Paul Keim

Proteome-wide discovery of novel diagnostic antigens for coccidioidomycosis

This study identifies novel diagnostic antigens for coccidioidomycosis using high-dimensional peptide serology, showing improved accuracy in distinguishing infected individuals from controls.

The historical domestication of a Clostridium botulinum strain used for the industrial production of botulinum neurotoxin

This paper reconstructs the genomic evolution of a Clostridium botulinum strain used for industrial botulinum neurotoxin production, identifying key mutations that drove its domestication and adaptation.

Genomic characterization of Francisella tularensis and other diverse Francisella species from complex samples

This study develops a capture-enrichment system to detect and genotype Francisella species in complex samples, enabling robust identification and analysis of low-level Francisella DNA.

A chromosomal-level reference genome of the widely utilized Coccidioides posadasii laboratory strain "Silveira"

The paper presents a chromosomal-level genome assembly of the Coccidioides posadasii Silveira strain using SMRT sequencing, improving genome annotation and enabling future genomic studies.

Forensic analysis of Soil Microbiomes: Linking Evidence to a Geographic Location

This study links a soil microbiome from a suspect's sock to a crime scene location, showing potential for forensic use.

Phylogenetic Analysis of St. Louis Encephalitis Virus within Two Southwestern United State Counties: a case for a bulk introduction event into the southwest United States

The paper uses phylogenetic analysis to determine if St. Louis Encephalitis Virus (SLEV) in Arizona and California originated from local cycling or new imports, finding evidence of annual imports in California and local cycling in Arizona.

A global to local genomics analysis of Clostridioides difficile ST1/RT027 identifies cryptic transmission events in a northern Arizona healthcare network

This study uses whole genome sequencing to analyze C. difficile isolates and identifies multiple introductions and transmission events in a healthcare network, highlighting genetic variability and antimicrobial resistance.

Botulinum-neurotoxin-like sequences identified from an Enterococcus sp. genome assembly

The paper identifies a botulinum-neurotoxin-like gene cluster in an Enterococcus sp. genome, similar to known BoNT gene clusters but with unknown pathogenic potential.

The Northern Arizona SNP Pipeline (NASP): accurate, flexible, and rapid identification of SNPs in WGS datasets

NASP is a WGS pipeline for SNP detection in bacterial genomes, showing comparable or better performance than existing tools with greater flexibility.

A Bacillus anthracis Genome Sequence from the Sverdlovsk 1979 Autopsy Specimens

The paper generates a draft genome of the Sverdlovsk 1979 Bacillus anthracis strain and places it phylogenetically within a clade of vaccine strains, finding no evidence of genetic manipulation.

Whole genome SNP typing to investigate methicillin-resistant Staphylococcus aureus carriage in a health-care provider as the source of multiple surgical site infections.

This study uses whole genome SNP typing to investigate whether a healthcare provider was the source of multiple surgical site infections, finding no genetic link between the provider's isolate and the infections.

KlebSeq: A Diagnostic Tool for Healthcare Surveillance and Antimicrobial Resistance Monitoring of Klebsiella pneumoniae

KlebSeq is a diagnostic tool that detects Klebsiella pneumoniae and identifies antimicrobial resistance and virulence traits using amplicon sequencing for healthcare surveillance.