Complete Genome Sequence of Campylobacter coli Bacteriophage CAM-P21.

Bacteriophage CAM-P21, isolated from a beef mince sample in Japan using Campylobacter coli, has a 12,587-bp genome encoding 18 putative coding sequences with an average GC content of 31.19%.

ANNOUNCEMENT

Campylobacteriosis is one of the most notorious foodborne diseases worldwide and is caused by Campylobacter spp., especially the major pathogenic species, Campylobacter coli and Campylobacter jejuni (1). Although phages of C. jejuni have been intensively studied, there is limited information available on phages of C. coli (2).

Phage CAM-P21 was isolated from a beef mince sample collected in Fukuoka, Japan, using the double-layer agar method (3) with C. coli CAN10 as the host strain (Fukuoka City Institute of Health and Environment), grown at 42°C in brain heart infusion (BHI) broth supplemented with 10 mM CaCl2 under microaerobic conditions. The phage lysate was serially diluted in saline magnesium (SM) buffer (0.05 M Tris-HCl buffer [pH 7.5] containing 0.1 M NaCl, 0.008 M MgSO4, and 0.01% gelatin) and then further purified using polyethylene glycol (PEG) 8000 precipitation. Genomic DNA from CAM-P21 was extracted using the High Pure viral nucleic acid kit (Roche, Mannheim, Germany). The library preparation and whole-genome sequencing were carried out by Novogene (Japan). The genomic DNA of phage CAM-P21 was completely sequenced with an Illumina HiSeq 4000 platform using the 2 × 150-bp paired-end strategy. The library was purified using the AMPure XP system (Beckman Coulter, USA) and assessed using a Qubit v2.0 fluorometer (Thermo Fisher Scientific) and a 2100 Bioanalyzer (Agilent Technologies, CA, USA).

After filtering the reads by quality score (4), a total of 7,818,238 high-quality reads (effective rate, 99.91%) were generated, and the average read length was 150 bp. For all software, default parameters were used except where otherwise noted. The read quality was checked using FastQC v0.11.9 (5), and the de novo assembly was performed using VelvetOptimiser v1.2.10 (6) with an optimal k-mer value of 139 and the parameters –s 19, –e 151, and –x 8. Annotation of the open reading frames (ORFs) was carried out using Prokka v1.11.0 (7) and the RAST v2.0 server (8) and further confirmed by BLAST analysis. Putative tRNA-encoding genes were scanned using tRNAscan-SE v2.0 (9), and searches for genes linked to antimicrobial resistance and virulence factors were conducted with the ResFinder v3.1 (10) and VirulenceFinder v2.0 (11) servers, respectively.

CAM-P21 has a linear double-stranded DNA (dsDNA) genome 12,587 bp long with an average GC content of 31.19%. It was predicted to encode 18 open reading frames (ORFs) but no tRNA genes; of the ORFs, 9 (50.0%) have putative functions, and the others are hypothetical proteins. Genes associated with antibiotic resistance, toxins, and virulence factors were not found in the genome of CAM-P21. Based on BLASTn results, the highest degree of similarity was observed with Campylobacter phage CGC-2007 (GenBank accession number EF694691), with a coverage of 76% (similarity, 96.31%), which seems to be a prophage specific to C. jejuni.

Data availability.

The fully sequenced genome of phage CAM-P21 has been deposited in the GenBank database under the accession number MW462221. The associated BioProject, BioSample, and SRA accession numbers are PRJNA714202, SAMN18292496, and SRR13959829, respectively.