title: Detecting Staphylococcus aureus Virulence and Resistance Genes: a Comparison of Whole-Genome Sequencing and DNA Microarray Technology.
abstract: Staphylococcus aureusis a major bacterial pathogen causing a variety of diseases ranging from wound infections to severe bacteremia or intoxications. Besides host factors, the course and severity of disease is also widely dependent on the genotype of the bacterium. Whole-genome sequencing (WGS), followed by bioinformatic sequence analysis, is currently the most extensive genotyping method available. To identify clinically relevant staphylococcal virulence and resistance genes in WGS data, we developed anin silicotyping scheme for the software SeqSphere(+)(Ridom GmbH, Münster, Germany). The implemented target genes (n= 182) correspond to those queried by the IdentibacS. aureusGenotyping DNA microarray (Alere Technologies, Jena, Germany). Thein silicoscheme was evaluated by comparing the typing results of microarray and of WGS for 154 humanS. aureusisolates. A total of 96.8% (n= 27,119) of all typing results were equally identified with microarray and WGS (40.6% present and 56.2% absent). Discrepancies (3.2% in total) were caused by WGS errors (1.7%), microarray hybridization failures (1.3%), wrong prediction of ambiguous microarray results (0.1%), or unknown causes (0.1%). Superior to the microarray, WGS enabled the distinction of allelic variants, which may be essential for the prediction of bacterial virulence and resistance phenotypes. Multilocus sequence typing clonal complexes and staphylococcal cassette chromosomemecelement types inferred from microarray hybridization patterns were equally determined by WGS. In conclusion, WGS may substitute array-based methods due to its universal methodology, open and expandable nature, and rapid parallel analysis capacity for different characteristics in once-generated sequences.
authors.affiliation: Institute of Hygiene, Westphalian Wilhelms-University, Münster, Germany.
authors.forename: Lena
authors.initials: L
authors.lastname: Strauß
authors.affiliation: Institute of Medical Microbiology and Hygiene, University of Saarland, Homburg, Germany.
authors.forename: Ulla
authors.initials: U
authors.lastname: Ruffing
authors.affiliation: Ifakara Health Research and Development Centre, Bagamoyo, Tanzania.
authors.forename: Salim
authors.initials: S
authors.lastname: Abdulla
authors.affiliation: Albert Schweitzer Hospital, Lambaréné, Gabon Institute of Tropical Medicine, Eberhard Karls University, Tübingen, Germany.
authors.forename: Abraham
authors.initials: A
authors.lastname: Alabi
authors.affiliation: Center for Bioinformatics, University of Saarland, Saarbrücken, Germany.
authors.forename: Ruslan
authors.initials: R
authors.lastname: Akulenko
authors.affiliation: Manhiça Health Research Centre, Manhiça, Mozambique.
authors.forename: Marcelino
authors.initials: M
authors.lastname: Garrine
authors.affiliation: Fraunhofer Institute for Biomedical Engineering, Sulzbach, Germany.
authors.forename: Anja
authors.initials: A
authors.lastname: Germann
authors.affiliation: Institute of Tropical Medicine, Eberhard Karls University, Tübingen, Germany Center of Tropical Medicine and Travel Medicine, Department of Infectious Diseases, Division of Internal Medicine, Amsterdam Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
authors.forename: Martin Peter
authors.initials: MP
authors.lastname: Grobusch
authors.affiliation: Center for Bioinformatics, University of Saarland, Saarbrücken, Germany.
authors.forename: Volkhard
authors.initials: V
authors.lastname: Helms
authors.affiliation: Institute of Medical Microbiology and Hygiene, University of Saarland, Homburg, Germany.
authors.forename: Mathias
authors.initials: M
authors.lastname: Herrmann
authors.affiliation: Ifakara Health Research and Development Centre, Bagamoyo, Tanzania.
authors.forename: Theckla
authors.initials: T
authors.lastname: Kazimoto
authors.affiliation: Division of Infectious Diseases, Department of Medicine, University of Freiburg, Freiburg, Germany.
authors.forename: Winfried
authors.initials: W
authors.lastname: Kern
authors.affiliation: Manhiça Health Research Centre, Manhiça, Mozambique.
authors.forename: Inácio
authors.initials: I
authors.lastname: Mandomando
authors.affiliation: Institute of Medical Microbiology, Westphalian Wilhelms-University, Münster, Germany.
authors.forename: Georg
authors.initials: G
authors.lastname: Peters
authors.affiliation: Institute of Medical Microbiology, Westphalian Wilhelms-University, Münster, Germany.
authors.forename: Frieder
authors.initials: F
authors.lastname: Schaumburg
authors.affiliation: Institute of Medical Microbiology and Hygiene, University of Saarland, Homburg, Germany.
authors.forename: Lutz
authors.initials: L
authors.lastname: von Müller
authors.affiliation: Institute of Hygiene, Westphalian Wilhelms-University, Münster, Germany mellmann@uni-muenster.de.
authors.forename: Alexander
authors.identifier: http://orcid.org/0000-0002-0649-5185
authors.initials: A
authors.lastname: Mellmann
mesh_terms: D001431:Bacteriological Techniques / Q000379:methods*; D016680:Genome, Bacterial; D005838:Genotype; D005858:Germany; D064368:Healthy Volunteers; D006801:Humans; D058889:Molecular Typing / Q000379:methods; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D013203:Staphylococcal Infections / Q000382:microbiology*; D013211:Staphylococcus aureus / Q000235:genetics* / Q000302:isolation & purification / Q000472:pathogenicity*; D014774:Virulence; D037521:Virulence Factors / Q000032:analysis* / Q000235:genetics
chemical_list: D037521:Virulence Factors
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