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Title: Genomic and evolutionary analysis of two Salmonella enterica serovar Kentucky sequence types isolated from bovine and poultry sources in North America

item Haley, Bradd
item KIM, SEON WOO - US Department Of Agriculture (USDA)
item PETTENGILL, JAMES - Food And Drug Administration(FDA)
item LUO, YAN - Food And Drug Administration(FDA)
item Karns, Jeffrey
item Van Kessel, Jo Ann

Submitted to: PLoS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/3/2016
Publication Date: 10/3/2016
Citation: Haley, B.J., Kim, S., Pettengill, J., Luo, Y., Karns, J.S., Van Kessel, J.S. 2016. Genomic and evolutionary analysis of two Salmonella enterica serovar Kentucky wequence types isolated from bovine and poultry sources in North America. PLoS One. doi: 10.1371/journal.pone.0161225.

Interpretive Summary: Salmonella enterica is a leading cause of foodborne disease in the United States. Some Salmonella serovars (or types) cause disease in other animals, while some do not. Salmonella enterica serovar Kentucky is frequently isolated from the feces of dairy cows and poultry, two distantly related animals. Cows and poultry colonized by Salmonella Kentucky do not show overt signs of disease, and there is therefore the potential for these stains to contaminate the food supply without prior detection. However, some strains of Salmonella Kentucky have been isolated from humans in the United States, Southeast Asia, and Africa. In an attempt to understand the differences between strains isolated from poultry, cows, and humans, the genomes of 104 isolates were sequenced and compared. Results of our analysis revealed that Salmonella Kentucky strains isolated from poultry recently evolved from strains that colonize cows after a series of two mutations in the chromosome and the acquisition of two plasmids. Salmonella Kentucky strains that are implicated in human illness globally have genes in their genomes that are associated with virulence, such as sialic acid metabolism regions and intestinal colonization factors. These results will help to improve our understanding of the differences between Salmonella strains that infect humans, cows, and poultry, and may be used to help develop intervention strategies in the future. This information will be useful to other scientists and regulatory agencies.

Technical Abstract: Salmonella enterica subsp. enterica serovar Kentucky is frequently isolated from healthy poultry and dairy cows and is occasionally isolated from people with clinical disease. A genomic analysis of 119 isolates collected in the United States from dairy cows, ground beef, poultry and poultry products, and human clinical cases was conducted. Results of the analysis demonstrated that the majority of poultry and bovine-associated S. Kentucky were sequence type (ST) 152. Several bovine-associated (n=3) and food product isolates (n=3) collected from the United States and the majority of human clinical isolates were ST198, a sequence type that is frequently isolated from poultry and occasionally from human clinical cases in Northern Africa, Eastern Europe and Southeast Asia. A phylogenetic analysis indicated that both STs are more closely related to other Salmonella serovars than they are to each other. Additionally, there was strong evidence of an evolutionary divergence between the poultry-associated and bovine-associated ST152 isolates that was due to polymorphisms in four core genome genes. The three ST198 isolates recovered from dairy farms in the United States were phylogenetically distinct from those collected from human clinical cases with 66 core genome SNPs differentiating the two groups of isolates but more isolates are needed to determine the significance of this distinction. Identification of S. Kentucky ST198 from dairy animals in the United States suggests that the presence of this pathogen should be monitored in food-producing animals.