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Genomic Epidemiology of Salmonella enterica Serotype Enteritidis based on Population Structure of Prevalent Lineages

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Abstract

Salmonella enterica serotype Enteritidis is one of the most commonly reported causes of human salmonellosis. Its low genetic diversity, measured by fingerprinting methods, has made subtyping a challenge. We used whole-genome sequencing to characterize 125 S. enterica Enteritidis and 3 S. enterica serotype Nitra strains. Single-nucleotide polymorphisms were filtered to identify 4,887 reliable loci that distinguished all isolates from each other. Our whole-genome single-nucleotide polymorphism typing approach was robust for S. enterica Enteritidis subtyping with combined data for different strains from 2 different sequencing platforms. Five major genetic lineages were recognized, which revealed possible patterns of geographic and epidemiologic distribution. Analyses on the population dynamics and evolutionary history estimated that major lineages emerged during the 17th-18th centuries and diversified during the 1920s and 1950s.

genetic diversity salmonellosis bacterial disease pathology epidemiology Facultatively Anaerobic Gram-Negative Rods Eubacteria Bacteria Microorganisms (Bacteria Eubacteria Microorganisms) - Enterobacteriaceae [06702] Salmonella enterica species pathogen serotype Enteritidis strain-Nitra Primates Mammalia Vertebrata Chordata Animalia (Animals Chordates Humans Mammals Primates Vertebrates) - Hominidae [86215] human common host 03508 Genetics - Human 03509 Genetics - Population genetics 12502 Pathology - General 31000 Physiology and biochemistry of bacteria 36002 Medical and clinical microbiology - Bacteriology 37052 Public health: epidemiology - Communicable diseases 37056 Public health: epidemiology - Miscellaneous Medical Sciences Population Studies fingerprinting analysis laboratory techniques genetic techniques sequencing laboratory techniques genetic techniques single-nucleotide polymorphism typing laboratory techniques genetic techniques Epidemiology Human Medicine Infection Population Genetics IMMUNOLOGY INFECTIOUS TANDEM REPEAT ANALYSIS UNITED-STATES EVOLUTIONARY RECOMBINATION PHYLOGENETICS TRANSMISSION PATHOGENS OUTBREAKS SELECTION ORIGINS FOOD SAFETY GENETICS GENOMICS GENOTYPE POLYMORPHISM SALMONELLA SALMONELLA ENTERITIDIS Hygiene and toxicology Microbiological aspects