A method of detecting in a sample a methicillin-resistant Staphylococcus aureus (MRSA) having an insertion of an SCCmec cassette within Staphylococcus aureus chromosomal DNA, the method comprising A) performing on a sample an amplification reaction to detect MRSA which can amplify only a junction of an inserted SCC mec cassette and Staphylococcus aureus chromosomal DNA and a region of mecA, and B) detecting, within the products of the amplification, the presence or absence of each of the junction and mecA, wherein if the sample contains MRSA, the presence of both the junction and mecA in the sample is detected, wherein the method comprises the steps of: bringing, in a single container, the biological sample in contact with a) a first oligonucleotide set comprising a first oligonucleotide having a nucleic acid sequence that specifically hybridizes to an extremity junction region of a SCC mec cassette, and a second oligonucleotide having a nucleic acid sequence that specifically hybridizes to a Staphylococcus aureus chromosomal DNA region flanking said SCCmec cassette to form a first reaction product of the biological sample and the first and second oligonucleotides, and b) a second oligonucleotide set comprising a third oligonucleotide having a nucleotide sequence that specifically hybridizes to a first region of mecA nucleic acid and a fourth oligonucleotide having a nucleotide sequence that specifically hybridizes to a second region of mecA nucleic acid to form a second reaction product of the biological sample and the third and fourth oligonucleotides wherein the contacting step further comprises performing a transcription-based amplification reaction such as NASBA or DNA-NASBA using oligonucleotide sets (a) and (b) as primers; and identifying the presence of MRSA by detecting both a first and a second reaction product wherein the identifying step comprises detecting the presence or absence of an amplification product from both oligonucleotide sets. A) performing on a sample an amplification reaction to detect MRSA which can amplify only a junction of an inserted SCC mec cassette and Staphylococcus aureus chromosomal DNA and a region of mecA, and B) detecting, within the products of the amplification, the presence or absence of each of the junction and mecA, a) a first oligonucleotide set comprising a first oligonucleotide having a nucleic acid sequence that specifically hybridizes to an extremity junction region of a SCC mec cassette, and a second oligonucleotide having a nucleic acid sequence that specifically hybridizes to a Staphylococcus aureus chromosomal DNA region flanking said SCCmec cassette to form a first reaction product of the biological sample and the first and second oligonucleotides, and a first oligonucleotide having a nucleic acid sequence that specifically hybridizes to an extremity junction region of a SCC mec cassette, and a second oligonucleotide having a nucleic acid sequence that specifically hybridizes to a Staphylococcus aureus chromosomal DNA region flanking said SCCmec cassette to form a first reaction product of the biological sample and the first and second oligonucleotides, and b) a second oligonucleotide set comprising a third oligonucleotide having a nucleotide sequence that specifically hybridizes to a first region of mecA nucleic acid and a fourth oligonucleotide having a nucleotide sequence that specifically hybridizes to a second region of mecA nucleic acid to form a second reaction product of the biological sample and the third and fourth oligonucleotides wherein the contacting step further comprises performing a transcription-based amplification reaction such as NASBA or DNA-NASBA using oligonucleotide sets (a) and (b) as primers; and identifying the presence of MRSA by detecting both a first and a second reaction product wherein the identifying step comprises detecting the presence or absence of an amplification product from both oligonucleotide sets. a third oligonucleotide having a nucleotide sequence that specifically hybridizes to a first region of mecA nucleic acid and a fourth oligonucleotide having a nucleotide sequence that specifically hybridizes to a second region of mecA nucleic acid to form a second reaction product of the biological sample and the third and fourth oligonucleotides wherein the contacting step further comprises performing a transcription-based amplification reaction such as NASBA or DNA-NASBA using oligonucleotide sets (a) and (b) as primers; and