Data from: Rapid and robust phylotyping of spa t003, a dominant MRSA clone in Luxembourg and other European countries

Background: spa typing is a common genotyping tool for
methicillin-resistant Staphylococcus aureus (MRSA) in Europe. Given the
high prevalence of dominant clones, spa-typing is proving to be limited in
its ability to distinguish outbreak isolates from background isolates. New
molecular tools need to be employed to improve subtyping of dominant local
MRSA strains (e.g., spa type t003). Methods: Phylogenetically critical, or
canonical, SNPs (can-SNPs) were identified as subtyping targets through
sequence analysis of 40 MRSA whole genomes from Luxembourg. Real-time PCR
assays were designed around target SNPs and validated using a repository
of 240 previously sub-typed and epidemiologically characterized Luxembourg
MRSA isolates, including 153 community and hospital isolates, 69 isolates
from long term care (LTC) facilities, and 21 prospectively analyzed MRSA
isolates. Selected isolates were also analyzed by whole genome SNP typing
(WGST) for comparison to the SNP assays and other subtyping techniques.
Results: Fourteen real-time PCR assays were developed and validated,
including two assays to determine presence of spa t003 or t008. The other
twelve assays successfully provided a high degree of resolution within the
t003 subtype. WGST analysis of the LTC facility isolates provided greater
resolution than other subtyping tools, identifying clusters indicative of
ongoing transmission within LTC facilities. Conclusions: canSNP-based PCR
assays are useful for local level MRSA phylotyping, especially in the
presence of one or more dominant clones. The assays designed here can be
easily adapted for investigating t003 MRSA strains in other regions in
Western Europe. WGST provides substantially better resolution than other
typing methods.