Investigation of Salmonella Phage–Bacteria Infection Profiles: Network Structure Reveals a Gradient of Target-Range from Generalist to Specialist Phage Clones in Nested Subsets

Salmonella enterica serovars Enteritidis and Typhimurium are major foodborne pathogens of worldwide concern, which often cause severe diarrheal diseases sometimes with fatal outcomes. According to the WHO report, 550 million people are infected annually, including 220 million children under the age of five [1]. The majority of these cases of domestically acquired salmonellosis are caused by various Salmonella serovars transmitted through the food chain (The US Centers for Disease Control and Prevention) [2]. Increasing antibiotic-resistance of this bacterium is aggravating the epidemic situation [3]. Due to the increasing problem of antibiotic resistance, the development of new strategies to sustainably control food-borne pathogens is urgently needed. Bacteriophages (phages) are potential alternative tools to target Salmonella infection. In post-Soviet Union countries, phage preparations have a long history of application for treatment and prophylaxis against dysenterial diseases, such as shigellosis, escherichiosis, and salmonellosis. These preparations have been successfully used for prophylaxis of salmonellosis among civilian population as well as in Red Army units [4,5,6]. In Western countries phage applications are used for biocontrol in foods [3]. Better understanding of phage–bacteria interactions will facilitate the development of a more rational approach to select appropriate phages for therapy, prophylaxis or biocontrol of Salmonella infections. Therefore, investigating the host range of Salmonella phages is a key to understand their impact on bacterial ecology, coevolution and inform intervention strategies.

One way to study a phage’s host ranges and ecological interactions is through the investigation of phage–bacteria infection networks [7,8,9] (PBINs). Essentially, these networks (or graphs) represent predator–prey interactions between phages and bacteria, respectively. These ecological relationships are graphed as a bipartite network where edges connect nodes from two different subsets, i.e., phages and bacteria. In such networks, an interaction between a single bacterium and a phage could have an impact on other members of the network too. Studying the structure of PBINs essentially addresses the question of “who-kills-whom” and provides important information regarding the ecological, biological and coevolutionary mechanisms underlying the network’s structure [10,11,12,13,14]. For example, large variation in host range species suggests that some phages have evolved to infect many hosts (generalists with wide host ranges), while others have evolved to infect a few select hosts (specialists with narrow host ranges). Equally, large variation in susceptibility host species suggests that the network consists of hosts with generalist and specialist resistance repertoires. At an evolutionary scale, large variation in host and susceptibility range sizes could indicate that particular modes of coevolution are occurring [10,15].

In this study, we investigate the in vitro infection profiles of different Salmonella phages against a wide range of Salmonella bacterium strains. We further use these data to construct a Salmonella phage–bacteria infection network (PBIN) and study its structure. Based on the above, we define a set of different Salmonella phage infection groups (or clusters) and explore their association to known Salmonella phage characteristics. Our aim is to better understand the underlying ecological and evolutionary dynamics that shape the Salmonella phages’ host-range.