The present invention is based on the discovery of novel polymorphisms (SNPs) in the penicillin binding protein (pbp3) gene in Staphylococcus aureus. The presence of G88A and/or G2047A SNPs provides an accurate, reliable biomarker for the presence of Methicillin Resistant Staphylococcus aureus (MRSA), specifically the community-associated MRSA (CA-MRSA). The present invention provides reagents used for detecting the SNPs as well as methods of identifying and using these variants to screen subjects for presence of CA-MRSA. The methods involve isolating a biological sample from a mammal (preferably a human) and testing for the presence of a SNP in the pbp3 gene which is associated with CA-MRSA.