Staphylococcal Interspersed Repeat Unit Typing of Staphylococcus aureus : Evaluation of a New Multilocus Variable-Number Tandem-Repeat Analysis Typing Method

Abstract

The present study evaluates the performance of the staphylococcal interspersed repeat unit (SIRU) method applied to a diverse collection of 104 Staphylococcus aureus isolates previously characterized by pulsed-field gel electrophoresis (PFGE), spa typing, multilocus sequence typing (MLST), and staphylococcal cassette chromosome mec typing for methicillin-resistant S. aureus. The SIRU method distributed the 104 strains into 81 SIRU profiles that could be clustered into 12 groups and 29 singletons. The discriminatory power of the method at the profile level, translated by Simpson's index of diversity (SID), was similar to that of PFGE subtyping (SID ‫؍‬ 99.23% versus 99.85%) and slightly higher than that of spa typing (SID ‫؍‬ 97.61%). At the group level, the SIRU SID (93.24%) was lower than that of PFGE typing (95.41%) but higher than that of MLST (SID ‫؍‬ 91.77%). The adjusted Rand (AR) coefficient showed that SIRU typing at the group level had the highest congruence with MLST (AR ‫؍‬ 0.5736) and with clonal complex (CC) (AR ‫؍‬ 0.4963) but the lowest congruence with PFGE subtype (AR ‫؍‬ 0.0242). The Wallace coefficient indicated that in the present collection, two strains with the same SIRU profile have a 100% probability of belonging to the same CC, a 90% probability of sharing the same spa type, and an 83% probability of being classified in the same sequence type. The high discriminatory power of the SIRU method, along with its apparent concordance with MLST results, makes it potentially valuable for S. aureus short-term epidemiological investigations and population dynamics as well.

Comparison of Two Multilocus Variable-Number Tandem-Repeat Methods and Pulsed-Field Gel Electrophoresis for Differentiating Highly Clonal Methicillin-Resistant Staphylococcus aureus Isolates

“…Previously, Hardy et al (5) showed the clustering of these epidemic strains was the same by SIRU typing and PFGE; however, subtyping differed between the two. Other studies comparing VNTR methods with PFGE have shown much greater concordance between methods at the group level compared to the subtyping level (3,10).…”

Comparisons between Geographically Diverse Samples of Carried Staphylococcus aureus

“…These can be readily identified as clusters of related genotypes which have diversified radially from "founder" genotypes (9), and because this organism is largely clonal (8), assignments of isolates to these groups is broadly robust to the many different typing methods employed (4,10,27). The high level of divergence between these lineages suggests that they are relatively ancient and temporally stable (7), and it is possible that isolated host populations may have been colonized by different S. aureus lineages in the past.…”

An Improved MLVF Method and Its Comparison with Traditional MLVF, spa Typing, MLST/SCCmec and PFGE for the Typing of Methicillin-Resistant Staphylococcus aureus

“…However, the concordance between CGE/MLVF and PFGE and other typing methods at the subtyping level was low. Other studies comparing VNTR methods with PFGE also have shown much greater concordance between methods at the cluster level compared to subtyping level [ 11 , 14 , 24 ].…”