Microdiversity of Salmonella Kentucky during an outbreak in a dairy herd

Authors: Salaheen, Serajus; Kim, Seonwoo; KARNS, JEFF - US Department Of Agriculture (USDA); Van Kessel, Jo Ann; Haley, Bradd

Submitted to: Foodborne Pathogens and Disease
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/11/2023
Publication Date: 5/10/2024
Citation: Salaheen, S., Kim, S., Karns, J., Van Kessel, J.S., Haley, B.J. 2024. Microdiversity of Salmonella Kentucky during an outbreak in a dairy herd. Foodborne Pathogens and Disease. 21(5): e0090. https://doi.org/10.1089/fpd.2023.0090.
DOI: https://doi.org/10.1089/fpd.2023.0090

Interpretive Summary: Salmonella Kentucky is among the most frequently isolated Salmonella serotypes from food producing animals in the United States. The underlying reasons for its success in these animals is not well known. To better understand this phenomenon, S. Kentucky isolates recovered from dairy cows in a single herd over an eight year period were analyzed using molecular fingerprinting, comparative genomics, and cell culture assays; the latter to mimic the interaction between S. Kentucky and the cow host cells. Results of this study demonstrated that what was thought to be a single outbreak caused by an individual strain, actually consisted of three strains. The initial strain was briefly identified on the farm and was quickly replaced by a second strain that persisted for approximately 4 years. This strain was then replaced by a third strain that persisted from 2010 until at least the end of the study in 2012. A comparative genomic analysis identified that a gene that controls virulence was found as only a single copy in the genomes of the ephemeral initial strain, but was found as two copies in the genomes of the two longer lasting outbreak strains. Further, numerous mutations in important regulatory genes were identified in the initial strains compared with the two longer lasting outbreak strains. We hypothesize that these genomic variations between the initial strains and the two latter strains may be responsible for the differences in their abilities to persist within the herd. This study demonstrates the importance of identifying the microdiversity of Salmonella strains within food animals to determine the mechanisms that are involved in their survival in food producing animals. This work helps to further identify genomic regions that may be explored as targets of potential interventions to reduce the carriage of foodborne pathogens in the US food supply.

Technical Abstract: A multi-year outbreak of Salmonella enterica subsp. enterica serovar Kentucky was observed in a commercial dairy herd in the United States that was enrolled in a longitudinal study where feces of asymptomatic dairy cattle were sampled intensively over an eight-year period. The genomes of five S. Kentucky isolates recovered from the farm two years prior to the outbreak and 13 isolates collected during the outbreak were sequenced. A phylogenetic analysis inferred that the S. Kentucky strains from the farm were distinct from poultry strains and three subclades (K, A1, and A2) were identified among the farm isolates, each appearing at different times during the study. Based on the phylogenetic analysis, three separate lineages of highly similar S. Kentucky were present in succession during the course of the outbreak. Genomic heterogeneity between the clades helped identify regions, most notably transcriptional regulators, of the S. Kentucky genome that may be involved in competition between highly similar strains. Notably, a region annotated as a hemolysin expression modulating protein (Hha), was identified in the putative plasmid region of strains that colonized a large portion of cows in the herd, suggesting that it may play a role in asymptomatic persistence within the bovine intestine. A cell culture assay of isolates from the three clades with bovine epithelial cells demonstrated a trend of decreased invasiveness of S. Kentucky isolates over time suggesting that clade-specific interactions with the animals on the farm may have played a role in the dynamics of strain succession during the course of the outbreak. Results of this analysis further demonstrate an underappreciated level of genomic diversity within strains of the same Salmonella serotype, particularly those isolated during the course of an outbreak within a single dairy herd.