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

Engelthaler, David M. and Kelley, Erin and Driebe, Elizabeth M. and Bowers, Jolene and Eberhard, Carl F. and Trujillo, Jesse and Decruyenaere, Frederic and Schupp, James M. and Mossong, Joel and Keim, Paul and Even, Jos (2013) Rapid and robust phylotyping of spa t003, a dominant MRSA clone in Luxembourg and other European countries. BMC Infectious Diseases, 13 (1). p. 339. ISSN 1471-2334

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Abstract

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.

Item Type:	Article
ID number or DOI:	10.1186/1471-2334-13-339
Keywords:	Cloning; Europe; Evolution; Genomes; Luxembourg; Methicilian-resistant staphylococcus aureus; Molecular epidemiology; Molecular epidemiology; MRSA; Phylotyping; Polymerase chain reaction; resistant staphylococcus-aureus; SNP assays; software; spa t003; spread; WGST
Subjects:	Q Science > QH Natural history > QH301 Biology Q Science > QH Natural history > QH426 Genetics
NAU Depositing Author Academic Status:	Faculty/Staff
Department/Unit:	College of Engineering, Forestry, and Natural Science > Biological Sciences Research Centers > Center for Microbial Genetics and Genomics
Date Deposited:	30 Sep 2015 21:03
URI:	http://openknowledge.nau.edu/id/eprint/469

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