Genome Sequence of a Urease-Positive Campylobacter lari Strain.

Campylobacter lari is frequently isolated from shore birds and can cause illness in humans. Here, we report the draft whole-genome sequence of a urease-positive strain of C. lari that was isolated in estuarial water on the coast of Delaware, USA.

GENOME ANNOUNCEMENT

Campylobacter lari is a member of the thermophilic cluster of the genus Campylobacter, and as such is closely related to C. jejuni, C. coli, C. upsaliensis, C. insulaenigrae, and C. helviticus. A genomic sequence has previously been described for C. lari RM2100 (GenBank number NC012039), an isolate of the nalidixic acid-resistant thermophilic campylobacters (NARTC) group that was originally isolated from a toddler with watery diarrhea (1). C. lari frequently has been isolated from shore birds and survives better than other Campylobacter species in surface waters (2).

Using a previously described procedure for isolating Campylobacter from environmental water (3), we isolated a Campylobacter-like organism in estuarine waters near Slaughter Beach, Delaware, USA (N38.91398°, W75.30843°). For selection, this isolation included incubation at 42°C with cefoperazone. C. lari is not usually cefoperazone-resistant, and initial PCR assays to identify the isolate were positive for a Campylobacter genus-specific probe and negative for a specific probe for C. lari glyA (4). However, sequencing of the 16S ribosomal fragment gene revealed a sequence characteristic of C. lari.

The genomic sequence of the strain was determined by sequencing with Pacific Biosciences XL-C2 chemistries and assembled with long-versus-long error correction (PacBioToCA), followed by the Celera Assembler version 7 into a single circular contig of 1,563,032 bases. This sequence was used as a scaffold for assembling data from three runs on a Roche 454 Jr. using the GS FLX Rapid Library prep kit followed by the GS Junior Titanium emPCR (Lib-L) kit (Roche, Branford, CT, USA) (257,885 total fragments, 404-base average read length) and there were less than one base per thousand disagreements. The sequence was also confirmed by genomic optical mapping (OpGen) with approximately 97% agreement. There was no evidence of the presence of any plasmids.

The Slaughter Beach strain sequence had a GC ratio of 29.8%. Annotation was performed by Glimmer (5), which predicted 1,584 open reading frames (ORFs). Three ribosomal operons were identified, each with tRNA-Ile and tRNA-Ala genes in the 16S–23S intergenic fragment.

The sequence showed almost exact synteny with the sequence for C. lari RM2100 with several insertions and deletions. A larger fragment present in the Slaughter Beach strain carried two ORFs with significant similarity to urease genes. Thus, the Slaughter Beach strain is a member of the urease-producing thermophilic campylobacters (UPTC) group. The glyA gene of the Slaughter Beach strain differed from that of C. lari RM2100 by 3.7%, critically differing at the GC-clamps of the 3ʹ end of both primers used for species identification.

Nucleotide sequence accession number.

This whole-genome shotgun project has been deposited in DDBJ/ENA/GenBank under the accession number CP011372. The version described in this paper is the first version.