Methods, kits, and compositions useful in selecting an antibiotic to treat MRSA

1. A profiling assay for determining a Staphylococcus strain's resistance to one or more antibiotic agents, the profiling assay comprising a sequence-specific vanA assay, a sequence-specific aacA assay, and one or more sequence-specific assays chosen from a group consisting of a sequence-specific, blaZ assay, a sequence-specific ermA assay, a sequence-specific ermC assay, a sequence-specific tetK assay, a sequence-specific tetM assay, and a sequence-specific msrA assay, wherein the profiling assay is configured to screen the Staphylococcus strain using the sequence-specific assays to amplify selected target genes and to analyze results of the sequence-specific assays using relative quantification of expression of the genes targeted by the sequence-specific assays,

wherein the sequence-specific vanA assay is used to determine the Staphylococcus strain's resistance to aminoglycoside and comprises an oligonucleotide sequence consisting of SEQ ID NO: 1 and an oligonucleotide sequence consisting of SEQ ID NO: 2, and a probe comprising a label and a sequence consisting of SEQ ID NO: 3;

wherein the sequence-specific aacA assay is used to determine the Staphylococcus strain's resistance to vancomycin and comprises an oligonucleotide sequence consisting of SEQ ID NO: 4 and an oligonucleotide sequence consisting of SEQ ID NO: 5, and a probe comprising a label and a sequence consisting of SEQ ID NO: 6;

wherein the sequence-specific blaZ assay is used to determine the Staphylococcus strain's resistance to penicillin and comprises an oligonucleotide sequence consisting of SEQ ID NO: 7 and an oligonucleotide sequence consisting of SEQ ID NO: 8 and a probe comprising a label and a sequence consisting of SEQ ID NO: 9;

wherein the sequence-specific ermA assay is used to determine the Staphylococcus strain's resistance to macrolide and comprises an oligonucleotide sequence consisting of SEQ ID NO: 10 and an oligonucleotide sequence consisting of SEQ ID NO: 11 and a probe comprising a label and a sequence consisting of SEQ ID NO: 12;

wherein the sequence-specific ermC assay is used to determine the Staphylococcus strain's resistance to macrolide and comprises an oligonucleotide sequence consisting of SEQ ID NO: 13and an oligonucleotide sequence consisting of SEQ ID NO: 14 and a probe comprising a label and a sequence consisting of SEQ ID NO: 15;

wherein the sequence-specific tetK assay is used to determine the Staphylococcus strain's susceptibility to tetracycline and comprises an oligonucleotide sequence consisting of SEQ ID NO: 16 and an oligonucleotide sequence consisting of SEQ ID NO:17 and a probe comprising a label and a sequence consisting SEQ ID NO: 18;

wherein the sequence-specific tetM assay is used to determine the Staphylococcus strain's susceptibility to tetracycline and comprises an oligonucleotide sequence consisting of the sequence set forth in SEQ ID NO: 19 and an oligonucleotide sequence consisting of SEQ ID NO: 20 and a probe comprising a label and a sequence consisting of SEQ ID NO: 21; and

wherein the sequence-specific msrA assay is used to determine the Staphylococcus strain's resistance to macrolide and comprises an oligonucleotide sequence consisting of SEQ ID NO: 22 and an oligonucleotide sequence consisting of SEQ ID NO: 23 and a probe comprising a label and a sequence consisting of SEQ ID NO: 24.

2. The profiling assay of claim 1 , wherein the Staphylococcus strain is selected from the group consisting of MRSA, MSSA, MRSE, and MSSE.

3. The profiling assay of claim 1 , the assay is a type of analysis chosen from PCR and RT-PCR.

4. The profiling assay of claim 1 , wherein the assays comprise the sequence-specific vanA assay, the sequence-specific aacA assay, the sequence-specific ermA assay, and the sequence-specific ermC assay.

5. The profiling assay of claim 4 , wherein sequence-specific ermA assay and the sequence-specific ermC assay are performed together as a multiplex assay.

6. The profiling assay of claim 1 , wherein assays comprise the sequence-specific vanA assay, the sequence-specific aacA assay, the sequence-specific blaZ assay, the sequence-specific ermA assay, the sequence-specific ermC assay, the sequence-specific tetK assay, the sequence-specific tetM assay, and the sequence-specific msrA assay.

7. A method for determining a Staphylococcus strain's resistance to one or more antibiotic agents, comprising:

a. receiving a sample comprising Staphylococcus;

b. screening the sample by conducting sequence-specific PCR-based assays comprising vanA assay, aacA assay, and one or more sequence-specific assays selected from the group consisting of blaZ assay, ermA assay, ermC assay, tetK assay, tetM assay, and msrA assay, wherein:

the vanA assay comprises a primer set comprising:

a primer having a sequence consisting of SEQ ID No: 1;

a primer having a sequence consisting of SEQ ID NO: 2; and

a probe comprising a label and a sequence consisting of the sequence set forth in SEQ ID NO:3;

the aacA assay comprises a primer set comprising:

a primer having a sequence consisting of SEQ ID No: 4;

a primer having a sequence consisting of SEQ ID NO: 5; and

a probe comprising a label and a sequence consisting of SEQ ID NO:6;

the blaZ assay comprises a primer set comprising:

a primer having a sequence consisting of SEQ ID No: 7;

a primer having a sequence consisting of SEQ ID NO: 8; and

a probe comprising a label and a sequence consisting of SEQ ID NO:9;

the ermA assay comprises a primer set comprising:

a primer having a sequence consisting of SEQ ID No: 10;

a primer having a sequence consisting of SEQ ID NO: 11; and

a probe comprising a label and a sequence consisting of SEQ ID NO:12;

the ermC assay comprises a primer set comprising:

a primer having a sequence consisting of SEQ ID No: 13;

a primer having a sequence consisting of SEQ ID NO: 14; and

a probe comprising a label and a sequence consisting of SEQ ID NO:15;

the tetK assay comprises a primer set comprising:

a primer having a sequence consisting of SEQ ID No: 16;

a primer having a sequence consisting of SEQ ID NO: 17; and

a probe comprising a label and a sequence consisting of the sequence set forth in SEQ ID NO:18;

the tetM assay comprises a primer set comprising:

a primer having a sequence consisting of the sequence set forth in SEQ ID No: 19;

a primer having a sequence consisting of SEQ ID NO: 20; and

a probe comprising a label and a sequence consisting of SEQ ID NO:21;

the msrA assay comprises a primer set comprising:

a primer having a sequence consisting of SEQ ID No: 22;

a primer having a sequence consisting of SEQ ID NO: 23; and

a probe comprising a label and a sequence consisting of SEQ ID NO:24;

c. analyzing results obtained from the sequence-specific PCR-based assays to determine the presence or absence of a vanA gene, an aacA gene, and one or more genes selected from the group consisting of: a blaZ gene, an ermA gene, an ermC gene, a tetK gene, a tetM gene and a msrA gene, wherein analyzing the results comprises relative quantification of expression of the genes targeted by the sequence-specific PCR-based assays; and

d. identifying the Staphylococcus strain contained in the sample as resistant to one or more antibiotics based on the analysis of the selected sequence-specific PCR-based assays.

8. The method of claim 7 , wherein the presence of the vanA gene indicates vancomycin resistance;

wherein the presence of the aacA gene indicates aminoglycoside resistance;

wherein the presence of the blaZ gene indicates penicillin resistance;

wherein the presence of ermA and ermC indicate macrolide resistance;

wherein the absence of tetM and tetK indicate susceptibility to tetracycline; and

wherein the presence of msrA indicates macrolide resistance.

9. The method of claim 7 , wherein the sample comprises MRSA, MRSE, MSSA, or MSSE.

10. The method of claim 7 , wherein one or more of the probes comprise a label.

11. The method of claim 7 , wherein the ermA assay and the ermC assay are performed as a single multiplex assay.

12. The method of claim 7 , wherein the sequence-specific PCR-based assays comprising the vanA assay, the aacA assay, the ermA assay, and the ermC assay.

13. The method of claim 12 , wherein the ermA assay and the ermC assay are performed as a single multiplex assay.

14. The method of claim 7 , wherein the sequence-specific PCR-based assays comprising the vanA assay, the aacA assay, the ermA assay, the ermC assay, the blaZ assay, the tetM assay, the tetK assay, and the msrA assay.

15. The method of claim 14 , wherein the erm A and ermC assays and the tetM and tetK assays are performed as single multiplex assays, respectively.