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

Abstract

Since this book was originally published in 2007 there has been a significant increase in the number of Salmonella bacteriophages, particularly lytic virus, and Salmonella strains which have been fully sequenced. In addition, new insights into phage taxonomy have resulted in new phage genera, some of which have been recognized by the International Committee of Taxonomy of Viruses (ICTV). The properties of each of these genera are discussed, along with the role of phage as agents of genetic exchange, as therapeutic agents, and their involvement in phage typing.

Contributions of P2- and P22-like prophages to understanding the enormous diversity and abundance of tailed bacteriophages

“…Schmieger and co-workers (Schicklmaier et al , 1998; Schmieger, 1999) found that 173 S. enterica serovar Typhimurium isolates released a minimum of 136 functional phages, and the commonly used laboratory Typhimurium isolate LT2 carries four intact, fully functional prophages (Yamamoto, 1967 & 1969; Yamada et al , 1986; Figueroa-Bossi and Bossi, 1999; McClelland et al , 2001). Many studies have also shown that prophage content accounts for a substantial part of the natural variation among Salmonella isolates ( e.g., Reen et al , 2005; Cooke et al , 2007; Drahovska et al , 2007; Rychlik et al , 2008; Fricke et al , 2011; Moreno Switt et al , 2012; Pang et al , 2013; Bobay et al , 2014; Hiley et al , 2014; Switt et al , 2015). …”

A proposed new bacteriophage subfamily: “Jerseyvirinae”

“…This genus was recently proposed by Moreno Switt et al (2014). 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].…”

“…Not surprisingly, Salmonella phages are also numerous and varied. The morphology of 177 Salmonella phages was reviewed in 2007 [2] (updated in [55]), with most representatives belonging to the order Caudovirales (tailed phages with a dsDNA genome) and its three families, Siphoviridae, Myoviridae and Podoviridae. A small number of phages representing the families Inoviridae, Leviviridae, Microviridae and Tectiviridae have also been documented.…”

Novel Temperate Phages of Salmonella enterica subsp. salamae and subsp. diarizonae and Their Activity against Pathogenic S. enterica subsp. enterica Isolates

“…While phages and prophages of subsp. enterica have been intensively studied (reviewed in [18, 30, 32]), information on phages in other Salmonella subspecies is scarce. In fact, putative prophage sequences were only recently identified in the whole genome sequences of two strains belonging to non- enterica subspecies, i.e.…”