title: Comparison of two approaches for the classification of 16S rRNA gene sequences.
abstract: The use of 16S rRNA gene sequences for microbial identification in clinical microbiology is accepted widely, and requires databases and algorithms. We compared a new research database containing curated 16S rRNA gene sequences in combination with the lca (lowest common ancestor) algorithm (RDB-LCA) to a commercially available 16S rDNA Centroid approach. We used 1025 bacterial isolates characterized by biochemistry, matrix-assisted laser desorption/ionization time-of-flight MS and 16S rDNA sequencing. Nearly 80 % of isolates were identified unambiguously at the species level by both classification platforms used. The remaining isolates were mostly identified correctly at the genus level due to the limited resolution of 16S rDNA sequencing. Discrepancies between both 16S rDNA platforms were due to differences in database content and the algorithm used, and could amount to up to 10.5 %. Up to 1.4 % of the analyses were found to be inconclusive. It is important to realize that despite the overall good performance of the pipelines for analysis, some inconclusive results remain that require additional in-depth analysis performed using supplementary methods.
authors: bioMérieux SA, Unit Microbiology, R&D Microbiology, La Balme Les Grottes, France.
authors: Sonia
authors: S
authors: Chatellier
authors: bioMérieux SA, Unit Innovation and Systems, Marcy l'Etoile, France.
authors: Nathalie
authors: N
authors: Mugnier
authors: bioMérieux SA, Unit Microbiology, R&D Microbiology, La Balme Les Grottes, France.
authors: Françoise
authors: F
authors: Allard
authors: bioMérieux SA, Unit Innovation and Systems, Marcy l'Etoile, France.
authors: Bertrand
authors: B
authors: Bonnaud
authors: bioMérieux SA, Unit Microbiology, R&D Microbiology, La Balme Les Grottes, France.
authors: Valérie
authors: V
authors: Collin
authors: bioMérieux SA, Unit Microbiology, R&D Microbiology, La Balme Les Grottes, France.
authors: Alex
authors: A
authors: van Belkum
authors: bioMérieux SA, Unit Innovation and Systems, Marcy l'Etoile, France.
authors: Jean-Baptiste
authors: JB
authors: Veyrieras
authors: SmartGene, Zug, Switzerland.
authors: Stefan
authors: S
authors: Emler
mesh_terms: D000818:Animals; D001419:Bacteria / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D001424:Bacterial Infections / Q000175:diagnosis / Q000662:veterinary; D001431:Bacteriological Techniques / Q000379:methods*; D019295:Computational Biology / Q000379:methods*; D020459:Genes, rRNA; D006801:Humans; D025202:Molecular Diagnostic Techniques / Q000379:methods*; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D012336:RNA, Ribosomal, 16S