Identification and detection of USA300 methicillin-resistant Staphylococcus aureus clones with a partial deletion in the ccrB2 gene on the type IV SCCmec element. Staphylococcus aureus strain:TSI637

The staphylococcal cassette chromosome (SCC) mec typing is important method used to rapidly screen USA300 clones, which are highly pathogenetic methicillin-resistant Staphylococcus aureus (MRSA). Here, we report USA300-like strains (named as pseudo USA300), which could not be identified as SCCmec type IV by the conventional PCR method. Among the 82 USA300 strains, 23.2% (19 isolates) failed to identify as SCCmec type IV. Genome analysis revealed that the pseudo USA300 has a 12 bp deletion at the primer binding site of ccrB2, located on the SCCmec element. We developed a new primer and could accurately identify the SCCmec type of all USA300 and pseudo USA300 strains. Our findings showed that at least 20% of the USA300 clones have a partially defective ccrB2 gene. The new primer designed in this study is useful for screening USA300 clones.