Submitted to: Microorganisms
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/20/2022
Publication Date: 7/21/2022
Citation: Mcmillan, E.A., Frye, J.G., Weinroth, M.D. 2022. Proliferation of Salmonella Infantis in United States poultry production driven by clonal expansion of a single lineage carrying the pESI plasmid. Microorganisms. https://doi.org/10.3390/microorganisms10071478.
Interpretive Summary: Salmonella Infantis, a pathogen that has been implicated in foodborne illness, has become one of the most common types of Salmonella in U.S. poultry production. The recent expansion of Infantis is closely tied to its carriage of a large pESI plasmid. While expansion has been focused on the plasmid itself, less work has been done to understand if the chromosomes of these Infantis strains differ between each other. Our objective was to understand if there was a difference in the chromosomes between groups that did and did not carry the plasmid. We investigated the genetics of over 3200 Salmonella Infantis genomes that were available to the public from CDC FSIS and FDA. We found that the chromosomes of the group that carries the plasmids are far less diverse than the non-plasmid group; indicating a single plasmid acquisition event rather than several events is responsible for plasmid carriage. Further tests showed there are 58 single nucleotide changes between the two groups, although no genes were present in just one group. This work has helped us better understand the genetics of Salmonella Infantis and will inform future interventions for the reduction of it in poultry products.
Technical Abstract: Infantis has recently become one of the most common serotypes of Salmonella isolated from U.S. poultry sources. Investigations have determined that the majority of these isolates contain the pESI plasmid, but there has not been a large-scale investigation of the chromosome of these isolates. Here, we investigated 3,276 whole genome sequences of Salmonella Infantis with and without the pESI plasmid to understand chromosomal differences between plasmid carriage groups. Infantis genomes arranged into multiple clades with a single clade containing the isolates carrying the plasmid. Fifty-eight SNPs were identified in complete linkage disequilibrium between isolates that did and did not carry the plasmid. However, there were no unique genes present only in the genomes of isolates containing the plasmid. On average, isolates with the plasmid did contain more insertion sequences than those without (P<0.05). Given that Infantis isolates carrying pESI form a single clade, it can be inferred that the increase in carriage of this plasmid in the U.S. is due to rapid clonal expansion of a single strain rather than as a result of multiple transfer events. As this Infantis clone does not contain any unique chromosomal genes, its proliferation appears to be due to pESI plasmid encoded genes that are advantageous in the poultry environment.