ArticleBMC genomics2018
Whole genome sequencing analysis of multiple Salmonella serovars provides insights into phylogenetic relatedness, antimicrobial resistance, and virulence markers across humans, food animals and agriculture environmental sources.
Article in BMC genomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 79 papers, 2 of them syntheses that pooled it.
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79 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Computational paradigms for antimicrobial resistance prediction: integrating multi-omics, structural modeling, and foundation artificial intelligence systems.Briefings in bioinformatics · 2026Pooled it
- Does Irrigation with Treated and Untreated Wastewater Increase Antimicrobial Resistance in Soil and Water: A Systematic Review.International journal of environmental research and public health · 2021Pooled it
- Review
- Mobile genetic elements drive the evolution and multidrug resistance of Salmonella infantis along the United States poultry production line.BMC genomics · 2026Article
- Genotypic and Phenotypic Characterization of Salmonella Typhimurium Strains Isolated from Swine in the Southern Region of Brazil.Current microbiology · 2026Article
- Genomic Epidemiology ofMicroorganisms · 2026Article
- Activity of Lysozyme Against Multidrug-ResistantAnimals : an open access journal from MDPI · 2025Article
- Ecology and epidemiology of multidrug-resistantOne health (Amsterdam, Netherlands) · 2025Article
- Comparative genomics ofVirulence · 2025Article
- Detection, Genomic Characterization, and Antibiotic Susceptibility ofFoods (Basel, Switzerland) · 2025Article
- Integrating serotyping, MLST, and phenotypic data: decoding the evolutionary drivers ofApplied and environmental microbiology · 2025Article
- Advancing microbial risk assessment: perspectives from the evolution of detection technologies.NPJ science of food · 2025Review
- Ecological prevalence and genomic characterization of Salmonella isolated from selected poultry farms in Jiangxi province, China.Poultry science · 2025Article
- Molecular epidemiology and antimicrobial resistance ofVeterinary world · 2025Article
- Effect of egg cultivation methods onFood science and biotechnology · 2025Article
- Tracing the evolution: the rise ofmSystems · 2025Article
- Whole-Genome Shotgun Sequencing from Chicken Clinical Tracheal Samples for Bacterial and Novel Bacteriophage Identification.Veterinary sciences · 2025Article
- Article
- Article
- Comparative genomics analysis of Salmonella Enteritidis isolated from clinical cases associated with chicken.BMC microbiology · 2024Article
19 more citing papers are in PubMed but not listed here.
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3 authors.
Funding
Abstract
backgroundSalmonella enterica is a significant foodborne pathogen, which can be transmitted via several distinct routes, and reports on acquisition of antimicrobial resistance (AMR) are increasing. To better understand the association between human Salmonella clinical isolates and the potential environmental/animal reservoirs, whole genome sequencing (WGS) was used to investigate the epidemiology and AMR patterns within Salmonella isolates from two adjacent US states.
resultsWGS data of 200 S. enterica isolates recovered from human (n = 44), swine (n = 32), poultry (n = 22), and farm environment (n = 102) were used for in silico prediction of serovar, distribution of virulence genes, and phylogenetically clustered using core genome single nucleotide polymorphism (SNP) and feature frequency profiling (FFP). Furthermore, AMR was studied both by genotypic prediction using five curated AMR databases, and compared to phenotypic AMR using broth microdilution. Core genome SNP-based and FFP-based phylogenetic trees showed consistent clustering of isolates into the respective serovars, and suggested clustering of isolates based on the source of isolation. The overall correlation of phenotypic and genotypic AMR was 87.61% and 97.13% for sensitivity and specificity, respectively. AMR and virulence genes clustered with the Salmonella serovars, while there were also associations between the presence of virulence genes in both animal/environmental isolates and human clinical samples.
conclusionsWGS is a helpful tool for Salmonella phylogenetic analysis, AMR and virulence gene predictions. The clinical isolates clustered closely with animal and environmental isolates, suggesting that animals and environment are potential sources for dissemination of AMR and virulence genes between Salmonella serovars.
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