Salmonella and Campylobacter epidemiology

The paper examines how broiler house environments and litter management practices influence antimicrobial resistance and virulence factors in Campylobacter isolates from chicken flocks.

This study investigates the genomic structure and evolution of Salmonella ST34 in Southeast Asia, showing that multidrug resistance plasmids drive its clonal expansion and international spread.

This study uses multilevel genome typing to analyze Australian Salmonella Enteritidis isolates, finding strong epidemiological links to Asian strains and a local outbreak linked to European isolates.

This paper analyzes 180,098 Salmonella genomes to refine genomic typing nomenclature by identifying polyphyletic serovars and proposing a stable population structure based on core genome MLST thresholds.

This study analyzes spatial-temporal and phylogenetic data from typhoid fever cases in Samoa to identify transmission patterns and the role of asymptomatic carriers.

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

The paper analyzes the population structure and evolution of Salmonella enterica serotype Typhi in Zimbabwe before a typhoid vaccine campaign, identifying dominant resistant genotypes and their AMR mechanisms.

The paper develops a real-time PCR assay to differentiate Salmonella Enteritidis clades for public health surveillance in resource-limited settings.

The paper compares gene expression in caecal tonsils of two chicken lines infected with Salmonella Enteritidis to identify genes and pathways associated with differences in bacterial carriage.

This study investigates the genetic basis of survival differences in Salmonella Typhimurium infections across genetically diverse Collaborative Cross mouse strains, identifying new genomic regions associated with susceptibility and survival.

The paper identifies genetic variants and HLA types associated with susceptibility to enteric fever in human volunteers challenged with Salmonella.

The paper characterizes genomic diversity and antimicrobial resistance in non-typhoidal Salmonella from The Gambia, identifying multidrug-resistant strains and their epidemiological implications.

This study uses whole genome sequencing to characterize Salmonella isolates from the Philippines, revealing AMR patterns and population structure compared to traditional methods.

MGTdb provides a web service for assigning and analyzing multilevel genome types of bacterial isolates, supporting epidemiological studies of Salmonella and Vibrio species.

The paper analyzes whole genome sequences of invasive Salmonella isolates in The Gambia to study changes in serovar distribution and virulence factors over time.

This paper uses machine learning on whole genome data to improve source attribution of Campylobacter jejuni infections, achieving higher accuracy than traditional methods.

The paper reports the persistent circulation of third-generation cephalosporin-resistant Salmonella Typhi in Mumbai, India, linked to an IncX3 plasmid carrying resistance genes.

This study develops a multilevel genome typing method for Salmonella Enteritidis and analyzes 26,670 genomes to reveal global and local genomic epidemiology, including multidrug resistance and outbreak patterns.

The paper presents the genome sequences of two laboratory Salmonella strains and traces their ancestry, revealing hybridization events and their historical use in research.

The paper introduces Pathogenwatch, a tool for genomic surveillance of Salmonella Typhi, enabling AMR prediction and population-level risk assessment through global data sharing.

The paper identifies host-specific genetic variants in Campylobacter jejuni genomes from Germany and Canada, showing associations between genome characteristics and host adaptation.

This study analyzes antimicrobial resistance in non-typhoidal Salmonella from cattle and ground beef in Mexico, finding higher prevalence of multi-drug resistant strains in ground beef and association with specific serovars and resistance genes.

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 analyzes the pangenome of Campylobacter hyointestinalis subspecies to reveal genetic isolation and host adaptation differences.

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

The paper identifies azithromycin-resistant Salmonella Typhi in Northern India, showing independent emergence of resistance and highlighting the need for typhoid conjugate vaccines.

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.

The paper identifies that Nextera XT library preparation introduces low GC sequencing bias, affecting O antigen prediction by SeqSero2 in Salmonella genomes.

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