Salmonella spp. is one of the most common foodborne pathogens worldwide; therefore, its control is highly relevant for the food industry. Phages of the Felixounavirus genus have the characteristic that one phage can infect a large number of different Salmonella serovars and, thus, are proposed as an alternative to antimicrobials in food production. Here, we describe two new members of the Felixounavirus genus named vB_Si_35FD and vB_Si_DR94, which can infect Salmonella Infantis. These new members were isolated and sequenced, and a subsequent comparative genomic analysis was conducted including 23 publicly available genomes of Felixounaviruses that infect Salmonella. The genomes of vB_Si_35FD and vB_Si_DR94 are 85,818 and 85,730 bp large and contain 129 and 125 coding sequences, respectively. The genomes did not show genes associated with virulence or antimicrobial resistance, which could be useful for candidates to use as biocontrol agents. Comparative genomics revealed that closely related Felixounavirus are found in distinct geographical locations and that this genus has a conserved genomic structure despite its worldwide distribution. Our study revealed a highly conserved structure of the phage genomes, and the two newly described phages could represent promising biocontrol candidates against Salmonella spp. from a genomic viewpoint.

Retron were described in 1984 as DNA sequences that code for a reverse transcriptase and a unique single-stranded DNA/RNA hybrid called multicopy single-stranded DNA (msDNA). It would not be until 2020 that a function was shown for retrons, when compelling evidence was presented that retrons activate an abortive infection pathway in response to bacteriophage (phage) infection. When infected with the virulent mutant of the phage lambda, λ ^VIR , and to a lesser extent, other phages, a retron designated Ec48 is activated, the Escherichia coli bearing this element dies, and the infecting phage is lost. With the aid of a mathematical model, we explore the a priori conditions under which retrons will protect bacterial populations from predation by phage and the conditions under which retron-bearing bacteria will evolve in populations without this element. Using E. coli with and without Ec48 and l ^VIR , we estimated the parameters of our model and tested the hypotheses generated from our analysis of its properties. Our models and experiments demonstrate that cells expressing a retron-mediated abortive infection system can protect bacterial populations. Our results demonstrate that retron bearing bacteria only have a competitive advantage under a limited set of conditions.

Summary: One major concern in hospitalized patients is infections with pathogens borne on surfaces, patients, and healthcare workers. Fundamental to controlling nosocomial infections is identifying the sources of pathogens, monitoring the processes responsible for their transmission, and evaluating the efficacy of the procedures employed for restricting their transmission. Here we present a method using the bacteriophage Lambda (λ) to achieve these ends. Defined densities of multiple genetically marked λ phages were inoculated at known hotspots for contamination on high-fidelity mannequins. Healthcare workers (HCWs) then entered a pre-sanitized simulated hospital room and performed a series of patient care tasks on the mannequins. Sampling occurred on the scrubs and hands of the HCWs, as well as previously defined high-touch surfaces in hospital rooms. Following sampling, the rooms were decontaminated using procedures designed and demonstrated to be effective. Following the conclusion of the simulation, the samples were tested for the presence, identity, and densities of these Lambda phages. The data generated enabled the determination of the sources and magnitude of contamination caused by the breakdown of established infection prevention practices by HCW. This technique enabled the standardized tracking of multiple contaminants during a single episode of patient care. While our application of these methods focused on nosocomial infections and the role of HCW behaviors in their spread, these methods could be employed for identifying the sources and sites of microbial contamination in other settings.

The most significant difference between bacteriophages functionally and ecologically is whether they are purely lytic (virulent) or temperate. Virulent phages can only be transmitted horizontally by infection, most commonly with the death of their hosts. Temperate phages can also be transmitted horizontally, but upon infection of susceptible bacteria, their genomes can be incorporated into that of their host’s as a prophage and be transmitted vertically in the course of cell division by their lysogenic hosts. From what we know from studies with the temperate phage Lambda and other temperate phages, in laboratory culture, lysogenic bacteria are protected from killing by the phage coded for by their prophage by immunity; where upon infecting lysogens, the free temperate phage coded by their prophage are lost. Why are lysogens not also resistant as well as immune to the phage coded by their prophage since immunity does not confer protection against virulent phages? To address this question, we used a mathematical model and performed experiments with temperate and virulent mutants of the phage Lambda in laboratory culture. Our models predict and experiments confirm that selection would favor the evolution of resistant as well as immune lysogens, particularly if the environment includes virulent phage that share the same receptors as the temperate. To explore the validity and generality of this prediction, we examined ten lysogenic Escherichia coli from natural populations. All ten were capable of forming immune lysogens but their original hosts were resistant to the phage coded by their prophage. Significance Statement: This jointly theoretical and experimental study predicted that lysogenic bacteria, will be resistant as well as immune to the phage coded for by their prophage. All ten naturally occurring lysogenic Escherichia coli tested were resistant to the temperate phage coded for by their prophage.