Systematic Derivation of Marker Sets for Staphylococcal Cassette Chromosome mec Typing

Abstract

The aim of this study was to identify optimized sets of genotyping targets for the staphylococcal cassette chromosome mec (SCC mec ). We analyzed the gene contents of 46 SCC mec variants in order to identify minimal subsets of targets that provide useful resolution. This was achieved by firstly identifying and characterizing each available SCC mec element based on the presence or absence of 34 binary targets. This information was used as input for the software “Minimum SNPs,” which identifies the minimum number of targets required to differentiate a set of genotypes up to a predefined Simpson's index of diversity ( D ) value. It was determined that 22 of the 34 targets were required to genotype the 46 SCC mec variants to a D of 1. The first 6, 9, 12, and 15 targets were found to define 21, 29, 35, and 39 SCC mec variants, respectively. The genotypes defined by these marker subsets were largely consistent with the relationships between SCC mec variants and the accepted nomenclature. Consistency was made virtually complete by forcing the computer program to include ccr1 and ccr5 in the target set. An alternative target set biased towards discriminating abundant SCC mec variants was derived by analyzing an input file in which common SCC mec variants were repeated, thus ensuring that markers that discriminate abundant variants had a large effect on D . Finally, it was determined that mecA single nucleotide polymorphisms (SNPs) can increase the overall genotyping resolution, as different mecA alleles were found in otherwise identical SCC mec variants.