Phenotypic and genotypic variations within a single bacteriophage species

Abstract

Background: Although horizontal gene transfer plays a pivotal role in bacteriophage evolution, many lytic phage genomes are clearly shaped by vertical evolution. We investigated the influence of minor genomic deletions and insertions on various phage-related phenotypic and serological properties.

Findings: We collected ten different isolates of Pseudomonas aeruginosa bacteriophage ϕKMV. All sequenced genomes (42-43 kb, long direct terminal repeats) are nearly identical, which intuitively implied strongly similar infections cycles. However, their latent periods vary between 21 and 28 minutes and they are able to lyse between 5 and 58% of a collection of 107 clinical P. aeruginosa strains. We also noted that phages with identical tail structures displayed profound differences in host spectra. Moreover, point mutations in tail and spike proteins were sufficient to evade neutralization by two phage-specific antisera, isolated from rabbits.

Conclusion: Although all analyzed phages are 83-97% identical at the genome level, they display a surprisingly large variation in various phenotypic properties. The small overlap in host spectrum and their ability to readily escape immune defences against a nearly identical phage are promising elements for the application of these phages in phage therapy.

Figure 1

Host range analysis of the ϕKMV-like viruses. A. Host range analysis of 'phiKMV-like viruses' using a collection of 114 clinical P. aeruginosa strains. In this assay, 10⁶ pfu were spotted on a bacterial lawn and checked for lysis. See additional files for more information on the P. aeruginosa strains and for detailed spectra. B. Host range comparison of four phages displaying >94% nucleotide identity throughout their genomes, stating the number of strains which are uniquely or commonly lysed by PNM, PT2, PT5 and phiKMV.

Figure 2

Comparative genomic analysis of the ϕKMV-like viruses. The predicted open reading frames of all sequenced ϕKMV-like phages are shown. Their amino acid identity to the corresponding ORF of ϕKMV is indicated in different shades of grey. ORFs unique to each phage are not colored, while predicted functions of the annotated genes are indicated on top. Functional equivalent genes are connected with broken lines. Gene annotation was performed as described elsewhere (Ceyssens et al., 2006).