Compositions for use in identification of bacteria

• US 8,013,142 B2
• Filed: 03/13/2007
• Issued: 09/06/2011
• Est. Priority Date: 09/11/2003
• Status: Expired due to Fees

• Current Assignee: Ibis Biosciences Incorporated
• Original Assignee: Ibis Biosciences Incorporated
• Inventors: Sampath, Rangarajan, Hall, Thomas A., Blyn, Lawrence, Ecker, David J.
• Primary Examiner(s): WOOLWINE, SAMUEL C
• Application Number:
  US11/685,610
• Publication Number:
  US 20070243544A1
• Time in Patent Office: 1,638 Days
• Field of Search: None
• US Class Current: 536/24.33
• CPC Class Codes: C12Q 1/6816 characterised by the detection means C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6858 Allele-specific amplification
• CPC Class Codes: C12Q 1/689 for bacteria
• CPC Class Codes: C12Q 2537/143 Multiplexing, i.e. use of multiple primers or probes in a single reaction, usually for simultaneously analyse of multiple analysis
• CPC Class Codes: C12Q 2565/627 being a mass spectrometer
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers

Abstract

The present invention provides compositions, kits and methods for rapid identification and quantification of bacteria by molecular mass and base composition analysis.

Claims

1. An oligonucleotide primer pair comprising a forward primer and a reverse primer, wherein said forward primer comprises a sequence 95% identical to SEQ ID NO:

399, and wherein said reverse primer comprises the sequence of SEQ ID NO;

1041.

2. The oligonucleotide primer pair of claim 1, wherein said forward primer comprises the sequence of SEQ ID NO:

399.

3. The oligonucleotide primer pair of claim 1, wherein said forward primer is SEQ ID NO:

399.

4. The oligonucleotide primer pair of claim 1, wherein said reverse primer is SEQ ID NO:

1041.

5. The oligonucleotide primer pair of claim 1, wherein at least one of said forward primer and said reverse primer comprises at least one modified nucleobase.

6. The oligonucleotide primer pair of claim 5, wherein at least one of said at least one modified nucleobase is a mass modified nucleobase.

7. The oligonucleotide primer pair of claim 6, wherein said mass modified nucleobase is 5-Iodo-C.

8. The composition of claim 6, wherein said mass modified nucleobase comprises a molecular mass modifying tag.

9. The oligonucleotide primer pair of claim 5, wherein at least one of said at least one modified nucleobase is a universal nucleobase.

10. The oligonucleotide primer pair of claim 9, wherein said universal nucleobase is inosine.

11. The oligonucleotide primer pair of claim 1, wherein at least one of said forward primer and said reverse primer comprises a T residue at its 5′

end.

12. A kit for identifying a Staphylococcus aureus bioagent comprising the oligonucleotide primer pair of claim 1, and at least one additional primer pair, wherein the primers of each of said at least one additional primer pair are designed to hybridize to sequence regions within a Staphylococcus aureus gene selected from the group consisting of mecA, mecR1, ermA, tufB, pvluk, mupR and nuc.

13. The kit of claim 12 wherein said at least one additional primer pair is one or more primer pairs selected from the group consisting of SEQ ID NO:

217;

SEQ ID NO;

1167, SEQ ID NO;

430;

SEQ ID NO;

1321, SEQ ID NO;

456;

SEQ ID NO;

1261, SEQ ID NO;

174;

SEQ ID NO;

853, SEQ ID NO;

288;

SEQ ID NO;

1269, SEQ ID NO;

698;

SEQ ID NO;

1420, or SEQ ID NO;

205;

SEQ ID NO;

876.

14. The kit of claim 12 wherein each primer of said at least one additional primer pair has at least 70% sequence identity with one of SEQ ID NO:

217, SEQ ID NO;

1167, SEQ ID NO;

399, SEQ ID NO;

1041, SEQ ID NO;

456, SEQ ID NO;

1261, SEQ ID NO;

430, SEQ ID NO;

1321, SEQ ID NO;

288, SEQ ID NO;

1269, SEQ ID NO;

698, SEQ ID NO;

1420, SEQ ID NO;

205, SEQ ID NO;

876, SEQ ID NO;

174, and SEQ ID NO;

853.