Complete Genome Sequence of the Hippuricase-Positive Campylobacter avium Type Strain LMG 24591

GENOME ANNOUNCEMENT

Campylobacter spp., primarily C. jejuni and C. coli, are commonly associated with acute bacterial gastroenteritis in humans (1), and transmission is often via contaminated poultry products (1, 2). In 2006, hippuricase-positive Campylobacter strains were isolated from poultry on three farms in Italy (3). Although initially identified as C. jejuni, based on their hippuricase activity, additional molecular and phenotypic tests identified these organisms as a novel species, termed Campylobacter avium (3). In this study, we present the first closed genome sequence of the C. avium type strain LMG 24591.

The genome of C. avium strain LMG 24591^T was completed using the Roche 454, Illumina HiSeq, and PacBio next-generation sequencing platforms, as previously described (4). Illumina HiSeq reads for strain LMG 24591^T were obtained from SeqWright (Houston, TX). The final coverage across the genome was 1,191×. The LMG 24591^T assembly was additionally verified using a bacterial optical restriction map (XbaI; OpGen, Gaithersburg, MD). Putative coding sequences (CDSs) were identified using GeneMark (5). Final annotation, including manual start codon curation, determination of homopolymeric GC tract variability, and the identification of rRNA- and tRNA-coding genes and pseudogenes, was performed as previously described (6).

C. avium strain LMG 24591^T has a circular genome of 1,738.6 kbp, with a GC content of 34.2%. The genome contains 1,645 putative protein-coding genes, 48 pseudogenes, 2 rRNA loci, and 3 putative genetic islands, with one encoding a partial type VI secretion system. Forty-four GC tracts of ≥8 bp were identified in the LMG 24591^T genome; 40 of these were determined to be hypervariable. No plasmids were identified in LMG 24591^T.

Noteworthy in C. avium is the absence of the selenocysteinyl tRNA and genes encoding selenium-associated proteins, e.g., selenocysteine insertion proteins, selenoproteins, and selenoprotein-associated chaperones. The absence of selenium metabolism was reported previously for Campylobacter lanienae and related taxa (7). An ortholog of the C. jejuni fibronectin-binding protein CadF is also not encoded by C. avium. Because CadF is required for C. jejuni host cell invasion and colonization (8, 9), its absence might indicate reduced virulence in C. avium. Other proteins that are not encoded by C. avium include the ferredoxins FdxA and FdxB, methionine sulfoxide reductase (MsrA, MsrB, or MsrAB), and the globin Cgb, suggesting that, when compared to C. jejuni, C. avium might have a lower aerotolerance and is more sensitive to oxidative and nitrosative stress (10–12).

Prior to the identification of C. avium, C. jejuni was unique among Campylobacter spp. in its ability to hydrolyze hippuric acid (13). Hippuric acid (N-benzoylglycine) is cleaved by HipO (14) to produce glycine and benzoic acid, with glycine production measured by a simple colorimetric assay (15). Although we confirmed that C. avium is hippuricase positive, the hipO gene was not detected in strain LMG 24591^T. Thus, it is likely that C. avium encodes an alternate hippuricase with low similarity to HipO. C. jejunihipO contains a peptidase M20 domain and encodes a predicted zinc-dependent aminoacylase/carboxypeptidase. Analysis of the C. avium LMG 24591^T genome identified a candidate hippuricase gene with a similar domain structure, which we have termed hipA.