Comparing genome versus proteome-based identification of clinical bacterial isolates.
Identifieur interne : 000A34 ( Main/Exploration ); précédent : 000A33; suivant : 000A35Comparing genome versus proteome-based identification of clinical bacterial isolates.
Auteurs : Valentina Galata [Allemagne] ; Christina Backes [Allemagne] ; Cédric Christian Laczny [Allemagne] ; Georg Hemmrich-Stanisak [Allemagne] ; Howard Li [États-Unis] ; Laura Smoot [États-Unis] ; Andreas Emanuel Posch [Allemagne] ; Susanne Schmolke [Allemagne] ; Markus Bischoff [Allemagne] ; Lutz Von Müller [Allemagne] ; Achim Plum [Allemagne] ; Andre Franke [Allemagne] ; Andreas Keller [Allemagne]Source :
- Briefings in bioinformatics [ 1477-4054 ] ; 2018.
Descripteurs français
- KwdFr :
- MESH :
- génétique : Bactéries à Gram négatif, Protéines bactériennes.
- isolement et purification : Bactéries à Gram négatif.
- métabolisme : Bactéries à Gram négatif, Protéines bactériennes.
- Génome bactérien, Humains, Protéome.
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : Bacterial Proteins.
- chemical , metabolism : Bacterial Proteins.
- genetics : Gram-Negative Bacteria.
- isolation & purification : Gram-Negative Bacteria.
- metabolism : Gram-Negative Bacteria.
- methods : Whole Genome Sequencing.
- Genome, Bacterial, Humans, Proteome.
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.
DOI: 10.1093/bib/bbw122
PubMed: 28013236
Affiliations:
- Allemagne, États-Unis
- Bade-Wurtemberg, Bavière, Californie, District de Moyenne-Franconie, District de Stuttgart, Sarre (Land), Schleswig-Holstein
- Erlangen, Kiel, Sarrebruck, Stuttgart
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Le document en format XML
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xml:lang="fr">Allemagne</country><wicri:regionArea>Chair for Clinical Bioinformatics, Saarland University, Campus Building E2.1, 66123 Saarbrücken</wicri:regionArea><placeName><region type="land" nuts="2">Sarre (Land)</region><settlement type="city">Sarrebruck</settlement></placeName></affiliation></author><author><name sortKey="Backes, Christina" sort="Backes, Christina" uniqKey="Backes C" first="Christina" last="Backes">Christina Backes</name><affiliation wicri:level="3"><nlm:affiliation>Chair for Clinical Bioinformatics, Saarland University, Campus Building E2.1, 66123 Saarbrücken, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Chair for Clinical Bioinformatics, Saarland University, Campus Building E2.1, 66123 Saarbrücken</wicri:regionArea><placeName><region type="land" nuts="2">Sarre (Land)</region><settlement type="city">Sarrebruck</settlement></placeName></affiliation></author><author><name sortKey="Laczny, Cedric Christian" sort="Laczny, 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xml:lang="fr">Allemagne</country><wicri:regionArea>Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Schittenhelmstr. 12, 24105 Kiel</wicri:regionArea><placeName><region type="land" nuts="2">Schleswig-Holstein</region><settlement type="city">Kiel</settlement></placeName></affiliation></author><author><name sortKey="Li, Howard" sort="Li, Howard" uniqKey="Li H" first="Howard" last="Li">Howard Li</name><affiliation wicri:level="2"><nlm:affiliation>Siemens Healthcare, R&D, 725 Potter Street, Berkeley, CA 94710, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Siemens Healthcare, R&D, 725 Potter Street, Berkeley, CA 94710</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Smoot, Laura" sort="Smoot, Laura" uniqKey="Smoot L" first="Laura" last="Smoot">Laura Smoot</name><affiliation wicri:level="2"><nlm:affiliation>Siemens Healthcare, R&D, 1584 Enterprise Blvd., West Sacramento, CA 95691, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Siemens Healthcare, R&D, 1584 Enterprise Blvd., West Sacramento, CA 95691</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Posch, Andreas Emanuel" sort="Posch, Andreas Emanuel" uniqKey="Posch A" first="Andreas Emanuel" last="Posch">Andreas Emanuel Posch</name><affiliation wicri:level="1"><nlm:affiliation>Siemens Healthcare GmbH, Strategy and Innovation, Hartmannstr. 16, 91052 Erlangen, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Siemens Healthcare GmbH, Strategy and Innovation, Hartmannstr. 16, 91052 Erlangen</wicri:regionArea><wicri:noRegion>91052 Erlangen</wicri:noRegion><placeName><settlement type="city">Erlangen</settlement><region type="land" nuts="1">Bavière</region><region type="district" nuts="2">District de Moyenne-Franconie</region></placeName></affiliation></author><author><name sortKey="Schmolke, Susanne" sort="Schmolke, Susanne" uniqKey="Schmolke S" first="Susanne" last="Schmolke">Susanne Schmolke</name><affiliation wicri:level="1"><nlm:affiliation>Siemens Healthcare GmbH, Strategy and Innovation, Hartmannstr. 16, 91052 Erlangen, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Siemens Healthcare GmbH, Strategy and Innovation, Hartmannstr. 16, 91052 Erlangen</wicri:regionArea><wicri:noRegion>91052 Erlangen</wicri:noRegion><placeName><settlement type="city">Erlangen</settlement><region type="land" nuts="1">Bavière</region><region type="district" nuts="2">District de Moyenne-Franconie</region></placeName></affiliation></author><author><name sortKey="Bischoff, Markus" sort="Bischoff, Markus" uniqKey="Bischoff M" first="Markus" last="Bischoff">Markus Bischoff</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Medical Microbiology and Hygiene, Saarland University, Kirrberger Straße, Campus Building 43, 66421 Homburg/Saar, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Institute of Medical Microbiology and Hygiene, Saarland University, Kirrberger Straße, Campus Building 43, 66421 Homburg/Saar</wicri:regionArea><wicri:noRegion>66421 Homburg/Saar</wicri:noRegion><wicri:noRegion>66421 Homburg/Saar</wicri:noRegion><wicri:noRegion>66421 Homburg/Saar</wicri:noRegion></affiliation></author><author><name sortKey="Von Muller, Lutz" sort="Von Muller, Lutz" uniqKey="Von Muller L" first="Lutz" last="Von Müller">Lutz Von Müller</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Medical Microbiology and Hygiene, Saarland University, Kirrberger Straße, Campus Building 43, 66421 Homburg/Saar, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Institute of Medical Microbiology and Hygiene, Saarland University, Kirrberger Straße, Campus Building 43, 66421 Homburg/Saar</wicri:regionArea><wicri:noRegion>66421 Homburg/Saar</wicri:noRegion><wicri:noRegion>66421 Homburg/Saar</wicri:noRegion><wicri:noRegion>66421 Homburg/Saar</wicri:noRegion></affiliation></author><author><name sortKey="Plum, Achim" sort="Plum, Achim" uniqKey="Plum A" first="Achim" last="Plum">Achim Plum</name><affiliation wicri:level="3"><nlm:affiliation>Curetis GmbH, Max-Eyth-Str. 42, 71088 Holzgeringen, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Curetis GmbH, Max-Eyth-Str. 42, 71088 Holzgeringen</wicri:regionArea><placeName><region type="land" nuts="1">Bade-Wurtemberg</region><region type="district" nuts="2">District de Stuttgart</region><settlement type="city">Stuttgart</settlement></placeName></affiliation></author><author><name sortKey="Franke, Andre" sort="Franke, Andre" uniqKey="Franke A" first="Andre" last="Franke">Andre Franke</name><affiliation wicri:level="3"><nlm:affiliation>Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Schittenhelmstr. 12, 24105 Kiel, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Schittenhelmstr. 12, 24105 Kiel</wicri:regionArea><placeName><region type="land" nuts="2">Schleswig-Holstein</region><settlement type="city">Kiel</settlement></placeName></affiliation></author><author><name sortKey="Keller, Andreas" sort="Keller, Andreas" uniqKey="Keller A" first="Andreas" last="Keller">Andreas Keller</name><affiliation wicri:level="3"><nlm:affiliation>Chair for Clinical Bioinformatics, Saarland University, Campus Building E2.1, 66123 Saarbrücken, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Chair for Clinical Bioinformatics, Saarland University, Campus Building E2.1, 66123 Saarbrücken</wicri:regionArea><placeName><region type="land" nuts="2">Sarre (Land)</region><settlement type="city">Sarrebruck</settlement></placeName></affiliation></author></analytic><series><title level="j">Briefings in bioinformatics</title><idno type="eISSN">1477-4054</idno><imprint><date when="2018" type="published">2018</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Bacterial Proteins (genetics)</term><term>Bacterial Proteins (metabolism)</term><term>Genome, Bacterial</term><term>Gram-Negative Bacteria (genetics)</term><term>Gram-Negative Bacteria (isolation & purification)</term><term>Gram-Negative Bacteria (metabolism)</term><term>Humans</term><term>Proteome</term><term>Whole Genome Sequencing (methods)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Bactéries à Gram négatif (génétique)</term><term>Bactéries à Gram négatif (isolement et purification)</term><term>Bactéries à Gram négatif (métabolisme)</term><term>Génome bactérien</term><term>Humains</term><term>Protéines bactériennes (génétique)</term><term>Protéines bactériennes (métabolisme)</term><term>Protéome</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Bacterial Proteins</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Bacterial Proteins</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Gram-Negative Bacteria</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Bactéries à Gram négatif</term><term>Protéines bactériennes</term></keywords><keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en"><term>Gram-Negative Bacteria</term></keywords><keywords scheme="MESH" qualifier="isolement et purification" xml:lang="fr"><term>Bactéries à Gram négatif</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Gram-Negative Bacteria</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Whole Genome Sequencing</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Bactéries à Gram négatif</term><term>Protéines bactériennes</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Genome, Bacterial</term><term>Humans</term><term>Proteome</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Génome bactérien</term><term>Humains</term><term>Protéome</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">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.</div></front></TEI><affiliations><list><country><li>Allemagne</li><li>États-Unis</li></country><region><li>Bade-Wurtemberg</li><li>Bavière</li><li>Californie</li><li>District de Moyenne-Franconie</li><li>District de Stuttgart</li><li>Sarre (Land)</li><li>Schleswig-Holstein</li></region><settlement><li>Erlangen</li><li>Kiel</li><li>Sarrebruck</li><li>Stuttgart</li></settlement></list><tree><country name="Allemagne"><region name="Sarre (Land)"><name sortKey="Galata, Valentina" sort="Galata, Valentina" uniqKey="Galata V" first="Valentina" last="Galata">Valentina Galata</name></region><name sortKey="Backes, Christina" sort="Backes, Christina" uniqKey="Backes C" first="Christina" last="Backes">Christina Backes</name><name sortKey="Bischoff, Markus" sort="Bischoff, Markus" uniqKey="Bischoff M" first="Markus" last="Bischoff">Markus Bischoff</name><name sortKey="Franke, Andre" sort="Franke, Andre" uniqKey="Franke A" first="Andre" last="Franke">Andre Franke</name><name sortKey="Hemmrich Stanisak, Georg" sort="Hemmrich Stanisak, Georg" uniqKey="Hemmrich Stanisak G" first="Georg" last="Hemmrich-Stanisak">Georg Hemmrich-Stanisak</name><name sortKey="Keller, Andreas" sort="Keller, Andreas" uniqKey="Keller A" first="Andreas" last="Keller">Andreas Keller</name><name sortKey="Laczny, Cedric Christian" sort="Laczny, Cedric Christian" uniqKey="Laczny C" first="Cédric Christian" last="Laczny">Cédric Christian Laczny</name><name sortKey="Plum, Achim" sort="Plum, Achim" uniqKey="Plum A" first="Achim" last="Plum">Achim Plum</name><name sortKey="Posch, Andreas Emanuel" sort="Posch, Andreas Emanuel" uniqKey="Posch A" first="Andreas Emanuel" last="Posch">Andreas Emanuel Posch</name><name sortKey="Schmolke, Susanne" sort="Schmolke, Susanne" uniqKey="Schmolke S" first="Susanne" last="Schmolke">Susanne Schmolke</name><name sortKey="Von Muller, Lutz" sort="Von Muller, Lutz" uniqKey="Von Muller L" first="Lutz" last="Von Müller">Lutz Von Müller</name></country><country name="États-Unis"><region name="Californie"><name sortKey="Li, Howard" sort="Li, Howard" uniqKey="Li H" first="Howard" last="Li">Howard Li</name></region><name sortKey="Smoot, Laura" sort="Smoot, Laura" uniqKey="Smoot L" first="Laura" last="Smoot">Laura Smoot</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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