Metagenomic analyses of single phages and phage cocktails reveal contamination with temperate phages and bacterial DNA. undefined

Abstract: Increasing incidence of antibiotic resistance has led to renewed attention being paid to bacteriophage therapy, a practice that is common in some parts of the world but remains experi-mental in the west. Commercial phage cocktails are available but often their contents are not well defined. Some metagenomic studies have been done to retrospectively characterise these cocktails, but little is known about the replication cycle of the included phages. In this study, published metagenomic sequences were analysed using recent advances in viromics tools and approaches and temperate phage contigs were found in all cocktail metagenomes. Given that temperate phag-es are unlikely to have been included deliberately, there are three possible explanations for their presence: temperate phages have been misidentified as lytic and included accidentally; there is contaminating host DNA present in the cocktails; or prophages have been induced in the propa-gating host. Regardless of how the temperate phage DNA was introduced to the cocktail, it poses a risk as it may lead to horizontal gene transfer of virulence factors to pathogens. Steps should be taken to ensure no temperate phages or temperate phage DNA is present before the cocktails are used therapeutically.