Salmonella and Campylobacter epidemiology

The paper introduces a method to calculate PFGE resolution using Dice percentage and evaluates its impact on comparing PFGE profiles with in-silico digestion models derived from WGS.

The paper investigates Salmonella prevalence in organic pig farms in northern Thailand, finding high antibiotic resistance and linking contamination to conventional farming practices.

This study investigates the genomic epidemiology of multi-drug resistant nontyphoidal Salmonella in sub-Saharan Africa, identifying key serotypes and transmission patterns.

The paper estimates molecular clock rates in Campylobacter using a birthday problem analogy to quantify lineage turnover and diversification in environmental bacteria.

This study identifies a bovine genotype, SYNJ1/SNYJ1::mcr1/mcr1, associated with reduced susceptibility to Salmonella and E. coli O157:H7 in cattle.

The paper introduces new algorithms to analyze PFGE data, links PFGE results to WGS through simulations, and evaluates the impact of co-migrating DNA fragments on typing accuracy.

This study evaluates the use of staA, viaB, and sopE genes for detecting Salmonella spp. using conventional PCR, finding that staA and viaB are specific to S. Typhi while sopE is specific to all Salmonella strains.

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

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

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

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.