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Sáenz V, Lizcano Salas AF, Gené J, Celis Ramírez AM. Fusarium and Neocosmospora: fungal priority pathogens in laboratory diagnosis. Crit Rev Microbiol 2024:1-14. [PMID: 38949272 DOI: 10.1080/1040841x.2024.2369693] [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: 10/12/2023] [Accepted: 06/11/2024] [Indexed: 07/02/2024]
Abstract
Fusarium and Neocosmospora are two fungal genera recently recognized in the list of fungal priority pathogens. They cause a wide range of diseases that affect humans, animals, and plants. In clinical laboratories, there is increasing concern about diagnosis due to limitations in sample collection and morphological identification. Despite the advances in molecular diagnosis, due to the cost, some countries cannot implement these methodologies. However, recent changes in taxonomy and intrinsic resistance to antifungals reveal the necessity of accurate species-level identification. In this review, we discuss the current phenotypic and molecular tools available for diagnosis in clinical laboratory settings and their advantages and disadvantages.
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Affiliation(s)
- Valeri Sáenz
- Grupo de Investigación Celular y Molecular de Microorganismos Patógenos (CeMoP), Departamento de Ciencias Biológicas, Universidad de Los Andes, Bogotá, Colombia
| | - Andrés Felipe Lizcano Salas
- Grupo de Investigación Celular y Molecular de Microorganismos Patógenos (CeMoP), Departamento de Ciencias Biológicas, Universidad de Los Andes, Bogotá, Colombia
| | - Josepa Gené
- Unitat de Micologia i Microbiologia Ambiental (MicroAmb), Facultat de Medicina i Ciències de la Salut i Institut d'Investigació Sanitària Pere Virgili (IISPV), Universitat Rovira i Virgili, Reus, Spain
| | - Adriana Marcela Celis Ramírez
- Grupo de Investigación Celular y Molecular de Microorganismos Patógenos (CeMoP), Departamento de Ciencias Biológicas, Universidad de Los Andes, Bogotá, Colombia
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Lee H, Koo J, Oh J, Cho SI, Lee H, Lee HJ, Sung GH, Kim J. Clinical Evaluation of VITEK MS PRIME with PICKME Pen for Bacteria and Yeasts, and RUO Database for Filamentous Fungi. Microorganisms 2024; 12:964. [PMID: 38792793 PMCID: PMC11124449 DOI: 10.3390/microorganisms12050964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 05/01/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
The VITEK MS PRIME (bioMérieux, Marcy-l'Étoile, France), a newly developed matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) system, alongside the VITEK PICKME pen (PICKME), offers easy sample preparation for bacteria and yeasts. The VITEK MS PRIME also offers two software platforms for filamentous fungi: the IVD database and the RUO database. Our study evaluated its identification agreement on 320 clinical isolates of bacteria and yeasts, comparing PICKME and traditional wooden toothpick sampling techniques against MicroIDSys Elite (ASTA) results. Additionally, we assessed the IVD (v3.2) and SARAMIS (v4.16) RUO databases on 289 filamentous fungi against molecular sequencing. The concordance rates for species-level identification of bacteria and yeasts were about 89.4% (286/320) between the PICKME and wooden toothpick, and about 83.4-85.3% between the VITEK MS PRIME and ASTA MicroIDSys Elite. Retesting with PICKME improved concordance to 91.9%. For filamentous fungi, species-level identification reached 71.3% with the IVD database and 85.8% with RUO, which significantly enhanced basidiomycetes' identification from 35.3% to 100%. Some strains in the IVD database, like Aspergillus versicolor, Exophiala xenobiotica, and Nannizzia gypsea, failed to be identified. The VITEK MS PRIME with PICKME offers reliable and efficient microorganism identification. For filamentous fungi, combined use of the RUO database can be beneficial, especially for basidiomycetes.
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Affiliation(s)
- Hyeyoung Lee
- Department of Laboratory Medicine, International St. Mary’s Hospital, College of Medicine, Catholic Kwandong University, Incheon 22711, Republic of Korea; (H.L.); (J.K.); (S.-I.C.); (H.L.); (H.J.L.)
| | - Jehyun Koo
- Department of Laboratory Medicine, International St. Mary’s Hospital, College of Medicine, Catholic Kwandong University, Incheon 22711, Republic of Korea; (H.L.); (J.K.); (S.-I.C.); (H.L.); (H.J.L.)
| | - Junsang Oh
- Biomedical Institute of Mycological Resource, International St. Mary’s Hospital, College of Medicine, Catholic Kwandong University, Incheon 22711, Republic of Korea;
- Department of Convergence Science, College of Medicine, Catholic Kwandong University, Gangneung 25601, Republic of Korea
| | - Sung-Il Cho
- Department of Laboratory Medicine, International St. Mary’s Hospital, College of Medicine, Catholic Kwandong University, Incheon 22711, Republic of Korea; (H.L.); (J.K.); (S.-I.C.); (H.L.); (H.J.L.)
| | - Hyunjoo Lee
- Department of Laboratory Medicine, International St. Mary’s Hospital, College of Medicine, Catholic Kwandong University, Incheon 22711, Republic of Korea; (H.L.); (J.K.); (S.-I.C.); (H.L.); (H.J.L.)
| | - Hyun Ji Lee
- Department of Laboratory Medicine, International St. Mary’s Hospital, College of Medicine, Catholic Kwandong University, Incheon 22711, Republic of Korea; (H.L.); (J.K.); (S.-I.C.); (H.L.); (H.J.L.)
| | - Gi-Ho Sung
- Biomedical Institute of Mycological Resource, International St. Mary’s Hospital, College of Medicine, Catholic Kwandong University, Incheon 22711, Republic of Korea;
- Department of Convergence Science, College of Medicine, Catholic Kwandong University, Gangneung 25601, Republic of Korea
| | - Jayoung Kim
- Department of Laboratory Medicine, International St. Mary’s Hospital, College of Medicine, Catholic Kwandong University, Incheon 22711, Republic of Korea; (H.L.); (J.K.); (S.-I.C.); (H.L.); (H.J.L.)
- Biomedical Institute of Mycological Resource, International St. Mary’s Hospital, College of Medicine, Catholic Kwandong University, Incheon 22711, Republic of Korea;
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Ao K, Li X, Zhang W, Chen Z, Liu Y, Shu L, Xiao Y, Wu S, Xie Y, Kang M. Evaluation of the Autof ms1000 mass spectrometry for rapid clinical identification of filamentous fungi. BMC Microbiol 2023; 23:228. [PMID: 37608359 PMCID: PMC10464221 DOI: 10.1186/s12866-023-02968-w] [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: 08/11/2022] [Accepted: 08/02/2023] [Indexed: 08/24/2023] Open
Abstract
BACKGROUND Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has revolutionized microbial identification. However, there is a lack of data on its performance in identifying filamentous fungi. The objective of our study was to evaluate the accuracy of the Autof ms1000 mass spectrometry for identifying filamentous fungi in the clinical microbiology laboratory. RESULTS Among 106 samples tested using the Autof ms1000 system, 101 (95.28%) were identified at the genus or species level, and 81 (76.41%) were accurately identified at the species level. Additionally, we developed a new rapid formic acid extraction method with simple pretreatment for filamentous fungi that saved time and provided accurate results. CONCLUSIONS The Autof ms1000 mass spectrometer proved to be a valuable tool for identifying filamentous fungi. However, upgrading the database is recommended for correctly identifying rare strains.
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Affiliation(s)
- Keping Ao
- Department of Laboratory Medicine, West China Hospital, Sichuan University, No. 37 Guoxue Lane, Chengdu, 610041, China
| | - Xiaohan Li
- Department of Laboratory Medicine, West China Hospital, Sichuan University, No. 37 Guoxue Lane, Chengdu, 610041, China
| | - Weili Zhang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, No. 37 Guoxue Lane, Chengdu, 610041, China
| | - Zhixing Chen
- Department of Laboratory Medicine, West China Hospital, Sichuan University, No. 37 Guoxue Lane, Chengdu, 610041, China
| | - Ya Liu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, No. 37 Guoxue Lane, Chengdu, 610041, China
| | - Ling Shu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, No. 37 Guoxue Lane, Chengdu, 610041, China
| | - Yuling Xiao
- Department of Laboratory Medicine, West China Hospital, Sichuan University, No. 37 Guoxue Lane, Chengdu, 610041, China
| | - Siying Wu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, No. 37 Guoxue Lane, Chengdu, 610041, China
| | - Yi Xie
- Department of Laboratory Medicine, West China Hospital, Sichuan University, No. 37 Guoxue Lane, Chengdu, 610041, China
| | - Mei Kang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, No. 37 Guoxue Lane, Chengdu, 610041, China.
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Sarvestani HK, Ramandi A, Getso MI, Razavyoon T, Javidnia J, Golrizi MB, Saboor-Yaraghi AA, Ansari S. Mass spectrometry in research laboratories and clinical diagnostic: a new era in medical mycology. Braz J Microbiol 2022; 53:689-707. [PMID: 35344203 PMCID: PMC9151960 DOI: 10.1007/s42770-022-00715-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 02/14/2022] [Indexed: 02/01/2023] Open
Abstract
Diagnosis by clinical mycology laboratory plays a critical role in patient care by providing definitive knowledge of the cause of infection and antimicrobial susceptibility data to physicians. Rapid diagnostic methods are likely to improve patient. Aggressive resuscitation bundles, adequate source control, and appropriate antibiotic therapy are cornerstones for success in the treatment of patients. Routine methods for identifying clinical specimen fungal pathogen are based on the cultivation on different media with the subsequent examination of its phenotypic characteristics comprising a combination of microscopic and colony morphologies. As some fungi cannot be readily identified using these methods, molecular diagnostic methods may be required. These methods are fast, but it can cost a lot. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is suitable for high-throughput and rapid diagnostics at low costs. It can be considered an alternative for conventional biochemical and molecular identification systems in a microbiological laboratory. The reliability and accuracy of this method have been scrutinized in many surveys and have been compared with several methods including sequencing and molecular methods. According to these findings, the reliability and accuracy of this method are very high and can be trusted. With all the benefits of this technique, the libraries of MALDI-TOF MS need to be strengthened to enhance its performance. This review provides an overview of the most recent research literature that has investigated the applications and usage of MT-MS to the identification of microorganisms, mycotoxins, antifungal susceptibility examination, and mycobiome research.
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Affiliation(s)
- Hasti Kamali Sarvestani
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Alireza Ramandi
- Students' Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Muhammad Ibrahim Getso
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
- Department of Medical Microbiology and Parasitology, College of Health Sciences, Bayero University, PMB, Kano, 3011, Nigeria
| | - Taraneh Razavyoon
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Javad Javidnia
- Student Research Committee, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
- Department of Medical Mycology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Miaad Banay Golrizi
- Student Research Committee, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Ali-Akbar Saboor-Yaraghi
- Department of Nutrition and Biochemistry, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
- Department of Medical Parasitology and Mycology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Saham Ansari
- Department of Medical Parasitology and Mycology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Salah H, Kolecka A, Rozaliyani A, Wahyuningsih R, Taj-Aldeen SJ, Boekhout T, Houbraken J. A New Filter Based Cultivation Approach for Improving Aspergillus Identification using Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS). Mycopathologia 2022; 187:39-52. [PMID: 35006478 PMCID: PMC8807449 DOI: 10.1007/s11046-021-00603-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 10/27/2021] [Indexed: 11/30/2022]
Abstract
Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) is widely used in clinical laboratories for routine identification of bacteria and yeasts. However, methodological difficulties are still apparent when applied to filamentous fungi. The liquid cultivation method recommended by Bruker Daltonics GmbH for identification of filamentous fungi by MALDI-TOF MS is labour intensive and time-consuming. In this study, growth of Aspergillus species on different (porous) surfaces was investigated with the aim to develop a more reliable, quicker and less laborious identification method using MALDI-TOF MS. Mycelial growth without sporulation mimicking liquid cultivation and reliable MALDI-TOF MS spectra were obtained when A. fumigatus strains were grown on and in between a polycarbonate membrane filter on Sabouraud dextrose agar. A database of in-house reference spectra was created by growing Aspergillus reference strains (mainly focusing on sections Fumigati and Flavi) under these selected conditions. A test set of 50 molecularly identified strains grown under different conditions was used to select the best growth condition for identification and to perform an initial validation of the in-house database. Based on these results, the cultivation method on top of a polycarbonate filter proved to be most successful for species identification. This method was therefore selected for the identification of two sets of clinical isolates that mainly consisted of Aspergilli (100 strains originating from Indonesia, 70 isolates from Qatar). The results showed that this cultivation method is reliable for identification of clinically relevant Aspergillus species, with 67% and 76% correct identification of strains from Indonesia and Qatar, respectively. In conclusion, cultivation of Aspergilli on top of a polycarbonate filter showed improved results compared to the liquid cultivation protocol recommended by Bruker in terms of percentage of correct identification, ease of MSP creation, time consumption, cost and labour intensity. This method can be reliably applied for identification of clinically important Aspergilli and has potential for identification of other filamentous fungi.
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Affiliation(s)
- Husam Salah
- Division of Microbiology, Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar.,Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Anna Kolecka
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Anna Rozaliyani
- Department of Parasitology Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Retno Wahyuningsih
- Department of Parasitology Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia.,Department of Parasitology Faculty of Medicine, Universitas Kristen Indonesia, Jakarta, Indonesia
| | - Saad J Taj-Aldeen
- Division of Microbiology, Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar.,University of Babylon, Hilla, Iraq
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Jos Houbraken
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.
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ZHOU J, ZHOU D, CHEN W, XIE H, HU P, ZHOU Y. Study on the clinical application of Streptococcus pneumoniae serotype detection based on MALDI-TOF MS technology. FOOD SCIENCE AND TECHNOLOGY 2022. [DOI: 10.1590/fst.34922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
| | - Dajin ZHOU
- Second People's Hospital of Lishui, China
| | | | - Hejie XIE
- Second People's Hospital of Lishui, China
| | | | - Yan ZHOU
- Second People's Hospital of Lishui, China
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Hashim Z, Neyaz Z, Marak RSK, Nath A, Nityanand S, Tripathy NK. Practice Guidelines for the Diagnosis of COVID-19-Associated Pulmonary Aspergillosis in an Intensive Care Setting. J Intensive Care Med 2021; 37:985-997. [PMID: 34678103 PMCID: PMC9353310 DOI: 10.1177/08850666211047166] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Coronavirus disease-2019 (COVID-19)-associated pulmonary aspergillosis (CAPA) is a new disease characterized by secondary Aspergillus mold infection in patients with COVID-19. It primarily affects patients with COVID-19 in critical state with acute respiratory distress syndrome, requiring intensive care and mechanical ventilation. CAPA has a higher mortality rate than COVID-19, posing a serious threat to affected individuals. COVID-19 is a potential risk factor for CAPA and has already claimed a massive death toll worldwide since its outbreak in December 2019. Its second wave is currently progressing towards a peak, while the third wave of this devastating pandemic is expected to follow. Therefore, an early and accurate diagnosis of CAPA is of utmost importance for effective clinical management of this highly fatal disease. However, there are no uniform criteria for diagnosing CAPA in an intensive care setting. Therefore, based on a review of existing information and our own experience, we have proposed new criteria in the form of practice guidelines for diagnosing CAPA, focusing on the points relevant for intensivists and pulmonary and critical care physicians. The main highlights of these guidelines include the role of CAPA-appropriate test specimens, clinical risk factors, computed tomography of the thorax, and non-culture-based indirect and direct mycological evidence for diagnosing CAPA in the intensive care unit. These guidelines classify the diagnosis of CAPA into suspected, possible, and probable categories to facilitate clinical decision-making. We hope that these practice guidelines will adequately address the diagnostic challenges of CAPA, providing an easy-to-use and practical algorithm to clinicians for rapid diagnosis and clinical management of the disease.
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Affiliation(s)
- Zia Hashim
- 30093Sanjay Gandhi Postgraduate Institute of Medical Sciences (SGPGIMS), Lucknow, India
| | - Zafar Neyaz
- 30093Sanjay Gandhi Postgraduate Institute of Medical Sciences (SGPGIMS), Lucknow, India
| | - Rungmei S K Marak
- 30093Sanjay Gandhi Postgraduate Institute of Medical Sciences (SGPGIMS), Lucknow, India
| | - Alok Nath
- 30093Sanjay Gandhi Postgraduate Institute of Medical Sciences (SGPGIMS), Lucknow, India
| | - Soniya Nityanand
- 30093Sanjay Gandhi Postgraduate Institute of Medical Sciences (SGPGIMS), Lucknow, India
| | - Naresh K Tripathy
- 30093Sanjay Gandhi Postgraduate Institute of Medical Sciences (SGPGIMS), Lucknow, India
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Comparative Evaluation of Bruker Biotyper and ASTA MicroIDSys for Species Identification in a Clinical Microbiology Laboratory. Diagnostics (Basel) 2021; 11:diagnostics11091683. [PMID: 34574024 PMCID: PMC8470862 DOI: 10.3390/diagnostics11091683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 08/27/2021] [Accepted: 09/14/2021] [Indexed: 11/17/2022] Open
Abstract
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI–TOF MS) has been widely used for microbial identification, because of its speed and accuracy, since its introduction to clinical microbiology laboratories. In this study, we evaluated the performance of ASTA MicroIDSys, a newly developed MALDI–TOF, and compared it with the widely used Bruker Biotyper. Microbial identification with the Bruker Biotyper system was performed by using a direct smear method and the Bruker Biotyper database (reference library version 6.0.0.0). The isolates were also tested in parallel, using the ASTA MicroIDSys system with a direct smear method and the MicroIDSys database, CoreDB v1.26. A total of 914 clinical isolates were recovered from the clinical specimens. Identical results with confidence scores (≥2.0, for the Bruker Biotyper) and acceptable scores (≥140 for the ASTA MicroIDSys) were obtained for 840 (91.9%) isolates. The minor errors were defined as misidentification at the species level, and the rate was 1.1% (9/792) for Bruker Biotyper and 1.6% (13/792) for ASTA MicroIDSys. Major errors were defined as misidentification at the genus level, and the rate was 0.3% (2/792) for both Bruker Biotyper and ASTA MicroIDSys. ASTA MicroIDSys showed reliable performance for microbial identification, which was comparable to that of the Bruker Biotyper. Therefore, ASTA MicroIDSys can be applied for the identification of microorganisms in clinical microbiology laboratories.
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