Methods for concurrent identification and quantification of an unknown bioagent

• US 9,447,462 B2
• Filed: 01/27/2014
• Issued: 09/20/2016
• Est. Priority Date: 02/18/2004
• Status: Expired due to Fees

• Current Assignee: Ibis Biosciences Incorporated (Abbott Laboratories)
• Original Assignee: Ibis Biosciences Incorporated (Abbott Laboratories)
• Inventors: Ecker, David J., Sampath, Rangarajan, Blyn, Lawrence B., Hofstadler, Steven A., Hall, Thomas A.
• Primary Examiner(s): THOMAS, DAVID C
• Application Number:
  US14/164,559
• Publication Number:
  US 20140141502A1
• Time in Patent Office: 967 Days
• Field of Search: None
• US Class Current: 1/1
• CPC Class Codes: C07H 21/04 with deoxyribosyl as saccharide radical
• CPC Class Codes: C12Q 1/6851 Quantitative amplification
• CPC Class Codes: C12Q 1/6872 involving mass spectrometry
• CPC Class Codes: C12Q 2545/101 with an internal standard/control

Abstract

The present invention provides methods for the quantification of an unknown bioagent in a sample by amplification of nucleic acid of the bioagent, and concurrent amplification of a known quantity of a calibration polynucleotide from which are obtained a bioagent identifying amplicon and a calibration amplicon. Upon molecular mass analysis, mass and abundance data are obtained. The identity of the bioagent is then determined from the molecular mass of the bioagent identifying amplicon and the quantity of the identified bioagent in the sample is determined from the abundance data of the bioagent identifying amplicon and the abundance data of the calibration amplicon.

Claims

1. A system, comprising:

a) a nucleic acid amplification component, comprising a pair of primers designed to produce a bioagent identifying amplicon from a bioagent nucleic acid sequence acid under amplification conditions, a known quantity of a calibration polynucleotide comprising a calibration sequence designed to produce a calibration amplicon as a result of amplification with said primers under said amplification conditions wherein the 5′ and

3′

ends of said amplicons are the sequences of said pair of primers or complements thereof, and an amplification reaction vessel wherein said bioagent identifying amplicon and said calibration amplicon are concurrently amplified;

b) a molecular mass determination component; and

c) a molecular mass identification component comprising at least one computer comprising a processor and software, and a database of molecular masses of bioagent identifying amplicons from a plurality known bioagents wherein a match between the molecular mass of said bioagent identifying amplicon and the molecular mass of a bioagent identifying amplicon from a known bioagent in said database of molecular masses identifies said bioagent, a molecular mass of said calibration amplicon identifies said calibration amplicon, and molecular mass abundance data of said bioagent identifying ampicon and molecular mass abundance data of said calibration amplicon indicates the quantity of said bioagent.

2. The system of claim 1, wherein said calibration sequence:

a) comprises a chosen standard sequence of a bioagent identifying amplicon with the exception of a deletion of about 2 to about 8 consecutive nucleotide residues of said standard sequence;

b) comprises a chosen standard sequence of a bioagent identifying amplicon with the exception of an insertion of about 2 to about 8 consecutive nucleotide residues of said standard sequence;

or c) has at least 80% sequence identity with a chosen standard sequence of a bioagent identifying amplicon.

3. The system of claim 1, wherein said molecular mass determination component comprises a mass spectrometer.

4. The system of claim 1, wherein said molecular mass abundance data of said calibration amplicon comprises a standard curve wherein the amount of said calibration polynucleotide in said amplification reaction vessel is varied.

5. The system of claim 1, wherein said nucleic acid amplification component comprises a plurality of primer pairs which amplify a corresponding plurality of bioagent nucleic acid sequences and calibration sequences.

6. The system of claim 5, wherein said plurality of primer pairs comprise survey primers, division-wide primers, clade group primers and sub-species characteristic primers.

7. The system of claim 5, wherein said plurality of primer pairs comprise a plurality of bioagent identifying primer pairs within a plurality of core gene primer pairs.

8. The system of claim 7, wherein said core gene primer pairs hybridize to conserved regions of nucleic acid of genes encoding 16S and 23S rRNAs, RNA polymerase subunits, t-RNA synthetases, elongation factors, ribosomal proteins, protein chain initiation factors, cell division proteins, chaperonin groEL, chaperonin dnaK, phosphoglycerate kinase, NADH dehydrogenase, DNA ligases, and DNA topoisomerases.

9. The system of claim 1, further comprising a nucleic acid purification component.

10. The system of claim 9, wherein said nucleic acid purification component comprises one or more buffer manipulations, one or more salt manipulations, one or more thermal manipulations, one or more pH manipulations, one or more mechanical manipulations, one or more centrifugation manipulations, or one or more magnetic manipulations.

11. The system of claim 1, wherein said nucleic acid amplification component comprises a thermocycler.

12. The system of claim 1, wherein said nucleic acid amplification component comprises one or more salts, one or more buffers, one or more purified oligonucleotide primers, one or more dNTPs, or one or more enzymes.

13. The system of claim 1, further comprising a computer program on a computer readable medium configured to direct said processor to coordinate the operation of said nucleic acid amplification component, said molecular mass determination component, and said molecular mass identification component.

14. A system, comprising:

a) a nucleic acid amplification component, comprising a pair of primers designed to produce a bioagent identifying amplicon from a bioagent nucleic acid sequence acid under amplification conditions, a known quantity of a calibration polynucleotide comprising a calibration sequence designed to produce a calibration amplicon as a result of amplification with said primers under said amplification conditions wherein the 5′ and

3′

ends of said amplicons are the sequences of said pair of primers or complements thereof, and an amplification reaction vessel wherein said bioagent identifying amplicon and said calibration amplicon are concurrently amplified;

b) a base composition determination component comprising a component that measures the molecular masses of said bioagent identifying amplicon and said calibration amplicon, and a computer comprising a processor and software that calculates the base compositions of said molecular masses; and

c) a base composition identification component comprising at least one computer comprising a processor and software, and a database of base compositions of bioagent identifying amplions from a plurality of known bioagents wherein a match between the base composition of said bioagent identifying amplicon and the base composition of a bioagent identifying amplicon from a known bioagent in said database of base compositions identifies said bioagent, a base composition of said calibration amplicon identifies said calibration amplicon, and molecular mass abundance data of said bioagent identifying ampicon and molecular mass abundance data of said calibration amplicon indicates the quantity of said bioagent.

15. The system of claim 14, wherein said calibration sequence:

a) comprises a chosen standard sequence of a bioagent identifying amplicon with the exception of a deletion of about 2 to about 8 consecutive nucleotide residues of said standard sequence;

b) comprises a chosen standard sequence of a bioagent identifying amplicon with the exception of an insertion of about 2 to about 8 consecutive nucleotide residues of said standard sequence;

or c) has at least 80% sequence identity with a chosen standard sequence of a bioagent identifying amplicon.

16. The system of claim 14, wherein said molecular mass determination component comprises a mass spectrometer.

17. The system of claim 14, wherein said molecular mass abundance data of said calibration amplicon comprises a standard curve wherein the amount of said calibration polynucleotide in said amplification reaction vessel is varied.

18. The system of claim 14, wherein said nucleic acid amplification component comprises a plurality of primer pairs which amplify a corresponding plurality of bioagent nucleic acid sequences and calibration sequences.

19. The system of claim 14, wherein said plurality of primer pairs comprise survey primers, division-wide primers, clade group primers and sub-species characteristic primers.

20. The system of claim 14, wherein said plurality of primer pairs comprise a plurality of bioagent identifying primer pairs within a plurality of core gene primer pairs.