1 National Food Institute, Technical University of Denmark2 Division of Epidemiology and Microbial Genomics, National Food Institute, Technical University of Denmark3 University of Georgia4 University of California, Irvine5 Cornell University6 Centers for Disease Control and Prevention7 United States Department of Agriculture8 University of California, Davis9 Washington University School of Medicine10 University of Georgia11 Cornell University12 Centers for Disease Control and Prevention
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.
Emerging Infectious Diseases, 2014, Vol 20, Issue 9, p. 1481-1489
genetic diversity; salmonellosis bacterial disease pathology, epidemiology; Facultatively Anaerobic Gram-Negative Rods Eubacteria Bacteria Microorganisms (Bacteria, Eubacteria, Microorganisms) - Enterobacteriaceae  Salmonella enterica species pathogen serotype Enteritidis, strain-Nitra; Primates Mammalia Vertebrata Chordata Animalia (Animals, Chordates, Humans, Mammals, Primates, Vertebrates) - Hominidae  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