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Neoh CF, Chen SCA, Lanternier F, Tio SY, Halliday CL, Kidd SE, Kong DCM, Meyer W, Hoenigl M, Slavin MA. Scedosporiosis and lomentosporiosis: modern perspectives on these difficult-to-treat rare mold infections. Clin Microbiol Rev 2024; 37:e0000423. [PMID: 38551323 DOI: 10.1128/cmr.00004-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2024] Open
Abstract
SUMMARYAlthough Scedosporium species and Lomentospora prolificans are uncommon causes of invasive fungal diseases (IFDs), these infections are associated with high mortality and are costly to treat with a limited armamentarium of antifungal drugs. In light of recent advances, including in the area of new antifungals, the present review provides a timely and updated overview of these IFDs, with a focus on the taxonomy, clinical epidemiology, pathogenesis and host immune response, disease manifestations, diagnosis, antifungal susceptibility, and treatment. An expansion of hosts at risk for these difficult-to-treat infections has emerged over the last two decades given the increased use of, and broader population treated with, immunomodulatory and targeted molecular agents as well as wider adoption of antifungal prophylaxis. Clinical presentations differ not only between genera but also across the different Scedosporium species. L. prolificans is intrinsically resistant to most currently available antifungal agents, and the prognosis of immunocompromised patients with lomentosporiosis is poor. Development of, and improved access to, diagnostic modalities for early detection of these rare mold infections is paramount for timely targeted antifungal therapy and surgery if indicated. New antifungal agents (e.g., olorofim, fosmanogepix) with novel mechanisms of action and less cross-resistance to existing classes, availability of formulations for oral administration, and fewer drug-drug interactions are now in late-stage clinical trials, and soon, could extend options to treat scedosporiosis/lomentosporiosis. Much work remains to increase our understanding of these infections, especially in the pediatric setting. Knowledge gaps for future research are highlighted in the review.
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Affiliation(s)
- Chin Fen Neoh
- National Centre for Infections in Cancer, Peter MacCallum Cancer Centre, Melbourne, Australia
- Department of Infectious Diseases, Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia
| | - Sharon C-A Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales Health Pathology, Westmead Hospital, Sydney, Australia
- The University of Sydney, Sydney, Australia
- Department of Infectious Diseases, Westmead Hospital, Sydney, Australia
| | - Fanny Lanternier
- Service de Maladies Infectieuses et Tropicales, Hôpital universitaire Necker-Enfants malades, Paris, France
- National Reference Center for Invasive Mycoses and Antifungals, Translational Mycology research group, Mycology Department, Institut Pasteur, Université Paris Cité, Paris, France
| | - Shio Yen Tio
- National Centre for Infections in Cancer, Peter MacCallum Cancer Centre, Melbourne, Australia
- Department of Infectious Diseases, Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia
| | - Catriona L Halliday
- Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales Health Pathology, Westmead Hospital, Sydney, Australia
| | - Sarah E Kidd
- National Mycology Reference Centre, SA Pathology, Adelaide, Australia
- School of Biological Sciences, Faculty of Sciences, University of Adelaide, Adelaide, Australia
| | - David C M Kong
- National Centre for Infections in Cancer, Peter MacCallum Cancer Centre, Melbourne, Australia
- The National Centre for Antimicrobial Stewardship, The Peter Doherty Institute for Infections and Immunity, Melbourne, Australia
- Centre for Medicine Use and Safety, Monash Institute of Pharmaceutical Sciences, Faculty of Pharmacy and Pharmaceutical Sciences, Monash University, Melbourne, Australia
- School of Medicine, Deakin University, Waurn Ponds, Geelong, Australia
| | - Wieland Meyer
- The University of Sydney, Sydney, Australia
- Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands
| | - Martin Hoenigl
- Division of Infectious Diseases, Department of Internal Medicine, Medical University of Graz, Graz, Austria
- Translational Medical Mycology Research Group, ECMM Excellence Center for Clinical Mycology, Medical University of Graz, Graz, Austria
| | - Monica A Slavin
- National Centre for Infections in Cancer, Peter MacCallum Cancer Centre, Melbourne, Australia
- Department of Infectious Diseases, Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia
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2
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Douglas AP, Stewart AG, Halliday CL, Chen SCA. Outbreaks of Fungal Infections in Hospitals: Epidemiology, Detection, and Management. J Fungi (Basel) 2023; 9:1059. [PMID: 37998865 PMCID: PMC10672668 DOI: 10.3390/jof9111059] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 10/17/2023] [Accepted: 10/26/2023] [Indexed: 11/25/2023] Open
Abstract
Nosocomial clusters of fungal infections, whilst uncommon, cannot be predicted and are associated with significant morbidity and mortality. Here, we review reports of nosocomial outbreaks of invasive fungal disease to glean insight into their epidemiology, risks for infection, methods employed in outbreak detection including genomic testing to confirm the outbreak, and approaches to clinical and infection control management. Both yeasts and filamentous fungi cause outbreaks, with each having general and specific risks. The early detection and confirmation of the outbreak are essential for diagnosis, treatment of affected patients, and termination of the outbreak. Environmental sampling, including the air in mould outbreaks, for the pathogen may be indicated. The genetic analysis of epidemiologically linked isolates is strongly recommended through a sufficiently discriminatory approach such as whole genome sequencing or a method that is acceptably discriminatory for that pathogen. An analysis of both linked isolates and epidemiologically unrelated strains is required to enable genetic similarity comparisons. The management of the outbreak encompasses input from a multi-disciplinary team with epidemiological investigation and infection control measures, including screening for additional cases, patient cohorting, and strict hygiene and cleaning procedures. Automated methods for fungal infection surveillance would greatly aid earlier outbreak detection and should be a focus of research.
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Affiliation(s)
- Abby P. Douglas
- National Centre for Infections in Cancer, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
- Department of Infectious Diseases, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC 3000, Australia
- Department of Infectious Diseases, Austin Health, Heidelberg, VIC 3084, Australia
| | - Adam G. Stewart
- Centre for Clinical Research, Faculty of Medicine, Royal Brisbane and Women’s Hospital Campus, The University of Queensland, Herston, QLD 4006, Australia;
| | - Catriona L. Halliday
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead Hospital, Sydney, NSW 2145, Australia; (C.L.H.); (S.C.-A.C.)
| | - Sharon C.-A. Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead Hospital, Sydney, NSW 2145, Australia; (C.L.H.); (S.C.-A.C.)
- Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2050, Australia
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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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Hankins JD, Amerson-Brown MH, Brown CA, Riegler AN, Muldrew KL, Dunn JJ. Comparison of Bruker Biotyper ® and Vitek ® MS matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry platforms for the identification of filamentous fungi. Future Microbiol 2023; 18:553-561. [PMID: 37317856 DOI: 10.2217/fmb-2023-0084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023] Open
Abstract
Aims: To evaluate the performance of two matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry platforms to identify molds isolated from clinical specimens. Methods: Fifty mold isolates were analyzed on Bruker Biotyper® and Vitek® MS platforms. Two Bruker Biotyper extraction protocols were assessed alongside the US FDA-approved extraction protocol for Vitek MS. Results: The Bruker Biotyper modified NIH-developed extraction protocol correctly identified more isolates than Bruker's protocol (56 vs 33%). For species in the manufacturers' databases, Vitek MS correctly identified 85% of isolates, with 8% misidentifications. The Bruker Biotyper identified 64%, with no misidentifications. For isolates not in the databases, the Bruker Biotyper did not misidentify any, and Vitek MS misidentified 36%. Conclusion: Both the Vitek MS and Bruker Biotyper accurately identified the fungal isolates, however Vitek MS was more likely to misidentify isolates than the Bruker Biotyper.
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Affiliation(s)
- Julia D Hankins
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Pathology, Texas Children's Hospital, Houston, TX 77030, USA
| | - Megan H Amerson-Brown
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Pathology, Texas Children's Hospital, Houston, TX 77030, USA
- Department of Pathology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Cameron A Brown
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Pathology, Harris Health Ben Taub Hospital, Houston, TX 77030, USA
| | - Ashleigh N Riegler
- Department of Pathology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Kenneth L Muldrew
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Pathology, Harris Health Ben Taub Hospital, Houston, TX 77030, USA
- Department of Internal Medicine, Infectious Diseases, Baylor College of Medicine, Houston, TX 77030, USA
| | - James J Dunn
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Pathology, Texas Children's Hospital, Houston, TX 77030, USA
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5
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Trivitt GE, Lau AF. Performance of the MSI-2 Database for Fungal Identification by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry from Cleanroom Environments. J Clin Microbiol 2023; 61:e0135322. [PMID: 36853008 PMCID: PMC10035329 DOI: 10.1128/jcm.01353-22] [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: 09/13/2022] [Accepted: 01/30/2023] [Indexed: 03/01/2023] Open
Abstract
Accurate mold identification by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is dependent on robust organism representation in available databases. The Mass Spectrometry Identification (MSI) platform has proven successful for mold identification in clinical and veterinary settings but has yet to be studied with a large set of environmental isolates. Here, we performed a retrospective study using spectra collected by the Bruker MALDI Biotyper (MBT) v4.1 microflex LT instrument to evaluate the MSI-2 database alongside the combined use of the Bruker MBT (including the MBT Filamentous Fungi Library) and the National Institutes of Health (NIH) mold database (MBT/NIH databases). Analysis was performed for 462 environmental fungal isolates (representing 73 different fungi) cultured from the hospital pharmacy and cellular therapy suites as part of the current good manufacturing practices (cGMP) environmental monitoring program at the NIH. When used alone, MSI-2 identified 237 spectra (51.3%) at its higher score threshold (index A), while the MBT/NIH databases identified only 183 spectra (39.6%; P < 0.001) at the equivalent threshold of ≥2.0. The combination of all three databases at the respective high thresholds improved identification sensitivity to 327 spectra (70.8%). The combination of MSI-2 with the MBT/NIH databases at a lowered threshold (index B or ≥1.7, respectively) identified 400/462 environmental spectra (86.6%). Our results show that the MSI-2 database, in combination with existing databases, may be useful for environmental surveillance, particularly by clinical or industry laboratories involved in cGMP or current good tissue practices (cGTP) applications, such as cellular therapy manufacturing facilities and sterile compounding pharmacies.
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Affiliation(s)
- Gloria E. Trivitt
- Sterility Testing Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Anna F. Lau
- Sterility Testing Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
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6
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Zhao Y, Chen D, Duan H, Li P, Wu W, Wang X, Poapolathep A, Poapolathep S, Logrieco AF, Pascale M, Wang C, Zhang Z. Sample preparation and mass spectrometry for determining mycotoxins, hazardous fungi, and their metabolites in the environment, food, and healthcare. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.116962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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7
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Xiao C, Qiao D, Xiong L, Tian W, Wang D, Deng S, Guo J. Clinical and Microbiological Characteristics of Aspergillosis at a Chinese Tertiary Teaching Hospital. Infect Drug Resist 2022; 15:7249-7257. [PMID: 36533254 PMCID: PMC9753761 DOI: 10.2147/idr.s391069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 11/23/2022] [Indexed: 07/25/2023] Open
Abstract
BACKGROUND Aspergillus spp. infection in immunocompromised patients results in increasing morbidity and mortality. This study investigated clinical and microbiological characteristics of aspergillosis in a Chinese tertiary teaching hospital. METHODS A total of 114 patients with aspergillosis were included over a 5-year period at Ruijin Hospital. In sum, 114 Aspergillus strains were isolated and identified at species level using matrix-assisted laser desorption ionization time-of-flight mass spectrometry, confirmed by ITS gene region and β-tubulin (BenA) gene sequencing. Sensititre YeastOne was used in vitro to test susceptibility to antifungal drugs: amphotericin B, itraconazole, voriconazole, posaconazole, isavuconazole, micafungin, anidulafungin, and caspofungin. RESULTS The median age of the patients was 61 (19) years, men accounted for 53.5% (n=61) of the sample, about 64% were immunocompromised, and 36% had underlying diseases. Pulmonary diseases accounted for 27.2%. Aspergillus isolates were mainly isolated from sputum (n=42, 36.8%). Antifungal therapy was administered to 106 (93.0%) patients and voriconazole (n=76, 66.7%) was the most frequently used as empirical therapy. Aspergillus fumigatus (n=69, 60.5%) was the most common species. There was a 73.7% concordance between MALDI-TOF MS and molecular identification. All Aspergillus isolates showed good susceptibility to anidulafungin and caspofungin. CONCLUSION Immunocompromised patients are an at-risk population for aspergillosis, and voriconazole was used as empirical therapy in Ruijin Hospital, China. A. fumigatus was the predominant Aspergillus species causing aspergillosis, and A. flavus - as non-A. fumigatus species are increasing - the second-leading cause of aspergillosis. Anidulafungin and caspofungin were the most active in vitro against the Aspergillus isolates tested. The MALDI-TOF MS method showed good accuracy for identification of common Aspergillus spp. In vitro antifungal-susceptibility testing is crucially important for decisions on effective therapy with aspergillosis.
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Affiliation(s)
- Chenlu Xiao
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
- Department of Clinical Microbiology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, People’s Republic of China
| | - Dan Qiao
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
| | - Lijuan Xiong
- Department of Laboratory Medicine, Second Affiliated Hospital of Traditional Chinese Medicine of Guizhou University, Guizhou, People’s Republic of China
| | - Wenjie Tian
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, People’s Republic of China
| | - Dongjiang Wang
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, People’s Republic of China
| | - Shuwen Deng
- Department of Medical Microbiology, People’s Hospital of Suzhou New District, Suzhou, Jiangsu, People’s Republic of China
| | - Jian Guo
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, People’s Republic of China
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8
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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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Identification of molds with MALDI-TOF mass spectrometry: performance of the newly developed MSI-2 application in comparison with the Bruker filamentous fungi database and MSI-1. J Clin Microbiol 2021; 59:e0129921. [PMID: 34319807 DOI: 10.1128/jcm.01299-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS) represents a promising tool for the rapid and efficient identification of molds, but improvements are still necessary to achieve satisfactory results when identifying cryptic species. Here, we aimed to validate a new web application, MSI-2, which replaces MSI-1, an application that was built and deployed online in 2017. For the evaluation, we gathered 633 challenging isolates obtained from daily hospital practice that were first identified with DNA-based methods, and we submitted their corresponding mass spectra to three identification programs (Bruker, MSI-1 and MSI-2). The MSI-2 application had a better identification performance at the species level than MSI-1 and Bruker, reaching 83.25% correct identifications compared with 63.19% (MSI-1), 38.07% (Bruker with 1.7 threshold) and 21.8% (Bruker with 2.0 threshold). The MSI-2 application performed especially well for Aspergillus and Fusarium species, including for many cryptic species, reaching 90% correct identifications for Aspergillus species and 78% for Fusarium species compared to 69% and 43% with MSI-1. Such improvement may have a positive impact on patient management by facilitating the identification of cryptic species potentially associated with a specific antifungal resistance profile.
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10
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Sun Y, Guo J, Chen R, Hu L, Xia Q, Wu W, Wang J, Hu F. Multicenter evaluation of three different MALDI-TOF MS systems for identification of clinically relevant filamentous fungi. Med Mycol 2021; 59:81-86. [PMID: 32437532 DOI: 10.1093/mmy/myaa037] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 04/09/2020] [Accepted: 04/23/2020] [Indexed: 12/18/2022] Open
Abstract
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) holds promise as a potential tool for clinical identification of filamentous fungi. However, due to the lack of an appropriate extraction protocol and the difficulty of database building, the identification power of each system differs. In this study, we selected 126 clinical mould isolates comprising 28 species identified using internal transcribed spacer (ITS) sequencing as the reference method to evaluate three MALDI-TOF MS systems. When using cultures and sample preparation as recommended by the respective vendors, of the 126 strains tested, VITEK MS identified 121 (96.0%) to species-level and 124 (98.4%) to genus-level; Biotyper identified 53 (42.1%) to species-level and 54 (42.9%) to genus-level; Autof identified 74 (58.7%) to species-level and 76 (60.3%) to genus-level. For the Autof system, the tube extraction method recommended by the vendor performed better (59%) than the on-plate lysis (51%). Our study demonstrates that MALDI-TOF MS systems can successfully identify most clinically relevant fungi, while performance is still highly dependent on the database and sample preparation protocol.
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Affiliation(s)
- Yue Sun
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China.,Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
| | - Jian Guo
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Rong Chen
- Department of Clinical Microbiology Laboratory, Shanghai Center for Clinical Laboratory, Shanghai, China
| | - Liang Hu
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Qihang Xia
- Department of Clinical Microbiology Laboratory, Shanghai Center for Clinical Laboratory, Shanghai, China
| | - Wenjuan Wu
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jinghua Wang
- Department of Clinical Microbiology Laboratory, Shanghai Center for Clinical Laboratory, Shanghai, China
| | - Fupin Hu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China.,Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
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11
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Detection of azole resistance in Aspergillus fumigatus complex isolates using MALDI-TOF mass spectrometry. Clin Microbiol Infect 2021; 28:260-266. [PMID: 34147673 DOI: 10.1016/j.cmi.2021.06.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 05/26/2021] [Accepted: 06/03/2021] [Indexed: 01/24/2023]
Abstract
OBJECTIVES The main goal of this study was to accurately detect azole resistance in species of the Aspergillus fumigatus complex by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). METHODS Identification of isolates (n = 868) was done with MALDI-TOF MS using both commercial and in-house libraries. To determine azole susceptibility, the EUCAST E.Def. 9.3.2 method was applied as the reference standard. Identification of resistant isolates was confirmed by DNA sequence analysis. Protein spectra obtained by MALDI-TOF MS were analysed to differentiate species within the A. fumigatus complex and to detect azole-resistant A. fumigatus sensu stricto isolates. RESULTS Correct discrimination of A. fumigatus sensu stricto from cryptic species was accomplished in 100% of the cases applying principal component analysis (PCA) to protein spectra generated by MALDI-TOF MS. Furthermore, a specific peak (4586 m/z) was found to be present only in cryptic species. The application of partial least squares (PLS) discriminant analysis allowed 98.43% (±0.038) discrimination between susceptible and azole-resistant A. fumigatus sensu stricto isolates. Finally, based on PLS and SVM, A. fumigatus sensu stricto isolates with different cyp51A gene mutations were correctly clustered in 91.5% of the cases. CONCLUSIONS MALDI-TOF MS combined with peak analysis is a novel tool that allows the differentiation of A. fumigatus sensu stricto from other species within the A. fumigatus complex, as well as the detection of azole-resistant A. fumigatus sensu stricto. Although further studies are still needed, the results reported here show the great potential of MALDI-TOF and machine learning for the rapid detection of azole-resistant Aspergillus fumigatus isolates from clinical origins.
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12
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Lau AF. Matrix-Assisted Laser Desorption Ionization Time-of-Flight for Fungal Identification. Clin Lab Med 2021; 41:267-283. [PMID: 34020763 DOI: 10.1016/j.cll.2021.03.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Many studies have shown successful performance of matrix-assisted laser desorption ionization time-of-flight mass spectrometry for rapid yeast and mold identification, yet few laboratories have chosen to apply this technology into their routine clinical mycology workflow. This review provides an overview of the current status of matrix-assisted laser desorption ionization time-of-flight mass spectrometry for fungal identification, including key findings in the literature, processing and database considerations, updates in technology, and exciting future prospects. Significant advances toward standardization have taken place recently; thus, accurate species-level identification of yeasts and molds should be highly attainable, achievable, and practical in most clinical laboratories.
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Affiliation(s)
- Anna F Lau
- Sterility Testing Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, 10 Center Drive, Room 2C306, Bethesda, MD 20892, USA.
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13
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Moreno-Sabater A, Autaa G, Sterlin D, Jerbi A, Villette R, Holm JB, Parizot C, Selim S, Senghor Y, Ghillani-Dalbin P, Bachmeyer C, Hennequin C, Gorochov G, Larsen M. Systemic anti-commensal response to fungi analyzed by flow cytometry is related to gut mycobiome ecology. MICROBIOME 2020; 8:159. [PMID: 33190643 PMCID: PMC7667786 DOI: 10.1186/s40168-020-00924-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 09/15/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND Interest for the study of gut mycobiota in relation with human health and immune homeostasis has increased in the last years. From this perspective, new tools to study the immune/fungal interface are warranted. Systemic humoral immune responses could reflect the dynamic relationships between gut mycobiota and immunity. Using a novel flow cytometry technology (Fungi-Flow) to determine immunoglobulin (Ig) responses to fungi, we studied the relationships between gut mycobiota and systemic humoral anti-commensal immunity. RESULTS The Fungi-Flow method allows a sensitive and specific measurement of systemic IgG responses against 17 commensal and environmental fungi from the two main divisions; Ascomycota and Basidiomycota. IgG responses exhibited a high inter-individual variability. Anti-commensal IgG responses were contrasted with the relative abundance, alpha-diversity, and intra-genus richness of fungal species in gut mycobiota of twenty healthy donors. Categorization of gut mycobiota composition revealed two differentiated fungal ecosystems. Significant difference of anti-Saccharomyces systemic IgG responses were observed in healthy donors stratified according to the fungal ecosystem colonizing their gut. A positive and significant correlation was observed between the variety of IgG responses against fungal commensals and intestinal alpha-diversity. At the level of intra-genus species richness, intense IgG responses were associated with a low intra-genus richness for known pathobionts, but not commensals. CONCLUSIONS Fungi-Flow allows an easy and reliable measure of personalized humoral responses against commensal fungi. Combining sequencing technology with our novel Fungi-Flow immunological method, we propose that there are at least two defined ecosystems in the human gut mycobiome associated with systemic humoral responses. Fungi-Flow opens new opportunities to improve our knowledge about the impact of mycobiota in humoral anti-commensal immunity and homeostasis. Video Abstract.
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Affiliation(s)
- Alicia Moreno-Sabater
- Sorbonne Université, Inserm U1135, Centre d’Immunologie et des Maladies Infectieuses (CIMI-Paris), 75013 Paris, France
- Service de Parasitologie-Mycologie AP-HP, Hôpital Saint-Antoine, 75012 Paris, France
| | - Gaelle Autaa
- Sorbonne Université, Inserm U1135, Centre d’Immunologie et des Maladies Infectieuses (CIMI-Paris), 75013 Paris, France
| | - Delphine Sterlin
- Sorbonne Université, Inserm U1135, Centre d’Immunologie et des Maladies Infectieuses (CIMI-Paris), 75013 Paris, France
- Service d’immunologie, AP-HP, Hôpital Pitié-Salpêtrière, 75013 Paris, France
- Unit of Antibodies in Therapy and Pathology, Institut Pasteur, UMR1222 Inserm, 75015 Paris, France
| | - Amenie Jerbi
- Service d’immunologie, AP-HP, Hôpital Pitié-Salpêtrière, 75013 Paris, France
| | - Remy Villette
- Sorbonne Université, Inserm U1135, Centre d’Immunologie et des Maladies Infectieuses (CIMI-Paris), 75013 Paris, France
| | - Johanna B. Holm
- Institute for Genome Sciences and Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD USA
| | - Christophe Parizot
- Service d’immunologie, AP-HP, Hôpital Pitié-Salpêtrière, 75013 Paris, France
| | - Sameh Selim
- College of Agricultural Sciences AGHYLE Res, Unit. Institut Polytechnique UniLaSalle, 60026 Beauvais, France
| | - Yaye Senghor
- Service de Parasitologie-Mycologie AP-HP, Hôpital Saint-Antoine, 75012 Paris, France
| | | | | | - Christophe Hennequin
- Service de Parasitologie-Mycologie AP-HP, Hôpital Saint-Antoine, 75012 Paris, France
- Centre de Recherche Saint-Antoine, CRSA, AP-HP, Sorbonne Université, Inserm, 75012 Paris, France
| | - Guy Gorochov
- Sorbonne Université, Inserm U1135, Centre d’Immunologie et des Maladies Infectieuses (CIMI-Paris), 75013 Paris, France
- Service d’immunologie, AP-HP, Hôpital Pitié-Salpêtrière, 75013 Paris, France
| | - Martin Larsen
- Sorbonne Université, Inserm U1135, Centre d’Immunologie et des Maladies Infectieuses (CIMI-Paris), 75013 Paris, France
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Multilaboratory Evaluation of the MALDI-TOF Mass Spectrometry System, MicroIDSys Elite, for the Identification of Medically Important Filamentous Fungi. Mycopathologia 2020; 186:15-26. [PMID: 33180204 DOI: 10.1007/s11046-020-00507-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 10/30/2020] [Indexed: 12/17/2022]
Abstract
With the increasing number of fungal infections and immunocompromised patients, rapid and accurate fungal identification is required in clinical microbiology laboratories. We evaluated the applicability of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) system, MicroIDSys Elite (ASTA Corp., South Korea) for the identification of medically important filamentous fungi. A total of 505 strains comprising 37 genera and 90 species collected from 11 Korean hospitals were sent to the microbiology laboratory of International St. Mary's Hospital. All isolates were tested using MicroIDSys Elite, and data were analyzed using the MoldDB v.1.22 database (ASTA). Correct identification rates were compared with the multigene sequencing results. MicroIDSys Elite correctly identified 86.5% (437/505) and 88.9% (449/505) of all tested isolates at the species and genus level, respectively. About 98.2% of Aspergillus isolates were identified at the species level, including cryptic and rare species of A. calidoustus, A. tamarii, A. lentulus, A. versicolor and A. aculeatus. MicroIDSys Elite identified 75.0% of basidiomycetes, including Schizophyllum commune, and 84.3% of the dermatophytes. It also distinguished Sprothrix globosa at the species level. The mean scores of total isolates corresponding to correct species identification were significantly higher than those obtained for genus-level identification (253.5 ± 50.7 vs. 168.6 ± 30.3, P < 0.001). MicroIDSys Elite showed high accuracy for the identification of filamentous fungi, including cryptic and rare Aspergillus species. It is suitable for use in clinical laboratories as a rapid and efficient tool for clinical mold identification. Further evaluations are recommended for MicroIDSys Elite as a rapid and efficient tool for the identification of medically important filamentous fungi.
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Li Y, Wang H, Hou X, Huang JJ, Wang PC, Xu YC. Identification by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry and Antifungal Susceptibility Testing of Non- Aspergillus Molds. Front Microbiol 2020; 11:922. [PMID: 32582045 PMCID: PMC7283379 DOI: 10.3389/fmicb.2020.00922] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 04/17/2020] [Indexed: 12/28/2022] Open
Abstract
Non-Aspergillus molds including Mucorales, Fusarium, and Scedosporium, etc. are emerging pathogens leading to higher mortality in immunocompromised patients. Fifty-two isolates of genetically confirmed non-Aspergillus molds representing 16 species from 8 genera were collected to evaluate the performance of the Bruker matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) in identification of non-Aspergillus molds. Antifungal susceptibilities were determined through the Clinical & Laboratory Standards Institute (CLSI) M38-A2 broth microdilution method and the Sensititre YeastOne colorimetric method. Bruker MALDI-TOF MS identified 57.7% (30/52) of isolates cultured in broth and 15.4% (8/52) of isolates cultured on solid agar media to the species level, respectively, according to standard interpretation criteria. Lowering the species level cut-off value (COV) from ≥2.0 to ≥1.7 could improve the MALDI-TOF MS species-level identification rate to 67.3% (38/52) for isolates cultured on solid media, with a slight increase of false identification rate of 2.6% (1/38). Amphotericin B was the most in vitro fungistatic-active agent for 98.1% (51/52) of the tested non-Aspergillus molds, with minimum inhibitory concentrations (MICs) of ≤2 μg/mL. The susceptibilities to triazoles varied, with MICs of 0.12 to >16 μg/mL among different species of non-Aspergillus molds. The correlation between the CLSI method and Sensititre YeastOne on antifungal susceptibility testing of non-Aspergillus molds was good, with essential agreement (EA) rates of >90% for triazoles and echinocandins except amphotericin B, which had a lower EA rate of 84.6%. In conclusion, a favorable performance of the Bruker MALDI-TOF MS in identification of clinical non-Aspergillus isolates directly inoculated on solid agar media could be achieved with the adoption of alternative interpretation criteria. Antifungal susceptibility testing is important for non-Aspergillus molds, especially when information on triazole susceptibility is required, and the Sensititre YeastOne is a practical and reliable method to determine antifungal susceptibilities of non-Aspergillus molds.
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Affiliation(s)
- Ying Li
- Department of Clinical Laboratory, Xuanwu Hospital, Capital Medical University, Beijing, China.,Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - He Wang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Xin Hou
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Jing-Jing Huang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Pei-Chang Wang
- Department of Clinical Laboratory, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Ying-Chun Xu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
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16
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Tie Y, Adams E, Deconinck E, Vanhee C. Substandard and falsified antimicrobials: A potential biohazard in disguise? Drug Test Anal 2019; 12:285-291. [PMID: 31758727 DOI: 10.1002/dta.2740] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 11/04/2019] [Accepted: 11/04/2019] [Indexed: 11/07/2022]
Affiliation(s)
- Yaxin Tie
- Scientific Direction Chemical and Physical Health Risks, Section Medicines and Health Products, Sciensano, Brussels, Belgium
- Department of Pharmaceutical and Pharmacological Sciences, Pharmaceutical Analysis, KU Leuven, University of Leuven, Leuven, Belgium
| | - Erwin Adams
- Department of Pharmaceutical and Pharmacological Sciences, Pharmaceutical Analysis, KU Leuven, University of Leuven, Leuven, Belgium
| | - Eric Deconinck
- Scientific Direction Chemical and Physical Health Risks, Section Medicines and Health Products, Sciensano, Brussels, Belgium
| | - Celine Vanhee
- Scientific Direction Chemical and Physical Health Risks, Section Medicines and Health Products, Sciensano, Brussels, Belgium
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17
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Lau AF, Walchak RC, Miller HB, Slechta ES, Kamboj K, Riebe K, Robertson AE, Gilbreath JJ, Mitchell KF, Wallace MA, Bryson AL, Balada-Llasat JM, Bulman A, Buchan BW, Burnham CAD, Butler-Wu S, Desai U, Doern CD, Hanson KE, Henderson CM, Kostrzewa M, Ledeboer NA, Maier T, Pancholi P, Schuetz AN, Shi G, Wengenack NL, Zhang SX, Zelazny AM, Frank KM. Multicenter Study Demonstrates Standardization Requirements for Mold Identification by MALDI-TOF MS. Front Microbiol 2019; 10:2098. [PMID: 31616388 PMCID: PMC6764242 DOI: 10.3389/fmicb.2019.02098] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 08/26/2019] [Indexed: 12/20/2022] Open
Abstract
Objectives Rapid and accurate mold identification is critical for guiding therapy for mold infections. MALDI-TOF MS has been widely adopted for bacterial and yeast identification; however, few clinical laboratories have applied this technology for routine mold identification due to limited database availability and lack of standardized processes. Here, we evaluated the versatility of the NIH Mold Database in a multicenter evaluation. Methods The NIH Mold Database was evaluated by eight US academic centers using a solid media extraction method and a challenge set of 80 clinical mold isolates. Multiple instrument parameters important for spectra optimization were evaluated, leading to the development of two specialized acquisition programs (NIH method and the Alternate-B method). Results A wide range in performance (33–77%) was initially observed across the eight centers when routine spectral acquisition parameters were applied. Use of the NIH or the Alternate-B specialized acquisition programs, which are different than those used routinely for bacterial and yeast spectral acquisition (MBT_AutoX), in combination with optimized instrument maintenance, improved performance, illustrating that acquisition parameters may be one of the key limiting variable in achieving successful performance. Conclusion Successful mold identification using the NIH Database for MALDI-TOF MS on Biotyper systems was demonstrated across multiple institutions for the first time following identification of critical program parameters combined with instrument optimization. This significantly advances our potential to implement MALDI-TOF MS for mold identification across many institutions. Because instrument variability is inevitable, development of an instrument performance standard specific for mold spectral acquisition is suggested to improve reproducibility across instruments.
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Affiliation(s)
- Anna F Lau
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, United States
| | - Robert C Walchak
- Division of Clinical Microbiology, Mayo Clinic, Rochester, MN, United States
| | - Heather B Miller
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - E Susan Slechta
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, United States
| | - Kamal Kamboj
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH, United States
| | - Katherine Riebe
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Amy E Robertson
- Clinical Microbiology Laboratory, Weill Cornell Medical Center/New York Presbyterian Hospital, New York, NY, United States
| | - Jeremy J Gilbreath
- Department of Laboratory Medicine, University of Washington, Seattle, WA, United States
| | - Kaitlin F Mitchell
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, United States
| | - Meghan A Wallace
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, United States
| | - Alexandra L Bryson
- Department of Pathology, Virginia Commonwealth University School of Medicine, Richmond, VA, United States
| | - Joan-Miquel Balada-Llasat
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH, United States
| | - Amanda Bulman
- Bruker Daltonics, Inc., Billerica, MA, United States
| | - Blake W Buchan
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Carey-Ann D Burnham
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, United States
| | - Susan Butler-Wu
- Department of Laboratory Medicine, University of Washington, Seattle, WA, United States
| | - Uma Desai
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, United States
| | - Christopher D Doern
- Department of Pathology, Virginia Commonwealth University School of Medicine, Richmond, VA, United States
| | - Kimberly E Hanson
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, United States.,Department of Pathology, Division of Clinical Microbiology, The University of Utah, Salt Lake City, UT, United States
| | - Christina M Henderson
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, United States
| | | | - Nathan A Ledeboer
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Thomas Maier
- Bruker Daltonics, Inc., Billerica, MA, United States
| | - Preeti Pancholi
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH, United States
| | - Audrey N Schuetz
- Clinical Microbiology Laboratory, Weill Cornell Medical Center/New York Presbyterian Hospital, New York, NY, United States
| | - Gongyi Shi
- Bruker Daltonics, Inc., Billerica, MA, United States
| | - Nancy L Wengenack
- Division of Clinical Microbiology, Mayo Clinic, Rochester, MN, United States
| | - Sean X Zhang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Adrian M Zelazny
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, United States
| | - Karen M Frank
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, United States
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18
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Pinheiro D, Monteiro C, Faria MA, Pinto E. Vitek ® MS v3.0 System in the Identification of Filamentous Fungi. Mycopathologia 2019; 184:645-651. [PMID: 31506883 DOI: 10.1007/s11046-019-00377-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 08/21/2019] [Indexed: 12/19/2022]
Abstract
Infections caused by filamentous fungi are rising in incidence and became a serious health concern. Their rapid and reliable identification in the clinical laboratory is essential for an early and accurate diagnosis to guide timely therapy. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been reported as a rapid and reliable method for identification of bacteria and yeasts isolated from clinical samples. However, it has less used for molds identification. The aim of this study was to evaluate Vitek® MS (a MALDI-TOF MS system) ability to identify molds and differentiate species within a complex. A collection of 90 filamentous fungi, 70 clinical and 20 environmental isolates, was studied by morphological and molecular methods and by Vitek® MS. Seventy-four isolates (82.2%) were identified using Vitek® MS v3.0 at Genus/Complex/Species group level; within these, 47/74 (63.5%) were correctly identified at species level and only one was misidentified. In contrast, 16/90 isolates (17.8%) were not identified, of which 13 were not present in the database. Results here expressed favor Vitek® MS v3.0 as a very useful system for identification of most common clinical isolates of filamentous fungi. Accordingly, it may be an important tool for clinical microbiology laboratories in their task to answer to clinicians, adequately and rapidly, helping in proper patient's management.
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Affiliation(s)
- Dolores Pinheiro
- Laboratory of Microbiology, Service of Clinical Pathology, Centro Hospitalar Universitário de S. João, Alameda Prof. Hernâni Monteiro, 4200-319, Porto, Portugal.
| | - Carolina Monteiro
- Laboratory of Microbiology, Biological Sciences Department, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Miguel A Faria
- LAQV-REQUIMTE, Laboratory of Bromatology and Hydrology, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313, Porto, Portugal
| | - Eugénia Pinto
- Laboratory of Microbiology, Biological Sciences Department, Faculty of Pharmacy, University of Porto, Porto, Portugal.,Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Edifício do Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal
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Welker M, Van Belkum A, Girard V, Charrier JP, Pincus D. An update on the routine application of MALDI-TOF MS in clinical microbiology. Expert Rev Proteomics 2019; 16:695-710. [PMID: 31315000 DOI: 10.1080/14789450.2019.1645603] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Introduction: Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has entered clinical diagnostics and is today a generally accepted and integral part of the workflow for microbial identification. MALDI-TOF MS identification systems received approval from national and international institutions, such as the USA-FDA, and are continuously improved and adopted to other fields like veterinary and industrial microbiology. The question is whether MALDI-TOF MS also has the potential to replace other conventional and molecular techniques operated in routine diagnostic laboratories. Areas covered: We give an overview of new advancements of mass spectral analysis in the context of microbial diagnostics. In particular, the expansion of databases to increase the range of readily identifiable bacteria and fungi, the refined discrimination of species complexes, subspecies, and types, the testing for antibiotic resistance or susceptibility, progress in sample preparation including automation, and applications of other mass spectrometry techniques are discussed. Expert opinion: Although many new approaches of MALDI-TOF MS are still in the stage of proof of principle, it is expectable that MALDI-TOF MS will expand its role in the clinical microbiology laboratory of the future. New databases, instruments and analytical software modules will continue to be developed to further improve diagnostic efficacy.
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Affiliation(s)
- Martin Welker
- bioMérieux, Microbiology R&D , La Balme Les Grottes , France
| | - Alex Van Belkum
- bioMérieux, Microbiology R&D , La Balme Les Grottes , France
| | - Victoria Girard
- bioMérieux, Microbiology R&D , La Balme Les Grottes , France
| | | | - David Pincus
- bioMérieux, Microbiology Innovation , Hazelwood , MO , USA
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20
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Bryson AL, Hill EM, Doern CD. Matrix-Assisted Laser Desorption/Ionization Time-of-Flight: The Revolution in Progress. Clin Lab Med 2019; 39:391-404. [PMID: 31383264 DOI: 10.1016/j.cll.2019.05.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
This article summarizes recent advances in the application of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to new areas of infectious diseases diagnostics. We discuss progress toward routine identification of mycobacteria and filamentous fungi and direct identification of pathogens from clinical specimens. Of greatest interest is the use of MALDI-TOF MS for identifying organisms from positive blood cultures and from clinical specimens such as urine. Last, We highlight some exciting new possibilities for MALDI-TOF MS phenotypic susceptibility testing for bacteria and yeast.
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Affiliation(s)
- Alexandra L Bryson
- Department of Pathology, Virginia Commonwealth University Health System, 403 North 13th Street, Richmond, VA 23298, USA
| | - Emily M Hill
- Pathology & Laboratory Medicine, Hunter Holmes McGuire VA Medical Center, 1201 Broad Rock Boulevard, Richmond, VA 23224, USA
| | - Christopher D Doern
- Department of Pathology, Virginia Commonwealth University Health System, 403 North 13th Street, Richmond, VA 23298, USA.
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