Genomic comparison of diverse Salmonella serovars isolated from swine

Authors: GUPTA, SUSHIM - Orise Fellow; SHARMA, POONAM - Orise Fellow; MCMILLAN, ELIZABETH - University Of Georgia; Hiott, Lari; Woodley, Tiffanie; Humayoun, Shaheen; Barrett, John; MCCLELLAND, MICHAEL - University Of California; Jackson, Charlene; Frye, Jonathan

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/15/2019
Publication Date: 11/1/2019
Citation: Gupta, S., Sharma, P., Mcmillan, E., Hiott, L.M., Woodley, T.A., Humayoun, S.B., Barrett, J.B., Mcclelland, M., Jackson, C.R., Frye, J.G. 2019. Genomic comparison of diverse Salmonella serovars isolated from swine. PLoS One. https://doi.org/10.1371/journal.pone.0224518.
DOI: https://doi.org/10.1371/journal.pone.0224518

Interpretive Summary: Salmonella has the ability to survive at different stages of food production, processing and storage as well as grow in improperly cooked food. Some Salmonella serotypes are host specific while others have broad host range due to genetic factors associated with colonization and infection. Hence, in order to understand the genetic variations among different Salmonella serotypes, the whole-genome sequence (WGS) of fourteen Salmonella serotypes were analyzed to assess the genetic variations among them. The WGS data was assessed for resistance and virulence determinants, and their association with mobile genetic elements was predicted. Analysis determined that despite all isolates being swine associated, a great deal of genetic diversity was detected in the different Salmonella serotypes. The findings of this study will help researchers understand the genetic diversity in Salmonella serotypes, and how specific genes help adapt some serotypes to certain host animals. The processes these genes perform can be further studied to determine how they could be blocked to prevent colonization and infection of food animals.

Technical Abstract: Salmonella enterica is an important foodborne pathogen that causes gastroenteritis in humans. In order to understand the genetic variations among different Salmonella serotypes, Whole Genome Sequences (WGS) of fourteen Salmonella serotypes from swine products were analyzed. More than 3/4th of the genes were part of the core genome. High concordance was detected between phenotypically confirmed antibiotic resistance and identified antibiotic resistance genes from WGS. The resistance determinants were mainly located on mobile genetic elements (MGE) and in some instances they were integrated into the chromosome. Most of the virulence genes were part of the core genome and a small fraction of virulence genes were detected on MGE. The predicted lysogenic phages were highly diverse and mostly harbor virulence, metals, and antibiotic resistance genes along with necessary genes for viable phage. Further analysis confirmed the common ancestry or infection history among Salmonella serotypes. Overall genomic analysis revealed a great deal of diversity among Salmonella serotypes and it was due to acquired genes that enabled them to thrive and survive during infection.