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US 7,741,036 B2Granted
Method for rapid detection and identification of bioagents
AssigneeIbis Biosciences, Inc.
InventorsDavid J. Ecker, Richard H. Griffey, Rangarajan Sampath, Steven Hofstadler, John McNeil
Life of this patent
Estimating the term…
Abstract
Method for detecting and identifying unknown bioagents, including bacteria, viruses and the like, by a combination of nucleic acid amplification and molecular weight determination using primers which hybridize to conserved sequence regions of nucleic acids derived from a bioagent and which bracket variable sequence regions that uniquely identify the bioagent. The result is a “base composition signature” (BCS) which is then matched against a database of base composition signatures, by which the bioagent is identified.
Claims74
A method of identifying a bacterium comprising:
- amplifying nucleic acid from said bacterium with at least one pair of oligonucleotide primers to produce an amplification product, wherein said pair of oligonucleotide primers are not specific for a particular bacterial genus, wherein one member of said pair of primers hybridizes to a first conserved region of nucleic acid encoding ribosomal RNA and the other member of said pair of primers hybridizes to a second conserved region of said nucleic acid encoding ribosomal RNA wherein said first and second conserved regions flank a variable nucleic acid region which varies among bacteria;
- determining the molecular mass of said amplification product by mass spectrometry;
- and
- comparing said molecular mass to calculated or measured molecular masses of amplification products of known bacteria produced by using said pair of oligonucleotide primers, thereby identifying said bacterium.
1 more element
A method of identifying a bacterium comprising:
- amplifying nucleic acid from said bacterium with at least one pair of oligonucleotide primers to produce an amplification product, wherein said pair of oligonucleotide primers are not specific for a particular bacterial genus, wherein one member of said pair of primers hybridizes to a first conserved region of nucleic acid encoding a protein involved in translation, replication, recombination and repair, transcription, nucleotide metabolism, amino acid metabolism, lipid metabolism, energy generation, uptake or secretion and the other member of said pair of primers hybridized to a second conserved region of said nucleic acid encoding a protein involved in translation, replication, recombination and repair, transcription, nucleotide metabolism, amino acid metabolism, lipid metabolism, energy generation, uptake or secretion wherein said first and second conserved regions flank a variable nucleic acid region which varies among bacteria;
- determining the molecular mass of said amplification product by mass spectrometry;
- and
- comparing said molecular mass to calculated or measured molecular masses of amplification products of known bacteria produced by using said pair of oligonucleotide primers, thereby identifying said bacterium.
1 more element
A method of identifying a bacterium comprising:
- amplifying nucleic acid from said bacterium with at least one pair of oligonucleotide primers to produce an amplification product, wherein said pair of oligonucleotide primers are not specific for a particular bacterial genus, wherein one member of said pair of primers hybridizes to a first conserved region of nucleic acid encoding ribosomal RNA and the other member of said pair of primers hybridizes to a second conserved region of said nucleic acid encoding ribosomal RNA wherein said first and second conserved regions flank a variable nucleic acid region which varies among bacteria;
- determining the molecular mass of said amplification product by mass spectrometry;
- calculating the base composition of said amplification product from said molecular mass;
- and
- comparing said base composition to calculated or measured base compositions of amplification products of known bacteria produced by using said pair of oligonucleotide primers, thereby identifying said bacterium.
2 more elements
A method of identifying a bacterium comprising:
- amplifying nucleic acid from said bacterium with at least one pair of oligonucleotide primers to produce an amplification product, wherein said pair of oligonucleotide primers are not specific for a particular bacterial genus, wherein one member of said pair of primers hybridizes to a first conserved region of nucleic acid encoding a protein involved in translation, replication, recombination and repair, transcription, nucleotide metabolism, amino acid metabolism, lipid metabolism, energy generation, uptake or secretion and the other member of said pair of primers hybridized to a second conserved region of said nucleic acid encoding a protein involved in translation, replication, recombination and repair, transcription, nucleotide metabolism, amino acid metabolism, lipid metabolism, energy generation, uptake or secretion wherein said first and second conserved regions flank a variable nucleic acid region which varies among bacteria;
- determining the molecular mass of said amplification product by mass spectrometry;
- calculating the base composition of said amplification product from said molecular mass;
- and
- comparing said base composition to calculated or measured base compositions of amplification products of known bacteria produced by using said pair of oligonucleotide primers, thereby identifying said bacterium.
2 more elements
Dependencies are inferred from the claim text.