Improved MLVA assay for Staphylococcus aureus providing a highly informative genotyping technique together with strong phylogenetic value.
Résumé
We describe an improved Multiple Locus Variable Number of Tandem repeats (VNTR) Analysis (MLVA) scheme for the genotyping of Staphylococcus aureus. We compare its performance to Multilocus Sequence Typing (MLST) and spa typing in a survey of 309 strains. This collection includes 87 epidemic Methicillin-resistant S. aureus (MRSA) strains of the Harmony collection, 75 clinical strains representing the major MLST clonal complexes (CC) (50 Methicillin-sensitive S. aureus (MSSA), 25 MRSA), 135 strains of nasal carriage (133 MSSA, 2 MRSA) and 13 published S. aureus genome sequences. The results show excellent concordance between the techniques and demonstrate the higher discriminatory power of MLVA as compared to both MLST and spa typing. Two hundred and forty-two genotypes are discriminated with 14 VNTR loci (diversity index: 0.9965, 95% confidence interval (CI) 0.9947-0.9984). Using a cut-off value of 45%, 21 clusters are observed corresponding to the clonal complexes (CC) previously defined by MLST. The variability of the different tandem repeats allows epidemiological studies as well as the follow-up of the evolution of clonal complexes and the identification of potential ancestors. The 14 loci can conveniently be analysed in two steps, based upon a first-line simplified assay comprising a subset of 10 loci (panel1) and a second panel of 4 loci (panel2) providing higher resolution when needed. In conclusion, the MLVA scheme proposed here in combination with available on-line genotyping databases (including http://mlva.u-psud.fr/), multiplexing and automatic sizing can provide the basis for the almost real-time large scale population monitoring of S. aureus.