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US 11,993,812 B2Granted
Systems and methods of diagnosing and characterizing infections
AssigneesThe Translational Genomics Research Institute, Arizona Board of Regents acting for and on behalf of Northern Arizona University
InventorsElizabeth Driebe, Jolene Bowers, David Engelthaler, Paul Keim
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Abstract
Embodiments of the invention include methods of identifying microorganisms and/or diagnosing infections in subjects cause by microorganisms. Embodiments of the invention may also include further characterizing (e.g., determining the presence of one or more antibiotic resistance markers) the microorganisms and determining a strain identity of the microorganisms.
Claims20
A method of detecting and characterizing one or more microorganisms within a sample, the method comprising the steps of:
- receiving the sample;
- extracting a template from the sample;
- performing a multiplex polymerase chain reaction assay comprising the steps of:
- amplifying a first marker from the template to create a first amplicon, comprising mixing the template with a first oligonucleotide comprising a sequence selected from SEQ ID Nos:
- 1-49, 54-109;
- and a second oligonucleotide comprising a sequence selected from SEQ ID Nos:
- 1-49, 54-109, wherein the first oligonucleotide and the second oligonucleotide independently comprise sequences selected from SEQ ID Nos:
- 1-49, 54-109 and wherein the first marker is specific for at least a genus of microorganism;
- amplifying a second marker from the template to create a second amplicon, comprising mixing the template with a third oligonucleotide and a fourth oligonucleotide, wherein the second marker is specific for at least one antibiotic resistance gene;
- amplifying a third marker from the template to create a third amplicon, comprising mixing the template with a fifth oligonucleotide and a sixth oligonucleotide comprising, wherein the third marker is specific for strain identity and/or lineage of the one or more microorganisms;
- wherein the multiplex polymerase chain reaction assay is performed within a single reaction vessel;
- and
- sequencing the first, second, and third amplicons to detect and characterize the one or more microorganisms.
10 more elements
A method of detecting and characterizing one or more microorganisms within a sample, the method comprising the steps of:
- receiving the sample;
- extracting a template from the sample;
- performing a multiplex polymerase chain reaction assay comprising the steps of:
- amplifying a first marker from the template to create a first amplicon, comprising mixing the template with a first oligonucleotide comprising a sequence selected from SEQ ID Nos:
- 54-57;
- and a second oligonucleotide comprising a sequence selected from SEQ ID Nos:
- 54-57, wherein the first oligonucleotide and the second oligonucleotide independently comprise sequences selected from SEQ ID Nos:
- 54-57 and wherein the first marker is specific for at least a genus of microorganism;
- amplifying a second marker from the template to create a second amplicon, comprising mixing the template with a third oligonucleotide and a fourth oligonucleotide, wherein the second marker is specific for at least one antibiotic resistance gene;
- amplifying a third marker from the template to create a third amplicon, comprising mixing the template with a fifth oligonucleotide and a sixth oligonucleotide, wherein the third marker is specific for strain identity and/or lineage of the one or more microorganisms;
- wherein the multiplex polymerase chain reaction assay is performed within a single reaction vessel;
- and
- sequencing the first, second, and third amplicons to detect and characterize the one or more microorganisms.
10 more elements
A method of detecting and characterizing one or more microorganisms within a sample, the method comprising the steps of:
- extracting a template from the sample;
- performing a multiplex polymerase chain reaction assay comprising the steps of:
- amplifying a first marker from the template to create a first amplicon, comprising mixing the template with a first oligonucleotide comprising a sequence selected from SEQ ID Nos:
- 1-49, 54-109;
- and a second oligonucleotide comprising a sequence selected from SEQ ID Nos:
- 1-49, 54-109, wherein the first oligonucleotide and the second oligonucleotide independently comprise sequences selected from SEQ ID Nos:
- 1-49, 54-109 and wherein the first marker is specific for at least a genus of microorganism;
- amplifying a second marker from the template to create a second amplicon, comprising mixing the template with a third oligonucleotide and a fourth oligonucleotide, wherein the second marker is specific for at least one antibiotic resistance gene;
- and
- amplifying a third marker from the template to create a third amplicon, comprising mixing the template with a fifth oligonucleotide and a sixth oligonucleotide comprising, wherein the third marker is specific for strain identity and/or lineage of the one or more microorganisms;
- and
- sequencing the first, second, and third amplicons to detect and characterize the one or more microorganisms.
9 more elements
Dependencies are inferred from the claim text.