DNA Microarray Profiling of a Diverse Collection of Nosocomial Methicillin-Resistant Staphylococcus aureus Isolates Assigns the Majority to the Correct Sequence Type and Staphylococcal Cassette Chromosomemec(SCCmec) Type and Results in the Subsequent Identification and Characterization of Novel SCCmec-SCCM1Composite Islands

Abstract

ABSTRACTOne hundred seventy-five isolates representative of methicillin-resistantStaphylococcus aureus(MRSA) clones that predominated in Irish hospitals between 1971 and 2004 and that previously underwent multilocus sequence typing (MLST) and staphylococcal cassette chromosomemec(SCCmec) typing were characterized byspatyping (175 isolates) and DNA microarray profiling (107 isolates). The isolates belonged to 26 sequence type (ST)-SCCmectypes and subtypes and 35spatypes. The array assigned all isolates to the correct MLST clonal complex (CC), and 94% (100/107) were assigned an ST, with 98% (98/100) correlating with MLST. The array assigned all isolates to the correct SCCmectype, but subtyping of only some SCCmecelements was possible. Additional SCCmec/SCC genes or DNA sequence variation not detected by SCCmectyping was detected by array profiling, including the SCC-fusidic acid resistance determinant Q6GD50/fusC. Novel SCCmec/SCC composite islands (CIs) were detected among CC8 isolates and comprised SCCmecIIA-IIE, IVE, IVF, or IVg and accrAB4-SCC element with 99% DNA sequence identity to SCCM1from ST8/t024-MRSA, SCCmecVIII, and SCC-CI inStaphylococcus epidermidis. The array showed that the majority of isolates harbored one or more superantigen (94%; 100/107) and immune evasion cluster (91%; 97/107) genes. Apart from fusidic acid and trimethoprim resistance, the correlation between isolate antimicrobial resistance phenotype and the presence of specific resistance genes was ≥97%. Array profiling allowed high-throughput, accurate assignment of MRSA to CCs/STs and SCCmectypes and provided further evidence of the diversity of SCCmec/SCC. In most cases, array profiling can accurately predict the resistance phenotype of an isolate.