ABSTRACT

Campylobacter spp. are frequently found associated with the avian intestinal tract. Most are commensals, but some can cause human campylobacteriosis. Here, we report the draft genome sequences of three strains of a novel Campylobacter sp. isolated from urban birds and a rural river in New Zealand.

ANNOUNCEMENT

Campylobacter species are frequent commensals of the avian gastrointestinal tract, and C. jejuni isolated from birds is associated with zoonotic campylobacteriosis in humans (1, 2). Additionally, wild birds are a rich source of novel Campylobacter species (3, 4). Swabs of deposited feces from starlings and mallard ducks in Palmerston North, Manawatu, New Zealand, as well as a 0.45-μm mixed cellulose ester filter (Millipore, Germany) of 100 ml of water from the Pareora River in Canterbury, New Zealand, were enriched in Bolton broth (LabM, Hampshire, UK) in a microaerobic atmosphere at 42°C and subcultured onto modified charcoal-cefoperazone-deoxycholate agar (mCCDA) (Fort Richard Laboratories, Auckland, New Zealand). Three strains of nonstandard colonial morphology (B423b from a mallard duck, B1491 from a starling, and W677a from the Pareora River) had crude DNA extracted by boiling and 16S rRNA PCR performed using the methodology of Linton and coauthors (5). The products were Sanger sequenced at the Massey Genome Service (Massey University, Palmerston North, New Zealand). Genomic DNA was extracted from a single colony using the QIAamp DNA minikit (Qiagen, Germany) for W677a and the Wizard genomic DNA kit (Promega, WI) for B423b and B1491. DNA was sequenced at New Zealand Genomics Ltd. (Massey University) using a MiSeq instrument (Illumina, Inc.) with paired read lengths of 250 base pairs after library preparation using the Nextera XT library kit (Illumina). Sequence data were trimmed, assembled, and annotated using the “reads to report” Nullarbor pipeline (https://github.com/tseemann/nullarbor), which uses Trimmomatic with default settings (6) and SPAdes v.3.9.0 in careful mode (7). Annotation statistics were extracted from the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) after being uploaded to the NCBI server and are described in Table 1.
TABLE 1
TABLE 1 Campylobacter sp. strain data
StrainLength (bp)No. of contigsN50 (bp)No. of readsCoverage (×)No. of CDSaGC content (%)Assembly accession no.GenBank accession no.SRA accession no.
W677a1,638,7113787,075859,904811,64727.48GCA_004323835QPGP00000000SRR8367113
B14911,647,5682877,2322,092,4243081,66627.44GCA_004323825QPGQ00000000SRR8367114
B423b1,571,81959119,547776,8201151,61427.45GCA_004323845QPGR00000000SRR8367115
a
CDS, coding DNA sequences.
Similarity to known Campylobacter spp. was measured by BLAST analysis of the 16S rRNA gene, and genomic average nucleotide identity (ANI) was calculated using the Kosta laboratory’s ANI calculator (http://enve-omics.ce.gatech.edu/ani/). The three presented isolates showed 99% ANI and 100% 16S pairwise identity compared to each other, suggesting a monophyletic lineage. Both BLAST and ANI methods identified the most closely related species as being members of C. jejuni, showing 98.15% 16S pairwise identity to C. jejuni NCTC13268 and ∼79% ANI to C. jejuni (GenBank accession number GCA_000011865), suggesting that the isolates are likely members of a previously undescribed taxonomic group.
The isolates had a genome with an estimated mean size of 1.62 Mb ± 0.04 Mb standard deviation and 1,642 (±26) predicted coding sequences. The average GC content was 27.46% (±0.02%). This is lower than that observed in other Campylobacter spp., which typically falls between 30 and 46% (8), with the previously described lowest being 27.9% for C. hepaticus (9). Single copies of 5S, 16S, and 23S rRNA genes were identified in each genome. ABRicate (https://github.com/tseemann/abricate) was used to query the Virulence Factors Database (10) using default settings. Neither the cdtABC operon responsible for cytolethal distending toxin production nor the pVir plasmid associated with described pathogenicity in other Campylobacter species was found, suggesting that these isolates potentially belong to an avirulent commensal taxonomic group.

Data availability.

The genome assemblies have been deposited in GenBank, and the accession numbers are detailed in Table 1.

ACKNOWLEDGMENTS

We thank Vathsala Mohan, Sarah Moore, and Anthony Pita for performing the sampling.
Sampling was funded by the Royal Society of New Zealand Marsden Fund (MAU0802), the New Zealand Food Safety Authority project FDI/236/2005 (Enhancing Surveillance of Potentially Food-borne Enteric Diseases in New Zealand: Human Campylobacteriosis in the Manawatu), and a New Zealand Ministry of Health, Aquatic Protozoa Analysis and Advice Services contract, while the whole-genome work was funded by the Massey University Research Fund. David A. Wilkinson and Nigel P. French were supported by the New Zealand Food Safety Science and Research Centre.
We declare no conflicts of interest.

REFERENCES

1.
Mullner P, Spencer SEF, Wilson DJ, Jones G, Noble AD, Midwinter AC, Collins-Emerson JM, Carter P, Hathaway S, French NP. 2009. Assigning the source of human campylobacteriosis in New Zealand: a comparative genetic and epidemiological approach. Infect Genet Evol 9:1311–1319.
2.
French NP, Midwinter A, Holland B, Collins-Emerson J, Pattison R, Colles F, Carter P. 2009. Molecular epidemiology of Campylobacter jejuni isolates from wild-bird fecal material in children’s playgrounds. Appl Environ Microbiol 75:779–783.
3.
Cáceres A, Muñoz I, Iraola G, Díaz-Viraqué F, Collado L. 2017. Campylobacter ornithocola sp. nov., a novel member of the Campylobacter lari group isolated from wild bird faecal samples. Int J Syst Evol Microbiol 67:1643–1649.
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Debruyne L, Broman T, Bergström S, Olsen B, On SLW, Vandamme P. 2010. Campylobacter subantarcticus sp. nov., isolated from birds in the sub-Antarctic region. Int J Syst Evol Microbiol 60:815–819.
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Linton D, Owen RJ, Stanley J. 1996. Rapid identification by PCR of the genus Campylobacter and of five Campylobacter species enteropathogenic for man and animals. Res Microbiol 147:707–718.
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Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120.
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Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477.
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Vandamme P, Falsen E, Rossau R, Hoste B, Segers P, Tytgat R, De Ley J. 1991. Revision of Campylobacter, Helicobacter, and Wolinella taxonomy: emendation of generic descriptions and proposal of Arcobacter gen. nov. Int J Syst Evol Microbiol 41:88–103.
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Van TTH, Elshagmani E, Gor MC, Scott PC, Moore RJ. 2016. Campylobacter hepaticus sp. nov., isolated from chickens with spotty liver disease. Int J Syst Evol Microbiol 66:4518–4524.
10.
Chen L, Zheng D, Liu B, Yang J, Jin Q. 2016. VFDB 2016: hierarchical and refined dataset for big data analysis—10 years on. Nucleic Acids Res 44:D694–D697.

Information & Contributors

Information

Published In

cover image Microbiology Resource Announcements
Microbiology Resource Announcements
Volume 8Number 182 May 2019
eLocator: 10.1128/mra.00258-19
Editor: J. Cameron Thrash, University of Southern California

History

Received: 8 March 2019
Accepted: 2 April 2019
Published online: 2 May 2019

Contributors

Authors

School of Veterinary Science, Massey University, Palmerston North, New Zealand
New Zealand Food Safety Science and Research Centre, Massey University, Palmerston North, New Zealand
School of Veterinary Science, Massey University, Palmerston North, New Zealand
Errol Kwan
School of Veterinary Science, Massey University, Palmerston North, New Zealand
Samuel J. Bloomfield
School of Veterinary Science, Massey University, Palmerston North, New Zealand
Quadram Institute, Norwich, United Kingdom
School of Veterinary Science, Massey University, Palmerston North, New Zealand
New Zealand Food Safety Science and Research Centre, Massey University, Palmerston North, New Zealand
Patrick J. Biggs
School of Veterinary Science, Massey University, Palmerston North, New Zealand
New Zealand Food Safety Science and Research Centre, Massey University, Palmerston North, New Zealand
School of Fundamental Sciences, Massey University, Palmerston North, New Zealand

Editor

J. Cameron Thrash
Editor
University of Southern California

Notes

Address correspondence to David A. Wilkinson, [email protected].

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