Salmonella bacteriophage diversity reflects host diversity on dairy farms

Abstract

Salmonella is an animal and human pathogen of worldwide concern. Surveillance programs indicate that the incidence of Salmonella serovars fluctuates over time. While bacteriophages are likely to play a role in driving microbial diversity, our understanding of the ecology and diversity of Salmonella phages is limited. Here we report the isolation of Salmonella phages from manure samples from 13 dairy farms with a history of Salmonella presence. Salmonella phages were isolated from 10 of the 13 farms; overall 108 phage isolates were obtained on serovar Newport, Typhimurium, Dublin, Kentucky, Anatum, Mbandaka, and Cerro hosts. Host range characterization found that 51% of phage isolates had a narrow host range, while 49% showed a broad host range. The phage isolates represented 65 lysis profiles; genome size profiling of 94 phage isolates allowed for classification of phage isolates into 11 groups with subsequent restriction fragment length polymorphism analysis showing considerable variation within a given group. Our data not only show an abundance of diverse Salmonella phage isolates in dairy farms, but also show that phage isolates that lyse the most common serovars causing salmonellosis in cattle are frequently obtained, suggesting that phages may play an important role in the ecology of Salmonella on dairy farms.

A proposed new bacteriophage subfamily: “Jerseyvirinae”

“…To date, three members (FSL SP-031, FSL SP-038, and FSL SP-049) have been reported, though only the genome of phage FLS SP-031 is fully sequenced, hence the proposed genus "Sp3unalikevirus" [42]. Phages in the genus "Sp03unalikevirus" were isolated from dairy farms in the state of New York with a history of Salmonella isolation [43]. Sp031-like viruses have a GC content of 51.1 %, closer to the Salmonella G+C value of approximately 52 % [46].…”

Salmonella Phages and Prophages: Genomics, Taxonomy, and Applied Aspects

“…This phage genus needs to be proposed to ICTV; currently only three Salmonella phages (e.g., FSL SP-031, FSL SP-038, and FSL SP-049) belong to this genus, and all of them were isolated from dairy farms in New York State [ 59 ]. Genomic characteristics of this phage genus include a genome size of approx.…”

“…One phenotypic characteristic that is distinguishable for the phages in this genus is a very narrow host range. When 25 Salmonella serovars were tested, only one strain representing Salmonella Cerro was infected [ 59 ].…”

“…FSL SP-062 and FSL SP-069, the two phages in this genus, were isolated recently by Moreno Switt et al from manure samples of dairy farms with history of Salmonella isolation [ 59 ]. Sp062-like viruses morphologically resemble coliphage lambda, possess a 56 kb genome (mol.% G + C of 42.8), and encode 102 CDSs [ 14 ].…”

“…The unique feature of these phages is the presence of 1-2 copies of a large (3,500 amino acid residues; 382,495 Da) rifampicin-resistant single-subunit RNA polymerase within the phage particles, which is responsible for early transcription [ 85 ]. The two Salmonella phages, FSL SP-058 and FSL SP-076, were both isolated from manure samples in New York State [ 59 ]. A genome size of 72 kb, with a mol.% G + C of 39.5, encoding for ten tRNAs and a 97 CDSs are characteristics of this genus [ 14 ].…”