The Translational Genomics Research Institute

Northern Arizona University

University of California

Centers for Disease Control and Prevention

Universite Du Luxembourg

David Engelthaler

Paul S Keim

Elizabeth Driebe

Jolene Bowers

James M Schupp

Erin Kelley

Michael J Valentine

Bridget Barker

Hongwei “Holly” Yin

Donald Chow

Darrin Lemmer

Rebecca E Colman

Antonino Catanzaro

Timothy Rodwell

John D Gillece

David R Smith

Lance B Price

Cindy Liu

Paul Wilmes

Nathan Christopher Nieto

Nathan Hicks

Brandi Limbago

James K Rasheed

Linda McDougal

Valerie S Albrecht

Emilie Muller

Jason Sahl

Viacheslav Fofanov

David Smith

David Wagner

The present invention provides methods of detecting a biothreat agent in a sample, comprising detecting at least one biothreat-specific amplicon in the sample. The methods also encompass confirming the absence of the biothreat agent by detecting Near Neighbor specific amplicons to avoid false positive results.

Methods and assays for detection and subtyping of microbial pathogens

The present invention provides a method of detecting a heteroresistant population of a pathogen in a sample, the method comprising: a) providing a sample comprising a population of a pathogen; b) extracting nucleic acids from the sample; c) amplifying a target locus of the genome of the pathogen in the extracted nucleic acids, wherein the target locus comprises at least one minor variant associated with drug resistance in the pathogen; d) consecutively sequencing both overlapping nucleic acid strands from a single DNA molecule amplified from the target locus on a Next Generation Sequencing (NGS) platform; e) applying an alignment algorithm to sequencing data from the overlapping nucleic acid strands; and f) performing an analysis of the aligned sequencing data to detect the at least one minor variant and heteroresistant population of the pathogen.

Single molecule-overlapping read analysis for minor variant mutation detection in pathogen samples

The present invention provides a method of detecting one or morespecies 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 morespecies. The present invention also provides a kit for detection of one or morespecies,clonal groups, AMR genes, and/or virulence genes, the kit comprising primer pairs targeting species-specific canSNPs,genes M1 and M2, clonal group-specific canSNPs, AMR genes, and/or virulence genes.

Methods and kits to identifystrains

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.

Systems and methods of diagnosing and characterizing infections

The present invention provides a method of detectingin 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 detectablepolynucleotide probes useful in detecting the presence of

Methods and assays for subtypingclonal complex 8 strains

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.

Compositions and methods for the treatment of fungal infections

An Amplicon Sequencing Analysis Pipeline (ASAP) system () characterizes a genetic sample. The ASAP system () receives assay configuration data individually associating reference sequences and genetic characteristics. The ASAP system () 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 () 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.

Enhanced amplicon sequencing analysis

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.

Methods for the detection of enterovirus D68 in complex samples

The present invention relates to method of detecting and characterizing one or morespecies 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 of16S 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 morespecies.

Systems and methods for the detection of infectious diseases

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

Methods and kits to identify Klebsiella strains

Embodiments of the invention provide a method of genotyping asample, which can include forming a plurality of mixtures for nucleic amplification. The method can include amplification of specific sequences within thegenome that can provide definitive genotype information to distinguish between one or more types or subtypes of

Methods to detect and genotypespecies

Methods for the production of lipids and biofuels with a culture ofspp. grown on a medium such as wastewater or sewage sludge are provided. Thespp. may be cultured with additional microorganisms that contribute to the accumulation of lipids from the growth medium such as Zoog!oea spp.,spp.,spp.,spp., ODI genera incertae sedis. Further discloses are transformed organisms comprising genes isolated from, as well as methods and processes for producing lipids, fatty acids, or biofuels in vitro using the protein products of the isolated genes.

Growing community of inventors

Flagstaff, AZ, United States of America

David Engelthaler