Jason W. Sahl

Clinical and molecular characterization of an outbreak of leptospirosis in dogs from Los Angeles County, California, USA, 2021

This study characterizes a leptospirosis outbreak in dogs in Los Angeles County, finding that all isolates were Leptospira interrogans serovar Canicola, with urine PCR as the most sensitive test and ICFs as a potential source.

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.

Population sequencing for diversity and transmission analyses

This paper introduces and validates population sequencing methods to analyze phylogenetic diversity in bacterial populations without haplotype reconstruction, demonstrating applications in tracking transmission and understanding pathogen dynamics.

Host population structure and rare dispersal events drive leptospirosis transmission patterns among Rattus norvegicus in Boston, Massachusetts, US

The paper investigates leptospirosis transmission among brown rats in Boston, finding high genetic structure and limited dispersal, with Leptospira clades linked to specific rat populations and a human case linked to rats.

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.

Persistence of rare Salmonella Typhi genotypes susceptible to first-line antibiotics in the remote islands of Samoa

This study characterizes the genomic structure and evolutionary history of Salmonella Typhi in Samoa, revealing dominant rare genotypes with low antimicrobial resistance.

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.

Bacterial Genome wide association studies (bGWAS) and transcriptomics identifies cryptic antimicrobial resistance mechanisms in Acinetobacter baumannii

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.

Bacterial genome reduction as a result of short read sequence assembly

The paper simulates short read assemblies of bacterial genomes to assess genome reduction effects and finds up to 25% reduction in some assemblies, correlated with repeat structure.

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.

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.

The In Silico Genotyper (ISG): an open-source pipeline to rapidly identify and annotate nucleotide variants for comparative genomics applications

The paper introduces ISG, an open-source pipeline for identifying and annotating nucleotide variants in bacterial genomes, showing it is faster and more flexible than existing tools.