Complete Genome Sequence of the Campylobacter helveticus Type Strain ATCC 51209.

Campylobacter helveticus has been isolated from domestic dogs and cats. Although C. helveticus is closely related to the emerging human pathogen C. upsaliensis, no C. helveticus-associated cases of human illness have been reported. This study describes the whole-genome sequence of the C. helveticus type strain ATCC 51209 (=CCUG 30682T).

GENOME ANNOUNCEMENT

Campylobacter helveticus is a catalase-negative, thermotolerant campylobacter that is generally isolated from cats and occasionally from dogs (1–4). However, although it is isolated from pets and is related to the human emerging pathogen C. upsaliensis (5), there have been no reports of C. helveticus-associated human disease (5, 6). The C. helveticus type strain ATCC 51209 was isolated in Switzerland from a domestic cat with diarrheal illness (7). In this study, we report the first closed genome sequence of strain ATCC 51209T.

The Roche GS-FLX, Illumina HiSeq, and PacBio RS next-generation sequencing platforms were used to complete the strain ATCC 51209T genome. Shotgun and paired-end Roche 454 reads were assembled (using Newbler version 2.6) into 6 scaffolds (1 chromosomal and 5 plasmid) of 46 contigs interspersed with unique and repeat contigs. Three plasmid scaffolds contained a single contig each and were closed/circularized using HiSeq reads (SeqWright, Houston, TX, USA). Two of the remaining three scaffolds were closed into a single contig using a combination of PCR amplification/Sanger sequencing across the contig gaps and PacBio sequencing. Base calls on all six final contigs were validated using HiSeq reads. The final coverage across the genome was 1,314×. Assembly of the chromosome was further validated using an optical restriction map (restriction enzyme NheI; OpGen, Gaithersburg, MD, USA).

C. helveticus strain ATCC 51209T has a circular genome of 1,759 kb with an average GC content of 34.6%. Protein-, rRNA- and tRNA-encoding genes were identified as previously described (8). The genome contains 1,698 putative protein-coding genes and 75 pseudogenes. Three rRNA operons were identified; however, all three operons are split, where the 23S and 16S ribosomal RNA genes are separated by 21, 353, or 4 kb. Two large genetic islands of 107 and 83 kb were identified in the ATCC 51209T chromosome, as well as three smaller elements of 4, 6, and 10 kb. The chromosome also contains 82 GC tracts ≥8 bp.

Five plasmids were identified in the C. helveticus type strain: two large plasmids of 72 (pHELV-1) and 34 (pHELV-2) kb (GC = 30.1%), and three small plasmids of 3.3 (pHELV-3), 1.7 (pHELV-4), and 1.8 (pHELV-5) kb (GC = 30.5 to 32.8%). The pHELV-1 sequence could not be circularized using reads from any of the next-generation platforms. Furthermore, pHELV-1 contains a perfect 606-bp terminal inverted repeat, suggesting that pHELV-1 is a linear plasmid (9). pHELV-3 is a repAB family theta-replicating, iteron-containing plasmid (10). pHELV-5 is a RepL family plasmid; however, pHELV-5 RepL is more similar to RepL proteins in Firmicutes spp., with no similarity to RepL proteins identified previously in Campylobacter spp. (10).

A noteworthy feature of the C. helveticus type strain genome is the presence of a large suite of restriction/modification (R/M) genes. The ATCC 51209T genome is predicted to encode seven R/M systems: one type I, four type II, and two type III; two additional type II systems are also encoded, although in each case the R subunit is predicted to be a pseudogene. Besides these systems, 10 DNA methyltransferases, 2 restriction endonucleases, and 10 R/M-associated putative pseudogenes were identified.

Accession number(s).

The complete genome sequence of C. helveticus strain ATCC 51209T has been deposited in GenBank under the accession numbers CP020478 (chromosome) and CP020479 to CP020483 (plasmids pHELV-1 to pHELV-5).