Bacteriophages infecting Campylobacter jejuni can be divided into 2 genera, the Cp220likevirus and the Cp8unalikevirus of the Eucampyviridae family. Comparative genomics has shown that phages within each genus are highly conserved. However, only a limited number of Campylobacter phage genome sequences are publicly available and these phages originate from very distinct locations all over the world.

Here we aim to determine the genetic relationship of phages isolated from the same country and on the same farms. We therefore present whole genome sequences and comparative sequence analyses of phages isolated from three different free-range chicken farms in Denmark during the summer of 2011. All phages infect C. jejuni strain RM1221 and belong to the Cp220likevirus genus. Sequencing was performed using the Illumina MiSeq technology with sequencing libraries constructed from either a single plaque or purified genomic DNA. The genomic analysis revealed that the overall similarities of the phages were high, except in regions where putative mobile elements were identified, indicating that acquisition of novel genetic content is associated with such elements. All phage genomes were organized in conserved modules flanked by very large direct or inverted repeats that prevented assembly into one contig. Thus, subsequent PCR’s were performed to close the genomes, which interestingly demonstrated rearrangement of conserved modules in phages isolated from the same farm. We are currently using PacBio technology to further verify the assembly of contigs. Furthermore, we observed duplication of regions associated with the repeats, which has previously not been described for this group of phages. Our work has shown that it is possible to modify the standard protocols for phage DNA purification and sequencing to be applied for the modified DNA of Campylobacter phages. Overall, we found that phages isolated from the same farm are more genetically related than phages isolated from different farms.