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  • 1
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    Online Resource
    Evaluation of Microsatellite Typing, ITS Sequencing, AFLP Fingerprinting, MALDI-TOF MS, and Fourier-Transform Infrared Spectroscopy Analysis of Candida auris
    MDPI AG ; 2020
    In:  Journal of Fungi Vol. 6, No. 3 ( 2020-08-25), p. 146-
    Details
    In: Journal of Fungi, MDPI AG, Vol. 6, No. 3 ( 2020-08-25), p. 146-
    Abstract: Candida auris is an emerging opportunistic yeast species causing nosocomial outbreaks at a global scale. A few studies have focused on the C. auris genotypic structure. Here, we compared five epidemiological typing tools using a set of 96 C. auris isolates from 14 geographical areas. Isolates were analyzed by microsatellite typing, ITS sequencing, amplified fragment length polymorphism (AFLP) fingerprint analysis, matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS), and Fourier-transform infrared (FTIR) spectroscopy methods. Microsatellite typing grouped the isolates into four main clusters, corresponding to the four known clades in concordance with whole genome sequencing studies. The other investigated typing tools showed poor performance compared with microsatellite typing. A comparison between the five methods showed the highest agreement between microsatellite typing and ITS sequencing with 45% similarity, followed by microsatellite typing and the FTIR method with 33% similarity. The lowest agreement was observed between FTIR spectroscopy, MALDI-TOF MS, and ITS sequencing. This study indicates that microsatellite typing is the tool of choice for C. auris outbreak investigations. Additionally, FTIR spectroscopy requires further optimization and evaluation before it can be used as an epidemiological typing method, comparable with microsatellite typing, as a rapid method for tracing nosocomial fungal outbreaks.
    Type of Medium: Online Resource
    ISSN: 2309-608X
    URL: Article
    DOI: 10.3390/jof6030146
    Language: English
    Publisher: MDPI AG
    Publication Date: 2020
    detail.hit.zdb_id: 2784229-0
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  • 2
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    Rapid identification of Burkholderia mallei and Burkholderia pseudomalleiby intact cell Matrix-assisted Laser Desorption/Ionisation mass spectrometric typing
    Springer Science and Business Media LLC ; 2012
    In:  BMC Microbiology Vol. 12, No. 1 ( 2012-12)
    Details
    In: BMC Microbiology, Springer Science and Business Media LLC, Vol. 12, No. 1 ( 2012-12)
    Abstract: Burkholderia (B.) pseudomallei and B. mallei are genetically closely related species. B. pseudomallei causes melioidosis in humans and animals, whereas B. mallei is the causative agent of glanders in equines and rarely also in humans. Both agents have been classified by the CDC as priority category B biological agents. Rapid identification is crucial, because both agents are intrinsically resistant to many antibiotics. Matrix-assisted laser desorption/ionisation mass spectrometry (MALDI-TOF MS) has the potential of rapid and reliable identification of pathogens, but is limited by the availability of a database containing validated reference spectra. The aim of this study was to evaluate the use of MALDI-TOF MS for the rapid and reliable identification and differentiation of B. pseudomallei and B. mallei and to build up a reliable reference database for both organisms. Results A collection of ten B. pseudomallei and seventeen B. mallei strains was used to generate a library of reference spectra. Samples of both species could be identified by MALDI-TOF MS, if a dedicated subset of the reference spectra library was used. In comparison with samples representing B. mallei , higher genetic diversity among B. pseudomallei was reflected in the higher average Eucledian distances between the mass spectra and a broader range of identification score values obtained with commercial software for the identification of microorganisms. The type strain of B. pseudomallei (ATCC 23343) was isolated decades ago and is outstanding in the spectrum-based dendrograms probably due to massive methylations as indicated by two intensive series of mass increments of 14 Da specifically and reproducibly found in the spectra of this strain. Conclusions Handling of pathogens under BSL 3 conditions is dangerous and cumbersome but can be minimized by inactivation of bacteria with ethanol, subsequent protein extraction under BSL 1 conditions and MALDI-TOF MS analysis being faster than nucleic amplification methods. Our spectra demonstrated a higher homogeneity in B. mallei than in B. pseudomallei isolates. As expected for closely related species, the identification process with MALDI Biotyper software (Bruker Daltonik GmbH, Bremen, Germany) requires the careful selection of spectra from reference strains. When a dedicated reference set is used and spectra of high quality are acquired, it is possible to distinguish both species unambiguously. The need for a careful curation of reference spectra databases is stressed.
    Type of Medium: Online Resource
    ISSN: 1471-2180
    URL: Article
    DOI: 10.1186/1471-2180-12-229
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2012
    detail.hit.zdb_id: 2041505-9
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  • 3
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    Improved Identification of Yeast Species Directly from Positive Blood Culture Media by Combining Sepsityper Specimen Processing and Microflex Analysis with the Matrix-Assisted Laser Desorption Ionization Biotyper System
    American Society for Microbiology ; 2011
    In:  Journal of Clinical Microbiology Vol. 49, No. 7 ( 2011-07), p. 2528-2532
    Details
    In: Journal of Clinical Microbiology, American Society for Microbiology, Vol. 49, No. 7 ( 2011-07), p. 2528-2532
    Abstract: Current methods for identification of yeast from blood cultures may take several days after these microorganisms have been observed by Gram stain smears from positive blood cultures. We explored the use of a matrix-assisted laser desorption ionization (MALDI) Biotyper system in combination with Sepsityper specimen processing and Microflex analysis for improved detection and identification of yeast species directly from positive blood culture specimens demonstrating yeast-like organisms by Gram stain. The limit of detection of yeast species in blood culture medium was determined to be 5.9 × 10 5 CFU, with intra- and interstrain coefficients of variation of 1.8 to 3.6% and 2.9%, respectively. A total of 42 yeast-containing positive blood culture specimens were processed, and the identification results were compared to those obtained by routinely used phenotypic methods. Specimens with discrepant results between the Biotyper and phenotypic methods were identified on the basis of internal transcribed spacer region sequencing. The MALDI Biotyper system correctly identified the 42 specimens to species level, including 28 (66.7%) Candida albicans , 8 (19.0%) Candida parapsilosis , and 5 (11.9%) Candida tropicalis isolates and 1 (2.4%) Cryptococcus neoformans isolate. The entire procedure, from specimen extraction to final result reporting, can be completed within 1 h. Our data indicated that the Sepsityper specimen processing and Microflex analysis by the MALDI Biotyper system provide a rapid and reliable tool for yeast species identification directly from positive blood culture media.
    Type of Medium: Online Resource
    ISSN: 0095-1137 , 1098-660X
    URL: Article
    DOI: 10.1128/JCM.00339-11
    RVK:
    XA 10000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2011
    detail.hit.zdb_id: 1498353-9
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  • 4
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    MALDI‐TOF MS: an upcoming tool for rapid detection of antibiotic resistance in microorganisms
    Wiley ; 2013
    In:  PROTEOMICS – Clinical Applications Vol. 7, No. 11-12 ( 2013-12), p. 767-778
    Details
    In: PROTEOMICS – Clinical Applications, Wiley, Vol. 7, No. 11-12 ( 2013-12), p. 767-778
    Abstract: MALDI‐TOF MS profiling for microorganism detection has already been demonstrated in the 1990s, but has evolved to the first‐line identification method in many laboratories just during the past five years. While this application of MALDI‐TOF MS has proven its broad applicability, accuracy, robustness, and cost‐effectiveness it is of particular interest to expand the capabilities of the mass spectrometric platform. Resistance detection is the most desirable further application of MALDI‐TOF MS in microbiology, but maybe also the most challenging. Different approaches have been published regarding diverse antibiotic drugs and distinct microorganism classes. The current review shall give an overview about the developments of the recent years and their potential to get transformed in clinical useful assays in the future.
    Type of Medium: Online Resource
    ISSN: 1862-8346 , 1862-8354
    URL: Issue
    URL: Article
    DOI: 10.1002/prca.v7.11-12
    DOI: 10.1002/prca.201300042
    Language: English
    Publisher: Wiley
    Publication Date: 2013
    detail.hit.zdb_id: 2317130-3
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  • 5
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    Fast and reliable MALDI-TOF MS–based microorganism identification
    Springer Science and Business Media LLC ; 2006
    In:  Nature Methods Vol. 3, No. 4 ( 2006-4), p. i-ii
    Details
    In: Nature Methods, Springer Science and Business Media LLC, Vol. 3, No. 4 ( 2006-4), p. i-ii
    Type of Medium: Online Resource
    ISSN: 1548-7091 , 1548-7105
    URL: Article
    DOI: 10.1038/nmeth870
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2006
    detail.hit.zdb_id: 2163081-1
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  • 6
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    A polyphasic approach for the differentiation of environmental Vibrio isolates from temperate waters : Vibrio parahaemolyticus in the North Sea
    Oxford University Press (OUP) ; 2011
    In:  FEMS Microbiology Ecology Vol. 75, No. 1 ( 2011-01), p. 145-162
    Details
    In: FEMS Microbiology Ecology, Oxford University Press (OUP), Vol. 75, No. 1 ( 2011-01), p. 145-162
    Type of Medium: Online Resource
    ISSN: 0168-6496
    URL: Issue
    URL: Article
    DOI: 10.1111/fem.2010.75.issue-1
    DOI: 10.1111/j.1574-6941.2010.00998.x
    RVK:
    WA 15000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2011
    detail.hit.zdb_id: 1501712-6
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  • 7
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    Nonculture‐based identification of bacteria in milk by protein fingerprinting
    Wiley ; 2012
    In:  PROTEOMICS Vol. 12, No. 17 ( 2012-08), p. 2739-2745
    Details
    In: PROTEOMICS, Wiley, Vol. 12, No. 17 ( 2012-08), p. 2739-2745
    Abstract: Traditional methods for bacterial identification include Gram staining, culturing, and biochemical assays for phenotypic characterization of the causative organism. These methods can be time‐consuming because they require in vitro cultivation of the microorganisms. Recently, however, it has become possible to obtain chemical profiles for lipids, peptides, and proteins that are present in an intact organism, particularly now that new developments have been made for the efficient ionization of biomolecules. MS has therefore become the state‐of‐the‐art technology for microorganism identification in microbiological clinical diagnosis. Here, we introduce an innovative sample preparation method for nonculture‐based identification of bacteria in milk. The technique detects characteristic profiles of intact proteins (mostly ribosomal) with the recently introduced MALDI S epsityper TM K it followed by MALDI ‐ MS . In combination with a dedicated bioinformatics software tool for databank matching, the method allows for almost real‐time and reliable genus and species identification. We demonstrate the sensitivity of this protocol by experimentally contaminating pasteurized and homogenized whole milk samples with bacterial loads of 10 3 –10 8 colony‐forming units (cfu) of laboratory strains of E scherichia coli , E nterococcus faecalis , and S taphylococcus aureus . For milk samples contaminated with a lower bacterial load (10 4 cfu mL −1 ), bacterial identification could be performed after initial incubation at 37°C for 4 h. The sensitivity of the method may be influenced by the bacterial species and count, and therefore, it must be optimized for the specific application. The proposed use of protein markers for nonculture‐based bacterial identification allows for high‐throughput detection of pathogens present in milk samples. This method could therefore be useful in the veterinary practice and in the dairy industry, such as for the diagnosis of subclinical mastitis and for the sanitary monitoring of raw and processed milk products.
    Type of Medium: Online Resource
    ISSN: 1615-9853 , 1615-9861
    URL: Issue
    URL: Article
    DOI: 10.1002/pmic.v12.17
    DOI: 10.1002/pmic.201200053
    Language: English
    Publisher: Wiley
    Publication Date: 2012
    detail.hit.zdb_id: 2037674-1
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  • 8
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    Rapid Identification and Typing of Listeria Species by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry
    American Society for Microbiology ; 2008
    In:  Applied and Environmental Microbiology Vol. 74, No. 17 ( 2008-09), p. 5402-5407
    Details
    In: Applied and Environmental Microbiology, American Society for Microbiology, Vol. 74, No. 17 ( 2008-09), p. 5402-5407
    Abstract: Listeria monocytogenes is a food-borne pathogen that is the causative agent of human listeriosis, an opportunistic infection that primarily infects pregnant women and immunologically compromised individuals. Rapid, accurate discrimination between Listeria strains is essential for appropriate therapeutic management and timely intervention for infection control. A rapid method involving matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) that shows promise for identification of Listeria species and typing and even allows for differentiation at the level of clonal lineages among pathogenic strains of L. monocytogenes is presented. A total of 146 strains of different Listeria species and serotypes as well as clinical isolates were analyzed. The method was compared with the pulsed-field gel electrophoresis analysis of 48 Listeria strains comprising L. monocytogenes strains isolated from food-borne epidemics and sporadic cases, isolates representing different serotypes, and a number of Listeria strains whose genomes have been completely sequenced. Following a short inactivation/extraction procedure, cell material from a bacterial colony was deposited on a sample target, dried, overlaid with a matrix necessary for the MALDI process, and analyzed by MALDI-TOF MS. This technique examines the chemistry of major proteins, yielding profile spectra consisting of a series of peaks, a characteristic “fingerprint” mainly derived from ribosomal proteins. Specimens can be prepared in a few minutes from plate or liquid cultures, and a spectrum can be obtained within 1 minute. Mass spectra derived from Listeria isolates showed characteristic peaks, conserved at both the species and lineage levels. MALDI-TOF MS fingerprinting may have potential for Listeria identification and subtyping and may improve infection control measures.
    Type of Medium: Online Resource
    ISSN: 0099-2240 , 1098-5336
    URL: Article
    DOI: 10.1128/AEM.02689-07
    RVK:
    WA 15000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2008
    detail.hit.zdb_id: 223011-2
    detail.hit.zdb_id: 1478346-0
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  • 9
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    Application of matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry for the study of Helicobacter pylori
    Wiley ; 2010
    In:  Rapid Communications in Mass Spectrometry Vol. 24, No. 3 ( 2010-02-15), p. 328-334
    Details
    In: Rapid Communications in Mass Spectrometry, Wiley, Vol. 24, No. 3 ( 2010-02-15), p. 328-334
    Abstract: The characteristics of matrix‐assisted laser desorption/ionization time‐of‐flight (MALDI‐TOF) mass spectrometry based investigation of extremely variable bacteria such as Helicobacter pylori were studied. H. pylori possesses a very high natural variability. Accurate tools for species identification and epidemiological characterization could help the scientific community to better understand the transmission pathways and virulence mechanisms of these bacteria. Seventeen clinical as well as two laboratory strains of H. pylori were analyzed by the MALDI Biotyper method for rapid species identification. Mass spectra collected were found containing 7–13 significant peaks per sample, and only six protein signals were identical for more than half of the strains. Four of them could be assigned to ribosomal proteins RL32, RL33, RL34, and RL36. The reproducible peak with m/z 6948 was identified as a histidine‐rich metal‐binding polypeptide by tandem mass spectrometry (MS/MS). In spite of the evident protein heterogeneity of H. pylori the mass spectra collected for a particular strain under several cultivations were highly reproducible. Moreover, all clinical strains were perfectly identified as H. pylori species through comparative analysis using the MALDI Biotyper software (Bruker Daltonics, Germany) by pattern matching against a database containing mass spectra from different microbial strains (n = 3287) including H. pylori 26695 and J99. The results of this study allow the conclusion that the MALDI‐TOF direct bacterial profiling is suited for H. pylori identification and could be supported by mass spectra fragmentation of the observed polypeptide if necessary. Copyright © 2010 John Wiley & Sons, Ltd.
    Type of Medium: Online Resource
    ISSN: 0951-4198 , 1097-0231
    URL: Issue
    URL: Article
    DOI: 10.1002/rcm.v24:3
    DOI: 10.1002/rcm.4394
    Language: English
    Publisher: Wiley
    Publication Date: 2010
    detail.hit.zdb_id: 2002158-6
    detail.hit.zdb_id: 58731-X
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  • 10
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    Nomenclatural issues concerning cultured yeasts and other fungi: why it is important to avoid unneeded name changes
    Springer Science and Business Media LLC ; 2021
    In:  IMA Fungus Vol. 12, No. 1 ( 2021-12)
    Details
    In: IMA Fungus, Springer Science and Business Media LLC, Vol. 12, No. 1 ( 2021-12)
    Abstract: The unambiguous application of fungal names is important to communicate scientific findings. Names are critical for (clinical) diagnostics, legal compliance, and regulatory controls, such as biosafety, food security, quarantine regulations, and industrial applications. Consequently, the stability of the taxonomic system and the traceability of nomenclatural changes is crucial for a broad range of users and taxonomists. The unambiguous application of names is assured by the preservation of nomenclatural history and the physical organisms representing a name. Fungi are extremely diverse in terms of ecology, lifestyle, and methods of study. Predominantly unicellular fungi known as yeasts are usually investigated as living cultures. Methods to characterize yeasts include physiological (growth) tests and experiments to induce a sexual morph; both methods require viable cultures. Thus, the preservation and availability of viable reference cultures are important, and cultures representing reference material are cited in species descriptions. Historical surveys revealed drawbacks and inconsistencies between past practices and modern requirements as stated in the International Code of Nomenclature for Algae, Fungi, and Plants (ICNafp). Improper typification of yeasts is a common problem, resulting in a large number invalid yeast species names. With this opinion letter, we address the problem that culturable microorganisms, notably some fungi and algae, require specific provisions under the ICNafp. We use yeasts as a prominent example of fungi known from cultures. But viable type material is important not only for yeasts, but also for other cultivable Fungi that are characterized by particular morphological structures (a specific type of spores), growth properties, and secondary metabolites. We summarize potential proposals which, in our opinion, will improve the stability of fungal names, in particular by protecting those names for which the reference material can be traced back to the original isolate.
    Type of Medium: Online Resource
    ISSN: 2210-6359
    URL: Article
    DOI: 10.1186/s43008-021-00067-x
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2021
    detail.hit.zdb_id: 2666116-0
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