Comparative Genomics of Salmonella Phage Diversity on Dairy Farms: Distinguishing the “Good” from the “Bad”

Introduction: Salmonella is a foodborne pathogen that is widely distributed among livestock. Salmonella on dairy farms is a concern because it can be found at high prevalence and in the absence of clinical signs, underscoring the difficulty in recognizing infected herds. Salmonella phages can act as predators of Salmonella (killing Salmonella, the “good”); however they can also act as a vector for horizontal transmission of genes (the “bad”). 

Purpose: The purpose of this study was to assess the genomic diversity and putative roles of lytic and lysogenic phages on dairy farms.

Methods: The genomes of 22 Salmonella phages from nine dairy farms with a history of Salmonella isolation were fully sequenced.  Comparative analyses of phage genomes isolated from the farms and previously sequenced phage genomes were conducted.  In addition, phylogenetic analysis was performed to classify the phages. 

Results: The Salmonella phages isolated from farms are highly diverse and can be classified into nine different groups, representing 13 lysogenic and nine lytic phages. We found that 9/22 of the phages represent types of Salmonella phages that have not previously been reported. In addition, we identified phage-borne virulence (adhesins, msgA) and antimicrobial resistance (tellurite and sulfonamide resistance) genes. Phages from the same group were found on farms hundreds of miles apart. Finally, lytic phages isolated from farms with a high prevalence of Salmonella (9-50%) were more likely to infect the most prevalent Salmonellaserovar present on that specific farm.

Significance: This represents the first comprehensive study on the genomic diversity of Salmonella phage isolated from dairy farms. The high diversity of lytic and lysogenic phages on farms and the presence of phage-borne resistance genes in some of the sequenced phages suggest that Salmonella phages play an important role as both predators and drivers of Salmonella evolution.