Salmonella and Campylobacter epidemiology

Genetic background influences survival of infections with Salmonella enterica serovar Typhimurium in the Collaborative Cross

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.

Genetic Susceptibility to Enteric Fever in Experimentally Challenged Human Volunteers

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

Genomic diversity and antimicrobial resistance among non-typhoidal Salmonella associated with human disease in The Gambia

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

Genomic Surveillance of Salmonella spp. in the Philippines, 2013-2014

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

MGTdb: A web service and database for studying the global and local genomic epidemiology of bacterial pathogens

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

Invasive atypical non-typhoidal Salmonella in The Gambia

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

Machine learning to predict the source of campylobacteriosis using whole genome data

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

Circulation of third-generation cephalosporin resistant Salmonella Typhi in Mumbai, India

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

Elucidation of global and local genomic epidemiology of Salmonella enterica Enteritidis through multilevel genome typing

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.

Genome archaeology of two laboratory Salmonella enterica enterica sv Typhimurium

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

A global resource for genomic predictions of antimicrobial resistance and surveillance of Salmonella Typhi at Pathogenwatch

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

Genome-wide insights into population structure and host specificity of Campylobacter jejuni

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

Genomic surveillance of antimicrobial resistance shows cattle are a moderate source of multi-drug resistant non-typhoidal Salmonella in Mexico

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.

PulseNet international: the missing link between PFGE and WGS

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.

Pangenome analysis reveals genetic isolation in Campylobacter hyointestinalis subspecies adapted to different mammalian hosts

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

Antimicrobial resistant Salmonella spp. circulating in antibiotic-free organic pig farms of northern-Thailand

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

Spontaneous emergence of azithromycin resistance in independent lineages of Salmonella Typhi in Northern India

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

The genomic epidemiology of multi-drug resistant nontyphoidal Salmonella causing invasive disease in sub-Saharan Africa

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

Quantifying bacterial evolution in the wild: a birthday problem for Campylobacter lineages

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

Impact of library preparation-induced low GC sequencing bias on Salmonella serotype prediction using SeqSero2

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

Identification of Bovine Genotypes Conferring Diminished Susceptibility to Salmonellosis and Colonization by Salmonella and E. coli O157:H7

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

Novel algorithms for PFGE bacterial typing: Number of co-migrated DNA fragments, linking PFGE to WGS results and computer simulations for evaluation of PulseNet international typing protocols

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.

Evaluation of staA, viaB and sopE genes in Salmonella detection using conventional polymerase chain reaction (PCR)

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.

Evolution of Salmonella enterica serotype Typhimurium driven by anthropogenic selection and niche adaptation

This study constructs a phylogenetic tree of 131 S. Typhimurium strains to reveal population structure and adaptation to domesticated and wild animal hosts.

Population structure and antimicrobial resistance patterns of Salmonella Typhi isolates in Bangladesh from 2004 to 2016

This paper analyzes Salmonella Typhi isolates from Bangladesh 2004-2016 to identify population structure and antimicrobial resistance patterns, finding a decline in H58 genotypes and rise in non-H58 genotypes with fluoroquinolone resistance.

Virulence and antibiotic resistance plasticity of Arcobacter butzleri: insights on the genomic diversity of an emerging human pathogen

This study performs a comprehensive genome analysis of Arcobacter butzleri, revealing its core- and pan-genome diversity, virulence factors, and antibiotic resistance mechanisms.

Persistent transmission of shigellosis in England is associated with a recently emerged multi-drug resistant strain of Shigella sonnei

The paper identifies a multi-drug resistant Shigella sonnei strain as the cause of persistent shigellosis in England, linked to sexual transmission among men who have sex with men.

Development of a multi-locus typing scheme for an Enterobacteriaceae linear plasmid that mediates inter-species transfer of flagella

The paper develops a multi-locus typing scheme for a plasmid mediating flagella transfer in Salmonella, identifies its homologs in 154 genomes, and demonstrates its utility in tracking plasmid lineages.

Diagnostic host gene signature to accurately distinguish enteric fever from other febrile diseases

The paper identifies a host gene signature using machine learning to distinguish enteric fever from other febrile diseases with high accuracy.

A mathematical model of Campylobacter dynamics within a broiler flock

This paper develops a mathematical model of Campylobacter dynamics in broiler flocks to explain infection transmission and identify key factors driving outbreaks.