Salmonella and Campylobacter epidemiology

Biological machine learning combined with bacterial population genomics reveals common and rare allelic variants of genes to cause disease

The paper combines GWAS, machine learning, and bacterial population genomics to identify and rank disease-associated alleles in Campylobacter jejuni.

Geography Shapes the Population Genomics of Salmonella enterica Dublin

This study analyzes the population genomics of Salmonella enterica Dublin, finding that geographical regions shape its genomic structure and antibiotic resistance profiles.

Whole genome sequence analysis of 91 Salmonella Enteritidis isolates from mice caught on poultry farms in the mid 1990s

This study uses whole-genome sequencing to analyze 91 Salmonella Enteritidis isolates from mice on poultry farms, identifying SNPs that distinguish isolates and provide biomarkers for outbreak detection.

Genomic and phylogenetic analysis of Salmonella Typhimurium and its monophasic variants responsible for invasive endemic infections in Colombia

The paper analyzes genomic and phylogenetic data of Salmonella Typhimurium and monophasic variants from Colombia to understand their population structure, evolution, and antibiotic resistance.

Using machine learning to predict antimicrobial minimum inhibitory concentrations and associated genomic features for nontyphoidal Salmonella

This study uses XGBoost to predict antimicrobial MICs for nontyphoidal Salmonella with high accuracy using genomic data.

Machine learning identifies signatures of host adaptation in the bacterial pathogen Salmonella enterica

The paper uses machine learning to identify genetic signatures of host adaptation in Salmonella enterica strains associated with extraintestinal disease.

Laboratory and Molecular Surveillance of Paediatric Typhoidal Salmonella in Nepal: Antimicrobial Resistance and Implications for Vaccine Policy

This study analyzes Salmonella isolates from Nepali children to assess antimicrobial resistance and inform vaccine policy.

Rapid Identification of Stable Clusters in Bacterial Populations Using the Adjusted Wallace Coefficient

The paper introduces nAWC to identify stable clusters in bacterial populations using WGS data, showing it produces robust clusters that reflect population structure.

The role of a single non-coding nucleotide in the evolution of an epidemic African clade of Salmonella

The paper identifies a non-coding SNP in the pgtE promoter of Salmonella ST313 that increases PgtE expression, contributing to serum resistance and virulence in a chicken model.

Whole genome sequence analysis of Salmonella Typhi isolated in Thailand before and after the introduction of a national immunization program

This study uses whole genome sequencing to analyze Salmonella Typhi isolates from Thailand before and after a national immunization program, showing that post-vaccine isolates were imported from neighboring countries rather than persisting locally.

Assessing Pathogens for Natural versus Laboratory Origins Using Genomic Data and Machine Learning

This study develops methods to determine if pathogens come from natural environments or laboratory culturing using genomic data and machine learning, identifying mutations as signatures of laboratory culturing.