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White JK, Nielsen JL, Madsen AM. Microbial species and biodiversity in settling dust within and between pig farms. ENVIRONMENTAL RESEARCH 2019; 171:558-567. [PMID: 30771719 DOI: 10.1016/j.envres.2019.01.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 11/30/2018] [Accepted: 01/04/2019] [Indexed: 05/14/2023]
Abstract
The airborne fungal and bacterial species present in pig farm dust have not been well characterised even though these bioaerosols are known to cause inflammation and other airway maladies. In this study, the microbial species and composition in airborne dust within and between pig farms were investigated. Passively sedimenting dust from six pig farms were collected using electrostatic dust collectors. The bacterial and fungal species were identified using matrix-assisted laser desorption-ionisation time-of-flight mass spectrometry (MALDI-TOF MS) and next generation sequencing (NGS). Dust samples taken within the same stable section revealed high resemblance and stability. Constrained statistical analysis of the microbial community compositions indicated that the types of stable did not appear to have a great effect on the bacterial and fungal β-diversity. In contrast to this, the farm from which samples were taken appeared to have the greatest effect on the bacterial β-diversity, but this trend was not observed for the fungal β-diversity. The most common bacteria and fungi according to NGS data were anaerobes typically associated with the pig intestinal tract and yeasts respectively. Bacterial sedimentation varied at a rate between 103 and 109 CFU/m2/day, with the most common species after aerobic incubation being Aerococcus viridans and Staphylococcus equorum, while Clostridium perfringens and Staphylococcus simulans were the most common species after anaerobic incubation. A total of 28 different species of bacteria and fungi were classifiable as pathogens. In conclusion, the biodiversity in pig farm dust shows a high diversity of bacterial species. However, samples from the same stable section resembled each other, but also different sections within the same farm also resembled each other, thus indicating a high degree of community stability in the dust source. In regards to fungal identification, the biodiversity was observed to be similar between samples from different stable sections and farms, indicating a higher degree of similarities in the mycobiomes found across pig farms studied.
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Affiliation(s)
- John Kerr White
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7 H, 9220 Aalborg Ø, Denmark; The National Research Centre for the Working Environment, Lersø Parkallé 105, 2100 Copenhagen Ø, Denmark.
| | - Jeppe Lund Nielsen
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7 H, 9220 Aalborg Ø, Denmark.
| | - Anne Mette Madsen
- The National Research Centre for the Working Environment, Lersø Parkallé 105, 2100 Copenhagen Ø, Denmark.
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52
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Arastehfar A, Bakhtiari M, Daneshnia F, Fang W, Sadati SK, Al-Hatmi AMS, Groenewald M, Sharifi-Mehr H, Liao W, Pan W, Zomorodian K, Hagen F, Boekhout T. First fungemia case due to environmental yeast Wickerhamomyces myanmarensis: detection by multiplex qPCR and antifungal susceptibility. Future Microbiol 2019; 14:267-274. [PMID: 30859860 PMCID: PMC6482385 DOI: 10.2217/fmb-2018-0253] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 01/09/2019] [Indexed: 11/21/2022] Open
Abstract
AIM Presenting the first clinical case of Wickerhamomyces myanmarensis. PATIENTS & METHODS Yeast cells were isolated from blood and central venous catheter of a 5.5-year-old male subject. API 20C AUX, MALDI-TOF MS, ITS and LSU rDNA sequencing, and our qPCR assay were used for identification and the MIC values were determined by CLSI M27-A3. RESULTS ITS and LSU rDNA sequencing identified both isolates as W. myanmarensis, while API 20C AUX and MALDI-TOF MS did not identify them correctly. Our qPCR specifically distinguished W. myanmarensis from W. anomalus. Isolate obtained from blood showed a higher MIC value for fluconazole, voriconazole and posaconazole. CONCLUSION Utilization of reliable identification tools might reveal the genuine spectrum of opportunistic yeast species.
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Affiliation(s)
- Amir Arastehfar
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Mina Bakhtiari
- Basic Sciences in Infectious Diseases Research Center, & Department of Medical Mycology & Parasitology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Farnaz Daneshnia
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Wenjie Fang
- 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
| | - Sara Khanjari Sadati
- Basic Sciences in Infectious Diseases Research Center, & Department of Medical Mycology & Parasitology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Abdullah MS Al-Hatmi
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
- Ministry of Health, Directorate General of Health Services, Ibri, Oman
| | | | - Hamid Sharifi-Mehr
- Biology Department, Faculty of Science, Sahid Bahonar University of Kerman, Kerman, Iran
| | - 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
| | - 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
| | - Kamiar Zomorodian
- Basic Sciences in Infectious Diseases Research Center, & Department of Medical Mycology & Parasitology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ferry Hagen
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
- Basic Sciences in Infectious Diseases Research Center, & Department of Medical Mycology & Parasitology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
- Institute of Biodiversity & Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
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53
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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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54
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Delavy M, Dos Santos AR, Heiman CM, Coste AT. Investigating Antifungal Susceptibility in Candida Species With MALDI-TOF MS-Based Assays. Front Cell Infect Microbiol 2019; 9:19. [PMID: 30792970 PMCID: PMC6375026 DOI: 10.3389/fcimb.2019.00019] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 01/22/2019] [Indexed: 12/21/2022] Open
Abstract
Half of invasive fungal infections lead to death. Amongst pathogenic fungi, the most widespread species belong to the Candida genus and vary in their susceptibility to antifungal drugs. The emergence of antifungal resistance has become a major clinical problem. Therefore, the definition of susceptibility patterns is crucial for the survival of patients and the monitoring of resistance epidemiology. Although, most routinely used methods of AntiFungal Susceptibility Testing (AFST) have reached their limits, the rediscovery of Matrix Associated Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) in the field of mycology provides a promising alternative for the study of antifungal resistance. MALDI-TOF MS is already used in mycology for fungal identification, which permits to highlight inherent antifungal resistance. However, the main concern of clinicians is the rise of acquired antifungal resistance and the time needed for their detection. For this purpose, MALDI-TOF MS has been shown to be an accurate tool for AFST, presenting numerous advantages in comparison to commonly used techniques. Finally, MALDI-TOF MS could be used directly to detect resistance mechanisms through typing. Consequently, MALDI-TOF MS offers new perspectives in the context of healthcare associated outbreaks of emerging multi-drug resistant fungi, such as C. auris. As a proof of concept, we will illustrate the current and future benefits in using and adapting MALDI-TOF MS-based assays to define the susceptibility pattern of C. auris, by species identification, AFST, and typing.
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Affiliation(s)
- Margot Delavy
- Institute of Microbiology, University of Lausanne and University Hospital of Lausanne, Lausanne, Switzerland
| | - Andrea R Dos Santos
- Institute of Microbiology, University of Lausanne and University Hospital of Lausanne, Lausanne, Switzerland
| | - Clara M Heiman
- Institute of Microbiology, University of Lausanne and University Hospital of Lausanne, Lausanne, Switzerland
| | - Alix T Coste
- Institute of Microbiology, University of Lausanne and University Hospital of Lausanne, Lausanne, Switzerland
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55
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McHugh KE, Gersey M, Rhoads DD, Procop GW, Zhang Y, Booth CN, Sturgis CD. Sensitivity of Cerebrospinal Fluid Cytology for the Diagnosis of Cryptococcal Infections: A 21-Year Single-Institution Retrospective Review. Am J Clin Pathol 2019; 151:198-204. [PMID: 30321269 DOI: 10.1093/ajcp/aqy133] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Objectives Cryptococcal meningoencephalitis is the most common fungal infection of the central nervous system diagnosed by cerebrospinal fluid cytology (CSF) studies. Existing literature suggests that routine CSF cytomorphologic evaluations are exquisitely specific; however, less is known about their sensitivity. Methods An electronic record review of the cytopathology and microbiology files was conducted for the 21-year interval from January 1, 1995, through December 31, 2015. Results In 21 years, 12,584 CSF samples were processed in the laboratory. Of these, 24 (0.2%) were reported positive for cryptococcal organisms by light microscopy, and 129 CSF fungal cultures were positive for Cryptococcus species. All cotested specimens with positive cytology results were positive on culture (15 specimens, 100% specificity). Twenty-four samples with positive culture results were negative by CSF cytology (sensitivity 39%). Conclusions When culture is used as a gold standard, CSF cytology is 100% specific and 39% sensitive, with a positive predictive value of 100% and a negative predictive value of 99.8%.
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Affiliation(s)
- Kelsey E McHugh
- Department of Laboratory Medicine, Cleveland Clinic, Cleveland, OH
| | - Melanie Gersey
- Department of Laboratory Medicine, Cleveland Clinic, Cleveland, OH
| | - Daniel D Rhoads
- Department of Pathology, Case Western Reserve University, Cleveland, OH
- Department of Pathology, University Hospitals Cleveland Medical Center, Cleveland, OH
| | - Gary W Procop
- Department of Laboratory Medicine, Cleveland Clinic, Cleveland, OH
| | - Yaxia Zhang
- Department of Pathology, Hospital for Special Surgery, New York, NY
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56
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Zhao Y, Tsang CC, Xiao M, Chan JFW, Lau SKP, Kong F, Xu Y, Woo PCY. Yeast identification by sequencing, biochemical kits, MALDI-TOF MS and rep-PCR DNA fingerprinting. Med Mycol 2018; 56:816-827. [PMID: 29228397 DOI: 10.1093/mmy/myx118] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 10/12/2017] [Indexed: 01/14/2023] Open
Abstract
No study has comprehensively evaluated the performance of 28S nrDNA and ITS sequencing, commercial biochemical test kits, MALDI-TOF MS platforms, and the emerging rep-PCR DNA fingerprinting technology using a cohort of yeast strains collected from a clinical microbiology laboratory. In this study, using 71 clinically important yeast isolates (excluding Candida albicans) collected from a single centre, we determined the concordance of 28S nrDNA and ITS sequencing and evaluated the performance of two commercial test kits, two MALDI-TOF MS platforms, and rep-PCR DNA fingerprinting. 28S nrDNA and ITS sequencing showed complete agreement on the identities of the 71 isolates. Using sequencing results as the standard, 78.9% and 71.8% isolates were correctly identified using the API 20C AUX and Vitek 2 YST ID Card systems, respectively; and 90.1% and 80.3% isolates were correctly identified using the Bruker and Vitek MALDI-TOF MS platforms, respectively. Of the 18 strains belonging to the Candida parapsilosis species complex tested by DiversiLab automated rep-PCR DNA fingerprinting, all were identified only as Candida parapsilosis with similarities ≥93.2%, indicating the misidentification of Candida metapsilosis and Candida orthopsilosis. However, hierarchical cluster analysis of the rep-PCR DNA fingerprints of these three species within this species complex formed three different discrete clusters, indicating that this technology can potentially differentiate the three species. To achieve higher accuracies of identification, the databases of commercial biochemical test kits, MALDI-TOF MS platforms, and DiversiLab automated rep-PCR DNA fingerprinting needs further enrichment, particularly for uncommonly encountered yeast species.
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Affiliation(s)
- Ying Zhao
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, China.,Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Chi-Ching Tsang
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Meng Xiao
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Jasper F W Chan
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong
| | - Susanna K P Lau
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong.,Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Hong Kong
| | - Fanrong Kong
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research - Pathology West, Westmead Hospital, Westmead, New South Wales, Australia
| | - Yingchun Xu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Patrick C Y Woo
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong.,Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Hong Kong
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57
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Hu Z, Zhang J, Chen Z, Jin Z, Leng P, Zhou J, Xie X. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometric identification and antifungal susceptibility analysis of Candida species isolated from patients with invasive yeast infections in five university hospitals. Braz J Microbiol 2018; 50:99-105. [PMID: 30637643 DOI: 10.1007/s42770-018-0027-0] [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: 07/25/2018] [Accepted: 10/15/2018] [Indexed: 11/29/2022] Open
Abstract
In this multicenter study, we compared the performance of the Bruker Biotyper MS system and VITEK 2 YST systems for invasive yeast identification, investigated the distribution of isolated species, and evaluated the antifungal susceptibility profiles of Candida albicans, Candida parapsilosis, and Candida tropicalis. In cases of discrepant results lack of identification with either method, molecular identification techniques were employed. We tested 216 clinical isolates, and concordance between the two methods was observed for 192/216 isolates (88.9%). For five unidentified strains (2.3%), an internal transcribed spacer (ITS) sequencing approach was used. In brief, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-ToF MS) provided short turnaround times and more reliable results than those of Vitek 2 YST. In Wuhan, C. albicans, C. parapsilosis, Candida glabrata, and C. tropicalis were the most common pathogens (93.0%) in patients with candidemia. Cryptococcus neoformans was mainly detected in cerebrospinal fluid samples (88.9%). Trichosporon asahii were all isolated from drainage fluids in the Surgery. Candida albicans was clearly susceptible to azoles, while C. parapsilosis and C. tropicalis displayed differences in susceptibility to azoles. Our findings provide a basis for the practical application of MALDI-ToF MS for identification and for the use of ATB FUNGUS 3 to characterize the susceptibility of Candida spp., thereby providing significant data for therapeutic decisions.
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Affiliation(s)
- Zhimin Hu
- Department of Clinical Microbiology Laboratory, Wuhan No. 1 Hospital of Tongji Medical College, Huazhong University of Science and Technology, No. 215 Zhongshan Ave., Wuhan, 430022, China.
| | - Juling Zhang
- Department of Clinical Laboratory, PLA 302 Hospital, No. 100 West Fourth Ring Road, Peking, 100166, China
| | - Zhongju Chen
- Department of Clinical Microbiology Laboratory, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, No. 1095 Liberation Ave., Wuhan, 430030, China
| | - Zhengjiang Jin
- Department of Clinical Microbiology Laboratory, Hubei Women and Children's Hospital, No. 745 Wuluo Road, Wuhan, 430070, China
| | - Pei Leng
- Department of Clinical Laboratory, Wuhan Women and Children Medical Care Center, No. 100 Xianggang Road, Wuhan, 430015, China
| | - Junying Zhou
- Department of Clinical Microbiology Laboratory, Zhongnan Hospital of Wuhan University, No. 169 Donghu Road, Wuhan, 430071, China
| | - Xiaofang Xie
- Department of Clinical Microbiology Laboratory, The First Affiliated Hospital of Soochow University, No. 188 Shizi Street, Soochow, 215006, China
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58
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Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) shows adaptation of grass pollen composition. Sci Rep 2018; 8:16591. [PMID: 30409982 PMCID: PMC6224550 DOI: 10.1038/s41598-018-34800-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 10/22/2018] [Indexed: 11/22/2022] Open
Abstract
MALDI time-of-flight mass spectrometry (MALDI-TOF MS) has become a widely used tool for the classification of biological samples. The complex chemical composition of pollen grains leads to highly specific, fingerprint-like mass spectra, with respect to the pollen species. Beyond the species-specific composition, the variances in pollen chemistry can be hierarchically structured, including the level of different populations, of environmental conditions or different genotypes. We demonstrate here the sensitivity of MALDI-TOF MS regarding the adaption of the chemical composition of three Poaceae (grass) pollen for different populations of parent plants by analyzing the mass spectra with partial least squares discriminant analysis (PLS-DA) and principal component analysis (PCA). Thereby, variances in species, population and specific growth conditions of the plants were observed simultaneously. In particular, the chemical pattern revealed by the MALDI spectra enabled discrimination of the different populations of one species. Specifically, the role of environmental changes and their effect on the pollen chemistry of three different grass species is discussed. Analysis of the group formation within the respective populations showed a varying influence of plant genotype on the classification, depending on the species, and permits conclusions regarding the respective rigidity or plasticity towards environmental changes.
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59
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Muste C, Owens KG. Cell-Free Identification of S. cerevisiae Strains by Analysis of Supernatant Using LC-MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:2260-2267. [PMID: 30105741 DOI: 10.1007/s13361-018-2046-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Revised: 07/13/2018] [Accepted: 07/26/2018] [Indexed: 06/08/2023]
Abstract
Current literature shows a gap for methods which can identify yeast sub-species (strains or serovars) in samples where there are no viable cells remaining. Presented here is a technique for the analysis of yeast supernatant, including solid phase extraction, data-dependent acquisition liquid chromatography/mass spectrometry (LC-MS), and two chemometric methods to identify and classify yeast strains. Five strains of Saccharomyces cerevisiae were successfully identified in various stages of growth. In addition, peptide/protein identification was performed, without the need for additional data acquisition. Graphical Abstract ᅟ.
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Affiliation(s)
- Cathy Muste
- Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, PA, 19104-2875, USA
| | - Kevin G Owens
- Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, PA, 19104-2875, USA.
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60
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Gorre E, Muste C, Owens KG. Introducing a Cell-Free Approach for the Identification of Brewing Yeast (Saccharomyces cerevisiae) Strains Using MALDI-TOF MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:2248-2259. [PMID: 30088233 DOI: 10.1007/s13361-018-2031-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 06/16/2018] [Accepted: 06/26/2018] [Indexed: 06/08/2023]
Abstract
Matrix-assisted laser desorption ionization (MALDI) time-of-flight mass spectrometry (TOF MS) is now accepted as a quick, easy-to-use, cost-effective, and accurate technique for the identification of microorganisms. However, the successful identification of microorganisms is dependent upon careful attention to factors such as growth conditions, extraction methods, mass spectral data collection, and data analysis procedures. Currently, most microorganism identification has been limited to the species level, and only a limited number of publications have been successful in achieving strain-level identification. In this work, a "cell-free" approach is introduced where peptide analytes secreted by several Saccharomyces cerevisiae strains during their growth period are analyzed. The analysis of the cell supernatant generates mass spectral patterns that are specific to each strain. The patterns generated in combination with a robust data analysis workflow using the open-source programs MALDIquant and Mass-Up allows for strain-level identification of S. cerevisiae. The cell-free approach using the yeast supernatant to accurately identify yeast strains is presented here as a proof of concept. Graphical Abstract.
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Affiliation(s)
- Elsa Gorre
- Department of Chemistry, Drexel University, 3141 Chestnut St, Philadelphia, PA, 19104-2875, USA
| | - Cathy Muste
- Department of Chemistry, Drexel University, 3141 Chestnut St, Philadelphia, PA, 19104-2875, USA
| | - Kevin G Owens
- Department of Chemistry, Drexel University, 3141 Chestnut St, Philadelphia, PA, 19104-2875, USA.
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61
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Vecchione A, Florio W, Celandroni F, Barnini S, Lupetti A, Ghelardi E. A Rapid Procedure for Identification and Antifungal Susceptibility Testing of Yeasts From Positive Blood Cultures. Front Microbiol 2018; 9:2400. [PMID: 30459718 PMCID: PMC6232941 DOI: 10.3389/fmicb.2018.02400] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 09/19/2018] [Indexed: 11/13/2022] Open
Abstract
The development of rapid diagnostic assays for the identification and analysis of antimicrobial resistance of fungal pathogens causing invasive mycoses is of utmost importance to reduce morbidity and mortality. We evaluated the performance of a novel rapid procedure directly applied to monomicrobial blood cultures from patients with bloodstream infection caused by yeast species, including nine Candida and three non-Candida species. For the rapid procedure herein developed, samples of positive blood cultures were transferred into serum separator tubes and treated with sodium dodecyl sulfate; the yeast layer was recovered and directly used for microbial identification by MALDI-TOF mass spectrometry and antifungal susceptibility testing (AFST) by the Sensititre YeastOne Y010 panel. The results were compared with those obtained by the same methods applied to colonies isolated on solid media. Using a score value of 1.700 as cut-off for valid identification, the rapid procedure identified 66 of 124 (53.2%) isolates, all of which concordantly with the reference method. However, adopting a cut-off ≥1.300 and ≥4 consecutive repetitions of the same species in the list of matches would extend concordant identification to 107/124 (86.3%) samples. Importantly, AFST revealed essential agreement between the two methods for all the isolate/antifungal drug combinations tested, including misidentified and not identified isolates. Therefore, the procedure herein developed represents a valid alternative for AFST of yeasts from positive blood cultures, yielding accurate and reliable results at least 24 h earlier than with the routine procedure, thus allowing clinicians to promptly streamline antifungal therapy.
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Affiliation(s)
- Alessandra Vecchione
- Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia, Università di Pisa, Pisa, Italy
| | - Walter Florio
- Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia, Università di Pisa, Pisa, Italy
| | - Francesco Celandroni
- Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia, Università di Pisa, Pisa, Italy
| | | | - Antonella Lupetti
- Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia, Università di Pisa, Pisa, Italy
| | - Emilia Ghelardi
- Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia, Università di Pisa, Pisa, Italy
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Lee H, Park JH, Oh J, Cho S, Koo J, Park IC, Kim J, Park S, Choi JS, Shin SY, Sung GH, Kim J. Evaluation of a new matrix-assisted laser desorption/ionization time-of-flight mass spectrometry system for the identification of yeast isolation. J Clin Lab Anal 2018; 33:e22685. [PMID: 30298531 DOI: 10.1002/jcla.22685] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 09/07/2018] [Accepted: 09/11/2018] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Currently, three commercial in vitro diagnostic matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) systems are widely used in clinical laboratories. The ASTA MicroIDSys system (ASTA Inc, South Korea) is a newly developed MALDI-TOF MS system used for the identification of pathogenic microorganisms. In the present study, we assessed the performance of the ASTA MALDI-TOF MS system for the identification of pathogenic yeast from clinical samples. METHODS We tested 284 clinical yeast isolates from various clinical specimens using ASTA MALDI-TOF MS, and the results were compared with those using molecular sequencing of the ITS or D1-D2 regions of rDNA and biochemical assays. RESULTS A total of 284 isolates were tested and found to be distributed across 14 species including Candida albicans (n = 100) and other yeast species (n = 184). ASTA MALDI-TOF MS correctly identified 95.1% (270/284) of the yeast species compared to molecular sequencing. Among them, 262 isolates showed acceptable MALDI-TOF MS scores (≥140), and 98.1% (257/262) isolates were identified correctly. In addition, among 22 isolates with a MALDI-TOF MS score <140, 59.1% (13/22) of the isolates showed concordance with molecular typing at the species level. Clustering analysis revealed the effectiveness of the new MALDI-TOF MS system for the identification of yeast species. CONCLUSIONS ASTA MALDI-TOF MS showed high accuracy in the identification of yeast species; it involves facile sample preparation and extraction procedures. ASTA MALDI-TOF MS is expected to be useful for yeast identification in clinical microbiology laboratories due to its reliability and cost-effectiveness.
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Affiliation(s)
- Hyeyoung Lee
- Department of Laboratory Medicine, International St. Mary's Hospital, College of Medicine, Catholic Kwandong University, Incheon, Korea
| | - Ji-Hyun Park
- Institute for Healthcare and Life Science, International St. Mary's Hospital, College of Medicine, Catholic Kwandong University, Incheon, Korea
| | - Junsang Oh
- Institute for Healthcare and Life Science, International St. Mary's Hospital, College of Medicine, Catholic Kwandong University, Incheon, Korea
| | - Sungil Cho
- Department of Laboratory Medicine, International St. Mary's Hospital, College of Medicine, Catholic Kwandong University, Incheon, Korea
| | - Jehyun Koo
- Department of Laboratory Medicine, International St. Mary's Hospital, College of Medicine, Catholic Kwandong University, Incheon, Korea
| | - Ik Chun Park
- Department of Laboratory Medicine, International St. Mary's Hospital, College of Medicine, Catholic Kwandong University, Incheon, Korea
| | - Jiwoo Kim
- Department of Laboratory Medicine, International St. Mary's Hospital, College of Medicine, Catholic Kwandong University, Incheon, Korea
| | - Sehyun Park
- Department of Laboratory Medicine, International St. Mary's Hospital, College of Medicine, Catholic Kwandong University, Incheon, Korea
| | - Ji Seon Choi
- Department of Laboratory Medicine, International St. Mary's Hospital, College of Medicine, Catholic Kwandong University, Incheon, Korea
| | - So Youn Shin
- Department of Infectious Diseases, International St. Mary Hospital, College of Medicine, Catholic Kwandong University, Incheon, Korea
| | - Gi-Ho Sung
- Institute for Healthcare and Life Science, International St. Mary's Hospital, College of Medicine, Catholic Kwandong University, Incheon, Korea.,Department of Microbiology, College of Medicine, Catholic Kwandong University, Gangneung, Korea
| | - Jayoung Kim
- Department of Laboratory Medicine, International St. Mary's Hospital, College of Medicine, Catholic Kwandong University, Incheon, Korea
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Ghosh PN, Fisher MC, Bates KA. Diagnosing Emerging Fungal Threats: A One Health Perspective. Front Genet 2018; 9:376. [PMID: 30254662 PMCID: PMC6141620 DOI: 10.3389/fgene.2018.00376] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 08/24/2018] [Indexed: 11/17/2022] Open
Abstract
Emerging fungal pathogens are a growing threat to global health, ecosystems, food security, and the world economy. Over the last century, environmental change and globalized transport, twinned with the increasing application of antifungal chemical drugs have led to increases in outbreaks of fungal diseases with sometimes catastrophic effects. In order to tackle contemporary epidemics and predemic threats, there is a pressing need for a unified approach in identification and monitoring of fungal pathogens. In this paper, we discuss current high throughput technologies, as well as new platforms capable of combining diverse data types to inform practical epidemiological strategies with a focus on emerging fungal pathogens of wildlife.
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Affiliation(s)
- Pria N. Ghosh
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | - Matthew C. Fisher
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Kieran A. Bates
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
- Institute of Zoology, Zoological Society of London, London, United Kingdom
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Ruhnke M, Behre G, Buchheidt D, Christopeit M, Hamprecht A, Heinz W, Heussel CP, Horger M, Kurzai O, Karthaus M, Löffler J, Maschmeyer G, Penack O, Rieger C, Rickerts V, Ritter J, Schmidt-Hieber M, Schuelper N, Schwartz S, Ullmann A, Vehreschild JJ, von Lilienfeld-Toal M, Weber T, Wolf HH. Diagnosis of invasive fungal diseases in haematology and oncology: 2018 update of the recommendations of the infectious diseases working party of the German society for hematology and medical oncology (AGIHO). Mycoses 2018; 61:796-813. [PMID: 30098069 DOI: 10.1111/myc.12838] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 08/05/2018] [Indexed: 01/05/2023]
Abstract
Invasive fungal diseases (IFD) are a primary cause of morbidity and mortality in patients with haematological malignancies. These infections are mostly life-threatening and an early diagnosis and initiation of appropriate antifungal therapy are essential for the clinical outcome. Most commonly, Aspergillus and Candida species are involved. However, other Non-Aspergillus moulds are increasingly identified in case of documented IFD. For definite diagnosis of IFD, a combination of diagnostic tools have to be applied, including conventional mycological culture and non-conventional microbiological tests such as antibody/antigen and molecular tests, as well as histopathology and radiology. Although varying widely in cancer patients, the risk of invasive fungal infection is highest in those with allogeneic stem cell transplantation and those with acute leukaemia and markedly lower in patients with solid cancer. Since the last edition of Diagnosis of Invasive Fungal Diseases recommendations of the German Society for Hematology and Oncology in 2012, integrated care pathways have been proposed for the management and therapy of IFDs with either a diagnostic driven strategy as opposed to a clinical or empirical driven strategy. This update discusses the impact of this additional evidence and effective revisions.
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Affiliation(s)
- Markus Ruhnke
- Department of Haematology & Oncology, Paracelsus-Klinik, Osnabrück, Germany
| | - Gerhard Behre
- Department of Haematology & Oncology, Universitätsklinik Leipzig, Leipzig, Germany
| | - Dieter Buchheidt
- Department of Internal Medicine III, Mannheim University Hospital, University of Heidelberg, Mannheim, Germany
| | - Maximilian Christopeit
- Department for Stem Cell Transplantation, University Medical Center Eppendorf, Hamburg, Germany
| | - Axel Hamprecht
- Institute for Medical Microbiology, Immunology and Hygiene, University Hospital of Cologne, Cologne, Germany
| | - Werner Heinz
- Department of Internal Medicine II, Julius Maximilians University, Würzburg, Germany
| | - Claus-Peter Heussel
- Department of Interventional & Diagnostic Radiology, Thorax Centre, University Hospital of Heidelberg, Heidelberg, Germany
| | - Marius Horger
- Department of Diagnostic and Interventional Radiology, Eberhard Karls University, Tübingen, Germany
| | - Oliver Kurzai
- National Reference Center for Invasive Fungal Infections NRZMyk, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knoell-Institute, Jena and Institute for Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | - Meinolf Karthaus
- Deparment of Haematology & Oncology, Municipal Hospital Neuperlach, Munich, Germany
| | - Jürgen Löffler
- Department of Internal Medicine II, Julius Maximilians University, Würzburg, Germany
| | - Georg Maschmeyer
- Department of Haematology, Oncology and Palliative Care, Klinikum Ernst von Bergmann, Municipal Hospital, Potsdam, Germany
| | - Olaf Penack
- Division of Haematology & Oncology, Department of Internal Medicine, Charité University Medicine, Berlin, Germany
| | | | - Volker Rickerts
- Konsiliarlabor Für Kryptokokkose und Seltene Systemmykosen, Robert-Koch-Institut Berlin, Berlin, Germany
| | - Jörg Ritter
- Division of Haematology & Oncology, Department of Paediatrics, University Hospital of Münster, Münster, Germany
| | - Martin Schmidt-Hieber
- Division of Haematology & Oncology, Department of Internal Medicine, Charité University Medicine, Berlin, Germany
| | - Nikolai Schuelper
- Department of Haematology and Medical Oncology, Göttingen University Medical Centre, Göttingen, Germany
| | - Stefan Schwartz
- Division of Haematology & Oncology, Department of Internal Medicine, Charité University Medicine, Berlin, Germany
| | - Andrew Ullmann
- Department of Internal Medicine II, Julius Maximilians University, Würzburg, Germany
| | - Jörg Janne Vehreschild
- Department of Internal Medicine I, German Centre for Infection Research, partner-site Bonn-Cologne, University Hospital of Cologne, Cologne, Germany
| | - Marie von Lilienfeld-Toal
- Department of Internal Medicine II, National Reference Center for Invasive Fungal Infections NRZMyk, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knoell-Institute, Universitätsklinik Jena, Jena, Germany
| | - Thomas Weber
- Department of Internal Medicine IV, Universitätsklinik Halle, Halle, Germany
| | - Hans H Wolf
- Department of Internal Medicine IV, Universitätsklinik Halle, Halle, Germany
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Clinical Utility of Rapid Pathogen Identification for Detecting the Causative Organisms in Sepsis: A Single-Center Study in Korea. CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY 2018; 2018:1698241. [PMID: 30224940 PMCID: PMC6129788 DOI: 10.1155/2018/1698241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 06/21/2018] [Accepted: 08/05/2018] [Indexed: 11/18/2022]
Abstract
Purpose The aim of this pre- and postintervention cohort study was evaluating how effectively rapid pathogen identification with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) detected the causative organisms in sepsis. Methods All consecutive adult patients who had bacteremia within 72 h of intensive care unit admission and met ≥2 quick Sequential Organ Failure Assessment criteria at intensive care unit admission were analyzed. The patients whose microorganisms were identified via MALDI-TOF MS between March 2014 and February 2016 formed the postintervention group. The patients whose microorganisms were identified by using conventional methods between March 2011 and February 2013 formed the preintervention group. Results The postintervention group (n=58) had a shorter mean time from blood draw to receiving the antimicrobial susceptibility results than the preintervention group (n=40) (90.2 ± 32.1 vs. 108.7 ± 43.1 h; p=0.02). The postintervention group was also more likely to have received active antimicrobial therapy by the time the susceptibility report became available (77% vs. 47%; p=0.005). Its 28-day mortality was also lower (40% vs. 70%; p=0.003). Univariate analysis showed that identification via MALDI-TOF MS (odds ratio, 0.28; 95% confidence interval, 0.12–0.66; p=0.004) and active therapy (odds ratio, 0.38; 95% confidence interval, 0.16–0.95; p=0.04) were associated with lower 28-day mortality. Conclusion Rapid microorganism identification via MALDI-TOF MS followed by appropriate antimicrobial therapy may improve the clinical outcomes of patients with sepsis.
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Ruiz de Alegría Puig C, Agüero-Balbín J, Fernández-Mazarrasa C, Martínez-Martínez L. Evaluation of the Vitek-MS™ system in the identification of Candida isolates from bloodstream infections. Rev Iberoam Micol 2018; 35:130-133. [DOI: 10.1016/j.riam.2018.02.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 01/17/2018] [Accepted: 02/26/2018] [Indexed: 01/13/2023] Open
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da Silva Amaral L, Rodrigues-Filho E, Kubicek CP, Herwig C, Marchetti-Deschmann M, Allmaier G. Optimization of sample preparation for intact cell mass spectrometry (matrix-assisted laser desorption/ionization linear time-of-flight mass spectrometry) of endophytic Xylaria. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2018; 32:815-823. [PMID: 29499079 DOI: 10.1002/rcm.8098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 02/08/2018] [Accepted: 02/21/2018] [Indexed: 06/08/2023]
Abstract
RATIONALE Although the fruiting-body of the fungi of the genus Xylaria shows a great variety of morphological characteristics, their mycelial forms are always very similar, imposing difficulties for their identification. Intact cell mass spectrometry (ICMS) using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) can be a fast and reliable strategy to support the differentiation/identification of Xylaria species in those cases where fruit-bodies are not available. METHODS Many experimental parameters such as sample preparation and culture media are crucial for filamentous fungi analysis by MALDI-TOFMS. For the purposes of this study, we used four matrices (CHCA, DHB, FA and SA) with five different concentrations (0.1, 0.3, 0.5, 1.0 and 2.5%) of TFA in the matrix, the influence of six different culture media (solid and liquid), and three mycelium peptide/protein extraction protocols (acid, basic and thymol-supported solution) to optimize the sample preparation of the endophytic fungus X. arbuscula. RESULTS It was observed that sinapinic acid (30 mg/mL) dissolved in acetonitrile/0.1% TFA and PDA were the best matrix solution and culture medium, respectively, for the ICMS of X. arbuscula. The formic acid and ammonium bicarbonate (AB) protocols provided similar mass spectra; however, a higher number of peaks were observed using AB extraction. Mass spectra obtained from different thymol-containing solutions (EtOH/aqueous 0.1% TFA and ACN/aqueous 0.1% TFA) show increasing peak abundances at m/z 3000-6500. CONCLUSIONS X. arbuscula could be analyzed by ICMS. However, an extraction step was required to provide suitable MALDI mass spectra. Formic acid-, AB- and thymol-containing solutions were demonstrated to be good cocktails for the extraction of peptide/protein biomarkers from these fungi.
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Affiliation(s)
- Luciana da Silva Amaral
- Departamento de Química, Universidade Federal de São Carlos CP 676, 13,565-905, São Carlos, SP, Brazil
- Institute of Chemical Technologies and Analytics, TU Wien (Vienna University of Technology), Getreidemarkt 9/164, A-1060, Vienna, Austria
| | - Edson Rodrigues-Filho
- Departamento de Química, Universidade Federal de São Carlos CP 676, 13,565-905, São Carlos, SP, Brazil
| | - Christian P Kubicek
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien (Vienna University of Technology), Getreidemarkt 9/166, A-1060, Vienna, Austria
| | - Christoph Herwig
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien (Vienna University of Technology), Getreidemarkt 9/166, A-1060, Vienna, Austria
| | - Martina Marchetti-Deschmann
- Institute of Chemical Technologies and Analytics, TU Wien (Vienna University of Technology), Getreidemarkt 9/164, A-1060, Vienna, Austria
| | - Günter Allmaier
- Institute of Chemical Technologies and Analytics, TU Wien (Vienna University of Technology), Getreidemarkt 9/164, A-1060, Vienna, Austria
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Honnavar P, Ghosh AK, Paul S, Shankarnarayan SA, Singh P, Dogra S, Chakrabarti A, Rudramurthy SM. Identification of Malassezia species by MALDI-TOF MS after expansion of database. Diagn Microbiol Infect Dis 2018; 92:118-123. [PMID: 30025965 DOI: 10.1016/j.diagmicrobio.2018.05.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 05/10/2018] [Accepted: 05/22/2018] [Indexed: 11/18/2022]
Abstract
The taxonomy of Malassezia species is evolving with introduction of molecular techniques, and difficulty is faced to identify the species by phenotypic methods. Among 15 known Malassezia species, the present Bruker database could identify only 2 species. The present study was aimed to improve Matrix -assisted laser desorption ionization time-flight mass spectrometry (MALDI-TOF MS) based identification of Malassezia species. A total of 88 isolates (DNA sequencing confirmed) for database preparation and, for the validation of database, 190 isolates confirmed by polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) were used. The main spectrum profile dendrogram showed the sufficient discrimination between all the species by MALDI-TOF MS. The updated Malassezia database could identify 94.7% and 5.3% strains to the species and genus level, respectively. MALDI-TOF MS is a significantly reliable technique, and results were comparable with PCR-RFLP with kappa value 0.9. In conclusion, MALDI-TOF MS could be a possible alternative tool to other molecular methods for rapid and accurate identification of Malassezia species.
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Affiliation(s)
- P Honnavar
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - A K Ghosh
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - S Paul
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - S A Shankarnarayan
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - P Singh
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - S Dogra
- Department of Dermatology, Venerology and Leprology, Postgraduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - A Chakrabarti
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - S M Rudramurthy
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, 160012, India.
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Florio W, Tavanti A, Barnini S, Ghelardi E, Lupetti A. Recent Advances and Ongoing Challenges in the Diagnosis of Microbial Infections by MALDI-TOF Mass Spectrometry. Front Microbiol 2018; 9:1097. [PMID: 29896172 PMCID: PMC5986882 DOI: 10.3389/fmicb.2018.01097] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 05/08/2018] [Indexed: 12/25/2022] Open
Abstract
Timeliness and accuracy in the diagnosis of microbial infections are associated with decreased mortality and reduced length of hospitalization, especially for severe, life-threatening infections. A rapid diagnosis also allows for early streamlining of empirical antimicrobial therapies, thus contributing to limit the emergence and spread of antimicrobial resistance. The introduction of matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry (MS) for routine identification of microbial pathogens has profoundly influenced microbiological diagnostics, and is progressively replacing biochemical identification methods. Compared to currently used identification methods, MALDI-TOF MS has the advantage of identifying bacteria and yeasts directly from colonies grown on culture plates for primary isolation in a few minutes and with considerable material and labor savings. The reliability and accuracy of MALDI-TOF MS in identification of clinically relevant bacteria and yeasts has been demonstrated by several studies showing that the performance of MALDI-TOF MS is comparable or superior to phenotypic methods currently in use in clinical microbiology laboratories, and can be further improved by database updates and analysis software upgrades. Besides microbial identification from isolated colonies, new perspectives are being explored for MALDI-TOF MS, such as identification of pathogens directly from positive blood cultures, sub-species typing, and detection of drug resistance determinants. In this review, we summarize the state of the art in routine identification of microbial pathogens by MALDI-TOF MS, and highlight recent advancements of this technology in special applications, such as strain typing, assessment of drug susceptibility, and detection of virulence factors.
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Affiliation(s)
- Walter Florio
- Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia, Università di Pisa, Pisa, Italy
| | | | | | - Emilia Ghelardi
- Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia, Università di Pisa, Pisa, Italy
| | - Antonella Lupetti
- Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia, Università di Pisa, Pisa, Italy
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Rating of the industrial application potential of yeast strains by molecular characterization. Eur Food Res Technol 2018. [DOI: 10.1007/s00217-018-3088-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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71
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Agustini BC, da Silva GA, Bonfim TMB. MALDI-TOF MS Supplementary database for species identification employing the yeast diversity encountered on southern Brazil grapes. Folia Microbiol (Praha) 2018; 63:685-693. [PMID: 29752627 DOI: 10.1007/s12223-018-0607-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 04/25/2018] [Indexed: 10/16/2022]
Abstract
The study of grape microflora is of interest when autochthonous yeasts, which are related to typical wine characteristics, are intended to be used in winemaking. The election of matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS) as the first method for yeast identification was based on its accuracy and rapidity compared to alternative laboratory protocols for identification. The aims of this study are to consolidate the MALDI-TOF MS Supplementary database for environmental yeasts already constructed, to expand it through the addition of standard spectra of not included yeast species, and to discuss the grape microflora encountered in Southern Brazil. A total of 358 strains, isolated from grape berries, were submitted to protein profiling employing Biotyper and Supplementary database. Molecular biology techniques were used as alternatives to identify 6.4% of strains not promptly designated by protein profiling. These strains corresponded to the species Candida californica, Zygoascus meyerae, Candida akabanensis, Candida azyma, and Hanseniaspora vineae. The MALDI-TOF MS spectra of the identified species were added to Supplementary database. The presented results strengthen the need for further expansion of the mass spectra database to broaden its microbiological application.
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Affiliation(s)
- Bruna Carla Agustini
- Laboratory of Applied Microbiology, Embrapa Grape and Wine, Bento Gonçalves, RS, Brazil.
| | | | - Tania Maria Bordin Bonfim
- Laboratory of Enzymology and Fermentation Technology, Pharmacy Department, Federal University of Paraná, Curitiba, PR, Brazil
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Rico-Munoz E, Samson RA, Houbraken J. Mould spoilage of foods and beverages: Using the right methodology. Food Microbiol 2018; 81:51-62. [PMID: 30910088 DOI: 10.1016/j.fm.2018.03.016] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 03/16/2018] [Accepted: 03/29/2018] [Indexed: 11/19/2022]
Abstract
Fungal spoilage of products manufactured by the food and beverage industry imposes significant annual global revenue losses. Mould spoilage can also be a food safety issue due to the production of mycotoxins by these moulds. To prevent mould spoilage, it is essential that the associated mycobiota be adequately isolated and accurately identified. The main fungal groups associated with spoilage are the xerophilic, heat-resistant, preservative-resistant, anaerobic and psychrophilic fungi. To assess mould spoilage, the appropriate methodology and media must be used. While classic mycological detection methods can detect a broad range of fungi using well validated protocols, they are time consuming and results can take days or even weeks. New molecular detection methods are faster but require good DNA isolation techniques, expensive equipment and may detect viable and non-viable fungi that probably will not spoil a specific product. Although there is no complete and easy method for the detection of fungi in food it is important to be aware of the limitation of the methodology. More research is needed on the development of methods of detection and identification that are both faster and highly sensitive.
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Affiliation(s)
- Emilia Rico-Munoz
- BCN Research Laboratories, Inc., 2491 Stock Creek Blvd., Rockford, TN 37853, USA.
| | - Robert A Samson
- Westerdijk Fungal Biodiversity Institute, Dept. Applied and Industrial Mycology, Uppsalalaan 8, Utrecht, CT 3584, The Netherlands
| | - Jos Houbraken
- Westerdijk Fungal Biodiversity Institute, Dept. Applied and Industrial Mycology, Uppsalalaan 8, Utrecht, CT 3584, The Netherlands
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El-Bouri K, Johnston S, Rees E, Thomas I, Bome-Mannathoko N, Jones C, Reid M, Ben-Ismaeil B, Davies AP, Harris LG, Mack D. Comparison of bacterial identification by MALDI-TOF mass spectrometry and conventional diagnostic microbiology methods: agreement, speed and cost implications. Br J Biomed Sci 2018. [DOI: 10.1080/09674845.2012.12002436] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- K. El-Bouri
- Public Health Wales Microbiology Laboratory ABM Swansea, Singleton Hospital, Abertawe-Bro Morgannwg University Health Board, Swansea, United Kingdom
| | - S. Johnston
- Public Health Wales Microbiology Laboratory ABM Swansea, Singleton Hospital, Abertawe-Bro Morgannwg University Health Board, Swansea, United Kingdom
| | - E. Rees
- Public Health Wales Microbiology Laboratory ABM Swansea, Singleton Hospital, Abertawe-Bro Morgannwg University Health Board, Swansea, United Kingdom
| | - I. Thomas
- Public Health Wales Microbiology Laboratory ABM Swansea, Singleton Hospital, Abertawe-Bro Morgannwg University Health Board, Swansea, United Kingdom
| | - N. Bome-Mannathoko
- Medical Microbiology and Infectious Diseases, Institute of Life Science, School of Medicine, Swansea University, Swansea, United Kingdom
| | - C. Jones
- Medical Microbiology and Infectious Diseases, Institute of Life Science, School of Medicine, Swansea University, Swansea, United Kingdom
| | - M. Reid
- Public Health Wales Microbiology Laboratory ABM Swansea, Singleton Hospital, Abertawe-Bro Morgannwg University Health Board, Swansea, United Kingdom
- Medical Microbiology and Infectious Diseases, Institute of Life Science, School of Medicine, Swansea University, Swansea, United Kingdom
| | - B. Ben-Ismaeil
- Public Health Wales Microbiology Laboratory ABM Swansea, Singleton Hospital, Abertawe-Bro Morgannwg University Health Board, Swansea, United Kingdom
| | - A. P. Davies
- Public Health Wales Microbiology Laboratory ABM Swansea, Singleton Hospital, Abertawe-Bro Morgannwg University Health Board, Swansea, United Kingdom
- Medical Microbiology and Infectious Diseases, Institute of Life Science, School of Medicine, Swansea University, Swansea, United Kingdom
| | - L. G. Harris
- Medical Microbiology and Infectious Diseases, Institute of Life Science, School of Medicine, Swansea University, Swansea, United Kingdom
| | - D. Mack
- Public Health Wales Microbiology Laboratory ABM Swansea, Singleton Hospital, Abertawe-Bro Morgannwg University Health Board, Swansea, United Kingdom
- Medical Microbiology and Infectious Diseases, Institute of Life Science, School of Medicine, Swansea University, Swansea, United Kingdom
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Kostrzewa M. Application of the MALDI Biotyper to clinical microbiology: progress and potential. Expert Rev Proteomics 2018; 15:193-202. [DOI: 10.1080/14789450.2018.1438193] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Markus Kostrzewa
- Microbiology and Diagnostics, Bruker Daltonik GmbH, Bremen, Germany
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75
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Quintilla R, Kolecka A, Casaregola S, Daniel HM, Houbraken J, Kostrzewa M, Boekhout T, Groenewald M. MALDI-TOF MS as a tool to identify foodborne yeasts and yeast-like fungi. Int J Food Microbiol 2018; 266:109-118. [DOI: 10.1016/j.ijfoodmicro.2017.11.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 10/23/2017] [Accepted: 11/20/2017] [Indexed: 01/09/2023]
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76
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Li MC, Chang TC, Chen HM, Wu CJ, Su SL, Lee SSJ, Chen PL, Lee NY, Lee CC, Li CW, Syue LS, Ko WC. Oligonucleotide Array and VITEK Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry in Species Identification of Blood Yeast Isolates. Front Microbiol 2018; 9:51. [PMID: 29434578 PMCID: PMC5790773 DOI: 10.3389/fmicb.2018.00051] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 01/10/2018] [Indexed: 01/03/2023] Open
Abstract
We evaluated matrix-assisted laser desorption ionization time-of-flight mass spectrometry using VITEK MS (IVD database) and an oligonucleotide array based on the internal transcribed spacer-1 (ITS-1) and ITS-2 sequences of rRNA genes for the identification of Candida spp. from blood cultures. Five-hundred and twelve consecutive bloodstream yeast isolates were collected daily and initially identified by the phenotypic automated method (VITEK YBC or VITEK2 YST card). Inconsistent results were confirmed by D1-D2 region of 28S rRNA genes and ITSs. Excluding two unidentified yeast isolates, the oligonucleotide array and VITEK MS correctly identified 99.6% (508) and 96.9% (494) of 510 yeast isolates, respectively. The oligonucleotide array and VITEK MS demonstrated high correct identification rates for four major Candida species (C. albicans 100%, 98.4%; C. glabrata 100%, 100%; C. parapsilosis 100%, 93.3%; C. tropicalis 100%, 97.3%), but lower correct identification rates for other Candida species (91.7 and 87.5%, respectively). In conclusion, the identification performance of the oligonucleotide array is comparable to that of VITEK MS, and can serve as a supplemental tool for the identification of Candida species.
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Affiliation(s)
- Ming-Chi Li
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Center for Infection Control, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Tsung C Chang
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Hung-Mo Chen
- Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chi-Jung Wu
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Tainan, Taiwan
| | - Shu-Li Su
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Susan S-J Lee
- Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan.,Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Po-Lin Chen
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Center for Infection Control, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Department of Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Nan-Yao Lee
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Center for Infection Control, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Department of Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ching-Chi Lee
- Department of Internal Medicine, Madou Sin-Lau Hospital, Tainan, Taiwan
| | - Chia-Wen Li
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Center for Infection Control, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ling-Shan Syue
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Center for Infection Control, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Wen-Chien Ko
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Center for Infection Control, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Department of Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
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77
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Borges FM, de Paula TO, Sarmiento MRA, de Oliveira MG, Pereira MLM, Toledo IV, Nascimento TC, Ferreira-Machado AB, Silva VL, Diniz CG. Fungal Diversity of Human Gut Microbiota Among Eutrophic, Overweight, and Obese Individuals Based on Aerobic Culture-Dependent Approach. Curr Microbiol 2018; 75:726-735. [PMID: 29368026 DOI: 10.1007/s00284-018-1438-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 01/16/2018] [Indexed: 12/14/2022]
Abstract
Fungi have a complex role in the intestinal tract, influencing health and disease, with dysbiosis contributing to obesity. Our objectives were to investigate fungal diversity in human gut microbiota among eutrophic, overweight, and obese. Epidemiological and nutritional information were collected from adult individuals, as well as stool samples processed for selective fungi isolation and identification by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (yeasts) or microculture (filamentous fungi). Further 18S rDNA sequencing was performed to confirm identification. The mean count of fungi was 241 CFU/g of feces. Differences in the population level of the filamentous fungi were observed within eutrophic and obese groups. Overall, 34 genera were identified. The predominant phylum was Ascomycota with 20 different genera, followed by Basidiomycota and Zygomycota. As for Ascomycota, the most prevalent species were Paecilomyces sp., Penicillium sp., Candida sp., Aspergillus sp., Fonsecaea sp., and Geotrichum sp. (76.39, 65.28, 59.72, 58.33, 12.50, and 9.72%, respectively). As for Basidiomycota, Trichosporon sp. and Rhodotorula sp. were the most prevalent (30.56 and 15.28%, respectively), and for Zygomycota, Rhizopus sp. and Mucor sp. were the most numerous (15.28 and 9.72%, respectively). As expected there is a mycobiota shift towards obesity, with slightly higher diversity associated to eutrophic individuals. This mycobiota shift seems also to be related to the nutritional behavior of the individuals, as observed that the macronutrients intake may be positively related to the different fungi occurrences. Other studies are needed to better understand relationships between mycobiota and obesity, which could be used in future obesity treatments.
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Affiliation(s)
- Francis M Borges
- Department of Parasitology, Microbiology and Immunology, Institute of Biological Sciences, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, 36036-900, Brazil
| | - Thaís O de Paula
- Department of Parasitology, Microbiology and Immunology, Institute of Biological Sciences, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, 36036-900, Brazil
| | - Marjorie R A Sarmiento
- Department of Parasitology, Microbiology and Immunology, Institute of Biological Sciences, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, 36036-900, Brazil
| | - Maycon G de Oliveira
- Department of Parasitology, Microbiology and Immunology, Institute of Biological Sciences, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, 36036-900, Brazil
| | - Maria L M Pereira
- Department of Parasitology, Microbiology and Immunology, Institute of Biological Sciences, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, 36036-900, Brazil
| | - Isabela V Toledo
- Department of Parasitology, Microbiology and Immunology, Institute of Biological Sciences, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, 36036-900, Brazil
| | - Thiago C Nascimento
- Department of Parasitology, Microbiology and Immunology, Institute of Biological Sciences, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, 36036-900, Brazil
| | - Alessandra B Ferreira-Machado
- Department of Parasitology, Microbiology and Immunology, Institute of Biological Sciences, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, 36036-900, Brazil
| | - Vânia L Silva
- Department of Parasitology, Microbiology and Immunology, Institute of Biological Sciences, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, 36036-900, Brazil
| | - Cláudio G Diniz
- Department of Parasitology, Microbiology and Immunology, Institute of Biological Sciences, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, 36036-900, Brazil.
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78
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Aslani N, Janbabaei G, Abastabar M, Meis JF, Babaeian M, Khodavaisy S, Boekhout T, Badali H. Identification of uncommon oral yeasts from cancer patients by MALDI-TOF mass spectrometry. BMC Infect Dis 2018; 18:24. [PMID: 29310582 PMCID: PMC5759378 DOI: 10.1186/s12879-017-2916-5] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 12/13/2017] [Indexed: 11/29/2022] Open
Abstract
Background Opportunistic infections due to Candida species occur frequently in cancer patients because of their inherent immunosuppression. The aim of the present study was to investigate the epidemiology of yeast species from the oral cavity of patients during treatment for oncological and haematological malignancies. Methods MALDI-TOF was performed to identify yeasts isolated from the oral cavity of 350 cancer patients. Moreover, antifungal susceptibility testing was performed in according to CLSI guidelines (M27-A3). Results Among 162 yeasts and yeast-like fungi isolated from the oral cavity of cancer patients, Candida albicans was the most common species (50.6%), followed by Candida glabrata (24.7%), Pichia kudriavzevii (Candida krusei (9.9%)), Candida tropicalis (4.3%), Candida dubliniensis (3.7%), Kluyveromyces marxianus (Candida kefyr (3.7%)) and Candida parapsilosis (1%). In addition, uncommon yeast species i.e., Saprochaete capitata, Saccharomyces cerevisiae, Clavispora lusitaniae (C. lusitaniae) and Pichia kluyveri (C. eremophila) were recovered from oral lesions. Oral colonization by C. albicans, non-albicans Candida species and uncommon yeasts were as follow; 55%, 44% and 1%, whereas oral infection due to C. albicans was 33.3%, non-albicans Candida species 60.6%, and uncommon yeasts 6.1%. Poor oral hygiene and xerostomia were identified as independent risk factors associated with oral yeast colonization. The overall resistance to fluconazole was 11.7% (19/162). Low MIC values were observed for anidulafungin for all Candida and uncommon yeast species. Conclusions This current study provides insight into the prevalence and susceptibility profiles of Candida species, including emerging Candida species and uncommon yeasts, isolated from the oral cavity of Iranian cancer patients. The incidence of oral candidiasis was higher amongst patients with hematological malignancies. The majority of oral infections were caused by non-albicans Candida species which were often more resistant to anti-fungal agents. Our findings suggest that anidulafungin should be used as antifungal of choice for prophylaxis in clinically high-risk patients with documented oral colonization or infection.
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Affiliation(s)
- Narges Aslani
- Student Research Committee, Mazandaran University of Medical Sciences, Sari, Iran.,Department of Medical Mycology and Parasitology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Ghasem Janbabaei
- Gastrointestinal Cancer Research Center, Mazandaran University of Medical Sciences, Sari, Iran
| | - Mahdi Abastabar
- Department of Medical Mycology and Parasitology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Jacques F Meis
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital (CWZ), Nijmegen, The Netherlands.,Center of Expertise in Mycology Radboudumc/CWZ, Nijmegen, The Netherlands
| | - Mahasti Babaeian
- Gastrointestinal Cancer Research Center, Mazandaran University of Medical Sciences, Sari, Iran
| | - Sadegh Khodavaisy
- Department of Medical Mycology and Parasitology, Tehran University of Medical Sciences, Tehran, Iran
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Hamid Badali
- Department of Medical Mycology and Parasitology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran. .,Invasive Fungi Research Center (IFRC), School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran.
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Shokohi T, Aslani N, Ahangarkani F, Meyabadi MF, Hagen F, Meis JF, Boekhout T, Kolecka A, Badali H. Candida infanticola and Candida spencermartinsiae yeasts: Possible emerging species in cancer patients. Microb Pathog 2017; 115:353-357. [PMID: 29292174 DOI: 10.1016/j.micpath.2017.12.069] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Revised: 11/22/2017] [Accepted: 12/28/2017] [Indexed: 02/05/2023]
Abstract
Opportunistic infections due to Candida species occur frequently in intensive care settings. We investigated the prevalence of Candida species among 65 clinical specimens obtained from 200 cancer patients by phenotypic and molecular (ITS sequencing and AFLP) methods. Among the 65 yeast isolates, Candida albicans was the most commonly isolated species (n = 34, 52.3%), whereas other Candida species comprised 47.7% (n = 31) and consisted of Candida glabrata (n = 14, 21.5%), Candida tropicalis (n = 5, 7.7%) and uncommon Candida species (n = 12, 18.5%) such as Candida pelliculosa (n = 3, 4.6%), Pichia kudriavzevii (= Candida krusei, n = 2, 3.1%), Candida orthopsilosis (n = 2, 3.1%), Candida parapsilosis (n = 1, 1.5%), Candida infanticola (n = 2, 3.1%), Candida spencermartinsiae (n = 1, 1.5%), and Kluyveromyces marxianus (=Candida kefyr, n = 1, 1.5%). Candida infanticola and Candida spencermartinsiae were recovered from oral lesions of cancer patients. Matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) easily confirmed these isolates as less common Candida isolates (4.6%). The in vitro antifungal susceptibilities of C. spencermartinsiae and the two strains of C. infanticola were determined according to CLSI guidelines (M27-A3). MIC results among these isolates showed they were susceptible to isavuconazole, posaconazole and voriconazole, however, fluconazole and caspofungin had high MIC values. These Candida species that may occur more commonly in infections remain unnoticed using commonly used phenotypical methods in routine microbiology laboratories. MALDI-TOF MS proved to be a more fast and robust diagnostic technique for identification of the yeasts isolated from different clinical specimens of cancer patients.
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Affiliation(s)
- Tahereh Shokohi
- Department of Medical Mycology and Parasitology/Invasive Fungi Research Center (IFRC), School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Narges Aslani
- Department of Medical Mycology and Parasitology/Invasive Fungi Research Center (IFRC), School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Fatemeh Ahangarkani
- Department of Medical Mycology and Parasitology/Invasive Fungi Research Center (IFRC), School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran; Student Research Committee, Mazandaran University of Medical Sciences, Sari, Iran
| | - Masoumeh Fatahi Meyabadi
- Department of Medical Mycology and Parasitology/Invasive Fungi Research Center (IFRC), School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Ferry Hagen
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands; Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital (CWZ), and Center of Expertise in Mycology Radboudumc/CWZ, Nijmegen, The Netherlands
| | - Jacques F Meis
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital (CWZ), and Center of Expertise in Mycology Radboudumc/CWZ, Nijmegen, The Netherlands
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands; Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands; Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Anna Kolecka
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Hamid Badali
- Department of Medical Mycology and Parasitology/Invasive Fungi Research Center (IFRC), School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran.
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80
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Bulane A, Hoosen A. Use of matrix-assisted laser desorption/ionisation-time of flight mass spectrometry analyser in a diagnostic microbiology laboratory in a developing country. Afr J Lab Med 2017; 6:598. [PMID: 29435422 PMCID: PMC5803516 DOI: 10.4102/ajlm.v6i1.598] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 06/30/2017] [Indexed: 01/10/2023] Open
Abstract
Background Rapid and accurate identification of pathogens is of utmost importance for management of patients. Current identification relies on conventional phenotypic methods which are time consuming. Matrix-assisted laser desorption/ionisation-time of flight mass spectrometry (MALDI-TOF MS) is based on proteomic profiling and allows for rapid identification of pathogens. Objective We compared MALDI-TOF MS against two commercial systems, MicroScan Walkaway and VITEK 2 MS. Methods Over a three-month period from July 2013 to September 2013, a total of 227 bacteria and yeasts were collected from an academic microbiology laboratory (N = 121; 87 Gram-negatives, seven Gram-positives, 27 yeasts) and other laboratories (N = 106; 35 Gram-negatives, 34 Gram-positives, 37 yeasts). Sixty-five positive blood cultures were initially processed with Bruker Sepsityper kit for direct identification. Results From the 65 blood culture bottles, four grew more than one bacterial pathogen and MALDI-TOF MS identified only one isolate. The blood cultures yielded 21 Gram-negatives, 43 Gram-positives and one Candida. There were 21 Escherirchia coli isolates which were reported by the MALDI-TOF MS as E. coli/Shigella. Of the total 292 isolates, discrepant results were found for one bacterial and three yeast isolates. Discrepant results were resolved by testing with the API system with MALDI-TOF MS showing 100% correlation. Conclusion The MALDI-TOF MS proved to be very useful for rapid and reliable identification of bacteria and yeasts directly from blood cultures and after culture of other specimens. The difference in time to identification was significant for all isolates. However, for positive blood cultures with minimal sample preparation time there was a massive difference in turn-around time with great appreciation by clinicians.
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Affiliation(s)
- Atang Bulane
- Department of Medical Microbiology & Virology, University of the Free State, Bloemfontein, South Africa
| | - Anwar Hoosen
- Department of Medical Microbiology & Virology, University of the Free State, Bloemfontein, South Africa
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81
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Alizadeh M, Kolecka A, Boekhout T, Zarrinfar H, Ghanbari Nahzag MA, Badiee P, Rezaei-Matehkolaei A, Fata A, Dolatabadi S, Najafzadeh MJ. Identification of Candida species isolated from vulvovaginitis using matrix assisted laser desorption ionization-time of flight mass spectrometry. Curr Med Mycol 2017; 3:21-25. [PMID: 29707675 PMCID: PMC5917097 DOI: 10.29252/cmm.3.4.21] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Background and Purpose: Vulvovaginal candidiasis (VVC) is a common problem in women. The purpose of this study was to identify Candida isolates by matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) from women with vulvovaginitis that were referred to Ghaem Hospital, Mashhad, Iran. Materials and Methods: This study was conducted on 65 clinical samples isolated from women that were referred to Ghaem Hospital. All specimens were identified using phenotyping techniques, such as microscopy and culture on Sabouraud dextrose agar and corn meal agar. In addition, all isolates were processed for MALDI-TOF MS identification. Results: Out of the 65 analyzed isolates, 61 (94%) samples were recognized by MALDI-TOF MS. However, the remaining four isolates (6%) had no reliable identification. According to the results, C. albicans (58.5%) was the most frequently isolated species, followed by C. tropicalis (16.9%), C. glabrata (7.7%), C. parapsilosis (7.7%), and guilliermondii (3.1%). Conclusion: As the findings indicated, MALDI TOF MS was successful in the identification of clinical Candida species. C. albicans was identified as the most common Candida species isolated from the women with VVC. Moreover, C. tropicalis was the most common species among the non-albicans Candida species.
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Affiliation(s)
- Majid Alizadeh
- Department of Parasitology and Mycology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Anna Kolecka
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Hossein Zarrinfar
- Allergy Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohamad A Ghanbari Nahzag
- Department of Parasitology and Mycology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Parisa Badiee
- Alborzi Clinical Microbiology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ali Rezaei-Matehkolaei
- Department of Medical Mycology, School of Medicine, Health Research Institute, Infectious and Tropical Diseases Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Abdolmajid Fata
- Department of Parasitology and Mycology, Research Center for Cutaneous Leishmaniasis, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Somayeh Dolatabadi
- Faculty of Engineering, Sabzevar University of New Technologies, Sabzevar, Iran
| | - Mohammad J Najafzadeh
- Department of Parasitology and Mycology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Cancer Molecular Pathology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
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82
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García-Agudo L, Rodríguez-Iglesias M, Carranza-González R. Nosocomial Candiduria in the Elderly: Microbiological Diagnosis. Mycopathologia 2017; 183:591-596. [PMID: 29196922 DOI: 10.1007/s11046-017-0232-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 11/25/2017] [Indexed: 10/18/2022]
Abstract
Candiduria is associated with high morbidity, mortality, and long hospitalization, involving high costs for the healthcare system. The use of increasingly aggressive treatments has prolonged the lives of patients susceptible to candiduria, namely the immunosuppressed, the premature, and the elderly. Our objective was to evaluate the incidence of nosocomial candiduria and the implicated species in hospitalized patients aged over 80 years old from three Spanish centers during 2012 and 2013. Urine samples received from these patients were cultured and analyzed by flow cytometry in search of leukocyturia, hematuria, proteinuria, and microbial nitrate reductase activity. The isolated yeast species were identified microscopically, by germ tube formation in serum, colony morphology after subculture onto CHROMagar Candida (Becton-Dickinson, UK), assimilation of carbon compounds ID32C (bioMérieux, France), matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDITOF) (Bruker Daltonics, Germany) and, in case of inconsistency, by sequencing of the ITS regions of ribosomal DNA (ITS1-5, 8S-ITS2). Susceptibility tests were also performed. The incidence of candiduria in the elderly population was 10.3%. A total of 155 strains of yeasts were isolated. The predominant species was Candida albicans, followed by Candida glabrata and then Candida tropicalis. Several infrequent species were found; among them, the first isolate of candiduria-producing Candida pulcherrima described in the literature. Our finding should raise concerns about the elderly population, which is probably the most important risk group for candiduria in the present moment, and the emergence of unusual yeast species producing candiduria, which are resistant against the commonly used antifungal agents.
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83
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Lyden A, Lombardi L, Sire W, Li P, Simpson JC, Butler G, Lee GU. Characterization of carboxylate nanoparticle adhesion with the fungal pathogen Candida albicans. NANOSCALE 2017; 9:15911-15922. [PMID: 29019498 DOI: 10.1039/c7nr04724j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Candida albicans is the lead fungal pathogen of nosocomial bloodstream infections worldwide and has mortality rates of 43%. Nanoparticles have been identified as a means to improve medical outcomes for Candida infections, enabling sample concentration, serving as contrast agents for in vivo imaging, and delivering therapeutics. However, little is known about how nanoparticles interact with the fungal cell wall. In this report we used laser scanning confocal microscopy to examine the interaction of fluorescent polystyrene nanoparticles of specific surface chemistry and diameter with C. albicans and mutant strains deficient in various C. albicans surface proteins. Carboxylate-functionalized nanoparticles adsorbed mainly to the hyphae of wild-type C. albicans. The dissociative binding constant of the nanoparticles was ∼150, ∼30 and ∼2.5 pM for 40, 100 nm and 200 nm diameter particles, respectively. A significant reduction in particle binding was observed with a Δals3 strain compared to wild-type strains, identifying the Als3 adhesin as the main mediator of this nanoparticle adhesion. In the absence of Als3, nanoparticles bound to germ tubes and yeast cells in a pattern resembling the localization of Als1, indicating Als1 also plays a role. Nanoparticle surface charge was shown to influence binding - positively charged amine-functionalized nanoparticles failed to bind to the hyphal cell wall. Binding of carboxylate-functionalized nanoparticles was observed in the presence of serum, though interactions were reduced. These observations show that Als3 and Als1 are important targets for nanoparticle-mediated diagnostics and therapeutics, and provide direction for optimal diameter and surface characteristics of nanoparticles that bind to the fungal cell wall.
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Affiliation(s)
- Amy Lyden
- School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland.
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84
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Wine yeasts identification by MALDI-TOF MS: Optimization of the preanalytical steps and development of an extensible open-source platform for processing and analysis of an in-house MS database. Int J Food Microbiol 2017; 254:1-10. [DOI: 10.1016/j.ijfoodmicro.2017.05.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 04/07/2017] [Accepted: 05/05/2017] [Indexed: 11/19/2022]
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85
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Dupont D, Huguenin A, Tisserand E, Reiter V, Morelon E, Badet L, Villena I, Wallon M, Toubas D. Donor Derived Candida stellimalicola in a Clinical Specimen: Preservation Fluid Contamination During Pancreas Procurement. Mycopathologia 2017; 183:573-577. [PMID: 28681316 DOI: 10.1007/s11046-017-0171-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Accepted: 06/27/2017] [Indexed: 11/29/2022]
Abstract
We report here a case of possible donor-derived Candida stellimalicola infection after pancreas transplantation. Candida stellimalicola, an environmental non-filamentous yeast, was isolated from both the peritoneal fluid of the graft donor and the preservation fluid of the transplanted pancreas. Interestingly, this strain exhibited high minimum inhibitory concentrations to azoles. These results justified the use of echinocandins as therapy instead of fluconazole. This switch permitted a favorable outcome. To our knowledge, this is the first report of C. stellimalicola from clinical samples and therefore the first reported case of a possible human infection. This case report highlights the need for standardized microbiological procedures in solid organ transplant settings. Moreover, it underlines the importance of using molecular identification technique when routine techniques do not allow successful identification of the pathogen. It is of utmost importance to determine sensitivity profile, even in the absence of species-level identification, because resistance to fluconazole is not uncommon, especially in emergent species.
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Affiliation(s)
- Damien Dupont
- Institut des Agents Infectieux, Parasitologie Mycologie, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, 69004, France. .,Integrative Physiology of the Brain Arousal Systems, Centre de Recherche en Neurosciences de Lyon, INSERM U1028-CNRS UMR 5292, Faculté de Médecine, Université Claude Bernard Lyon 1, Lyon, 69000, France.
| | - Antoine Huguenin
- Laboratoire de Parasitologie Mycologie, CHU de Reims, Université Reims Champagne Ardenne, Hôpital Maison Blanche, Reims, 51092, France
| | - Elodie Tisserand
- Pediatric Intensive Care Unit, CHU de Reims, Université Reims Champagne Ardenne, Hôpital Maison Blanche, Reims, 51092, France
| | - Véronique Reiter
- PMO, CHU de Reims, Université Reims Champagne Ardenne, Hôpital Maison Blanche, Reims, 51092, France
| | - Emmanuel Morelon
- Service de Transplantation, Néphrologie et Immunologie, Hôpital Edouard Herriot, Hospices Civils de Lyon, Lyon, 69003, France
| | - Lionel Badet
- Service d'Urologie et Transplantation, Hôpital Edouard Herriot, Hospices Civils de Lyon, Lyon, 69003, France
| | - Isabelle Villena
- Laboratoire de Parasitologie Mycologie, CHU de Reims, Université Reims Champagne Ardenne, Hôpital Maison Blanche, Reims, 51092, France.,Laboratoire de Parasitologie-Mycologie, EA3800, SFR Cap-Santé, UFR de Médecine, Université de Reims Champagne-Ardenne, Reims, 51100, France
| | - Martine Wallon
- Institut des Agents Infectieux, Parasitologie Mycologie, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, 69004, France.,Integrative Physiology of the Brain Arousal Systems, Centre de Recherche en Neurosciences de Lyon, INSERM U1028-CNRS UMR 5292, Faculté de Médecine, Université Claude Bernard Lyon 1, Lyon, 69000, France
| | - Dominique Toubas
- Laboratoire de Parasitologie Mycologie, CHU de Reims, Université Reims Champagne Ardenne, Hôpital Maison Blanche, Reims, 51092, France.,MéDIAN-Biophotonique et Technologies pour la Santé, CNRS UMR 7369 MEDyC, UFR de Médecine, SFR CAP Santé, Université de Reims Champagne-Ardenne, Reims, 51100, France
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86
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Yeasts. Microbiol Spectr 2017; 4. [PMID: 27726781 DOI: 10.1128/microbiolspec.dmih2-0030-2016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Yeasts are unicellular organisms that reproduce mostly by budding and less often by fission. Most medically important yeasts originate from Ascomycota or Basidiomycota. Here, we review taxonomy, epidemiology, disease spectrum, antifungal drug susceptibility patterns of medically important yeast, laboratory diagnosis, and diagnostic strategies.
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87
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Volatile organic compounds in the breath of oral candidiasis patients: a pilot study. Clin Oral Investig 2017; 22:721-731. [DOI: 10.1007/s00784-017-2147-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 06/01/2017] [Indexed: 10/19/2022]
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88
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Turvey ME, Weiland F, Keller EJ, Hoffmann P. The changing face of microbial quality control practices in the brewing industry: Introducing mass spectrometry proteomic fingerprinting for microbial identification. JOURNAL OF THE INSTITUTE OF BREWING 2017. [DOI: 10.1002/jib.428] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- M. E. Turvey
- Adelaide Proteomics Centre; The University of Adelaide; Australia
- Institute of Photonics and Advanced Sensing; Australia
- Singapore-MIT Alliance for Research and Technology Centre; Singapore
| | - F. Weiland
- Adelaide Proteomics Centre; The University of Adelaide; Australia
- Institute of Photonics and Advanced Sensing; Australia
| | - E. J. Keller
- Adelaide Proteomics Centre; The University of Adelaide; Australia
- Institute of Photonics and Advanced Sensing; Australia
| | - P. Hoffmann
- Adelaide Proteomics Centre; The University of Adelaide; Australia
- Institute of Photonics and Advanced Sensing; Australia
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89
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Hendrickx M. MALDI-TOF MS and Filamentous Fungal Identification: A Success Story? CURRENT FUNGAL INFECTION REPORTS 2017. [DOI: 10.1007/s12281-017-0277-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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90
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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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91
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Triest D, Hendrickx M, Piérard D, Piarroux R, Fraselle S, De Cremer K. Proof-of-concept study of a new LC-ESI-MS/MS-based assay to identify Aspergillus spp. in artificially mixed samples using species/genus-specific proteotypic peptides. Mycol Prog 2017. [DOI: 10.1007/s11557-017-1273-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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92
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Lopes RB, Faria M, Souza DA, Bloch C, Silva LP, Humber RA. MALDI-TOF mass spectrometry applied to identifying species of insect-pathogenic fungi from the Metarhizium anisopliae complex. Mycologia 2017; 106:865-78. [DOI: 10.3852/13-401] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | | | | | | | - Luciano P. Silva
- Embrapa Genetic Resources and Biotechnology, Brasilia DF, CP 02372, 70770-917, Brazil
| | - Richard A. Humber
- USDA-ARS Biological Integrated Pest Management Research, Robert W. Holley Center for Agriculture and Health, 538 Tower Road, Ithaca, New York 14853
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93
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Siller-Ruiz M, Hernández-Egido S, Sánchez-Juanes F, González-Buitrago JM, Muñoz-Bellido JL. Fast methods of fungal and bacterial identification. MALDI-TOF mass spectrometry, chromogenic media. Enferm Infecc Microbiol Clin 2017; 35:303-313. [PMID: 28108122 DOI: 10.1016/j.eimc.2016.12.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 12/20/2016] [Indexed: 11/16/2022]
Abstract
MALDI-TOF mass spectrometry is now a routine resource in Clinical Microbiology, because of its speed and reliability in the identification of microorganisms. Its performance in the identification of bacteria and yeasts is perfectly contrasted. The identification of mycobacteria and moulds is more complex, due to the heterogeneity of spectra within each species. The methodology is somewhat more complex, and expanding the size of species libraries, and the number of spectra of each species, will be crucial to achieve greater efficiency. Direct identification from blood cultures has been implemented, since its contribution to the management of severe patients is evident, but its application to other samples is more complex. Chromogenic media have also contributed to the rapid diagnosis in both bacteria and yeast, since they accelerate the diagnosis, facilitate the detection of mixed cultures and allow rapid diagnosis of resistant species.
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Affiliation(s)
- María Siller-Ruiz
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Complejo Asistencial Universitario de Salamanca, Universidad de Salamanca, CSIC, Salamanca, España
| | - Sara Hernández-Egido
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Complejo Asistencial Universitario de Salamanca, Universidad de Salamanca, CSIC, Salamanca, España
| | - Fernando Sánchez-Juanes
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Complejo Asistencial Universitario de Salamanca, Universidad de Salamanca, CSIC, Salamanca, España
| | - José Manuel González-Buitrago
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Complejo Asistencial Universitario de Salamanca, Universidad de Salamanca, CSIC, Salamanca, España; Servicio de Bioquímica Clínica, Complejo Asistencial Universitario de Salamanca, Salamanca, España; Departamento de Bioquímica y Biología Molecular, Universidad de Salamanca, Salamanca, España
| | - Juan Luis Muñoz-Bellido
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Complejo Asistencial Universitario de Salamanca, Universidad de Salamanca, CSIC, Salamanca, España; Servicio de Microbiología, Complejo Asistencial Universitario de Salamanca, Salamanca, España; Departamento de Ciencias Biomédicas y del Diagnóstico, Universidad de Salamanca, Salamanca, España.
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94
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Miniaturized Digestion and Extraction of Surface Proteins from Candida albicans following Treatment with Histatin 5 for Mass Spectrometry Analysis. INTERNATIONAL JOURNAL OF PROTEOMICS 2017; 2016:9812829. [PMID: 28044106 PMCID: PMC5156812 DOI: 10.1155/2016/9812829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 10/25/2016] [Accepted: 10/31/2016] [Indexed: 11/17/2022]
Abstract
A common approach to isolate surface proteins from fungal and bacterial cells is to perform a proteolytic cleavage of proteins on the surface of intact cells suspended in solution. This paper describes miniaturization of this technique, in which cells are adhered on glass surfaces, and all sample treatments are conducted at μL volumes. Specifically, Candida albicans cells were attached onto HSA-coated glass slides. By depositing the appropriate reagent solutions on the adhered cells, we successfully performed cell washing, treatment with antifugal peptide, Histatin 5, and a proteolysis on intact cells with trypsin. The resulting peptides were subsequently analysed by mass spectrometry. In general, the data obtained was similar to that collected with suspended cells in much larger sample volumes. However, our miniaturized workflow offers the benefit of greatly reducing the consumption of cells and reagents.
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95
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Detection and Management of Fungal Respiratory Infection by Using Molecular Markers. Fungal Biol 2017. [DOI: 10.1007/978-3-319-34106-4_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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96
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Himmelreich U, Sorrell TC, Daniel HM. Nuclear Magnetic Resonance Spectroscopy-Based Identification of Yeast. Methods Mol Biol 2017; 1508:289-304. [PMID: 27837512 DOI: 10.1007/978-1-4939-6515-1_17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Rapid and robust high-throughput identification of environmental, industrial, or clinical yeast isolates is important whenever relatively large numbers of samples need to be processed in a cost-efficient way. Nuclear magnetic resonance (NMR) spectroscopy generates complex data based on metabolite profiles, chemical composition and possibly on medium consumption, which can not only be used for the assessment of metabolic pathways but also for accurate identification of yeast down to the subspecies level. Initial results on NMR based yeast identification where comparable with conventional and DNA-based identification. Potential advantages of NMR spectroscopy in mycological laboratories include not only accurate identification but also the potential of automated sample delivery, automated analysis using computer-based methods, rapid turnaround time, high throughput, and low running costs.We describe here the sample preparation, data acquisition and analysis for NMR-based yeast identification. In addition, a roadmap for the development of classification strategies is given that will result in the acquisition of a database and analysis algorithms for yeast identification in different environments.
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Affiliation(s)
- Uwe Himmelreich
- Biomedical MRI Unit/MoSAIC, Department of Imaging and Pathology, Faculty of Medicine, University of Leuven, Herestraat 49, O&N 1, Box 505, Leuven, 3000, Belgium.
| | - Tania C Sorrell
- Westmead Millennium Institute, Centre for Infectious Diseases and Microbiology, University of Sydney, Sydney, NSW, Australia.,Department of Infectious Diseases, Westmead Hospital, Westmead, NSW, Australia
| | - Heide-Marie Daniel
- Laboratory of Mycology, Applied Microbiology, Earth and Life Institute, Mycothèque de l'Université catholique de Louvain (BCCM/MUCL), Université catholique de Lovain, Louvain-la-Neuve, Belgium
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97
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Cost Analysis of Implementing Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry Plus Real-Time Antimicrobial Stewardship Intervention for Bloodstream Infections. J Clin Microbiol 2016; 55:60-67. [PMID: 27795335 DOI: 10.1128/jcm.01452-16] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 10/06/2016] [Indexed: 11/20/2022] Open
Abstract
Studies evaluating rapid diagnostic testing plus stewardship intervention have consistently demonstrated improved clinical outcomes for patients with bloodstream infections. However, the cost of implementing new rapid diagnostic testing can be significant, and such testing usually does not generate additional revenue. There are minimal data evaluating the impact of adding matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) for rapid organism identification and dedicating pharmacy stewardship personnel time on the total hospital costs. A cost analysis was performed utilizing patient data generated from the hospital cost accounting system and included additional costs of MALDI-TOF equipment, supplies and personnel, and dedicated pharmacist time for blood culture review and of making interventions to antimicrobial therapy. The cost analysis was performed from a hospital perspective for 3-month blocks before and after implementation of MALDI-TOF plus stewardship intervention. A total of 480 patients with bloodstream infections were included in the analysis: 247 in the preintervention group and 233 in the intervention group. Thirty-day mortality was significantly improved in the intervention group (12% versus 21%, P < 0.01), and the mean length of stay was reduced, although the difference was not statistically significant (13.0 ± 16.5 days versus 14.2 ± 16.7 days, P = 0.44). The total hospital cost per bloodstream infection was lower in the intervention group ($42,580 versus $45,019). Intensive care unit cost per bloodstream infection accounted for the largest share of the total costs in each group and was also lower in the intervention group ($10,833 versus $13,727). Implementing MALDI-TOF plus stewardship review and intervention decreased mortality for patients with bloodstream infections. Despite the additional costs of implementing MALDI-TOF and of dedicating pharmacy stewardship personnel time to interventions, the total hospital costs decreased by $2,439 per bloodstream infection, for an approximate annual cost savings of $2.34 million.
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98
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Lasch P, Grunow R, Antonation K, Weller SA, Jacob D. Inactivation techniques for MALDI-TOF MS analysis of highly pathogenic bacteria – A critical review. Trends Analyt Chem 2016. [DOI: 10.1016/j.trac.2016.04.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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99
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Hirota K, Yumoto H, Sapaar B, Matsuo T, Ichikawa T, Miyake Y. Pathogenic factors in Candida biofilm-related infectious diseases. J Appl Microbiol 2016; 122:321-330. [PMID: 27770500 DOI: 10.1111/jam.13330] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 10/11/2016] [Accepted: 10/15/2016] [Indexed: 01/07/2023]
Abstract
Candida albicans is a commonly found member of the human microflora and is a major human opportunistic fungal pathogen. A perturbation of the microbiome can lead to infectious diseases caused by various micro-organisms, including C. albicans. Moreover, the interactions between C. albicans and bacteria are considered to play critical roles in human health. The major biological feature of C. albicans, which impacts human health, resides in its ability to form biofilms. In particular, the extracellular matrix (ECM) of Candida biofilm plays a multifaceted role and therefore may be considered as a highly attractive target to combat biofilm-related infectious diseases. In addition, extracellular DNA (eDNA) also plays a crucial role in Candida biofilm formation and its structural integrity and induces the morphological transition from yeast to the hyphal growth form during C. albicans biofilm development. This review focuses on pathogenic factors such as eDNA in Candida biofilm formation and its ECM production and provides meaningful information for future studies to develop a novel strategy to battle infectious diseases elicited by Candida-formed biofilm.
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Affiliation(s)
- K Hirota
- Department of Oral Microbiology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - H Yumoto
- Department of Conservative Dentistry, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - B Sapaar
- Department of Oral and Maxillofacial Prosthodontics, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - T Matsuo
- Department of Conservative Dentistry, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - T Ichikawa
- Department of Oral and Maxillofacial Prosthodontics, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Y Miyake
- Department of Oral Microbiology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
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100
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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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