Biology and Genomics of an Historic Therapeutic Escherichia coli Bacteriophage Collection

Abstract

We have performed microbiological and genomic characterization of an historic collection of nine bacteriophages, specifically infecting a K1 <i>E. coli</i> O18:K1:H7 ColV⁺ strain. These phages were isolated from sewage and tested for their efficacy <i>in vivo</i> for the treatment of systemic <i>E. coli</i> infection in a mouse infection model by Smith and Huggins (1982). The aim of the study was to identify common microbiological and genomic characteristics, which co-relate to the performance of these phages in <i>in vivo</i> study. These features will allow an informed selection of phages for use as therapeutic agents. Transmission electron microscopy showed that six of the nine phages were <i>Podoviridae</i> and the remaining three were <i>Siphoviridae</i>. The four best performing phages <i>in vivo</i> belonged to the <i>Podoviridae</i> family. <i>In vitro</i>, these phages exhibited very short latent and rise periods in our study. In agreement with their microbiological profiles, characterization by genome sequencing showed that all six podoviruses belong to the <i>Autographivirinae</i> subfamily. Of these, four were isolates of the same species (99% identity), whereas two had divergent genomes compared to other podoviruses. The <i>Siphoviridae</i> phages, which were moderate to poor performers <i>in vivo</i>, exhibited longer latent and rise periods <i>in vitro</i>. Two of the three siphoviruses were closely related to each other (99% identity), but all can be associated with the <i>Guernseyvirinae</i> subfamily. Genome sequence comparison of both types of phages showed that a gene encoding for DNA-dependent RNA polymerase was only present in phages with faster replication cycle, which may account for their better performance <i>in vivo</i>. These data define a combination of microbiological, genomic and <i>in vivo</i> characteristics which allow a more rational evaluation of the original <i>in vivo</i> data and pave the way for the selection of phages for future phage therapy trails.