Genomic and Phenotypic Analysis of Salmonella enterica Bacteriophages Identifies Two Novel Phage Species

Abstract

Bacteriophages (phages) are potential alternatives to chemical antimicrobials against pathogens of public health significance. Understanding the diversity and host specificity of phages is important for developing effective phage biocontrol approaches. Here, we assessed the host range, morphology, and genetic diversity of eight Salmonella enterica phages isolated from a wastewater treatment plant. The host range analysis revealed that six out of eight phages lysed more than 81% of the 43 Salmonella enterica isolates tested. The genomic sequences of all phages were determined. Whole-genome sequencing (WGS) data revealed that phage genome sizes ranged from 41 to 114 kb, with GC contents between 39.9 and 50.0%. Two of the phages SB13 and SB28 represent new species, Epseptimavirus SB13 and genera Macdonaldcampvirus, respectively, as designated by the International Committee for the Taxonomy of Viruses (ICTV) using genome-based taxonomic classification. One phage (SB18) belonged to the Myoviridae morphotype while the remaining phages belonged to the Siphoviridae morphotype. The gene content analyses showed that none of the phages possessed virulence, toxin, antibiotic resistance, type I–VI toxin–antitoxin modules, or lysogeny genes. Three (SB3, SB15, and SB18) out of the eight phages possessed tailspike proteins. Whole-genome-based phylogeny of the eight phages with their 113 homologs revealed three clusters A, B, and C and seven subclusters (A1, A2, A3, B1, B2, C1, and C2). While cluster C1 phages were predominantly isolated from animal sources, cluster B contained phages from both wastewater and animal sources. The broad host range of these phages highlights their potential use for controlling the presence of S. enterica in foods.

TSPDB: A curated resource of tailspike proteins with potential applications in phage research

“…The TSPDB was recently utilized in a study by (Bhandare et al, 2024), where the database was implemented within an ABRicate container to screen for the presence of TSPs in a collection of phage genomes using stringent parameters (≥ 90% identity and ≥ 70% coverage). Overall, the TSPDB contains a vast dataset of diverse TSPs found in phages, making it an essential tool for detecting TSPs within large genomic and metagenomic datasets.…”

“…Despite the known antimicrobial applications of TSPs, only a few have been fully characterized to date. This could be partly due to the laborious nature of detection techniques, which include plaque assays followed by examination under a transmission electron microscope (TEM) to identify “bulb-like” baseplate structures at the base of phage tails indicative of TSPs (Bhandare et al, 2024; Knecht et al, 2020). The decreasing costs of sequencing and the availability of improved bioinformatics tools have facilitated the construction of large-scale genome and metagenome datasets (Emond-Rheault et al, 2017; Wattam et al, 2014).…”