title: Comparing genome versus proteome-based identification of clinical bacterial isolates.
abstract: Whole-genome sequencing (WGS) is gaining importance in the analysis of bacterial cultures derived from patients with infectious diseases. Existing computational tools for WGS-based identification have, however, been evaluated on previously defined data relying thereby unwarily on the available taxonomic information.Here, we newly sequenced 846 clinical gram-negative bacterial isolates representing multiple distinct genera and compared the performance of five tools (CLARK, Kaiju, Kraken, DIAMOND/MEGAN and TUIT). To establish a faithful 'gold standard', the expert-driven taxonomy was compared with identifications based on matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) analysis. Additionally, the tools were also evaluated using a data set of 200 Staphylococcus aureus isolates.CLARK and Kraken (with k =31) performed best with 626 (100%) and 193 (99.5%) correct species classifications for the gram-negative and S. aureus isolates, respectively. Moreover, CLARK and Kraken demonstrated highest mean F-measure values (85.5/87.9% and 94.4/94.7% for the two data sets, respectively) in comparison with DIAMOND/MEGAN (71 and 85.3%), Kaiju (41.8 and 18.9%) and TUIT (34.5 and 86.5%). Finally, CLARK, Kaiju and Kraken outperformed the other tools by a factor of 30 to 170 fold in terms of runtime.We conclude that the application of nucleotide-based tools using k-mers-e.g. CLARK or Kraken-allows for accurate and fast taxonomic characterization of bacterial isolates from WGS data. Hence, our results suggest WGS-based genotyping to be a promising alternative to the MS-based biotyping in clinical settings. Moreover, we suggest that complementary information should be used for the evaluation of taxonomic classification tools, as public databases may suffer from suboptimal annotations.
authors.affiliation: Chair for Clinical Bioinformatics, Saarland University, Campus Building E2.1, 66123 Saarbrücken, Germany.
authors.forename: Valentina
authors.initials: V
authors.lastname: Galata
authors.affiliation: Chair for Clinical Bioinformatics, Saarland University, Campus Building E2.1, 66123 Saarbrücken, Germany.
authors.forename: Christina
authors.initials: C
authors.lastname: Backes
authors.affiliation: Chair for Clinical Bioinformatics, Saarland University, Campus Building E2.1, 66123 Saarbrücken, Germany.
authors.forename: Cédric Christian
authors.initials: CC
authors.lastname: Laczny
authors.affiliation: Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Schittenhelmstr. 12, 24105 Kiel, Germany.
authors.forename: Georg
authors.initials: G
authors.lastname: Hemmrich-Stanisak
authors.affiliation: Siemens Healthcare, R&D, 725 Potter Street, Berkeley, CA 94710, USA.
authors.forename: Howard
authors.initials: H
authors.lastname: Li
authors.affiliation: Siemens Healthcare, R&D, 1584 Enterprise Blvd., West Sacramento, CA 95691, USA.
authors.forename: Laura
authors.initials: L
authors.lastname: Smoot
authors.affiliation: Siemens Healthcare GmbH, Strategy and Innovation, Hartmannstr. 16, 91052 Erlangen, Germany.
authors.forename: Andreas Emanuel
authors.initials: AE
authors.lastname: Posch
authors.affiliation: Siemens Healthcare GmbH, Strategy and Innovation, Hartmannstr. 16, 91052 Erlangen, Germany.
authors.forename: Susanne
authors.initials: S
authors.lastname: Schmolke
authors.affiliation: Institute of Medical Microbiology and Hygiene, Saarland University, Kirrberger Straße, Campus Building 43, 66421 Homburg/Saar, Germany.
authors.forename: Markus
authors.initials: M
authors.lastname: Bischoff
authors.affiliation: Institute of Medical Microbiology and Hygiene, Saarland University, Kirrberger Straße, Campus Building 43, 66421 Homburg/Saar, Germany.
authors.forename: Lutz
authors.initials: L
authors.lastname: von Müller
authors.affiliation: Curetis GmbH, Max-Eyth-Str. 42, 71088 Holzgeringen, Germany.
authors.forename: Achim
authors.initials: A
authors.lastname: Plum
authors.affiliation: Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Schittenhelmstr. 12, 24105 Kiel, Germany.
authors.forename: Andre
authors.initials: A
authors.lastname: Franke
authors.affiliation: Chair for Clinical Bioinformatics, Saarland University, Campus Building E2.1, 66123 Saarbrücken, Germany.
authors.forename: Andreas
authors.initials: A
authors.lastname: Keller
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics* / Q000378:metabolism*; D016680:Genome, Bacterial; D006090:Gram-Negative Bacteria / Q000235:genetics* / Q000302:isolation & purification / Q000378:metabolism*; D006801:Humans; D020543:Proteome; D000073336:Whole Genome Sequencing / Q000379:methods*
chemical_list: D001426:Bacterial Proteins; D020543:Proteome