Abstract: The present invention comprises methods of treating an infection using a pharmaceutical composition comprising an active ingredient selected from Table 1. In some aspects, the infection can be caused by one or more pathogens, including fungal pathogens. For example, the infection may be Valley Fever.

Abstract: The present invention provides a method of detecting Staphylococcus aureus in a subject, by contacting a sample obtained from the subject with at least one detectably labeled probe of the invention or detecting in the sample identity to a sequence of the invention. The invention is also directed to kits, microarrays and detectable Staphylococcus aureus polynucleotide probes useful in detecting the presence of Staphylococcus aureus.

Abstract: Embodiments of the invention provide a method of detecting one or more strains of Klebsiella pneumoniae. The method may include forming a plurality of mixtures for nucleic amplification. The method can include amplification of specific sequences within the K. pneumonia genome that can provide definitive information to distinguish between one or more types or strains of K. pneumonia.

Abstract: The present invention comprises methods of treating an infection using a pharmaceutical composition comprising an active ingredient selected from Table 1. In some aspects, the infection can be caused by one or more pathogens, including fungal pathogens.

Abstract: The present invention provides a method of detecting one or more Klebsiella species within a sample from a subject, the method comprising: subjecting DNA and/or RNA from the sample to a PCR amplification reaction using primer pairs targeting species-specific canonical single nucleotide polymorphisms (canSNPs); and analyzing amplification products resulting from the PCR amplification reaction to detect the one or more Klebsiella species. The present invention also provides a kit for detection of one or more Klebsiella species, Klebsiella clonal groups, AMR genes, and/or virulence genes, the kit comprising primer pairs targeting species-specific canSNPs, K. pneumoniae genes M1 and M2, clonal group-specific canSNPs, AMR genes, and/or virulence genes.

Abstract: Embodiments of the invention provide a method of detecting one or more strains of Klebsiella pneumoniae. The method may include forming a plurality of mixtures for nucleic amplification. The method can include amplification of specific sequences within the K. pneumonia genome that can provide definitive information to distinguish between one or more types or strains of K. pneumonia.

Abstract: The present invention comprises methods of treating an infection using a pharmaceutical composition comprising an active ingredient selected from Table 1. In some aspects, the infection can be caused by one or more pathogens, including fungal pathogens. For example, the infection may be Valley Fever.

Abstract: The present invention relates to method of detecting and characterizing one or more Borrelia species causing Lyme Disease or tick-borne relapsing fever within a sample from a subject, the method comprising: a) subjecting DNA and/or RNA from the sample to a PCR amplification reaction using primer pairs targeting at least one region of Borrelia 16S rRNA and at least one region of flaB, ospA, ospB, ospC, glpQ, 16S-23S intergenic spacer (IGS1), 5S-23S intergenic spacer (IGS2), bbk32, dbpA, dbpB, and/or p66; and b) analyzing amplification products resulting from the PCR amplification reaction to detect the one or more Borrelia species.

Abstract: A method of detecting Enterovirus D68 is provided. The method may include adding to a mixture containing the sample from the subject, (a) a first forward primer comprising SEQ ID NO: 1, (b) a second forward primer comprising SEQ ID NO: 2, (c) a third forward primer comprising SEQ ID NO: 3, (d) a first reverse primer comprising SEQ ID NO: 4, and (e) a second reverse primer comprising SEQ ID NO: 5, subjecting the mixture to conditions that allow nucleic acid amplification, and detecting the presence or absence of Enterovirus D68 by analyzing the nucleic acid amplification products. The forward primers may include a first universal tail sequence and reverse primers may include a second universal tail sequence. The nucleic acid amplification products may be sequenced using next-generation sequencing.

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.

Abstract: The present invention provides multiplex assays, methods and kits that may be used to detect and confirm the presence of MRSA in a sample. The methods include real-time PCR assays, and the kits and compositions include oligonucleotides used as primers and probes. The present invention further comprises assays useful to identify and differentiate MRSA, MSSA, MRSE, MSSE, MRCNS and MSCNS in a sample.

Abstract: An Amplicon Sequencing Analysis Pipeline (ASAP) system (120, 600) characterizes a genetic sample. The ASAP system (120, 600) receives assay configuration data individually associating reference sequences and genetic characteristics. The ASAP system (120, 600) processes amplicon sequencing data and the reference sequences to characterize the genetic sample based on the individual associations between the reference sequences and the genetic characteristics in the assay configuration data. The ASAP (120, 600) system transfers genetic data indicating the genetic characteristics for the genetic sample and indicating interpretation metrics for amplicon sequencing read depth and quality related to the genetic characteristics.

Abstract: The present technology provides methods and kits that may be used to detect and quantify the presence of Coccidioides species. The methods include quantification real-time PCR assays, and the kits and compositions include oligonucleotides used as primers and probes.

Abstract: The present invention provides a method, a kit and composition for determining MRSA and other Staphylococcus strain resistance to one or more antibiotic agents through detecting the presence of the respective antibiotic resistance gene. The methods include real-time PCR assays, and the kits and compositions include oligonucleotides used as primers and probes.

Abstract: Embodiments of the invention provide a method of detecting one or more strains of Klebsiella pneumoniae. The method may include forming a plurality of mixtures for nucleic amplification. The method can include amplification of specific sequences within the K. pneumonia genome that can provide definitive information to distinguish between one or more types or strains of K. pneumonia.

Abstract: The present technology provides methods and kits that may be used to detect and quantify the presence of Coccidioides species. The methods include quantification real-time PCR assays, and the kits and compositions include oligonucleotides used as primers and probes.

Abstract: The present invention comprises methods of treating an infection using a pharmaceutical composition comprising an active ingredient selected from Table 1. In some aspects, the infection can be caused by one or more pathogens, including fungal pathogens. For example, the infection may be Valley Fever.

Abstract: The present invention provides assays, methods and kits that may be used to detect and differentiate MRSA isolates, e.g., USA100, USA300 and USA600 strains.

Abstract: The invention pertains to sequences, methods, and kits useful in the identification of and differentiation between Burkholderia pseudomallei and Burkholderia mallei. The methods generally involve the addition of oligonucleotides to mixtures containing nucleic acid isolated from a sample and performing nucleic acid amplification on the mixture.

Abstract: The present invention provides assays, methods and kits that may be used to detect and differentiate MRSA isolates, e.g., USA100, USA300 and USA600 strains.