The Search for Therapeutic Bacteriophages Uncovers One New Subfamily and Two New Genera of Pseudomonas-Infecting Myoviridae

Abstract

In a previous study, six virulent bacteriophages PAK_P1, PAK_P2, PAK_P3, PAK_P4, PAK_P5 and CHA_P1 were evaluated for their in vivo efficacy in treating Pseudomonas aeruginosa infections using a mouse model of lung infection. Here, we show that their genomes are closely related to five other Pseudomonas phages and allow a subdivision into two clades, PAK_P1-like and KPP10-like viruses, based on differences in genome size, %GC and genomic contents, as well as number of tRNAs. These two clades are well delineated, with a mean of 86% and 92% of proteins considered homologous within individual clades, and 25% proteins considered homologous between the two clades. By ESI-MS/MS analysis we determined that their virions are composed of at least 25 different proteins and electron microscopy revealed a morphology identical to the hallmark Salmonella phage Felix O1. A search for additional bacteriophage homologs, using profiles of protein families defined from the analysis of the 11 genomes, identified 10 additional candidates infecting hosts from different species. By carrying out a phylogenetic analysis using these 21 genomes we were able to define a new subfamily of viruses, the Felixounavirinae within the Myoviridae family. The new Felixounavirinae subfamily includes three genera: Felixounalikevirus, PAK_P1likevirus and KPP10likevirus. Sequencing genomes of bacteriophages with therapeutic potential increases the quantity of genomic data on closely related bacteriophages, leading to establishment of new taxonomic clades and the development of strategies for analyzing viral genomes as presented in this article.

Characterization of Pseudomonas aeruginosa phage K5 genome and identification of its receptor related genes

“…aeruginosa phage K5 has been previously shown to be a myovirus [9]. In this study, combined with the comparative genomic data and the phylogenetic data of the major capsid proteins, phage K5 is demonstrated as a new member of "PaP1-like" [25] or "PAK_P1-like" phages [29]. The phages in this genus typically have identical terminal direct repeats with the lengths ranging from 184 to 1238 bp, consistent with our data which is 1182 bp [30].…”

Characterization of Pseudomonas aeruginosa Phage C11 and Identification of Host Genes Required for Virion Maturation

“…P. aeruginosa phage C11 is highly similar to the genome of P. aeruginosa phage PaP1 and may be considered as a new member of the genus PaP1-like phages36 or PAK_P1-like phages37. Though the phages C11, JG004, PaP1, vB_PaeM_C2-10_Ab1, and PAK_P1 are genetically closely related to each other, they are the different phage isolates recovered across the world with their own evolutionary paths38.…”

“…These genes may have their own bacterial origins and possibly be obtained by phage C11 via the process of horizontal gene transfer (HGT)39. The complete genome sequence of phage C11 is shown to be a liner DNA molecule with the 1173 bp identical terminal direct repeats, similar to a variety of P. aeruginosa phages which have highly conserved direct repeat sequences with length ranging from 184 bp to 1238 bp3740.…”

Phage therapy of pulmonary infections

“…Additional characterization of the biology of the phages employed by Henry et al has recently been published where they question the need for "complete molecular characterization of new bacteriophages" prior to their medical use. 70 Semler et al 62 also employed a mouse B. cenocepacia lung infection model but are a different group from that of Carmody et al 54 Mice were prepared for infection by being chemically immunocompromised via cyclophosphamide application and both bacterial challenge and phage treatment were accomplished via nebulization. There was a 24-h delay between bacterial challenge and phage treatment, which as a delay in the initiation of therapy in animals can be viewed as fairly substantial.…”