1. Species identification of clinical isolates of Bacteroides by matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry
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Nagy, E., Maier, T., Urban, E., Terhes, G., Kostrzewa, M., Nord, C. E., Hedberg, M., Könönen, E., Dubreuil, L., Dosa, E., Kalenic, S., Piérard, D., Degener, J., Wildeboer Veloo, A., Chmelarova, E., Mazzariol, Annarita, Gürler, N., Güner, S., Papaparakevas, J., and Villa, J.
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sequence analysis ,Aerobic bacteria ,genus ,Bacteroides ovatus ,Bacteroides fragilis ,RNA, Ribosomal, 16S ,Bacteroides ,clinical isolates ,flight mass spectrometry ,identification ,MALDI-TOF MS ,sequencing ,Bacteroides sp ,strain difference ,0303 health sciences ,accuracy ,biology ,article ,food and beverages ,General Medicine ,matrix assisted laser desorption ionization time of flight mass spectrometry ,Bacteroides Infections ,Bacterial Typing Techniques ,Infectious Diseases ,priority journal ,bacterium identification ,Bacteroides thetaiotaomicron ,Microbiology (medical) ,DNA, Bacterial ,spectrophotometer ,Sequence analysis ,species identification ,Mass spectrometry ,DNA, Ribosomal ,Sensitivity and Specificity ,Bacteroides uniformis ,Microbiology ,03 medical and health sciences ,Humans ,controlled study ,intermethod comparison ,Bacteroidaceae ,030304 developmental biology ,Bacteriological Techniques ,nonhuman ,030306 microbiology ,Clinical isolates ,Identification ,Sequencing ,bacterial strain ,bacterium isolate ,chemical analysis ,optical resolution phenotype ,Sequence Analysis, DNA ,Ribosomal RNA ,biology.organism_classification ,Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization - Abstract
Bacteroides fragilis and related species are important human pathogens involved in mixed infections of different origins. The B. fragilis group isolates are phenotypically very similar, grow more slowly than aerobic bacteria and, accordingly, are frequently misidentifed with classical or automated phenotypical identification methods. Recent taxonomic changes and new species accepted as members of the Bacteroides genus are not included in the different databases of commercially available identification kits. The use of matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was therefore evaluated for the species identification of 277 clinical isolates of the Bacteroides genus. Species identification was carried out with MALDI Bruker Daltonik Biotyper software (Bruker Daltonik GmbH, Bremen, Germany) by comparing the mass spectrum of each strain with the mass spectra of the 3260 reference strains currently available. The results of conventional phenotypical identification of the isolates were used as a reference. 16S rRNA gene sequencing was performed for a selection of the strains that gave discrepant results and for all those inconclusively identified by MALDI-TOF MS; 270 isolates (97.5%) were unequivocally identified [log(score) ≥2.0] by comparison with the reference strains present in the MALDI Biotyper database. Of the 23 isolates for which the MALDI-TOF MS species identification differed from the conventional phenotypical identification, 11 were sequenced. The sequencing data confirmed the MALDI-TOF MS result in ten cases and, for the remaining isolate, the sequencing data did not lead to the determination of the species, but only to that of the genus (Bacteroides sp.). The discriminating power and identification accuracy of MALDI-TOF MS proved to be superior to that of biochemical testing for Bacteroides thetaiotaomicron, Bacteroides ovatus and Bacteroides uniformis.
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