Genomic analysis of a novel active prophage of Hafnia paralvei

Abstract

Relatively little is known about the prophages in Enterobacterales bacteria except Escherichia coli. A novel phage, Hafnia phage yong2, was induced from Hafnia paralvei by mitomycin C. The phage has an elliptical head of approximately 45 × 38 nm, a long noncontractile tail of approximately 157 × 4 nm. The complete genome of Hafnia phage yong2 is a 39,546 bp double-stranded DNA with a G+C content of 49.9%, containing 59 opening reading frames (ORFs), and having at least one fixed terminus (GGGGCAGCGACA) with R=107>100. In phylogenetic analysis, Hafnia phage yong2 clustered with 4 predicted Hafnia prophages and 1 predicted Enterobacteriaceae prophage. The prophages cluster and Drexlerviridae family together formed two distinct subclades nested within a clade, suggesting the existence of a novel class of prophages with conserved sequences and unique evolutionary status not yet studied before in Hafniaceae and Enterobacteriaceae bacteria. Bacteria of the genus Hafnia in family Hafniaceae, including Hafnia alvei and Hafnia paralvei, are normally found in food, plants, the gastrointestinal tract of animals and humans, etc [1, 2]. Rod-shaped Hafnia bacteria are facultatively anaerobic, gram-negative, considered to be an opportunistic pathogen to various animal species including fish, mammals and birds, and are capable of causing human infection under suspicion [1-4].Bacteriophages (phages) are viruses that can develop lytic or lysogenic infection in bacterial cells.