Date Published: January 24, 2017
Publisher: Public Library of Science
Author(s): Lenka Mikalová, Juraj Bosák, Hana Hříbková, Daniela Dědičová, Oldřich Benada, Jan Šmarda, David Šmajs, Mark J. van Raaij.
Forty strains of Salmonella enterica (S. enterica) subspecies salamae (II), arizonae (IIIa), diarizonae (IIIb), and houtenae (IV) were isolated from human or environmental samples and tested for bacteriophage production. Production of bacteriophages was observed in 15 S. enterica strains (37.5%) belonging to either the subspecies salamae (8 strains) or diarizonae (7 strains). Activity of phages was tested against 52 pathogenic S. enterica subsp. enterica isolates and showed that phages produced by subsp. salamae had broader activity against pathogenic salmonellae compared to phages from the subsp. diarizonae. All 15 phages were analyzed using PCR amplification of phage-specific regions and 9 different amplification profiles were identified. Five phages (SEN1, SEN4, SEN5, SEN22, and SEN34) were completely sequenced and classified as temperate phages. Phages SEN4 and SEN5 were genetically identical, thus representing a single phage type (i.e. SEN4/5). SEN1 and SEN4/5 fit into the group of P2-like phages, while the SEN22 phage showed sequence relatedness to P22-like phages. Interestingly, while phage SEN34 was genetically distantly related to Lambda-like phages (Siphoviridae), it had the morphology of the Myoviridae family. Based on sequence analysis and electron microscopy, phages SEN1 and SEN4/5 were members of the Myoviridae family and phage SEN22 belonged to the Podoviridae family.
At present, the Salmonella genus contains two species: S. enterica and S. bongori (V). S. enterica is further subdivided into six subspecies: enterica (I), salamae (II), arizonae (IIIa), diarizonae (IIIb), houtenae (IV), and indica (VI) [1–3]. Salmonelloses (infections transferred between humans and animals, mainly by contaminated food) represent an important, global, public health problem, with S. enterica subsp. enterica causing about 99% of the human cases [3–6]. Out of more than 2,600 S. enterica subsp. enterica serovars , relatively few serovars are important causative agents of salmonelloses . While S. enterica subsp. enterica is typically found in warm-blooded animals, S. enterica subsp. arizonae and S. bongori are associated with cold-blooded animals. The other four subspecies of S. enterica can be isolated from both host types and can occasionally cause human infections [8–13].
To date, almost 200 phage types have been identified in the genus Salmonella  and if prophages are included, the number is greater than 9,000 . Prophages appear to be very common in Salmonella, as shown by production of 136 functional phages from 173 S. enterica subsp. enterica (serovar Typhimurium) isolates . It has been calculated that there are, on average, 2.8 known prophages present per Salmonella genome . 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. in subsp. arizonae (GenBank: CP000880.1; prophage Sari1; ), and subsp. salamae (GenBank: ATFA01000000; ). This study focused on phage production within strains S. enterica subspecies salamae, arizonae, diarizonae, and houtenae. While fifteen phage producers were identified in subspecies salamae and diarizonae, no producers were identified in subspecies arizonae and houtenae; however, it is unclear if this difference is due to the relatively low number of investigated strains in the second group (9 out of 40) or due to other factors.
In this study, we determined phage production in S. enterica subspecies salamae, arizonae, diarizonae, and houtenae. Out of 15 identified phage producers, five complete phage genomes were determined and four different temperate phages were identified. Phages SEN1 and SEN4/5 clustered with P2-like phages, while phage SEN22 showed sequence relatedness to P22-like phages. Phage SEN34 was distantly related to Lambda-like phages (Siphoviridae), but had a morphology that was characteristic of Myoviridae.