For Publishers
DiscoveryMetadataPeer reviewHostingPublishing
For Researchers
JoinPublishReviewCollect
Register
Blog
About
Search
Advanced search
My ScienceOpen
Search
For Publishers
For Researchers
Blog
About
11
views
44
references
 Top references
cited by
16
    
0 reviews
 Review
0
comments
 Comment
0
recommends
+1 Recommend
0 collections
    0
    shares
      101
      similar
       All similar
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      Evaluation of MALDI-TOF mass spectrometry and MALDI BioTyper in comparison to 16S rDNA sequencing for the identification of bacteria isolated from Arctic sea water

      research-article

      Read this article at

      ScienceOpenPublisherPMC
      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          MALDI-TOF Mass Spectrometry in association with the MALDI BioTyper 3.1 software has been evaluated for the identification and classification of 45 Arctic bacteria isolated from Kandalaksha Bay (White Sea, Russia). The high reliability of this method has been already demonstrated, in clinical microbiology, by a number of studies showing high attribution concordance with other credited analyses. Recently, it has been employed also in other branches of microbiology with controversial performance. The phyloproteomic results reported in this study were validated with those obtained by the “gold standard” 16S rDNA analysis. Concordance between the two methods was 100% at the genus level, while at the species level it was 48%. These percentages appeared to be quite high compared with other studies regarding environmental bacteria. However, the performance of MALDI BioTyper changed in relation to the taxonomical group analyzed, reflecting known identification problems related to certain genera. In our case, attribution concordance for Pseudomonas species was rather low (29%), confirming the problematic taxonomy of this genus, whereas that of strains from other genera was quite high (> 60%). Among the isolates tested in this study, two strains ( Exiguobacterium oxidotolerans and Pseudomonas costantinii) were misidentified by MALDI BioTyper due to absence of reference spectra in the database. Accordingly, missing spectra were acquired for the database implementation.

          Related collections

          Most cited references44

          • Record: found
          • Abstract: found
          • Article: not found

          Ongoing revolution in bacteriology: routine identification of bacteria by matrix-assisted laser desorption ionization time-of-flight mass spectrometry.

          Piseth Seng, Michel Drancourt, Frédérique Gouriet … (2009)
          Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry accurately identifies both selected bacteria and bacteria in select clinical situations. It has not been evaluated for routine use in the clinic. We prospectively analyzed routine MALDI-TOF mass spectrometry identification in parallel with conventional phenotypic identification of bacteria regardless of phylum or source of isolation. Discrepancies were resolved by 16S ribosomal RNA and rpoB gene sequence-based molecular identification. Colonies (4 spots per isolate directly deposited on the MALDI-TOF plate) were analyzed using an Autoflex II Bruker Daltonik mass spectrometer. Peptidic spectra were compared with the Bruker BioTyper database, version 2.0, and the identification score was noted. Delays and costs of identification were measured. Of 1660 bacterial isolates analyzed, 95.4% were correctly identified by MALDI-TOF mass spectrometry; 84.1% were identified at the species level, and 11.3% were identified at the genus level. In most cases, absence of identification (2.8% of isolates) and erroneous identification (1.7% of isolates) were due to improper database entries. Accurate MALDI-TOF mass spectrometry identification was significantly correlated with having 10 reference spectra in the database (P=.01). The mean time required for MALDI-TOF mass spectrometry identification of 1 isolate was 6 minutes for an estimated 22%-32% cost of current methods of identification. MALDI-TOF mass spectrometry is a cost-effective, accurate method for routine identification of bacterial isolates in or =10 reference spectra per bacterial species and a 1.9 identification score (Brucker system). It may replace Gram staining and biochemical identification in the near future.
          Article 0 comments Cited 590 times – based on 0 reviews     Review now
            Bookmark
            • Record: found
            • Abstract: found
            • Article: not found

            Phylogenetic affiliation of the pseudomonads based on 16S rRNA sequence.

            Hyoun Geun Kim, David Park, Y Anzai … (2000)
            The broad and vague phenotypic definition allowed the genus Pseudomonas to become a dumping ground for incompletely characterized polarly flagellated, gram-negative, rod-shaped, aerobic bacteria, and a large number of species have been accommodated in the genus Pseudomonas. The 16S rRNA sequences of 128 valid and invalid Pseudomonas species, which included almost valid species of the genus Pseudomonas listed in the Approved Lists of Bacterial Names, were obtained: sequences of 59 species were determined and those of 69 species were obtained from the GenBank/EMBL/DDBJ databases. These sequences were compared with the sequences of other species of the Proteobacteria. Fifty-seven valid or invalid species including Pseudomonas aeruginosa (type species of the genus Pseudomonas Migula 1894) belonged to the genus Pseudomonas (sensu stricto). Seven subclusters were formed in the cluster of the genus Pseudomonas (sensu stricto), and the resulting clusters conformed well to the rRNA-DNA hybridization study by Palleroni (1984). The other species did not belong to the genus Pseudomonas (sensu stricto) and were related to other genera, which were placed in four subclasses of the Proteobacteria (alpha, beta, gamma and gamma-beta subclasses). Twenty-six examined species, which were not included in the cluster of the Pseudomonas (sensu stricto) and have not been transferred to other genera as yet, are listed alphabetically: 'Pseudomonas abikonensis', Pseudomonas antimicrobica, Pseudomonas beijerinckii, Pseudomonas beteli, Pseudomonas boreopolis, 'Pseudomonas butanovora', Pseudomonas carboxydohydrogena, Pseudomonas cissicola, Pseudomonas doudoroffii, Pseudomonas echinoides, Pseudomonas elongata, Pseudomonas flectens, Pseudomonas geniculata, Pseudomonas halophila, Pseudomonas hibiscicola, Pseudomonas huttiensis, Pseudomonas iners, Pseudomonas lanceolata, Pseudomonas lemoignei, Pseudomonas mephitica, Pseudomonas pictorum, Pseudomonas saccharophila, Pseudomonas spinosa, Pseudomonas stanier, Pseudomonas syzygii and Pseudomonas woodsii. The phylogenetic affiliations of these 26 pseudomonads species are shown.
            Article 0 comments Cited 167 times – based on 0 reviews     Review now
              Bookmark
              • Record: found
              • Abstract: found
              • Article: not found

              DNA sequence-based analysis of the Pseudomonas species.

              Magdalena Mulet, Jorge Lalucat, Elena García-Valdés (2010)
              Partial sequences of four core 'housekeeping' genes (16S rRNA, gyrB, rpoB and rpoD) of the type strains of 107 Pseudomonas species were analysed in order to obtain a comprehensive view regarding the phylogenetic relationships within the Pseudomonas genus. Gene trees allowed the discrimination of two lineages or intrageneric groups (IG), called IG P. aeruginosa and IG P. fluorescens. The first IG P. aeruginosa, was divided into three main groups, represented by the species P. aeruginosa, P. stutzeri and P. oleovorans. The second IG was divided into six groups, represented by the species P. fluorescens, P. syringae, P. lutea, P. putida, P. anguilliseptica and P. straminea. The P. fluorescens group was the most complex and included nine subgroups, represented by the species P. fluorescens, P. gessardi, P. fragi, P. mandelii, P. jesseni, P. koreensis, P. corrugata, P. chlororaphis and P. asplenii. Pseudomonas rhizospherae was affiliated with the P. fluorescens IG in the phylogenetic analysis but was independent of any group. Some species were located on phylogenetic branches that were distant from defined clusters, such as those represented by the P. oryzihabitans group and the type strains P. pachastrellae, P. pertucinogena and P. luteola. Additionally, 17 strains of P. aeruginosa, 'P. entomophila', P. fluorescens, P. putida, P. syringae and P. stutzeri, for which genome sequences have been determined, have been included to compare the results obtained in the analysis of four housekeeping genes with those obtained from whole genome analyses.
              Article 0 comments Cited 164 times – based on 0 reviews     Review now
                Bookmark
                All references

                Author and article information

                Contributors
                Jon M. Jacobs: Role: Editor
                Journal
                Journal ID (nlm-ta): PLoS One
                Journal ID (iso-abbrev): PLoS ONE
                Journal ID (publisher-id): plos
                Journal ID (pmc): plosone
                Title: PLoS ONE
                Publisher: Public Library of Science (San Francisco, CA USA )
                ISSN (Electronic): 1932-6203
                Publication date (Electronic): 24 July 2017
                Publication date Collection: 2017
                Volume: 12
                Issue: 7
                Electronic Location Identifier: e0181860
                Affiliations
                [1 ] Dipartimento di Ecologia e Biologia, University of Tuscia, Viterbo, Italy
                [2 ] Dipartimento di Scienze Agrarie e Forestali, University of Tuscia, Viterbo, Italy
                [3 ] Laboratorio di Microbiologia Marina Applicata, CONISMA, University of Tuscia, Viterbo, Italy
                Pacific Northwest National Laboratory, UNITED STATES
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                • Conceptualization: AMT SG MF.

                • Data curation: AMT SG MF.

                • Formal analysis: AMT MF.

                • Funding acquisition: MF.

                • Investigation: AMT SG MF.

                • Methodology: AMT SG MF.

                • Project administration: AMT SG MF.

                • Resources: AMT MF.

                • Software: AMT SG MF.

                • Supervision: AMT MF.

                • Visualization: SG MF.

                • Writing – original draft: AMT SG MF.

                • Writing – review & editing: AMT SG LZ MF.

                Author information
                http://orcid.org/0000-0001-8504-0885
                Article
                Publisher ID: PONE-D-17-01534
                DOI: 10.1371/journal.pone.0181860
                PMC ID: 5524297
                PubMed ID: 28738078
                SO-VID: c8ecb5be-1a4e-4a40-81a6-33b16d46a5f1
                Copyright © © 2017 Timperio et al
                License:

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                Date received : 12 January 2017
                Date accepted : 7 July 2017
                Page count
                Figures: 5, Tables: 1, Pages: 15
                Funding
                The authors received no specific funding for this work.
                Categories
                Subject: Research Article
                Subject: Research and Analysis Methods
                Subject: Database and Informatics Methods
                Subject: Biological Databases
                Subject: Sequence Databases
                Subject: Research and Analysis Methods
                Subject: Database and Informatics Methods
                Subject: Bioinformatics
                Subject: Sequence Analysis
                Subject: Sequence Databases
                Subject: Biology and Life Sciences
                Subject: Organisms
                Subject: Bacteria
                Subject: Pseudomonas
                Subject: Biology and Life Sciences
                Subject: Organisms
                Subject: Bacteria
                Subject: Enterobacteriaceae
                Subject: Serratia
                Subject: Biology and Life Sciences
                Subject: Organisms
                Subject: Bacteria
                Subject: Pseudomonas
                Subject: Pseudomonas Fluorescens
                Subject: Physical Sciences
                Subject: Chemistry
                Subject: Analytical Chemistry
                Subject: Mass Spectrometry
                Subject: Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry
                Subject: Research and Analysis Methods
                Subject: Spectrum Analysis Techniques
                Subject: Mass Spectrometry
                Subject: Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry
                Subject: Biology and Life Sciences
                Subject: Evolutionary Biology
                Subject: Evolutionary Systematics
                Subject: Phylogenetics
                Subject: Phylogenetic Analysis
                Subject: Biology and Life Sciences
                Subject: Taxonomy
                Subject: Evolutionary Systematics
                Subject: Phylogenetics
                Subject: Phylogenetic Analysis
                Subject: Computer and Information Sciences
                Subject: Data Management
                Subject: Taxonomy
                Subject: Evolutionary Systematics
                Subject: Phylogenetics
                Subject: Phylogenetic Analysis
                Subject: Biology and Life Sciences
                Subject: Organisms
                Subject: Bacteria
                Subject: Biology and Life Sciences
                Subject: Evolutionary Biology
                Subject: Evolutionary Systematics
                Subject: Phylogenetics
                Subject: Biology and Life Sciences
                Subject: Taxonomy
                Subject: Evolutionary Systematics
                Subject: Phylogenetics
                Subject: Computer and Information Sciences
                Subject: Data Management
                Subject: Taxonomy
                Subject: Evolutionary Systematics
                Subject: Phylogenetics
                Custom metadata
                Data Availability All relevant data are within the paper including GenBank accession numbers. Sequence data are available at GenBank database.

                ScienceOpen disciplines: Uncategorized
                Data availability:
                ScienceOpen disciplines: Uncategorized

                Comments

                Comment on this article

                scite_

                Similar content101

                See all similar

                Cited by15

                See all cited by

                Most referenced authors1,214

                See all reference authors