Genomic and functional characterization of five novel Salmonella-targeting bacteriophages

Abstract

Background The host-unrestricted, non-typhoidal Salmonella enterica serovar Enteritidis (S. Enteritidis) and the serovar Typhimurium (S. Typhimurium) are major causative agents of food-borne gastroenteritis, and the host-restricted Salmonella enterica serovar Gallinarum (S. Gallinarum) is responsible for fowl typhoid. Increasing drug resistance in Salmonella contributes to the reduction of effective therapeutic and/or preventive options. Bacteriophages appear to be promising antibacterial tools, able to combat infectious diseases caused by a wide range of Salmonella strains belonging to both host-unrestricted and host-restricted Salmonella serovars. Methods In this study, five novel lytic Salmonella phages, named UPWr_S1-5, were isolated and characterized, including host range determination by plaque formation, morphology visualization with transmission electron microscopy, and establishment of physiological parameters. Moreover, phage genomes were sequenced, annotated and analyzed, and their genomes were compared with reference Salmonella phages by use of average nucleotide identity, phylogeny, dot plot, single nucleotide variation and protein function analysis. Results It was found that UPWr_S1-5 phages belong to the genus Jerseyvirus within the Siphoviridae family. All UPWr_S phages were found to efficiently infect various Salmonella serovars. Host range determination revealed differences in host infection profiles and exhibited ability to infect Salmonella enterica serovars such as Enteritidis, Gallinarum, Senftenberg, Stanley and Chester. The lytic life cycle of UPWr_S phages was confirmed using the mitomycin C test assay. Genomic analysis revealed that genomes of UPWr_S phages are composed of 51 core and 19 accessory genes, with 33 of all predicted genes having assigned functions. UPWr_S genome organization comparison revealed 3 kinds of genomes and mosaic structure. UPWr_S phages showed very high sequence similarity to each other, with more than 95% average nucleotide identity. Conclusions Five novel UPWr_S1-5 bacteriophages were isolated and characterized. They exhibit host lysis range within 5 different serovars and are efficient in lysis of both host-unrestricted and host-restricted Salmonella serovars. Therefore, because of their ability to infect various Salmonella serovars and lytic life cycle, UPWr_S1-5 phages can be considered as useful tools in biological control of salmonellosis.

Bacteriophage Cocktail Can Effectively Control Salmonella Biofilm in Poultry Housing

“…UPWr_S1, UPWr_S3, and UPWr_S4 phages are capable of infecting zoonotic pathogens such as S. Enteritidis as well as S. Gallinarum, which is the etiological factor of fowl typhoid. Regardless of their ability to infect various Salmonella serovars and lytic life cycle, they can be considered useful tools in the biological control of salmonellosis (Kuzmińska-Bajor et al, 2021). In this study, we found that UPWr_S1, UPWr_S3, and UPWr_S4 phages alone and the UPWr_S134 phage cocktail exhibited a great ability to decrease the number of Salmonella from biofilm structures in a 96-well microtiter plate and on stainless steel washers formed by strong and moderate biofilm producers, S. Enteritidis ATCC 13076 and 372 lux strains, respectively.…”

“…This has many implications for phage biology as well as for their practical applications. Although UPWr_S1, UPWr_S3, and UPWr_S4 phages showed similar biofilm removal properties in comparison to the UPWr_S134 phage cocktail and they exhibited a similar lytic profile (Kuzmińska-Bajor et al, 2021 ), for studies on the potential anti-biofilm application in a poultry watering system, the UPWr_S134 phage cocktail was applied.…”

“…The bacteriophages used in this study, termed UPWr_S1, UPWr_S3, and UPWr_S4 were previously sequenced and described (Kuzmińska-Bajor et al, 2021 ). UPWr_S1, UPWr_S3, and UPWr_S4 phages exhibit a lytic life cycle and are deprived of the ability to promote lysogeny, toxin production, antibiotic resistance, or virulence.…”

Isolation, characterization, and genome investigation of vB_SenS_TUMS_E4, a polyvalent bacteriophage against Salmonella enteritidis

“…Subsampling of the reads was performed with seqtk (Galaxy Version 1.3.2) (24). De novo assembly was conducted with the Shovill pipeline (Version 3.12.0) using default parameters (7). Assembly validation was performed in Galaxy BWA-MEM (24) and Blastn was used to identify similarities between the assembled genome and other genomic sequences.…”

“…Using bacteriophages against food pathogens such as Salmonella to improve the food industry has received more attention. For that reason, most of the regulatory approvals are related to phage products of food pathogens (7).…”