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Li S, Han D, Chen X, Zheng D, Cai Y, Lin D, Zhang X, Ke P, Qu P, Chen C. Evaluation of the Zybio EXS3000 mass spectrometry in routine identification of Clinical isolates. Heliyon 2023; 9:e18990. [PMID: 37600400 PMCID: PMC10432711 DOI: 10.1016/j.heliyon.2023.e18990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 07/25/2023] [Accepted: 08/04/2023] [Indexed: 08/22/2023] Open
Abstract
The matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has been widely applied in routine clinical microbiology laboratories as an efficient and reliable technique for diagnostic purpose. In this work, we evaluated the performance of the newly developed Zybio EXS3000 (Zybio Inc., China) in microbial identification and compared it with VITEK MS (bioMérieux, France). For this study, a total of 1340 isolates from various clinical specimens were collected. These isolates were analyzed simultaneously on both EXS3000 and VITEK MS. The inconsistent or unidentifiable data were further identified using the help of either 16S rRNA gene or ITS region sequencing. During the study, we observed that EXS3000 and VITEK MS provided positive confirmatory diagnostics for 95.0% and 96.5% of the isolates, respectively, which were consistent with the sequencing results. However, it is worth noting that the EXS3000 system needs to improve the identification performance of Candida albicans in the follow-up. There are no significant differences between the two devices in terms of microbial identification performance. The advantage of EXS3000 over VITEK MS is in its ability to perform in significantly lesser time period. In conclusion, the results of this investigation showed that EXS3000 can be used to identify microorganisms in clinical microbiology laboratories.
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Affiliation(s)
- Song Li
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Clinical Laboratory, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Dexing Han
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xiaowei Chen
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Dexiang Zheng
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Clinical Laboratory, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Yimei Cai
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Clinical Laboratory, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Dongling Lin
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Clinical Laboratory, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Xuan Zhang
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Clinical Laboratory, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Peifeng Ke
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Clinical Laboratory, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Pinghua Qu
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Clinical Laboratory, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Cha Chen
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Clinical Laboratory, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
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Zhang L, Lu F, Wang Y, Ji J, Xu Y, Huang Y, Zhang M, Li M, Xia J, Wang B. Methodological comparison of bronchoalveolar lavage fluid-based detection of respiratory pathogens in diagnosis of bacterium/fungus-associated pneumonia in critically ill patients. Front Public Health 2023; 11:1168812. [PMID: 37255757 PMCID: PMC10225631 DOI: 10.3389/fpubh.2023.1168812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 04/12/2023] [Indexed: 06/01/2023] Open
Abstract
Background Bacterium/fungus-associated pneumonia (BAP/FAP) is the prominent cause of high mortality and morbidity with important clinical impacts globally. Effective diagnostic methods and proper specimen types hopefully facilitate early diagnosis of pneumonia and prevent spread of drug-resistant bacteria/fungi among critically ill patients. Methods In the present study, 342 bronchoalveolar lavage fluid (BALF) samples were collected from critically ill patients with pulmonary infections between November 2020 and March 2021. The BALF materials were comparatively employed to screen BAP/FAP through microscopy, culture, antigenic marker and PCR-based methods. The limit of detection (LOD) of cultures and PCR for bacteria/fungi was determined by serial dilution assays. Specimen slides were prepared with Gram staining for microscopic examinations. Microbial cultures and identifications underwent routine clinical protocols with the aid of mass spectrometry. (1,3)-β-D-glucan and galactomannan tests with BALF were carried out accordingly. Direct detection of pathogens in BALF was achieved through PCR, followed by sequencing and BLAST in GenBank database for pathogenic identification. The subjects' demographic and clinical characteristics were well evaluated. Results BAP/FAP was identified in approximately 47% of the subjects by the BALF-based PCR. The PCR-based diagnostic methods showed improved detection performance for fungi with good LOD, but performed similarly for bacteria, when compared to the cultures. There was poor agreement among traditional microscopy, culture and PCR assays for bacterial detections (kappa value, 0.184 to 0.277). For overall bacterial/fungal detections, the microscopy showed the lowest detecting rate, followed by the cultures, which displayed a slightly higher sensitivity than the microscopy did. The sensitivity of PCR was much higher than that of the other means of interest. However, the traditional cultures rather than antigenic marker-based approaches were moderately consistent with the PCR-based methods in fungal species identification, particularly for Candida and Aspergillus spp. Our findings further revealed that the age, length of hospital stay, invasive procedures and cerebral diseases were likely considered as main risk factors for BAP/FAP. Conclusion Screening for BALF in critically ill patients with suspected pneumonia pertaining high risk factors using combined PCR-based molecular detection strategies would hopefully contribute to early diagnosis of BAP/FAP and improved prognosis of the patients.
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Affiliation(s)
- Luwen Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Fanbo Lu
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Yuerong Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- Institute of Pediatrics, Children’s Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Juanjuan Ji
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Yuanhong Xu
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Ying Huang
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Min Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Moyan Li
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Jinxing Xia
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Bo Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, 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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Wang Y, Zhang L, Zhou L, Zhang M, Xu Y. Epidemiology, Drug Susceptibility, and Clinical Risk Factors in Patients With Invasive Aspergillosis. Front Public Health 2022; 10:835092. [PMID: 35493371 PMCID: PMC9051236 DOI: 10.3389/fpubh.2022.835092] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 03/04/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundThis study aimed to investigate the Aspergillus species distribution, antifungal sensitivities, clinical characteristics, and risk factors of patients with invasive aspergillosis (IA) in a tertiary teaching hospital in Anhui Province.MethodsIn the present study, 156 Aspergillus isolates were collected from patients admitted to a 2,800-bed comprehensive hospital between January 2019 and April 2021. The epidemiology of Aspergillus species was well-examined, and its antifungal susceptibility was specifically measured by the microbroth dilution method. The risk factors of patients with IA were documented and analyzed intensively. In addition, gene sequencing was employed to determine gene mutations of cytochrome P450 14-α sterol demethylase-Aspergillus (cyp51A) associated with azole resistance among Aspergillus fumigatus.ResultsThe Aspergillus species distribution was dominated by A. fumigatus (56.41%), Aspergillus flavus (20.51%), and Aspergillus niger (15.38%) locally. In particular, all Aspergillus species showed very low minimum inhibitory concentrations (MICs, ≤ 0.5 μg/ml) for azoles and echinocandins, slightly high MICs (1.66–2.91 μg/ml) for amphotericin B, and exceptionally high MICs (>64 μg/ml) for flucytosine. Azole-resistant rate of Aspergillus species in this local region reached up to 5.79%. Correlation analyses of multiple antifungals indicate a significant MIC relevance between isavuconazole and voriconazole (Pearson correlation coefficient was 0.81, P < 0.0001). The clinical risk factors for patients with IA were found primarily to be pulmonary diseases (P = 0.007) and patients' age (P < 0.001). Notably, three mutant loci (TR46/Y121F/T289A) of the cyp51A gene were identified in azole-resistant A. fumigatus.ConclusionsThe Aspergillus species emerged increasingly, of which A. fumigatus and A. flavus remained the main pathogens for invasive Aspergillus infections in the local region. The vast majority of Aspergillus species exhibited good susceptibility to all the antifungals, except flucytosine. The local occurrence of azole-resistant Aspergillus species grew gradually and needed monitoring in time. Pulmonary diseases and age were likely considered as highly associated risk factors for IA. To our knowledge, the clinically isolated azole-resistant A. fumigatus with TR46/Y121F/T289A mutations identified here were rarely reported in the area of China.
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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: 43] [Impact Index Per Article: 8.6] [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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Evaluation of Vitek MS for Differentiation of Cryptococcus neoformans and Cryptococcus gattii Genotypes. J Clin Microbiol 2019; 57:JCM.01282-18. [PMID: 30429250 DOI: 10.1128/jcm.01282-18] [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: 08/09/2018] [Accepted: 10/31/2018] [Indexed: 12/19/2022] Open
Abstract
Cryptococcus neoformans and Cryptococcus gattii are the main pathogenic species of invasive cryptococcosis among the Cryptococcus species. Taxonomic studies have shown that these two taxa have different genotypes or molecular types with biological and ecoepidemiological peculiarities. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has been proposed as an alternative method for labor-intensive methods for C. neoformans and C. gattii genotype differentiation. However, Vitek MS, one of the commercial MALDI-TOF MS instruments, has not been yet been evaluated for this purpose. Thus, we constructed an in-house database with reference strains belonging to the different C. neoformans (VNI, VNII, VNIII, and VNIV) and C. gattii (VGI, VGII, VGIII, and VGIV) major molecular types by using the software Saramis Premium (bioMérieux, Marcy-l'Etoile, France). Then, this new database was evaluated for discrimination of the different genotypes. Our in-house database provided correct identification for all C. neoformans and C. gattii genotypes; however, due to the intergenotypic mass spectral similarities, a careful postanalytic evaluation is necessary to provide correct genotype identification.
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