F.)
- Department of Pathology, NorthShore University HealthSystem, Evanston, IL 60201, USA
| | - Ashrit Multani
- Department of Medicine, Division of Infectious Diseases, University of California Los Angeles, Los Angeles, CA 90095, USA; (A.M.); (O.E.B.)
| | - Omer E. Beaird
- Department of Medicine, Division of Infectious Diseases, University of California Los Angeles, Los Angeles, CA 90095, USA; (A.M.); (O.E.B.)
| | - Ayrton J. Dayo
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA; (P.M.K.L.); (A.J.D.); (G.A.F.)
| | - Gregory A. Fishbein
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA; (P.M.K.L.); (A.J.D.); (G.A.F.)
| | - Shangxin Yang
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA; (P.M.K.L.); (A.J.D.); (G.A.F.)
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Šalplachta J, Horká M, Karásek P, Růžička F, Roth M. Identification of Aspergillus Conidia in Bronchoalveolar Lavage Using Offline Combination of Capillary Electrophoresis in Supercritical Water-Treated Fused Silica Capillary and Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry. Anal Chem 2020; 92:7588-7595. [PMID: 32384240 DOI: 10.1021/acs.analchem.0c00165] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Diagnosis of fungal infection in lung parenchyma is relatively difficult. Bronchoscopy with bronchoalveolar lavage is very useful in its diagnosing. Therefore, a method for rapid online concentration and analysis of Aspergillus conidia in bronchoalveolar lavage fluid using the combination of transient isotachophoresis (tITP) and micellar electrokinetic chromatography (MEKC) with subsequent off-line identification of the separated conidia by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is described in this study. In the proposed procedure, conidia were first dynamically adhered onto the roughened part of the inner surface of a fused silica capillary prepared by etching with supercritical water. Then the adhered conidia were desorbed, concentrated, and separated using a combination of tITP and MEKC. Finally, the fractions containing the separated conidia were collected from the capillary and analyzed by MALDI-TOF MS. The adhesion efficiency under the optimized experimental conditions was about 80%. This rapid diagnosis will contribute to timely initiation of therapy and increase the patient's chances of survival.
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Affiliation(s)
- Jiří Šalplachta
- Institute of Analytical Chemistry of the CAS, Veveří 97, 602 00 Brno, Czech Republic
| | - Marie Horká
- Institute of Analytical Chemistry of the CAS, Veveří 97, 602 00 Brno, Czech Republic
| | - Pavel Karásek
- Institute of Analytical Chemistry of the CAS, Veveří 97, 602 00 Brno, Czech Republic
| | - Filip Růžička
- Department of Microbiology, Faculty of Medicine, Masaryk University, Kamenice 53/5, 625 00 Brno, Czech Republic
| | - Michal Roth
- Institute of Analytical Chemistry of the CAS, Veveří 97, 602 00 Brno, Czech Republic
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Abstract
Appropriate diagnosis of invasive fungal infections (IFIs) is critical due to the high rates of morbidity and mortality, as well as the substantial economic burden, associated with the management of these diseases. The recognition of IFI and differentiation from other infections with similar clinical presentations can be challenging, which can lead to diagnostic error that not only has an impact on individual patient health outcomes but also on antimicrobial drug usage and the growing threat of antimicrobial resistance in bacteria. Therefore, there is a significant need for improved stewardship related to diagnostic testing for and treatment of IFIs. The purpose of this review is to highlight recent advances related to current fungal diagnostics, as well as explore some of the most innovative technology that has emerged with the potential to shift the paradigm of clinical mycology. In general, this review will discuss research related to enhanced fungal culture utilization and identification techniques, expanded applications of fungal antigen testing, and recently developed molecular assays and other novel nonculture fungal diagnostic approaches. Specifically, the application of mass spectrometry, novel glycobiomarker detection, and detection of fungal-specific volatile organic compounds will be reviewed, along with other key updates, to provide the reader with an updated review that extends beyond the basics of IFI laboratory diagnostics. Where appropriate, the reader will be directed to more comprehensive reviews of certain aspects of clinical mycology laboratory testing to provide a broader context for the critical consideration of these updates.
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Nomura F, Tsuchida S, Murata S, Satoh M, Matsushita K. Mass spectrometry-based microbiological testing for blood stream infection. Clin Proteomics 2020; 17:14. [PMID: 32435163 PMCID: PMC7222329 DOI: 10.1186/s12014-020-09278-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 05/04/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The most successful application of mass spectrometry (MS) in laboratory medicine is identification (ID) of microorganisms using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) in blood stream infection. We describe MALDI-TOF MS-based bacterial ID with particular emphasis on the methods so far developed to directly identify microorganisms from positive blood culture bottles with MALDI-TOF MS including our own protocols. We touch upon the increasing roles of Liquid chromatography (LC) coupled with tandem mass spectrometry (MS/MS) as well. MAIN BODY Because blood culture bottles contain a variety of nonbacterial proteins that may interfere with analysis and interpretation, appropriate pretreatments are prerequisites for successful ID. Pretreatments include purification of bacterial pellets and short-term subcultures to form microcolonies prior to MALDI-TOF MS analysis. Three commercial protocols are currently available: the Sepsityper® kit (Bruker Daltonics), the Vitek MS blood culture kit (bioMerieux, Inc.), and the rapid BACpro® II kit (Nittobo Medical Co., Tokyo). Because these commercially available kits are costly and bacterial ID rates using these kits are not satisfactory, particularly for Gram-positive bacteria, various home-brew protocols have been developed: 1. Stepwise differential sedimentation of blood cells and microorganisms, 2. Combination of centrifugation and lysis procedures, 3. Lysis-vacuum filtration, and 4. Centrifugation and membrane filtration technique (CMFT). We prospectively evaluated the performance of this CMFT protocol compared with that of Sepsityper® using 170 monomicrobial positive blood cultures. Although preliminary, the performance of the CMFT was significantly better than that of Sepsityper®, particularly for Gram-positive isolates. MALDI-TOF MS-based testing of polymicrobial blood specimens, however, is still challenging. Also, its contribution to assessment of susceptibility and resistance to antibiotics is still limited. For this purpose, liquid chromatography (LC) coupled with tandem mass spectrometry (MS/MS) should be more useful because this approach can identify as many as several thousand peptide sequences. CONCLUSION MALDI-TOF MS is now an essential tool for rapid bacterial ID of pathogens that cause blood stream infection. For the purpose of assessment of susceptibility and resistance to antibiotics of the pathogens, the roles of liquid chromatography (LC) coupled with tandem mass spectrometry (MS/MS) will increase in the future.
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Affiliation(s)
- Fumio Nomura
- Division of Clinical Mass Spectrometry, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8677 Japan
| | - Sachio Tsuchida
- Division of Clinical Mass Spectrometry, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8677 Japan
| | - Syota Murata
- Division of Laboratory Medicine, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8677 Japan
| | - Mamoru Satoh
- Division of Clinical Mass Spectrometry, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8677 Japan
| | - Kazuyuki Matsushita
- Division of Laboratory Medicine, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8677 Japan
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Ouarti B, Laroche M, Righi S, Meguini MN, Benakhla A, Raoult D, Parola P. Development of MALDI-TOF mass spectrometry for the identification of lice isolated from farm animals. ACTA ACUST UNITED AC 2020; 27:28. [PMID: 32351208 PMCID: PMC7191974 DOI: 10.1051/parasite/2020026] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 04/11/2020] [Indexed: 12/18/2022]
Abstract
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is now routinely used for the rapid identification of microorganisms isolated from clinical samples and has been recently successfully applied to the identification of arthropods. In the present study, this proteomics tool was used to identify lice collected from livestock and poultry in Algeria. The MALDI-TOF MS spectra of 408 adult specimens were measured for 14 species, including Bovicola bovis, B. ovis, B. caprae, Haematopinus eurysternus, Linognathus africanus, L. vituli, Solenopotes capillatus, Menacanthus stramineus, Menopon gallinae, Chelopistes meleagridis, Goniocotes gallinae, Goniodes gigas, Lipeurus caponis and laboratory reared Pediculus humanus corporis. Good quality spectra were obtained for 305 samples. Spectral analysis revealed intra-species reproducibility and inter-species specificity that were consistent with the morphological classification. A blind test of 248 specimens was performed against the in-lab database upgraded with new spectra and validated using molecular tools. With identification percentages ranging from 76% to 100% alongside high identification scores (mean = 2.115), this study proposes MALDI-TOF MS as an effective tool for discriminating lice species.
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Affiliation(s)
- Basma Ouarti
- Aix Marseille Univ., IRD, AP-HM, SSA, VITROME, 13005 Marseille, France - IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Maureen Laroche
- Aix Marseille Univ., IRD, AP-HM, SSA, VITROME, 13005 Marseille, France - IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Souad Righi
- Université Chadli Bendjdid, Département des sciences Vétérinaire, 36000 El Tarf, Algeria
| | - Mohamed Nadir Meguini
- Université Chadli Bendjdid, Département des sciences Vétérinaire, 36000 El Tarf, Algeria - Institut des Sciences Vétérinaire et Agronomiques, Université Mohamed Cherif Messaadia, 41000 Souk-Ahras, Algeria
| | - Ahmed Benakhla
- Université Chadli Bendjdid, Département des sciences Vétérinaire, 36000 El Tarf, Algeria
| | - Didier Raoult
- IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France - Aix Marseille Univ., IRD, AP-HM, MEPHI, 13005 Marseille, France
| | - Philippe Parola
- Aix Marseille Univ., IRD, AP-HM, SSA, VITROME, 13005 Marseille, France - IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
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