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Background   Salmonella  is a widely distributed foodborne pathogen that causes tens of millions of salmonellosis cases globally every year. While the genomic diversity of  Salmonella  is increasingly well studied, our knowledge of  Salmonella  phage genomic diversity is still rather limited, despite the contributions of both lysogenic and lytic phages to  Salmonella  virulence, diversity and ecology (e.g., through horizontal gene transfer and  Salmonella  lysis). To gain a better understanding of phage diversity in a specific ecological niche, we sequenced 22  Salmonella  phages isolated from a number of dairy farms from New York State (United States) and analyzed them using a comparative genomics approach.    Results  Classification of the 22 phages according to the presence/absence of orthologous genes allowed for classification into 8 well supported clusters. In addition to two phage clusters that represent novel virulent  Salmonella  phages, we also identified four phage clusters that each contained previously characterized phages from multiple continents. Our analyses also identified two clusters of phages that carry putative virulence (e.g., adhesins) and antimicrobial resistance (tellurite and bicyclomycin) genes as well as virulent and temperate transducing phages. Insights into phage evolution from our analyses include (i) identification of DNA metabolism genes that may facilitate nucleotide synthesis in phages with a G+C % distinct from  Salmonella , and (ii) evidence of  Salmonella  phage tailspike and fiber diversity due to both single nucleotide polymorphisms and major re-arrangements, which may affect the host specificity of  Salmonella  phages.    Conclusions  Genomics-based characterization of 22  Salmonella  phages isolated from dairy farms allowed for identification of a number of novel  Salmonella  phages. While the comparative genomics analyses of these phages provide a number of new insights in the evolution and diversity of  Salmonella  phages, they only represent a first glimpse into the diversity of  Salmonella  phages that is likely to be discovered when phages from different environments are characterized.

Genomic characterization provides new insight into Salmonella phage diversity