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Collins T, Muste C, Owens KG. Identification of Microbial Strains via 2D Cross-Correlation of LC-MS Data. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1352-1362. [PMID: 38742647 PMCID: PMC11197091 DOI: 10.1021/jasms.4c00101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 04/29/2024] [Accepted: 05/07/2024] [Indexed: 05/16/2024]
Abstract
Mass spectrometry is commonly used in the identification of species present in microbial samples, but the high similarity in the peptide composition between strains of a single species has made analysis at the subspecies level challenging. Prior research in this area has employed methods such as Principal Component Analysis (PCA), the k-Nearest Neighbors' (kNN) algorithm, and Pearson correlation. Previously, 1D cross-correlation of mass spectra has been shown to be useful in the classification of small molecule compounds as well as in the identification of peptide sequences via the SEQUEST algorithm and its variants. While direct application of cross-correlation to mass spectral data has been shown to aid in the identification of many other types of compounds, this type of analysis has not been demonstrated in the literature for the purpose of LC-MS based identification of microbial strains. A method of identifying microbial strains is presented here that applies the principle of 2D cross-correlation to LC-MS data. For a set of N = 30 yeast isolate samples representing 5 yeast strains (K-97, S-33, T-58, US-05, WB-06), high-resolution LC-MS-Orbitrap data were collected. Reference spectra were then generated for each strain from the combined data of each sample of that strain. Sample strains were then predicted by computing the 2D cross-correlation of each sample against the reference spectra, followed by application of correction factors measuring the asymmetry of the 2D correlation functions.
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Affiliation(s)
- Tucker
James Collins
- Department of Chemistry, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Cathy Muste
- Department of Chemistry, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Kevin G. Owens
- Department of Chemistry, Drexel University, Philadelphia, Pennsylvania 19104, United States
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2
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Maldonado I, Relloso S, Guelfand L, Fox B, Azula N, Romano V, Cantore A, Barrios R, Carnovale S, Nuske E, Minervini P. Evaluation of the MALDI-TOF mass spectrometry technique for the identification of dermatophytes: Use of an extended database. Rev Iberoam Micol 2023; 40:19-25. [PMID: 37951827 DOI: 10.1016/j.riam.2021.01.006] [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: 05/08/2020] [Revised: 11/23/2020] [Accepted: 01/26/2021] [Indexed: 11/14/2023] Open
Abstract
BACKGROUND Identification of dermatophytes is usually performed through morphological analyses. However, it may be hindered due to the discovery of new species and complexes and, with some isolates, by the absence of fructification. Matrix-assisted laser desorption/ionisation-time-of-flight mass spectrometry (MALDI-TOF MS) seems to be an option for improving identification. AIMS To develop a database (DB) for the identification of dermatophytes with MALDI-TOF MS, including 32 isolates from the Red de Micología de la Ciudad Autónoma de Buenos Aires [Mycology Network of the Autonomous City of Buenos Aires] (RMCABA) and one reference isolate (RMCABA DB), and evaluate its performance when added to the DB from the supplier, Bruker (Bruker DB). METHODS All the isolates in the RMCABA DB were identified based on morphology and sequencing. To evaluate the performance of the extended DB (Bruker DB plus RMCABA DB), 136 clinical isolates were included. RESULTS The percentages of identification at the species level increased from 45% to 88%, but the identification at the genus level decreased from 23% to 7%. CONCLUSIONS MALDI-TOF MS yielded better performance in the identification of dermatophytes after including the RMCABA DB, which encompassed local isolates.
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Affiliation(s)
| | - Silvia Relloso
- Centro de Educación Médica e Investigaciones Clínicas Norberto Quirno [Norberto Quirno Centre for Medical Education and Clinical Research] (CEMIC), Argentina
| | - Liliana Guelfand
- Hospital General de Agudos J. A. Fernández Buenos Aires [JA Fernández Acute Care General Hospital of Buenos Aires], Argentina
| | - Bárbara Fox
- Hospital Alemán [German Hospital], Argentina
| | - Natalia Azula
- Centro de Educación Médica e Investigaciones Clínicas Norberto Quirno [Norberto Quirno Centre for Medical Education and Clinical Research] (CEMIC), Argentina
| | - Vanesa Romano
- Centro de Educación Médica e Investigaciones Clínicas Norberto Quirno [Norberto Quirno Centre for Medical Education and Clinical Research] (CEMIC), Argentina
| | - Agostina Cantore
- Hospital General de Agudos J. A. Fernández Buenos Aires [JA Fernández Acute Care General Hospital of Buenos Aires], Argentina
| | | | - Susana Carnovale
- Faculty of Medicine of the Universidad de Buenos Aires [University of Buenos Aires] (UBA), Argentina
| | - Ezequiel Nuske
- Instituto de Investigaciones en Bacteriología y Virología Molecular [Bacteriology and Molecular Virology Research Institute] of the UBA, Argentina
| | - Patricia Minervini
- Hospital de Oftalmología Santa Lucia [Santa Lucia Ophthalmology Hospital], Argentina
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3
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Mina S, Yaakoub H, Annweiler C, Dubée V, Papon N. COVID-19 and Fungal Infections: A Double Debacle. Microbes Infect 2022; 24:105039. [PMID: 36030024 PMCID: PMC9400371 DOI: 10.1016/j.micinf.2022.105039] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 12/15/2022]
Abstract
Fungal infections remain hardly treatable because of unstandardized diagnostic tests, limited antifungal armamentarium, and more specifically, potential toxic interactions between antifungals and immunosuppressants used during anti-inflammatory therapies, such as those set up in critically ill COVID-19 patients. Taking into account pre-existing difficulties in treating vulnerable COVID-19 patients, any co-occurrence of infectious diseases like fungal infections constitutes a double debacle for patients, healthcare experts, and the public economy. Since the first appearance of SARS-CoV-2, a significant rise in threatening fungal co-infections in COVID-19 patients has been testified in the scientific literature. Better management of fungal infections in COVID-19 patients is, therefore, a priority and requires highlighting common risk factors, relationships with immunosuppression, as well as challenges in fungal diagnosis and treatment. The present review attempts to highlight these aspects in the three most identified causative agents of fungal co-infections in COVID-19 patients: Aspergillus, Candida, and Mucorales species.
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Affiliation(s)
- Sara Mina
- Department of Medical Laboratory Sciences, Faculty of Health Sciences, Beirut Arab University, Beirut, Lebanon.
| | - Hajar Yaakoub
- Univ Angers, Univ Brest, IRF, SFR ICAT, F-49000, Angers, France
| | - Cédric Annweiler
- Department of Geriatric Medicine and Memory Clinic, Research Center on Autonomy and Longevity, University Hospital of Angers, Angers, France; Univ Angers, Université de Nantes, LPPL, SFR CONFLUENCES, F-49000 Angers, France
| | - Vincent Dubée
- Univ Angers, Université de Nantes, Inserm, CRCINA, INCIT, SFR ICAT, F-49000 Angers, France; Infectious Diseases Department, Angers University Hospital, Angers, France
| | - Nicolas Papon
- Univ Angers, Univ Brest, IRF, SFR ICAT, F-49000, Angers, France.
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4
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García-Carnero LC, Mora-Montes HM. Mucormycosis and COVID-19-Associated Mucormycosis: Insights of a Deadly but Neglected Mycosis. J Fungi (Basel) 2022; 8:445. [PMID: 35628701 PMCID: PMC9144279 DOI: 10.3390/jof8050445] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/22/2022] [Accepted: 04/22/2022] [Indexed: 02/04/2023] Open
Abstract
The ongoing COVID-19 pandemic has quickly become a health threat worldwide, with high mortality and morbidity among patients with comorbidities. This viral infection promotes the perfect setting in patients for the development of opportunistic infections, such as those caused by fungi. Mucormycosis, a rare but deadly fungal infection, has recently increased its incidence, especially in endemic areas, since the onset of the pandemic. COVID-19-associated mucormycosis is an important complication of the pandemic because it is a mycosis hard to diagnose and treat, causing concern among COVID-19-infected patients and even in the already recovered population. The risk factors for the development of mucormycosis in these patients are related to the damage caused by the SARS-CoV-2 itself, the patient's overstimulated immune response, and the therapy used to treat COVID-19, causing alterations such as hyperglycemia, acidosis, endothelial and lung damage, and immunosuppression. In this review, the molecular aspects of mucormycosis and the main risk factors for the development of COVID-19-associated mucormycosis are explained to understand this virus-fungi-host interaction and highlight the importance of this neglected mycosis.
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Affiliation(s)
- Laura C. García-Carnero
- Departamento de Biología, División de Ciencias Naturales y Exactas, Campus Guanajuato, Universidad de Guanajuato, Noria Alta s/n, col. Noria Alta, C.P., Guanajuato 36050, Mexico
| | - Héctor M. Mora-Montes
- Departamento de Biología, División de Ciencias Naturales y Exactas, Campus Guanajuato, Universidad de Guanajuato, Noria Alta s/n, col. Noria Alta, C.P., Guanajuato 36050, Mexico
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5
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Dohlman JC, Rizzo JF. Diagnostics for Infectious Orbital and Ocular Adnexal Disease. Int Ophthalmol Clin 2022; 62:87-100. [PMID: 35325912 DOI: 10.1097/iio.0000000000000417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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6
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Darwish RM, AlMasri M, Al‐Masri MM. Mucormycosis: The Hidden and Forgotten Disease. J Appl Microbiol 2022; 132:4042-4057. [DOI: 10.1111/jam.15487] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/14/2022] [Accepted: 02/08/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Rula M. Darwish
- Department of Pharmaceutics and Pharmaceutical Technology, School of Pharmacy The University of Jordan Amman Jordan
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7
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Ghosh A, Sarkar A, Paul P, Patel P. The rise in cases of mucormycosis, candidiasis and aspergillosis amidst COVID19. FUNGAL BIOL REV 2021; 38:67-91. [PMID: 34548877 PMCID: PMC8445778 DOI: 10.1016/j.fbr.2021.09.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 09/05/2021] [Accepted: 09/08/2021] [Indexed: 12/15/2022]
Abstract
The Coronavirus outbreak globally has changed the medical system and also led to a shortage of medical facilities in both developing and underdeveloped countries. The COVID19 disease, being novel in nature along with high infectivity and frequent mutational rate, has been termed to be fatal across the globe. The advent of infection by SARS-CoV-2 has brought a myriad of secondary complications and comorbidities resulting in additional challenges to the health care system induced by novel therapeutic procedures. The emerging variant with respect to the Indian subcontinent and the associated genetic mutations have worsened the situation at hand. Proper clinical management along with epidemiological studies and clinical presentations in scientific studies and trials is necessary in order to combat the simultaneous waves of emerging strains. This article summarizes three of the major fungal outbreaks in India namely mucormycosis, candidiasis and aspergillosis, and elaborates their subtypes, pathogenesis, symptoms and treatment and detection techniques. A detail of future therapeutics under consideration are also elaborated along with a general hypothesis on how COVID19 is related to immunological advances leading to major widespread fungal infection in the country. The factors that contribute in promoting virus proliferation and invasive fungal infections include cell-mediated immunity, associated immunocompromised conditions and treatment protocols that slows down immune mechanisms. To better comprehend a fungal or bacterial outbreak, it is very important to conduct audits mediated through multicenter national and state research teams for recognizing patterns and studying current cases of fungal infection in both healthy and comorbid groups of COVID19 patients.
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Affiliation(s)
- Asmita Ghosh
- Department of Biotechnology, Heritage Institute of Technology, Kolkata 700107, West Bengal, India
| | - Anusua Sarkar
- Department of Biotechnology, Heritage Institute of Technology, Kolkata 700107, West Bengal, India
| | - Pubali Paul
- Department of Biotechnology, Heritage Institute of Technology, Kolkata 700107, West Bengal, India
| | - Parth Patel
- H. K. College of Pharmacy, Jogeshwari West, Mumbai 400102, Maharashtra, India
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Chen J, Zheng F, Sun X, Gao H, Lin S, Zeng Y. The qualitative accuracy of clinical dermatophytes via matrix-assisted laser desorption ionization-time of flight mass spectrometry: a meta-analysis. Med Mycol 2021; 59:1174-1180. [PMID: 34415045 DOI: 10.1093/mmy/myab049] [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: 05/13/2021] [Revised: 07/24/2021] [Accepted: 08/18/2021] [Indexed: 11/13/2022] Open
Abstract
Dermatophytes are an important part of superficial fungal infections, and accurate diagnosis is paramount for successful treatment. Recently, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has emerged as a powerful tool to identify clinical pathogens; its advantages are cost-effectiveness, rapid detection, and high accuracy. However, as the accurate identification of clinical dermatophytes via MALDI-TOF MS has still not been fully evaluated, we performed a meta-analysis for systematic evaluation it. Fifteen eligible studies were involved and showed high accuracy with an identification ratio of 0.96 (95%CI = 0.92─1.01) and 0.91 (95%CI = 0.86─0.96) at the genus and species levels, respectively. The results showed higher accuracy ratio of Vitek MS (91%) than MALDI Biotyper (85%). Dermatophytes such as Trichophyton interdigitale (0.99, 95%CI = 0.97─1.02), T. mentagrophytes var interdigitale (1.00, 95%CI = 0.98─1.02), and Microsporum canis (0.97, 95%CI = 0.89─1.04) showed high accuracy in detected clinical dermatophytes. Moreover, a library with self-built database set up by laboratories showed higher accuracy than commercial database, and 15-day cultivation for dermatophytes showed highest accuracy considering culture time. High heterogeneity was observed and decreased only with the subgroup analysis of species. The subgroup analysis of mass spectrometry, library database, and culture time also exhibited high heterogeneity. In summary, our results showed that MALDI-TOF MS could be used for highly accurate detection of clinically pathogenic dermatophytes, which could be an alternative diagnostic method in addition to morphological and molecular methods. LAY ABSTRACT This meta-analysis comprehensively investigated the qualitative accuracy of clinical dermatophytes through MALDI-TOF MS. Owing to the high accuracy observed at both genus and species levels, this approach could be an alternative diagnostic method in addition to morphological and molecular methods.
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Affiliation(s)
- Jin Chen
- Clinical Center for Molecular Diagnosis and Therapy, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
| | - Feng Zheng
- Department of Neurosurgery, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
| | - Xihuan Sun
- Clinical Microbiology Laboratory, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
| | - Hongzhi Gao
- Clinical Center for Molecular Diagnosis and Therapy, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
| | - Shu Lin
- Centre of Neurological and Metabolic Research, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China.,Diabetes and Metabolism Division, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, Sydney, NSW 2010, Australia
| | - Yiming Zeng
- Department of Respiratory Medicine, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
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9
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Effect of humidity during sample preparation on bacterial identification using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2021; 1176:122780. [PMID: 34052563 DOI: 10.1016/j.jchromb.2021.122780] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 05/14/2021] [Accepted: 05/17/2021] [Indexed: 01/08/2023]
Abstract
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a highly reliable and efficient technology for the identification of microbial pathogens. We previously found that 40% humidity was the optimal condition for the preparation of samples (co-crystallization of the sample and matrix) for serum peptidomic analysis via MALDI-TOF MS profiling. This optimum temperature was applied to obtain the highest reproducibility and throughput and greatest number of peaks. We therefore hypothesized that humidity control was also essential for MALDI-TOF MS bacterial identification. In this study, we constructed a simple sample preparation device that enables humidity control and used it for co-crystallization of the sample and matrix. Identification scores for five Gram-negative bacteria and six Gram-positive bacteria were determined using the MALDI BioTyper® system at three humidity ranges (10-20%, 30-40%, and 50-60%). As a result, higher identification scores were obtained at 30-40% humidity than at 10-20% or 50-60% humidity. At 30-40% humidity, 517/550 (94.0%) isolates scored greater than 2.0, indicating the success of species-level identification. Similarly, 537/550 (97.6%) isolates scored greater than 1.7, indicating the success of genus-level identification. Thus, 30-40% humidity generated optimal MALDI-TOF MS identification scores and the highest percentage of correct identifications. These results could lead to further improvements in the accuracy of MALDI-TOF MS bacterial identification.
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10
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Sun B, Wang W, Ma P, Gu B. Accuracy of matrix-assisted laser desorption ionization time-of-flight mass spectrometry for direct bacterial identification from culture-positive urine samples. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:647. [PMID: 33987345 PMCID: PMC8106043 DOI: 10.21037/atm-20-7310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Background Urinary tract infection (UTI) is one of the most frequent reasons for antimicrobial therapy. In typical clinical setting, 18–48 h is needed to identify pathogens by urine culture. A rapid method for pathogenic UTI diagnosis by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been developed in recent years. Methods This meta-analysis systematically evaluated the accuracy of MALDI-TOF MS for direct identification of bacteria from culture-positive urine samples. We queried the electronic database of Medline and Web of Science to obtain relevant articles. Results Nineteen articles involving 4,579 isolates were included after final selection in the meta-analysis. The random-effects pooled identification accuracy of MALDI-TOF MS was 0.82 with 95% confidence interval of 0.79 to 0.86 at the species level. For Gram-negative isolates, the correct identification performance of the species ranged from 0.54 to 0.98, with a cumulative rate of 0.87 (95% CI: 0.83 to 0.91). For Gram-positive isolates, the correct identification rate ranged from 0.32 to 0.80, with a cumulative rate of 0.59 (95% CI: 0.49 to 0.68). Conclusions MALDI-TOF MS provides a reliable direct identification of bacteria, particularly in cases of Gram-negative isolates, from clinical urine specimens. Nevertheless, the identification accuracy of this method is moderate for Gram-positive bacteria.
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Affiliation(s)
- Bin Sun
- Department of Laboratory Medicine, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Wei Wang
- Medical Technology School of Xuzhou Medical University, Xuzhou, China
| | - Ping Ma
- Department of Laboratory Medicine, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China.,Medical Technology School of Xuzhou Medical University, Xuzhou, China
| | - Bing Gu
- Department of Laboratory Medicine, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China.,Medical Technology School of Xuzhou Medical University, Xuzhou Key Laboratory of Laboratory Diagnostics, Xuzhou, China
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Nabet C, Imbert S, Normand AC, Blanchet D, Chanlin R, Becker P, Demar M, Piarroux R. Unexpected mould diversity in clinical isolates from French Guiana and associated identification difficulties. Med Mycol 2020; 59:myaa091. [PMID: 33111143 DOI: 10.1093/mmy/myaa091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/05/2020] [Accepted: 10/12/2020] [Indexed: 12/14/2022] Open
Abstract
New mold species are increasingly reported in invasive fungal infections. However, these fungi are often misdiagnosed or undiagnosed due to the use of inappropriate laboratory diagnostic tools. Tropical countries, such as French Guiana, harbor a vast diversity of environmental fungi representing a potential source of emerging pathogens. To assess the impact of this diversity on the accuracy of mold-infection diagnoses, we identified mold clinical isolates in French Guiana during a five-month follow-up using both microscopy and matrix-assisted laser desorption ionization time-of-flight mass spectrometry. In total, 38.8% of the 98 obtained molds isolates could not be identified and required a DNA-based identification. Fungal diversity was high, including 46 species, 26 genera, and 13 orders. Fungal ecology was unusual, as Aspergillus species accounted for only 27% of all isolates, and the Nigri section was the most abundant out of the six detected Aspergillus sections. Macromycetes (orders Agaricales, Polyporales, and Russulales) and endophytic fungi accounted for respectively 11% and 14% of all isolates. Thus, in tropical areas with high fungal diversity, such as French Guiana, routine mold identification tools are inadequate. Molecular identifications, as well as morphological descriptions, are necessary for the construction of region-specific mass spectrum databases. These advances will improve the diagnosis and clinical management of new fungal infections. LAY SUMMARY In French Guiana, environmental fungal diversity may be a source of emerging pathogens. We evaluated microscopy and mass spectrometry to identify mold clinical isolates. With 39% of unidentified isolates, a region-specific mass spectrum database would improve the diagnosis of new fungal infections.
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Affiliation(s)
- C Nabet
- Sorbonne Université, INSERM, Institut Pierre-Louis d'Epidémiologie et de Santé Publique, AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Service de Parasitologie-Mycologie, Paris, France
| | - S Imbert
- Sorbonne Université, INSERM, CNRS, Centre d'Immunologie et des Maladies Infectieuses, Cimi-Paris, AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Service de Parasitologie-Mycologie, Paris, France
| | - A C Normand
- Sorbonne Université, INSERM, Institut Pierre-Louis d'Epidémiologie et de Santé Publique, AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Service de Parasitologie-Mycologie, Paris, France
| | - D Blanchet
- Department of Parasitology-Mycology, Hôpital Andrée Rosemon, Cayenne, French Guiana
| | - R Chanlin
- Department of Parasitology-Mycology, Hôpital Andrée Rosemon, Cayenne, French Guiana
| | - P Becker
- Sciensano, BCCM/IHEM collection, Mycology and Aerobiology Unit, Brussels, Belgium
| | - M Demar
- Department of Parasitology-Mycology, Hôpital Andrée Rosemon, Cayenne, French Guiana
- EA 3593, Ecosystèmes Amazoniens et Pathologies Tropicales, Université de Guyane, Cayenne, French Guiana
| | - R Piarroux
- Sorbonne Université, INSERM, Institut Pierre-Louis d'Epidémiologie et de Santé Publique, AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Service de Parasitologie-Mycologie, Paris, France
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Humphrey VS, Li X, Choudhary S, Patton T. Fatal Disseminated Mucormycosis in a Hematological Immunocompromised Patient with Extensive Voriconazole Exposure: A Case Report and Review of the Literature. Case Rep Dermatol 2020; 12:168-173. [PMID: 33173476 PMCID: PMC7588686 DOI: 10.1159/000508457] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 05/02/2020] [Indexed: 12/20/2022] Open
Abstract
Disseminated mucormycosis is a rare, opportunistic, and aggressive infection typically presenting in immunocompromised patients. Herein, we report a 55-year-old male with a past medical history of Philadelphia-negative B-cell acute lymphoblastic leukemia who presented with a 2-month history of non-painful necrotic ulcers on the nose, knuckles, elbow, foot, and scrotum following 3 months of voriconazole (VRC) exposure in the setting of an unrelated fungal pneumonia. Our case reinforces the virulent and often fatal nature of the disease amongst immunocompromised patients, along with extensive VRC exposure as a possible supplementary risk factor. Disseminated cutaneous mucormycosis should be regarded as a differential diagnosis in all immunocompromised patients, especially those with hematologic malignancies or a history of VRC use, who present with cutaneous ulcerations and eschars.
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Affiliation(s)
| | - Xiaoxiao Li
- Department of Dermatology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Sonal Choudhary
- Department of Dermatology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Timothy Patton
- Department of Dermatology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
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Tang M, Yang J, Li Y, Zhang L, Peng Y, Chen W, Liu J. Diagnostic Accuracy of MALDI-TOF Mass Spectrometry for the Direct Identification of Clinical Pathogens from Urine. Open Med (Wars) 2020; 15:266-273. [PMID: 32292823 PMCID: PMC7147288 DOI: 10.1515/med-2020-0038] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 12/28/2019] [Indexed: 12/20/2022] Open
Abstract
Matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS) has become one of the most popular methods for the rapid and cost-effective detection of clinical pathogenic microorganisms. This study aimed to evaluate and compare the diagnostic performance of MALDI-TOF MS with that of conventional approaches for the direct identification of pathogens from urine samples. A systematic review was conducted based on a literature search of relevant databases. The pooled sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR) and area under the summary receiver operating characteristic (SROC) curve of the combined studies were estimated. Nine studies with a total of 3920 subjects were considered eligible and included in the meta-analysis. The pooled sensitivity was 0.85 (95% CI 0.79-0.90), and the pooled specificity was 0.93 (95% CI 0.82-0.97). The PLR and NLR were 11.51 (95% CI 4.53-29.26) and 0.16 (95% CI 0.11-0.24), respectively. The area under the SROC curve was 0.93 (95% CI 0.91-0.95). Sensitivity analysis showed that the results of this meta-analysis were stable. MALDI-TOF MS could directly identify microorganisms from urine samples with high sensitivity and specificity.
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Affiliation(s)
- Min Tang
- Department of Laboratory Medicine, Affiliated Hospital of Southwest Medical University, Luzhou City, Sichuan Province, China
| | - Jia Yang
- Department of Laboratory Medicine, Affiliated Hospital of Southwest Medical University, Luzhou City, Sichuan Province, China
| | - Ying Li
- Department of Pathogenic Biology, College of Preclinical Medicine, Southwest Medical University, Luzhou city, Sichuan Province, China
| | - Luhua Zhang
- Department of Pathogenic Biology, College of Preclinical Medicine, Southwest Medical University, Luzhou city, Sichuan Province, China
| | - Ying Peng
- Department of Laboratory Medicine, Affiliated Hospital of Southwest Medical University, Luzhou City, Sichuan Province, China
| | - Wenbi Chen
- Department of Pathogenic Biology, College of Preclinical Medicine, Southwest Medical University, Luzhou city, Sichuan Province, China
| | - Jinbo Liu
- Department of Laboratory Medicine, Affiliated Hospital of Southwest Medical University, Luzhou City, Sichuan Province, China
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Gülmez D, Alp S, Gursoy G, Ayaz CM, Dogan O, Arikan-Akdagli S, Akova M. Mixed fungaemia: an 18-year report from a tertiary-care university hospital and a systematic review. Clin Microbiol Infect 2020; 26:833-841. [PMID: 32246995 DOI: 10.1016/j.cmi.2020.03.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 03/16/2020] [Accepted: 03/26/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND While fungaemia caused by two or more different species of yeasts (mixed fungaemia, MF) is infrequent, it might be underestimated. AIMS This study aimed to determine the incidence of MF, clinical characteristics of the patients, and antifungal susceptibility profiles of the isolates with a systematic review of the literature. SOURCES Data sources were PubMed and Scopus. STUDY ELIGIBILITY CRITERIA Studies reporting ten or more mixed fungaemia episodes. CONTENT Study included MF episodes in adults between January 2000 and August 2018 in Hacettepe University Hospitals, Turkey. The isolation, identification and antifungal susceptibility testing (AFST) of the isolates were by standard mycological methods. Patient data were obtained retrospectively. Literature search was performed using relevant keywords according to PRISMA systematic review guidelines. A total of 32 patients with 33 MF episodes were identified. Among all fungaemia episodes, MF incidence was 3.7% (33/883). All patients had one or more underlying disorders among which solid-organ cancer (50.0%, 16/32) was the most common. Overall mortality was 51.5% (17/33). The most preferred antifungal agents for initial treatment were fluconazole (48.5%, 16/33) and echinocandins (39.4%, 13/33). Fluconazole susceptible-dose-dependent (S-DD) or -resistant Candida species were detected in 15 episodes, and an isolate of C. parapsilosis was classified as S-DD by AFST. All Candida isolates were susceptible to echinocandins. Non-candida yeasts with intrinsic resistance/reduced susceptibility to both echinocandins and fluconazole were detected in two episodes. Systematic review of the literature revealed 24 studies that reported more than ten MF episodes. Methodology was variable. Improvement of detection rates was reported when chromogenic agars were used. Most studies underlined detection of isolates with reduced susceptibility. IMPLICATIONS Although rare, the MF rate is affected by the detection methods, which have improved in recent years. Fluconazole and echinocandins were used for initial treatment in accordance with the current guideline recommendations; however, isolates non-susceptible to both were detected. Detection of a mixed infection offers an opportunity for optimum treatment.
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Affiliation(s)
- D Gülmez
- Hacettepe University Faculty of Medicine, Medical Microbiology, Ankara, Turkey.
| | - S Alp
- Hacettepe University Faculty of Medicine, Clinical Microbiology and Infectious Diseases, Ankara, Turkey
| | - G Gursoy
- Hacettepe University Faculty of Medicine, Clinical Microbiology and Infectious Diseases, Ankara, Turkey
| | - C M Ayaz
- Hacettepe University Faculty of Medicine, Clinical Microbiology and Infectious Diseases, Ankara, Turkey
| | - O Dogan
- Hacettepe University Faculty of Medicine, Medical Microbiology, Ankara, Turkey; Koç University Faculty of Medicine, Medical Microbiology, Topkapi-Istanbul, Turkey
| | - S Arikan-Akdagli
- Hacettepe University Faculty of Medicine, Medical Microbiology, Ankara, Turkey
| | - M Akova
- Hacettepe University Faculty of Medicine, Medical Microbiology, Ankara, Turkey
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15
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Abstract
Truffles are edible mushrooms with similar morphological characteristics, that make it difficult to distinguish between highly prized truffles (such as the Périgord black T. melanosporum) and inexpensive truffles (such as the Asian Black T. indicum). These biological and economic features have led to several misidentifications and/or fraudulent profit in the truffle markets. In this paper, we investigate Matrix-assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry (MALDI-TOF MS) biotyping to identify 34 commercial fresh truffles from Europe and Asia. The MALDI-TOF MS clustering rapidly distinguished seven Tuber species identified by ITS phylogenetic analysis. The tasty T. melanosporum was clearly differentiated from the Chinese and less expensive truffles. These cheaper mushrooms were marketed as T. indicum but corresponded to a mix of three species. In total, the method confirmed misidentifications in 26% of commercial specimens. Several unknown blind-coded truffles were rapidly identified, with scores >= 2, using the Bruker Biotyper algorithm against MS databases. This study demonstrates that MALDI-TOF MS is a reliable, rapid and cheaper new tool compared with molecular methods for the identification of truffle species and could be used to control frauds in the truffle markets. It could also be useful for the certification of truffle-inoculated seedlings and/or diversity in forest ecosystems.
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16
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Li Y, Shan M, Zhu Z, Mao X, Yan M, Chen Y, Zhu Q, Li H, Gu B. Application of MALDI-TOF MS to rapid identification of anaerobic bacteria. BMC Infect Dis 2019; 19:941. [PMID: 31699042 PMCID: PMC6836477 DOI: 10.1186/s12879-019-4584-0] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 10/21/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has been rapidly developed and widely used as an analytical technique in clinical laboratories with high accuracy in microorganism identification. OBJECTIVE To validate the efficacy of MALDI-TOF MS in identification of clinical pathogenic anaerobes. METHODS Twenty-eight studies covering 6685 strains of anaerobic bacteria were included in this meta-analysis. Fixed-effects models based on the P-value and the I-squared were used for meta-analysis to consider the possibility of heterogeneity between studies. Statistical analyses were performed by using STATA 12.0. RESULTS The identification accuracy of MALDI-TOF MS was 84% for species (I2 = 98.0%, P < 0.1), and 92% for genus (I2 = 96.6%, P < 0.1). Thereinto, the identification accuracy of Bacteroides was the highest at 96% with a 95% CI of 95-97%, followed by Lactobacillus spp., Parabacteroides spp., Clostridium spp., Propionibacterium spp., Prevotella spp., Veillonella spp. and Peptostreptococcus spp., and their correct identification rates were all above 90%, while the accuracy of rare anaerobic bacteria was relatively low. Meanwhile, the overall capabilities of two MALDI-TOF MS systems were different. The identification accuracy rate was 90% for VITEK MS vs. 86% for MALDI biotyper system. CONCLUSIONS Our research showed that MALDI-TOF-MS was satisfactory in genus identification of clinical pathogenic anaerobic bacteria. However, this method still suffers from different drawbacks in precise identification of rare anaerobe and species levels of common anaerobic bacteria.
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Affiliation(s)
- Ying Li
- School of Medical Technology, Xuzhou Medical University, Xuzhou, 221004, China
| | - Mingzhu Shan
- School of Medical Technology, Xuzhou Medical University, Xuzhou, 221004, China
| | - Zuobin Zhu
- Department of Genetics, Xuzhou Medical University, Xuzhou, 221004, China
| | - Xuhua Mao
- Department of Clinical Laboratory, Yixing People's Hospital, Wuxi, 214200, China
| | - Mingju Yan
- School of Medical Technology, Xuzhou Medical University, Xuzhou, 221004, China
| | - Ying Chen
- School of Medical Technology, Xuzhou Medical University, Xuzhou, 221004, China
| | - Qiuju Zhu
- Jiangsu Key Laboratory of Brain Disease Bioinformation, Xuzhou Medical University, Xuzhou, 221004, China
| | - Hongchun Li
- School of Medical Technology, Xuzhou Medical University, Xuzhou, 221004, China.,Department of Laboratory Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221002, China
| | - Bing Gu
- School of Medical Technology, Xuzhou Medical University, Xuzhou, 221004, China. .,Department of Laboratory Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221002, China.
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17
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Peng Y, Zhang Q, Xu C, Shi W. MALDI-TOF MS for the rapid identification and drug susceptibility testing of filamentous fungi. Exp Ther Med 2019; 18:4865-4873. [PMID: 31819764 PMCID: PMC6895777 DOI: 10.3892/etm.2019.8118] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 09/24/2019] [Indexed: 01/07/2023] Open
Abstract
The present study aimed to evaluate the applicability of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for identifying filamentous fungi and assessing the in vitro activities of common antifungal drugs against different kinds of filamentous fungi that are commonly encountered in a clinical setting. A total of 123 strains of filamentous fungi (24 species) were submitted for identification by MALDI-TOF MS, and the findings were compared with those obtained by conventional methods. The discrepancies were further investigated by internal transcribed spacer (ITS) sequence analysis. Then, 79 strains were randomly selected for further testing by the minimum inhibitory concentration Etest method. MALDI-TOF MS correctly identified 114 (92.70%) of the 123 filamentous fungi and failed to identify six isolates (4.9%). By contrast, the conventional identification methods made 113 (91.9%) correct identifications. In addition, 15 isolates of filamentous fungi were further identified by ribosomal DNA-ITS sequencing. In the in vitro antifungal susceptibility test, voriconazole showed the strongest antifungal activity among the tested drugs against a broad range of filamentous fungi. Caspofungin showed a better in vitro antifungal activity than fluconazole, itraconazole, and amphotericin B. MALDI-TOF MS offers a cost/time-saving, high-throughput and accurate working protocol for identifying filamentous fungi. Voriconazole could still serve as the first-line drug for treating serious infections caused by filamentous fungi, while caspofungin may be another treatment option for fungal infections.
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Affiliation(s)
- Yang Peng
- Department of Clinical Laboratory, The Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu 213003, P.R. China
| | - Qin Zhang
- Department of Clinical Laboratory, The Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu 213003, P.R. China
| | - Chao Xu
- Department of Clinical Laboratory, Shanghai Tenth People's Hospital Chongming Branch, Chongming, Shanghai 202157, P.R. China
| | - Weifeng Shi
- Department of Clinical Laboratory, The Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu 213003, P.R. China
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18
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Ivanova B, Spiteller M. Stochastic dynamic electrospray ionization mass spectrometric diffusion parameters and 3D structural determination of complexes of AgI–ion – Experimental and theoretical treatment. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111307] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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19
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Taverna CG, Mazza M, Bueno NS, Alvarez C, Amigot S, Andreani M, Azula N, Barrios R, Fernández N, Fox B, Guelfand L, Maldonado I, Murisengo OA, Relloso S, Vivot M, Davel G. Development and validation of an extended database for yeast identification by MALDI-TOF MS in Argentina. Med Mycol 2019; 57:215-225. [PMID: 29762695 DOI: 10.1093/mmy/myy021] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 04/04/2018] [Indexed: 12/22/2022] Open
Abstract
Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) has revolutionized the identification of microorganisms in clinical laboratories because it is rapid, relatively simple to use, accurate, and can be used for a wide number of microorganisms. Several studies have demonstrated the utility of this technique in the identification of yeasts; however, its performance is usually improved by the extension of the database. Here we developed an in-house database of 143 strains belonging to 42 yeast species in the MALDI Biotyper platform, and we validated the extended database with 388 regional strains and 15 reference strains belonging to 55 yeast species. We also performed an intra- and interlaboratory study to assess reproducibility and analyzed the use of the cutoff values of 1.700 and 2.000 to correctly identify at species level. The creation of an in-house database that extended the manufacturer's database was successful in view of no incorrect identification was introduced. The best performance was observed by using the extended database and a cutoff value of 1.700 with a sensitivity of .94 and specificity of .96. A reproducibility study showed utility to detect deviations and could be used for external quality control. The extended database was able to differentiate closely related species and it has potential in distinguishing the molecular genotypes of Cryptococcus neoformans and Cryptococcus gattii.
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Affiliation(s)
- Constanza Giselle Taverna
- Departamento Micología, Instituto Nacional de Enfermedades Infecciosas "Dr. Carlos G. Malbrán," Ciudad Autónoma de Buenos Aires
| | - Mariana Mazza
- Departamento Micología, Instituto Nacional de Enfermedades Infecciosas "Dr. Carlos G. Malbrán," Ciudad Autónoma de Buenos Aires
| | - Nadia Soledad Bueno
- Departamento Micología, Instituto Nacional de Enfermedades Infecciosas "Dr. Carlos G. Malbrán," Ciudad Autónoma de Buenos Aires
| | - Christian Alvarez
- División Micología, Laboratorio de Salud Pública de Tucumán, Tucumán
| | - Susana Amigot
- Centro de Especialidades Médicas Ambulatorias de Rosario, Santa Fe
| | - Mariana Andreani
- Hospital General de Agudos "Dr. Juan A. Fernández" Ciudad Autónoma de Buenos Aires
| | - Natalia Azula
- Centro de Educación Médica e Investigaciones Clínicas "Norberto Quirno," Ciudad Autónoma de Buenos Aires. Argentina
| | - Rubén Barrios
- BD Diagnostics Systems, Ciudad Autónoma de Buenos Aires
| | - Norma Fernández
- Hospital de Clínicas "José de San Martín," Ciudad Autónoma de Buenos Aires
| | - Barbara Fox
- Hospital Alemán, Ciudad Autónoma de Buenos Aires
| | - Liliana Guelfand
- Hospital General de Agudos "Dr. Juan A. Fernández" Ciudad Autónoma de Buenos Aires
| | | | - Omar Alejandro Murisengo
- Departamento Micología, Instituto Nacional de Enfermedades Infecciosas "Dr. Carlos G. Malbrán," Ciudad Autónoma de Buenos Aires
| | - Silvia Relloso
- Centro de Educación Médica e Investigaciones Clínicas "Norberto Quirno," Ciudad Autónoma de Buenos Aires. Argentina
| | - Matias Vivot
- Departamento Micología, Instituto Nacional de Enfermedades Infecciosas "Dr. Carlos G. Malbrán," Ciudad Autónoma de Buenos Aires
| | - Graciela Davel
- Departamento Micología, Instituto Nacional de Enfermedades Infecciosas "Dr. Carlos G. Malbrán," Ciudad Autónoma de Buenos Aires
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20
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Reagent-Free Identification of Clinical Yeasts by Use of Attenuated Total Reflectance Fourier Transform Infrared Spectroscopy. J Clin Microbiol 2019; 57:JCM.01739-18. [PMID: 30787141 DOI: 10.1128/jcm.01739-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Accepted: 02/06/2019] [Indexed: 12/23/2022] Open
Abstract
Invasive fungal infections by opportunistic yeasts have increased concomitantly with the growth of an immunocompromised patient population. Misidentification of yeasts can lead to inappropriate antifungal treatment and complications. Attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy is a promising method for rapid and accurate identification of microorganisms. ATR-FTIR spectroscopy is a standalone, inexpensive, reagent-free technique that provides results within minutes after initial culture. In this study, a comprehensive spectral reference database of 65 clinically relevant yeast species was constructed and tested prospectively on spectra recorded (from colonies taken from culture plates) for 318 routine yeasts isolated from various body fluids and specimens received from 38 microbiology laboratories over a 4-month period in our clinical laboratory. ATR-FTIR spectroscopy attained comparable identification performance with matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). In a preliminary validation of the ATR-FTIR method, correct identification rates of 100% and 95.6% at the genus and species levels, respectively, were achieved, with 3.5% unidentified and 0.9% misidentified. By expanding the number of spectra in the spectral reference database for species for which isolates could not be identified or had been misidentified, we were able to improve identification at the species level to 99.7%. Thus, ATR-FTIR spectroscopy provides a new standalone method that can rival MALDI-TOF MS for the accurate identification of a broad range of medically important yeasts. The simplicity of the ATR-FTIR spectroscopy workflow favors its use in clinical laboratories for timely and low-cost identification of life-threatening yeast strains for appropriate treatment.
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21
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Arastehfar A, Daneshnia F, Kord M, Roudbary M, Zarrinfar H, Fang W, Hashemi SJ, Najafzadeh MJ, Khodavaisy S, Pan W, Liao W, Badali H, Rezaie S, Zomorodian K, Hagen F, Boekhout T. Comparison of 21-Plex PCR and API 20C AUX, MALDI-TOF MS, and rDNA Sequencing for a Wide Range of Clinically Isolated Yeast Species: Improved Identification by Combining 21-Plex PCR and API 20C AUX as an Alternative Strategy for Developing Countries. Front Cell Infect Microbiol 2019; 9:21. [PMID: 30828570 PMCID: PMC6385604 DOI: 10.3389/fcimb.2019.00021] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 01/22/2019] [Indexed: 12/31/2022] Open
Abstract
Occurrence of non-Candida albicans Candida (NCAC) species that are associated with elevated MIC values and therapeutic failures are increasing. As a result, timely and accurate means of identification to the species level is becoming an essential part of diagnostic practices in clinical settings. In this study, 301 clinically isolated yeast strains recovered from various anatomical sites [Blood (n = 145), other sites (n = 156)] were used to assess the accuracy and practicality of API 20C AUX and 21-plex PCR compared to MALDI-TOF MS and large subunit rDNA (LSU rDNA). MALDI-TOF MS correctly identified 98.33% of yeast isolates, 100% of top five Candida species, 95.7% of rare yeast species, while 1.3% of isolates were misidentified. API 20C AUX correctly identified 83.7% of yeast isolates, 97.2% of top five Candida species, 61.8% of rare yeast species, while 16.2% of yeast isolates were misidentified. The 21-plex PCR, accurately identified 87.3% of yeast isolates, 100% of top five Candida species, 72% of rare yeast species, but it misidentified 1.3% of rare yeast species while 9.9% of whole yeast isolates were not identified. The combination of rapidity of 21-plex PCR and comprehensiveness of API 20C AUX, led to correct identification of 92% of included yeast isolates. Due to expensiveness of MALDI-TOF MS and sequencing, this combination strategy could be the most accurate and inexpensive alternative identification strategy for developing countries. Moreover, by the advent and development of cost-effective, reliable, and rapid PCR machines that cost 130 US dollars, 21-plex could be integrated in routine laboratories of developing and resource-limited countries to specifically identify 95% causative agents of yeast-related infections in human. Databases of MALDI-TOF MS, API 20C AUX, and the number of target species identified by 21-plex require further improvement to keep up with the diverse spectrum of yeast species.
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Affiliation(s)
- Amir Arastehfar
- Yeast Biodiversity Department, Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands
| | - Farnaz Daneshnia
- Yeast Biodiversity Department, Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands
| | - Mohammad Kord
- Department of Medical Parasitology and Mycology, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Roudbary
- Department of Medical Mycology and Parasitology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Hossein Zarrinfar
- Allergy Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Wenjie Fang
- Shanghai Key Laboratory of Molecular Medical Mycology, Department of Dermatology, Shanghai Institute of Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Sayed Jamal Hashemi
- Department of Medical Parasitology and Mycology, Tehran University of Medical Sciences, Tehran, Iran.,Food Microbiology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Javad Najafzadeh
- Department of Parasitology and Mycology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Sadegh Khodavaisy
- Department of Medical Parasitology and Mycology, Tehran University of Medical Sciences, Tehran, Iran.,Zoonoses Research Center, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Weihua Pan
- Shanghai Key Laboratory of Molecular Medical Mycology, Department of Dermatology, Shanghai Institute of Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Wanqing Liao
- Shanghai Key Laboratory of Molecular Medical Mycology, Department of Dermatology, Shanghai Institute of Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Hamid Badali
- Department of Medical Mycology, Invasive Fungi Research Center, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Sassan Rezaie
- Department of Medical Parasitology and Mycology, Tehran University of Medical Sciences, Tehran, Iran
| | - Kamiar Zomorodian
- Department of Medical Mycology and Parasitology, Basic Sciences in Infectious Diseases Research Center, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ferry Hagen
- Yeast Biodiversity Department, Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands
| | - Teun Boekhout
- Yeast Biodiversity Department, Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands.,Shanghai Key Laboratory of Molecular Medical Mycology, Department of Dermatology, Shanghai Institute of Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China.,Yeast Biodiversity Department, Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
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22
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Ayoade F, Cloke C, Quiroz T, Tjendra Y. A case of rhino-orbital mucormycosis in an immunocompetent patient following Hurricane Irma. IDCases 2019; 18:e00603. [PMID: 31388490 PMCID: PMC6669373 DOI: 10.1016/j.idcr.2019.e00603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 07/18/2019] [Accepted: 07/19/2019] [Indexed: 12/02/2022] Open
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23
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Ruiz-Aragón J, Ballestero-Téllez M, Gutiérrez-Gutiérrez B, de Cueto M, Rodríguez-Baño J, Pascual Á. Direct bacterial identification from positive blood cultures using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry: A systematic review and meta-analysis. Enferm Infecc Microbiol Clin 2018; 36:484-492. [DOI: 10.1016/j.eimc.2017.08.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 07/24/2017] [Accepted: 08/25/2017] [Indexed: 11/16/2022]
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24
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Arastehfar A, Fang W, Pan W, Lackner M, Liao W, Badiee P, Zomorodian K, Badali H, Hagen F, Lass-Flörl C, Boekhout T. YEAST PANEL multiplex PCR for identification of clinically important yeast species: stepwise diagnostic strategy, useful for developing countries. Diagn Microbiol Infect Dis 2018; 93:112-119. [PMID: 30377018 DOI: 10.1016/j.diagmicrobio.2018.09.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 09/07/2018] [Accepted: 09/12/2018] [Indexed: 12/14/2022]
Abstract
Identification of opportunistic yeasts in developing countries is mainly performed by phenotypic assays, which are time-consuming and prone to errors. Wrong species identification may result in suboptimal treatment and inaccurate epidemiological data. To improve rapidity and accuracy of species identification, a diagnostic strategy using a stepwise "YEAST PANEL multiplex PCR assays" targeting 21 clinically important yeast species of Candida, Trichosporon, Rhodotorula, Cryptococcus, and Geotrichum was designed. Four hundred CBS reference strains were used for optimization and specificity testing. Eight hundred clinical species were prepared in blinded sets for multiplex polymerase chain reaction (PCR) and matrix-assisted laser desorption time of flight mass spectrophotometry (MALDI-TOF MS) investigation. Results obtained from YEAST PANEL multiplex PCR assay were 100% consistent with those of MALDI-TOF MS. Utilization of pure colony testing showed distinct amplicons for each species, thus eliminating the need for DNA extraction. The targeted yeast species of this assay are responsible for 95% of the yeast infections. In conclusion, due to the high accuracy and coverage of a broad range of yeasts, this assay could be useful for identification in routine laboratories and epidemiological studies.
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Affiliation(s)
- Amir Arastehfar
- Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands
| | - Wenjie Fang
- Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands; Department of Dermatology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China; Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Weihua Pan
- Department of Dermatology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China; Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China.
| | - Michaela Lackner
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Wanqing Liao
- Department of Dermatology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China; Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Parisa Badiee
- Prof. Alborzi Clinical Microbiology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Kamiar Zomorodian
- Basic Sciences in Infectious Diseases Research Center, and Department of Medical Mycology and Parasitology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hamid Badali
- Department of Medical Mycology and Parasitology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Ferry Hagen
- Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands
| | - Cornelia Lass-Flörl
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands; Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China; Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, the Netherlands.
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25
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Li C, Ding S, Huang Y, Wang Z, Shen J, Ling H, Xu Y. Detection of AmpC β-lactamase-producing Gram-negative bacteria by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. J Hosp Infect 2018; 99:200-207. [DOI: 10.1016/j.jhin.2017.11.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 11/16/2017] [Indexed: 11/29/2022]
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26
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Accuracy of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Identification of Mycobacteria: a systematic review and meta-analysis. Sci Rep 2018. [PMID: 29515167 PMCID: PMC5841357 DOI: 10.1038/s41598-018-22642-w] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Mycobacterium species are a significant cause of morbidity and mortality worldwide. The present study was carried out to systematically evaluate the accuracy of Matrix-assisted laser desorption ionization-time of flight mass spectroscopy (MALDI-TOF MS) for the identification of clinical pathogenic mycobacteria. After a rigid selection process, 19 articles involving 2,593 mycobacteria isolates were included. The pooled result agreed with the reference method identification for 85% of the isolates to genus level, with 71% (95% CI of 69% to 72%) correct to the species level. The MALDI-TOF MS correctly identified 92% of the M.tuberculosis isolates (95% CI of 0.87 to 0.96), and 68% of M. bovisisolates (95% CI of 27% to 100%) to the species level. Mycobacterium tuberculosis complex in solid media with reference strains using augmented database showing more accurate identification. The identifying accuracy rate of bioMérieuxVitek MS was slight higher than Bruker MALDI Biotyper (75% vs 72%). However, opposite results were obtained in identifications of M. fortuitum, M. kansasii, M. marinum, and M. terrae with these two systems. In summary, our results demonstrate that application of MALDI-TOF MS in clinical pathogenic mycobacteria identification is less satisfactory to date. Increasing need for improvement is important especially at species level.
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Sanchez Ramos L, Rodloff AC. Identification of Clostridium species using the VITEK ® MS. Anaerobe 2018; 54:217-223. [PMID: 29391258 DOI: 10.1016/j.anaerobe.2018.01.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 01/18/2018] [Accepted: 01/22/2018] [Indexed: 10/18/2022]
Abstract
The genus Clostridium is of high clinical relevance, as some species may cause rapid and even lethal infections. Thus, a timely identification of these anaerobic bacteria is desirable. Conventional identification methods rely on biochemical properties of these organisms, however, establishing these is time-consuming and not always reliable. Alternatively, 16S rRNA gene sequence based diagnostic methods may be used, but they are expensive and not ubiquitously available. This study was designed to assess the possibility to identify Clostridium species employing the matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS). For this purpose, 848 Clostridium strains representing 42 species were analyzed with the VITEK® MS instrument (bioMérieux, Marcy l'Etoile, France), comparing mass spectra derived from these organisms with the spectra provided in the available database. 90.3% of the strains were correctly identified at species level and another 3.6% at genus level. Since the number of Clostridium species included in the database was rather limited (21 altogether), the spectra obtained were also analyzed employing the Shimadzu Pro Series software. Thus, it became possible to create a dendrogram of the species included in this study.
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Affiliation(s)
- Lucia Sanchez Ramos
- Institute for Medical Microbiology and Epidemiology of Infectious Diseases, University Hospital of Leipzig, Liebigstraße 21, 04103, Leipzig, Germany
| | - Arne C Rodloff
- Institute for Medical Microbiology and Epidemiology of Infectious Diseases, University Hospital of Leipzig, Liebigstraße 21, 04103, Leipzig, Germany.
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28
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A novel liquid media mycobacteria extraction method for MALDI-TOF MS identification using VITEK® MS. J Microbiol Methods 2017; 144:128-133. [PMID: 29158151 DOI: 10.1016/j.mimet.2017.11.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 10/30/2017] [Accepted: 11/16/2017] [Indexed: 11/22/2022]
Abstract
A low-cost identification method that can be performed directly from a positive liquid medium culture is needed for the diagnosis of mycobacterial infections. Here, we describe a novel, cost-effective, and validated method that allows for direct and rapid identification of mycobacteria from a positive liquid culture using VITEK® MS with a total process duration under 45min. From a liquid mycobacteria culture a 3.0mL aliquot is removed 24-72h post positivity and centrifuged to create a pellet. After decanting, the tube is blotted dry, the pellet is re-suspended in 0.5mL of 70% ethanol and then transferred into a 2.0mL tube containing glass beads. Mycobacteria are disrupted mechanically followed by a 10min. incubation at room temperature to complete inactivation. Inactivated material is pelleted by centrifugation and then re-suspended in 10μL of 70% formic acid and 10μL of acetonitrile. After centrifugation, 1μL of supernatant (protein extract) is deposited onto target slide, allowed to dry, and then 1μL CHCA matrix is added. A seeded study was conducted to demonstrate the reliability of the method, a total of 251 culture samples obtained from automated culture systems (BacT/ALERT® MP bottles, BACTEC MGIT™ 960 tubes, and VersaTREK® Myco bottles), were tested and resulted in 98.8% correct identification. Reproducibility was shown by testing three organisms across three reagent lots, between four laboratory technicians, over the course of five days for three liquid media systems resulting in a total of 180 deposits with an overall correct identification of 98.9% with the remaining results giving no identification. Additional studies were performed including comparison of different mechanical disruption techniques, stability of frozen extracts, and stability of slide deposits to allow for flexibility in a routine clinical workflow. The described method proved to be safe while providing consistent and reproducible results for different species of mycobacteria and is compatible with the three most widely used liquid media medium detection systems.
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29
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Yarbrough ML, Lainhart W, Burnham CAD. Identification of Nocardia, Streptomyces, and Tsukamurella using MALDI-TOF MS with the Bruker Biotyper. Diagn Microbiol Infect Dis 2017; 89:92-97. [PMID: 28811116 DOI: 10.1016/j.diagmicrobio.2017.06.019] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 05/16/2017] [Accepted: 06/20/2017] [Indexed: 11/19/2022]
Abstract
Nocardia species are the most commonly isolated aerobic actinomycetes from human clinical specimens. Our objective was to assess the identification of clinically relevant actinomycetes using the Bruker Biotyper MALDI-TOF system, including comparison of extraction methods, Biotyper library versions, score cutoffs, and media. Banked Streptomyces (n=10), Tsukamurella (n=2), and Nocardia isolates (n=60) were cultured and extracted using three methods: mycobacterial extraction, ethanol formic acid extraction, or direct on-target extraction. Following MALDI-TOF analysis, spectra were analyzed using versions 5 and 6 of the BDAL Biotyper library. Optimal species-level identifications for Nocardia were achieved using BDAL v6 at a score cutoff of ≥1.8 after direct extraction (49/60, 82%). Overall, the Biotyper platform with BDAL v6 accurately identified 12/16 species of Nocardia, demonstrating the utility of MALDI-TOF for identification of clinically relevant actinomycetes without the need for supplementation of the database.
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Affiliation(s)
- Melanie L Yarbrough
- Department of Pathology and Immunology, Washington University School of Medicine, 660 S. Euclid Ave, Campus Box 8118, Saint Louis, MO, 63110.
| | - William Lainhart
- Department of Pathology and Immunology, Washington University School of Medicine, 660 S. Euclid Ave, Campus Box 8118, Saint Louis, MO, 63110
| | - Carey-Ann D Burnham
- Department of Pathology and Immunology, Washington University School of Medicine, 660 S. Euclid Ave, Campus Box 8118, Saint Louis, MO, 63110
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30
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Li Y, Wang H, Zhao YP, Xu YC, Hsueh PR. Evaluation of the Bruker Biotyper Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry System for Identification of Aspergillus Species Directly from Growth on Solid Agar Media. Front Microbiol 2017; 8:1209. [PMID: 28706514 PMCID: PMC5489701 DOI: 10.3389/fmicb.2017.01209] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 06/14/2017] [Indexed: 11/26/2022] Open
Abstract
We evaluated the accuracy of the Bruker Biotyper matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) system at identifying clinical isolates of Aspergillus species that were grown on agar media. A total of 381 non-duplicate Aspergillus isolates representing 21 different Aspergillus species identified by molecular analysis were included in this study. The Bruker Biotyper MALDI-TOF MS system was able to identify 30.2% (115/381) of the isolates to the species level (score values of ≥2.000) and 49.3% to the genus level (score values of 1.700–1.999). When the identification cutoff value was lowered from ≥2.000 to ≥1.700, the species-level identification rate increased to 79.5% with a slight rise of false identification from 2.6 to 5.0%. From another aspect, a correct species-level identification rate of 89% could be reached by the Bruker Biotyper MALDI-TOF MS system regardless of the score values obtained. The Bruker Biotyper MALDI-TOF MS system had a moderate performance in identification of Aspergillus directly inoculated on solid agar media. Continued expansion of the Bruker Biotyper MALDI-TOF MS database and adoption of alternative cutoff values for interpretation are required to improve the performance of the system for identifying highly diverse species of clinically encountered Aspergillus isolates.
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Affiliation(s)
- Ying Li
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical SciencesBeijing, China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical SciencesBeijing, China
| | - He Wang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical SciencesBeijing, China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical SciencesBeijing, China
| | - Yu-Pei Zhao
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical SciencesBeijing, China
| | - Ying-Chun Xu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical SciencesBeijing, China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical SciencesBeijing, China
| | - Po-Ren Hsueh
- Departments of Laboratory Medicine and Internal Medicine, National Taiwan University Hospital, National Taiwan University College of MedicineTaipei, Taiwan
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Bassetti M, Garnacho-Montero J, Calandra T, Kullberg B, Dimopoulos G, Azoulay E, Chakrabarti A, Kett D, Leon C, Ostrosky-Zeichner L, Sanguinetti M, Timsit JF, Richardson MD, Shorr A, Cornely OA. Intensive care medicine research agenda on invasive fungal infection in critically ill patients. Intensive Care Med 2017; 43:1225-1238. [PMID: 28255613 DOI: 10.1007/s00134-017-4731-2] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 02/16/2017] [Indexed: 12/11/2022]
Abstract
PURPOSE To describe concisely the current standards of care, major recent advances, common beliefs that have been contradicted by recent trials, areas of uncertainty, and clinical studies that need to be performed over the next decade and their expected outcomes with regard to Candida and Aspergillus infections in non-neutropenic patients in the ICU setting. METHODS A systematic review of the medical literature taking account of national and international guidelines and expert opinion. RESULTS Severe invasive fungal infections (IFIs) are becoming increasingly frequent in critically ill patients. Approximately 80% of IFIs are due to Candida spp. and 0.3-19% to Aspergillus spp. Recent observations emphasize the necessity of building a worldwide sentinel network to monitor the emergence of new fungal species and changes in susceptibility. Robust data on the attributable mortality are essential for the design of clinical studies with mortality endpoints. Although early antifungal therapy for Candida has been recommended in patients with risk factors, sepsis of unknown cause, and positive Candida serum biomarkers [β-1 → 3-D-glucan (BDG) and Candida albicans germ tube antibody (CAGTA)], its usefulness and influence on outcome need to be confirmed. Future studies may specifically address the optimal diagnostic and therapeutic strategies for patients with abdominal candidiasis. Better knowledge of the pharmacokinetics of antifungal molecules and tissue penetration is a key issue for intensivists. Regarding invasive aspergillosis, further investigation is needed to determine its incidence in the ICU, its relationship with influenza outbreaks, the clinical impact of rapid diagnosis, and the significance of combination treatment. CONCLUSIONS Fundamental questions regarding IFI have to be addressed over the next decade. The clinical studies described in this research agenda should provide a template and set priorities for the clinical investigations that need to be performed.
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Affiliation(s)
- Matteo Bassetti
- Infectious Diseases Clinic, Santa Maria Misericordia Hospital, University of Udine, Udine, Italy. .,Clinica Malattie Infettive, Azienda Sanitaria Universitaria Integrata, Presidio Ospedaliero Santa Maria della Misericordia, Piazzale S. Maria della Misericordia, n. 15, 33100, Udine, Italy.
| | - Jose Garnacho-Montero
- Unidad Clínica de Cuidados Intensivos, Hospital Universitario Virgen Macarena and Institute of Biomedicine of Seville, IBiS/CSIC/University of Seville, seville, Spain
| | - Thierry Calandra
- Infectious Diseases Service, Department of Medicine, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
| | - Bartjan Kullberg
- Department of Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - George Dimopoulos
- Department of Critical Care, University Hospital ATTIKON, National and Kapodistrian University of Athens, Athens, Greece
| | - Elie Azoulay
- Medical Intensive Care Unit, Hôpital Saint-Louis, ECSTRA Team, Biostatistics and Clinical Epidemiology, Paris Diderot Sorbonne University, Paris, France
| | - Arunaloke Chakrabarti
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Daniel Kett
- Division of Pulmonary and Critical Care Medicine, The Leonard M. Miller School of Medicine at the University of Miami, Miami, FL, USA
| | - Cristobal Leon
- Intensive Care Unit, Hospital Universitario de Valme, Universidad de Sevilla, Seville, Spain
| | | | | | - Jean-Francois Timsit
- 1UMR1137-IAMETeam 5, Decision Sciences in Infectious Disease Prevention, Control and Care, Paris Diderot University-Inserm, Sorbonne Paris Cité and 2AP-HP, Medical and Infectious Diseases ICU, Bichat Hospital, Paris, France
| | - Malcom D Richardson
- Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
| | - Andrew Shorr
- Pulmonary and Critical Care Medicine, Medstar Washington Hospital Center, Washington, USA
| | - Oliver A Cornely
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Clinical Trials Centre Cologne (ZKS Köln), Department I of Internal Medicine, German Centre for Infection Research (DZIF), University of Cologne, Cologne, Germany
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32
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Huang Y, Wang J, Zhang M, Zhu M, Wang M, Sun Y, Gu H, Cao J, Li X, Zhang S, Lu X. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for rapid identification of fungal rhinosinusitis pathogens. J Med Microbiol 2017; 66:328-333. [PMID: 28100314 DOI: 10.1099/jmm.0.000435] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Yanfei Huang
- Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing, PR China
| | - Jinglin Wang
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, PR China
| | - Mingxin Zhang
- Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing, PR China
| | - Min Zhu
- Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing, PR China
| | - Mei Wang
- Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing, PR China
| | - Yufeng Sun
- Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing, PR China
| | - Haitong Gu
- Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing, PR China
| | - Jingjing Cao
- Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing, PR China
| | - Xue Li
- Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing, PR China
| | - Shaoya Zhang
- Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing, PR China
| | - Xinxin Lu
- Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing, PR China
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33
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Maldonado I, García Ramírez D, Striebeck P, Lafage M, Fernández Canigia L. Espectrometría de masas MALDI-TOF: evaluación de la etapa preanalítica para la identificación de hongos miceliales. Rev Argent Microbiol 2017; 49:7-14. [DOI: 10.1016/j.ram.2016.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 09/06/2016] [Accepted: 10/06/2016] [Indexed: 11/26/2022] Open
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34
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Stübiger G, Wuczkowski M, Mancera L, Lopandic K, Sterflinger K, Belgacem O. Characterization of Yeasts and Filamentous Fungi using MALDI Lipid Phenotyping. J Microbiol Methods 2016; 130:27-37. [DOI: 10.1016/j.mimet.2016.08.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 08/16/2016] [Accepted: 08/16/2016] [Indexed: 12/12/2022]
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35
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Angeletti S. Matrix assisted laser desorption time of flight mass spectrometry (MALDI-TOF MS) in clinical microbiology. J Microbiol Methods 2016; 138:20-29. [PMID: 27613479 DOI: 10.1016/j.mimet.2016.09.003] [Citation(s) in RCA: 143] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 09/01/2016] [Accepted: 09/03/2016] [Indexed: 10/21/2022]
Abstract
The microbiological management of patients with suspected bacterial infection includes the identification of the pathogen and the determination of the antibiotic susceptibility. These traditional approaches, based on the pure culture of the microorganism, require at least 36-48h. A new method, Matrix Assisted Laser Desorption Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS), has been recently developed to profile bacterial proteins from whole cell extracts and obtain a bacterial fingerprint able to discriminate microorganisms from different genera and species. By whole cell-mass spectrometry, microbial identification can be achieved within minutes from cultured isolate, rather than traditional phenotypic or genotypic characterizations. From the year 2009 an explosion of applications of this technology has been observed with promising results. Several studies have been performed and showed that MALDI-TOF represents a reliable alternative method for rapid bacteria and fungi identification in clinical setting. A future area of expansion is represented by the application of MALDI-TOF technology to the antibiotic susceptibility test. In conclusion, the revision of the literature available up to date demonstrated that MALDI-TOF MS represents an innovative technology for the rapid and accurate identification of bacterial and fungal isolates in clinical settings. By an earlier microbiological diagnosis, MALDI-TOF MS contributes to a reduced mortality and hospitalization time of the patients and consequently has a significant impact on cost savings and public health.
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Affiliation(s)
- Silvia Angeletti
- Clinical Pathology and Microbiology Unit, University Campus Bio-Medico of Rome, Italy.
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36
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Culture of Urine Specimens by Use of chromID CPS Elite Medium Can Expedite Escherichia coli Identification and Reduce Hands-On Time in the Clinical Laboratory. J Clin Microbiol 2016; 54:2767-2773. [PMID: 27582518 DOI: 10.1128/jcm.01376-16] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Accepted: 08/30/2016] [Indexed: 12/13/2022] Open
Abstract
Urine is one of the most common specimen types submitted to the clinical microbiology laboratory; the use of chromogenic agar is one method by which the laboratory might expedite culture results and reduce hands-on time and materials required for urine culture analysis. The objective of our study was to compare chromID CPS Elite (bioMérieux), a chromogenic medium, to conventional primary culture medium for evaluation of urine specimens. Remnant urine specimens (n = 200) were inoculated into conventional media and into chromID CPS Elite agar (chromID). The time to identification and consumables used were documented for both methods. Clinically significant pathogen(s) were recovered from 51 cultures using conventional media, with Escherichia coli being the most frequently recovered organism (n = 22). The rate of exact uropathogen agreement between conventional and chromogenic media was 82%, while overall categorical agreement was 83.5% The time interval between plating and final organism identification was decreased with chromID agar versus conventional media for E. coli (mean of 24.4 h versus 27.1 h, P < 0.001). Using chromID, clinically significant cultures required less hands-on time per culture (mean of 1 min and 2 s [1:02 min]) compared to conventional media (mean of 1:31 min). In addition, fewer consumables (2.4 versus 3.3 sticks and swabs) and rapid biochemical tests (1.0 versus 1.9) were necessary using chromID versus conventional media. Notably, antimicrobial susceptibility testing demonstrated good overall agreement (97.4%) between the chromID and conventional media for all antibiotics tested. chromID CPS Elite is accurate for uropathogen identification, reduces consumable usage, and may expedite the identification of E. coli in clinical specimens.
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Evaluation of the Vitek MS Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry System for Identification of Clinically Relevant Filamentous Fungi. J Clin Microbiol 2016; 54:2068-73. [PMID: 27225405 DOI: 10.1128/jcm.00825-16] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 05/19/2016] [Indexed: 12/22/2022] Open
Abstract
Invasive fungal infections have a high rate of morbidity and mortality, and accurate identification is necessary to guide appropriate antifungal therapy. With the increasing incidence of invasive disease attributed to filamentous fungi, rapid and accurate species-level identification of these pathogens is necessary. Traditional methods for identification of filamentous fungi can be slow and may lack resolution. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has emerged as a rapid and accurate method for identification of bacteria and yeasts, but a paucity of data exists on the performance characteristics of this method for identification of filamentous fungi. The objective of our study was to evaluate the accuracy of the Vitek MS for mold identification. A total of 319 mold isolates representing 43 genera recovered from clinical specimens were evaluated. Of these isolates, 213 (66.8%) were correctly identified using the Vitek MS Knowledge Base, version 3.0 database. When a modified SARAMIS (Spectral Archive and Microbial Identification System) database was used to augment the version 3.0 Knowledge Base, 245 (76.8%) isolates were correctly identified. Unidentified isolates were subcultured for repeat testing; 71/319 (22.3%) remained unidentified. Of the unidentified isolates, 69 were not in the database. Only 3 (0.9%) isolates were misidentified by MALDI-TOF MS (including Aspergillus amoenus [n = 2] and Aspergillus calidoustus [n = 1]) although 10 (3.1%) of the original phenotypic identifications were not correct. In addition, this methodology was able to accurately identify 133/144 (93.6%) Aspergillus sp. isolates to the species level. MALDI-TOF MS has the potential to expedite mold identification, and misidentifications are rare.
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38
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Lau SKP, Lam CSK, Ngan AHY, Chow WN, Wu AKL, Tsang DNC, Tse CWS, Que TL, Tang BSF, Woo PCY. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry for rapid identification of mold and yeast cultures of Penicillium marneffei. BMC Microbiol 2016; 16:36. [PMID: 26965891 PMCID: PMC4787007 DOI: 10.1186/s12866-016-0656-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 03/02/2016] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Penicillium marneffei is the most important thermal dimorphic fungus causing systemic mycosis in HIV-infected and other immunocompromised patients in Southeast Asia. However, laboratory diagnosis of penicilliosis, which relies on microscopic morphology and mycelial-to-yeast conversion, is time-consuming and expertise-dependent, thus delaying diagnosis and treatment. Although matrix -assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is useful for identification of various medically important fungi, its performance for identification of P. marneffei is less clear. RESULTS We evaluated the performance of the Bruker MALDI-TOF MS system for identification of mold and yeast cultures of 59 clinical strains and the type strain of P. marneffei using the direct transfer method, with results compared to four phylogenetically closely related species, P. brevi-compactum, P. chrysogenum, Talaromyces aurantiacus and T. stipitatus. Using the Bruker original database combined with BDAL v4.0.0.1 and Filamentous Fungi Library 1.0, MALDI-TOF MS failed to identify the 60 P. marneffei strains grown in mold and yeast phase (identified as P. funiculosum and P. purpurogenum with scores <1.7 respectively). However, when the combined database was expanded with inclusion of spectra from 21 P. marneffei strains in mold and/or yeast phase, all the remaining 39 P. marneffei strains grown in mold or phase were correctly identified to the species level with score >2.0. The MS spectra of P. marneffei exhibited significant difference to those of P. brevi-compactum, P. chrysogenum, T. aurantiacus and T. stipitatus. However, MALDI-TOF MS failed to identify these four fungi to the species level using the combined database with or without spectra from P. marneffei. CONCLUSIONS MALDI-TOF MS is useful for rapid identification of both yeast and mold cultures of P. marneffei and differentiation from related species. However, accurate identification to the species level requires database expansion using P. marneffei strains.
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Affiliation(s)
- Susanna K P Lau
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China. .,Research Centre of Infection and Immunology, The University of Hong Kong, University Pathology Building, Queen Mary Hospital, Hong Kong, China. .,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China. .,Department of Microbiology, The University of Hong Kong, Hong Kong, China.
| | | | - Antonio H Y Ngan
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Wang-Ngai Chow
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Alan K L Wu
- Department of Pathology, Pamela Youde Nethersole Eastern Hospital, Hong Kong, China
| | | | - Cindy W S Tse
- Department of Pathology, Kwong Wah Hospital, Hong Kong, China
| | - Tak-Lun Que
- Department of Pathology, Tuen Mun Hospital, Hong Kong, China
| | | | - Patrick C Y Woo
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China. .,Research Centre of Infection and Immunology, The University of Hong Kong, University Pathology Building, Queen Mary Hospital, Hong Kong, China. .,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China. .,Department of Microbiology, The University of Hong Kong, Hong Kong, China.
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Sanguinetti M, Posteraro B. Diagnostic of Fungal Infections Related to Biofilms. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 931:63-82. [PMID: 27300347 DOI: 10.1007/5584_2016_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Fungal biofilm-related infections, most notably those caused by the Candida and Aspergillus genera, need to be diagnosed accurately and rapidly to avoid often unfavorable outcomes. Despite diagnosis of these infections is still based on the traditional histopathology and culture, the use of newer, rapid methods has enormously enhanced the diagnostic capability of a modern clinical mycology laboratory. Thus, while accurate species-level identification of fungal isolates can be achieved with turnaround times considerably shortened, nucleic acid-based or antigen-based detection methods can be considered useful adjuncts for the diagnosis of invasive forms of candidiasis and aspergillosis. Furthermore, simple, reproducible, and fast methods have been developed to quantify biofilm production by fungal isolates in vitro. In this end, isolates can be categorized as low, moderate, or high biofilm-forming, and this categorization may reflect their differential response to the conventional antifungal therapy. By means of drug susceptibility testing performed on fungal biofilm-growing isolates, it is now possible to evaluate not only the activity of conventional antifungal agents, but also of novel anti-biofilm agents. Despite this, future diagnostic methods need to target specific biofilm components/molecules, in order to provide a direct proof of the presence of this growth phenotype on the site of infection. In the meantime, our knowledge of the processes underlying the adaptive drug resistance within the biofilm has put into evidence biofilm-specific molecules that could be potentially helpful as therapeutic targets. Surely, the successful management of clinically relevant fungal biofilms will rely upon the advancement and/or refinement of these approaches.
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Affiliation(s)
| | - Brunella Posteraro
- Institute of Public Health (Section of Hygiene), Università Cattolica del Sacro Cuore, Rome, Italy
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40
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Lo CI, Fall B, Sambe-Ba B, Diawara S, Gueye MW, Mediannikov O, Sokhna C, Faye N, Diemé Y, Wade B, Raoult D, Fenollar F. MALDI-TOF Mass Spectrometry: A Powerful Tool for Clinical Microbiology at Hôpital Principal de Dakar, Senegal (West Africa). PLoS One 2015; 10:e0145889. [PMID: 26716681 PMCID: PMC4696746 DOI: 10.1371/journal.pone.0145889] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 12/09/2015] [Indexed: 12/26/2022] Open
Abstract
Our team in Europe has developed the routine clinical laboratory identification of microorganisms by matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS). To evaluate the utility of MALDI-TOF MS in tropical Africa in collaboration with local teams, we installed an apparatus in the Hôpital Principal de Dakar (Senegal), performed routine identification of isolates, and confirmed or completed their identification in France. In the case of discordance or a lack of identification, molecular biology was performed. Overall, 153/191 (80.1%) and 174/191 (91.1%) isolates yielded an accurate and concordant identification for the species and genus, respectively, with the 2 different MALDI-TOF MSs in Dakar and Marseille. The 10 most common bacteria, representing 94.2% of all bacteria routinely identified in the laboratory in Dakar (Escherichia coli, Klebsiella pneumoniae, Streptococcus agalactiae, Acinetobacter baumannii, Pseudomonas aeruginosa, Staphylococcus aureus, Staphylococcus haemolyticus, Enterobacter cloacae, Enterococcus faecalis, and Staphylococcus epidermidis) were accurately identified with the MALDI-TOF MS in Dakar. The most frequent misidentification in Dakar was at the species level for Achromobacter xylosoxidans, which was inaccurately identified as Achromobacter denitrificans, and the bacteria absent from the database, such as Exiguobacterium aurientacum or Kytococcus schroeteri, could not be identified. A few difficulties were observed with MALDI-TOF MS for Bacillus sp. or oral streptococci. 16S rRNA sequencing identified a novel bacterium, “Necropsobacter massiliensis.” The robust identification of microorganisms by MALDI-TOF MS in Dakar and Marseille demonstrates that MALDI-TOF MS can be used as a first-line tool in clinical microbiology laboratories in tropical countries.
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Affiliation(s)
- Cheikh I. Lo
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, InsermU1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Marseille, France and Dakar, Senegal
| | | | | | | | | | - Oleg Mediannikov
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, InsermU1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Marseille, France and Dakar, Senegal
| | - Cheikh Sokhna
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, InsermU1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Marseille, France and Dakar, Senegal
| | - Ngor Faye
- Université Cheikh Anta Diop, Dakar, Senegal
| | - Yaya Diemé
- Hôpital Principal de Dakar, Dakar, Senegal
| | | | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, InsermU1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Marseille, France and Dakar, Senegal
| | - Florence Fenollar
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, InsermU1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Marseille, France and Dakar, Senegal
- * E-mail:
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Brady AC, Wong B, Pfeiffer CD. Utilizing Rapid Diagnostics for Detection of Candida Species. CURRENT TREATMENT OPTIONS IN INFECTIOUS DISEASES 2015. [DOI: 10.1007/s40506-015-0049-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Chen YS, Liu YH, Teng SH, Liao CH, Hung CC, Sheng WH, Teng LJ, Hsueh PR. Evaluation of the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry Bruker Biotyper for identification of Penicillium marneffei, Paecilomyces species, Fusarium solani, Rhizopus species, and Pseudallescheria boydii. Front Microbiol 2015. [PMID: 26217315 PMCID: PMC4495555 DOI: 10.3389/fmicb.2015.00679] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
We evaluated the performance of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), the MALDI Bruker Biotyper system (microflex LT; Bruker Daltonik GmbH, Bremen, Germany), on the identification of 50 isolates of clinically encountered molds, including Penicillium marneffei (n = 28), Paecilomyces species (n = 12), Fusarium solani (n = 6), Rhizopus species (n = 3), and Pseudallescheria boydii (n = 1). The isolates were identified to species levels by sequence analysis of the internal transcribed spacer (ITS) regions using primers ITS1 and ITS4. None of the 28 genetically well characterized isolates of P. marneffei were identified as P. marneffei by MALDI-TOF MS, because P. marneffei was not present in either Bruker general library (DB 5627) or Bruker filamentous fungi library V1.0. However, the rate of accurate identification as P. marneffei (score value ≥ 2.000) was 85.7% based on newly created database from one P. marneffei strain (NTUH-3370) by MALDI Biotyper system. Sequencing analysis of these 22 non-P. marneffei isolates of molds revealed seven Paecilomyces variotii, six F. solani, four Paecilomyces lilacinus, and one each of Paecilomyces sinensis, Rhizopus arrhizus, R. oryzae, R. microspores, and P. boydii. Although all the seven P. variotii isolates, four of the six F. solani, two of the four P. lilacinus, and two of the three isolates of Rhizopus species, and the P. boydii isolate had concordant identification results between MALDI-TOF MS and sequencing analysis, the score values of these isolates were all of <1.700. This study indicated that the MALDI Bruker Biotyper is ineffective for identifying P. marneffei and other unusual molds because of the current database limitations. Therefore, it is necessary to continuously update the MALDI-TOF MS databases.
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Affiliation(s)
- Ying-Sheng Chen
- Division of Infectious Diseases, Department of Internal Medicine, Cardinal Tien Hospital New Taipei City, Taiwan
| | - Yen-Hung Liu
- Division of Infectious Diseases, Department of Internal Medicine, Cardinal Tien Hospital New Taipei City, Taiwan ; Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University Taipei, Taiwan
| | - Shih-Hua Teng
- Department of Graduate Institute of Biomedical Sciences, Chang Gung University Tao-Yuan, Taiwan
| | - Chun-Hsing Liao
- Department of Internal Medicine, Far Eastern Memorial Hospital Taipei, Taiwan
| | - Chien-Ching Hung
- Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine Taipei, Taiwan
| | - Wang-Huei Sheng
- Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine Taipei, Taiwan
| | - Lee-Jene Teng
- Department of Laboratory Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine Taipei, Taiwan ; Department and Graduate Institute of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University Taipei, Taiwan
| | - Po-Ren Hsueh
- Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine Taipei, Taiwan ; Department of Laboratory Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine Taipei, Taiwan
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Are the Conventional Commercial Yeast Identification Methods Still Helpful in the Era of New Clinical Microbiology Diagnostics? A Meta-Analysis of Their Accuracy. J Clin Microbiol 2015; 53:2439-50. [PMID: 25994160 DOI: 10.1128/jcm.00802-15] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 05/11/2015] [Indexed: 12/29/2022] Open
Abstract
Accurate identification of pathogenic species is important for early appropriate patient management, but growing diversity of infectious species/strains makes the identification of clinical yeasts increasingly difficult. Among conventional methods that are commercially available, the API ID32C, AuxaColor, and Vitek 2 systems are currently the most used systems in routine clinical microbiology. We performed a systematic review and meta-analysis to estimate and to compare the accuracy of the three systems, in order to assess whether they are still of value for the species-level identification of medically relevant yeasts. After adopting rigorous selection criteria, we included 26 published studies involving Candida and non-Candida yeasts that were tested with the API ID32C (674 isolates), AuxaColor (1,740 isolates), and Vitek 2 (2,853 isolates) systems. The random-effects pooled identification ratios at the species level were 0.89 (95% confidence interval [CI], 0.80 to 0.95) for the API ID32C system, 0.89 (95% CI, 0.83 to 0.93) for the AuxaColor system, and 0.93 (95% CI, 0.89 to 0.96) for the Vitek 2 system (P for heterogeneity, 0.255). Overall, the accuracy of studies using phenotypic analysis-based comparison methods was comparable to that of studies using molecular analysis-based comparison methods. Subanalysis of studies conducted on Candida yeasts showed that the Vitek 2 system was significantly more accurate (pooled ratio, 0.94 [95% CI, 0.85 to 0.99]) than the API ID32C system (pooled ratio, 0.84 [95% CI, 0.61 to 0.99]) and the AuxaColor system (pooled ratio, 0.76 [95% CI, 0.67 to 0.84]) with respect to uncommon species (P for heterogeneity, <0.05). Subanalysis of studies conducted on non-Candida yeasts (i.e., Cryptococcus, Rhodotorula, Saccharomyces, and Trichosporon) revealed pooled identification accuracies of ≥98% for the Vitek 2, API ID32C (excluding Cryptococcus), and AuxaColor (only Rhodotorula) systems, with significant low or null levels of heterogeneity (P > 0.05). Nonetheless, clinical microbiologists should reconsider the usefulness of these systems, particularly in light of new diagnostic tools such as matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry, which allow for considerably shortened turnaround times and/or avoid the requirement for additional tests for species identity confirmation.
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Riat A, Hinrikson H, Barras V, Fernandez J, Schrenzel J. Confident identification of filamentous fungi by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry without subculture-based sample preparation. Int J Infect Dis 2015; 35:43-5. [PMID: 25917964 DOI: 10.1016/j.ijid.2015.04.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 04/02/2015] [Accepted: 04/18/2015] [Indexed: 10/23/2022] Open
Affiliation(s)
- Arnaud Riat
- Bacteriology Laboratory, Service of Laboratory Medicine, University of Geneva Hospitals (HUG), CH-1211 Geneva 14, Switzerland.
| | - Hanspeter Hinrikson
- Bacteriology Laboratory, Service of Laboratory Medicine, University of Geneva Hospitals (HUG), CH-1211 Geneva 14, Switzerland
| | - Valérie Barras
- Bacteriology Laboratory, Service of Laboratory Medicine, University of Geneva Hospitals (HUG), CH-1211 Geneva 14, Switzerland
| | - José Fernandez
- Bacteriology Laboratory, Service of Laboratory Medicine, University of Geneva Hospitals (HUG), CH-1211 Geneva 14, Switzerland
| | - Jacques Schrenzel
- Bacteriology Laboratory, Service of Laboratory Medicine, University of Geneva Hospitals (HUG), CH-1211 Geneva 14, Switzerland; Genomic Research Laboratory, Service of Infectious Diseases, Department of Medical Specialties, University of Geneva Hospitals (HUG), Geneva, Switzerland
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Zhou C, Tao L, Hu B, Ma J, Ye X, Huang S, Ma Y, Shan Y. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for the identification of beta-hemolytic streptococci. J Thorac Dis 2015; 7:591-5. [PMID: 25973224 PMCID: PMC4419311 DOI: 10.3978/j.issn.2072-1439.2015.03.02] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 01/21/2015] [Indexed: 01/22/2023]
Abstract
OBJECTIVE Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has emerged as promising technology for species identification. The purpose of this investigation was to compare the performance of MS and the traditional method for identification of beta-hemolytic streptococci (BHS). METHODS Clinical BHS isolates were identified by the BD Phoenix SMIC/ID Streptococcal panels, and two MALDI-TOF MS platforms: the VITEK MS and the Bruker MALDI Biotyper systems respectively. In case of discordant results, 16sRNA sequencing was performed to provide the reference ID. RESULTS A total of 96 isolates of BHS were analyzed. Thirty-six isolates (20.8%) were re-tested by BD Phoenix for identification failure; and four isolates (4.2%) were rerun on the Bruker system for low identification score. No isolate need a second run for identification by Vitek MS system. Overall, BD Phoenix, BioTyper and Vitek MS automated system accurately identified 76 strains (79.2%), 91 (94.7%) strains and 92 (95.8%) strains, respectively. CONCLUSIONS Our study suggests that MALDI-TOF MS is a superior method to conventional phenotypic methods for BHS identification.
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Fleurbaaij F, van Leeuwen HC, Klychnikov OI, Kuijper EJ, Hensbergen PJ. Mass Spectrometry in Clinical Microbiology and Infectious Diseases. Chromatographia 2015. [DOI: 10.1007/s10337-014-2839-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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