Distribution and characterization of staphylococcal interspersed repeat units (SIRUs) and potential use for strain differentiation

• Published in: Microbiology (Society for General Microbiology) 2004-12, Vol.150 (12), p.4045-4052
• Main Authors: Hardy, K. J, Ussery, D. W, Oppenheim, B. A, Hawkey, P. M
• Format: Article
• Language: English
• Subjects: Bacterial Typing Techniques; Bacteriology; Base Sequence; Biological and medical sciences; Disease Outbreaks; Evolution, Molecular; Fundamental and applied biological sciences. Psychology; Genome, Bacterial; Humans; Methicillin Resistance; Microbiology; Minisatellite Repeats - genetics; Miscellaneous; Molecular Sequence Data; Mycobacterium tuberculosis; Sequence Alignment; Staphylococcal Infections - epidemiology; Staphylococcal Infections - microbiology; Staphylococcus aureus; Staphylococcus aureus - classification; Staphylococcus aureus - drug effects; Staphylococcus aureus - genetics; United Kingdom - epidemiology
• ISSN: 1350-0872; 1465-2080
• DOI: 10.1099/mic.0.27413-0

1 West Midlands Public Health Laboratory, Health Protection Agency, Heartlands Hospital, Bordesley Green East, Birmingham B9 5SS, UK 2 Division of Infection and Immunity, University of Birmingham, Birmingham B15 2TT, UK 3 Center for Biological Sequence Analysis, Biocentrum-DTU, Building 208, The Technical University of Denmark, DK-2800 Denmark Correspondence K. J. Hardy Katie.Hardy{at}heartsol.wmids.nhs.uk Variable-number tandem repeats (VNTRs) have been shown to be a powerful tool in the determination of evolutionary relationships and population genetics of bacteria. The sequencing of a number of Staphylococcus aureus genomes has allowed the identification of novel VNTR sequences in S. aureus , which are similar to those used in the study of the evolution of Mycobacterium tuberculosis clades. Seven VNTRs, termed staphylococcal interspersed repeat units (SIRUs), distributed around the genome are described, occurring in both unique and multiple sites, and varying in length from 48 to 159 bp. Variations in copy numbers were observed in all loci, within both the sequenced genomes and the UK epidemic methicillin-resistant S. aureus (EMRSA) isolates. Clonally related UK EMRSA isolates were clustered using SIRUs, which provided a greater degree of discrimination than multi-locus sequence typing, indicating that VNTRs may be a more appropriate evolutionary marker for studying transmission events and the geographical spread of S. aureus clades. Abbreviations: EMRSA, epidemic methicillin-resistant Staphylococcus aureus ; MIRU, mycobacterial interspersed repeat unit; MLST, multi-locus sequence typing; MRSA, methicillin-resistant S. aureus ; MSSA, methicillin-sensitive S. aureus ; SIRU, staphylococcal interspersed repeat units; VNTR, variable-number tandem repeats