title: Whole genome sequence typing and microarray profiling of nasal and blood stream methicillin-resistant Staphylococcus aureus isolates: Clues to phylogeny and invasiveness.
abstract: Hospital-associated methicillin-resistant Staphylococcus aureus (MRSA) infections are frequently caused by predominant clusters of closely related isolates that cannot be discriminated by conventional diagnostic typing methods. Whole genome sequencing (WGS) and DNA microarray (MA) now allow for better discrimination within a prevalent clonal complex (CC). This single center exploratory study aims to distinguish invasive (blood stream infection) and non-invasive (nasal colonization) MRSA isolates of the same CC5 into phylogenetic- and virulence-associated genotypic subgroups by WGS and MA. A cohort of twelve blood stream and fifteen nasal MRSA isolates of CC5 (spa-types t003 and t504) was selected. Isolates were propagated at the same period of time from unrelated patients treated at the University of Saarland Medical Center, Germany. Rooted phylotyping based on WGS with core-genome single nucleotide polymorphism (SNP) analysis revealed two local clusters of closely related CC5 subgroups (t504 and Clade1 t003) which were separated from other local t003 isolates and from unrelated CC5 MRSA reference isolates of German origin. Phylogenetic subtyping was not associated with invasiveness when comparing blood stream and nasal isolates. Clustering based on MA profiles was not concordant with WGS phylotyping, but MA profiles may identify subgroups of isolates with nasal and blood stream origin. Among the new putative virulence associated genes identified by WGS, the strongest association with blood stream infections was shown for ebhB mutants. Analysis of the core-genome together with the accessory genome enables subtyping of closely related MRSA isolates according to phylogeny and presumably also to the potential virulence capacity of isolates.
authors: Center for Bioinformatics, Saarland University, Saarbruecken, Germany.
authors: Mohamed
authors: M
authors: Hamed
authors: Department of Medical Microbiology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany.
authors: Daniel Patric
authors: DP
authors: Nitsche-Schmitz
authors: Institute of Medical Microbiology and Hygiene, University of Saarland Medical Center, Homburg, Germany.
authors: Ulla
authors: U
authors: Ruffing
authors: Robert Koch Institute Wernigerode, Germany.
authors: Matthias
authors: M
authors: Steglich
authors: Wellcome Trust Sanger Institute, Hinxton, UK.
authors: Janina
authors: J
authors: Dordel
authors: Center for Bioinformatics, Saarland University, Saarbruecken, Germany.
authors: Duy
authors: D
authors: Nguyen
authors: Institute of Medical Microbiology and Hygiene, University of Saarland Medical Center, Homburg, Germany.
authors: Jan-Hendrik
authors: JH
authors: Brink
authors: Department of Medical Microbiology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany.
authors: Gursharan Singh
authors: GS
authors: Chhatwal
authors: Institute of Medical Microbiology and Hygiene, University of Saarland Medical Center, Homburg, Germany.
authors: Mathias
authors: M
authors: Herrmann
authors: Leibniz Institute DSMZ, Braunschweig, Germany.
authors: Ulrich
authors: U
authors: Nübel
authors: Center for Bioinformatics, Saarland University, Saarbruecken, Germany.
authors: Volkhard
authors: V
authors: Helms
authors: Institute of Medical Microbiology and Hygiene, University of Saarland Medical Center, Homburg, Germany. Electronic address: lutz.mueller@christophorus-kliniken.de.
authors: Lutz
authors: L
authors: von Müller
mesh_terms: D019943:Amino Acid Substitution; D016470:Bacteremia / Q000382:microbiology*; D016000:Cluster Analysis; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D055624:Methicillin-Resistant Staphylococcus aureus / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D009666:Nose / Q000382:microbiology*; D020411:Oligonucleotide Array Sequence Analysis; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D013203:Staphylococcal Infections / Q000382:microbiology*; D014774:Virulence / Q000235:genetics
keywords: DNA microarray; Invasiveness; MRSA; Phylogeny; Staphylococcus aureus; Whole genome sequencing