Genome-based taxonomic classification of Listeria phage and diversity analysis of major capsid protein, receptor-binding protein and endolysin

Abstract

Introduction: Listeria monocytogenes (Lm) poses a significant risk to food safety due to its adaptability and pathogenicity. In contrast, Listeria phages show great promise as biocontrol agents. Method: This study comprehensively analyzed 97 complete Listeria phage genomes from 14 countries across four continents, including 16 newly isolated phages exhibiting specific phenotypic characteristics. Results: The phages were grouped into nine genomic clusters that clearly distinguished between virulent and temperate lifestyles. Temperate phages demonstrated greater genomic diversity than virulent ones. Cluster 1 phages were assigned to the genus Pecentumvirus, exhibiting a broad geographical distribution with diverse sources, and appear to have an ecological advantage based on their genomic characteristics. Evolutionary analyses classified the major capsid protein (MCP), receptor-binding protein (RBP), and endolysin of Listeria phages into nine, seven, and eight distinct types, respectively. These three proteins exhibited high levels of conservation within the virulent clusters, but significant diversity within the temperate clusters. Notably, the RBPs of types R1, R2, R4, and R6 are associated with broad host ranges and distributed across Clusters 1, 2, 7, and 8 phages. Cluster 3 phages lacked identifiable RBP sequences, suggesting an absence of canonical domains that can be detected using standard prediction tools. Discussion: These findings refine the classification of Listeria phages, significantly advancing our understanding of their taxonomy, genomic diversity, and global distribution.