Abstract: Cystic Fibrosis (CF) is a common autosomal recessive disorder. The congenital mutation in the Cystic Fibrosis Transmembrane Conductance Regulator gene alters the chloride channel in epithelial cells, giving rise to dehydration and a thick mucus layer. This mucus provides a nutrient rich environment for opportunistic bacteria. Bronchiectasis (BR) is similar symptomatically to CF due to localised dilation and inflammation events of the bronchial tree that can be linked to lung trauma in some instances allergic response and subsequent bacterial infection. Pseudomonas aeruginosa (PA) and Burkholderia cepacia complex (BCC) are opportunistic pathogens that are major drivers of chronic lung infection that correlate to lowered lung function and poor clinical outcomes. Temperate bacteriophages infect and subvert their bacterial hosts through integration into the bacterial chromosome (prophage) and adapt alongside their host. We here compare the genomes of mixed temperate phage lysates induced from 94 PA (47 PA from CF, 47 PA) and 46 BCC isolates. Novel approaches were used to stratify mixed viral sequences for genome assembly and the genomes compared to the etiology of infection (CF < 15yr, CF Adult >15 years, BR <10 years since diagnosis and BR >10 years since diagnosis. When comparing to the genomes of PA phages and clinical disease >109 completed phage genomes were compared showing distinct phage genomovars. These methods were also used to isolate and compare the genomes of 26 BCC phages.

Methods: Khmer software was used to remove bacterial contamination from the samples. This was achieved by separating out k-mers in a probabilistic bloom filter. It also allowed stratification of induced phages prior to assembly based upon k-mer abundance. Genomes where assembled using SPAdes. Those that were not completely assembled using SPAdes were completed using PriceTI. Completed phage genomes were re-orientated and annotated using PROKKA. Genomes were compared using Dotter and MAFFT.