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Announcement
30 January 2020

Draft Genome Sequences of Eight Strains of Campylobacter helveticus Isolated from Cats and a Dog in New Zealand

ABSTRACT

The draft genome sequences for eight isolates of Campylobacter helveticus isolated from companion animals are described and compared with that of the type strain. On average, the genomes are 1,825,025 bp long and have a GC content of 34.4% and 1,885 coding DNA sequences (CDSs). CRISPRs were detected in only one isolate and phages in none.

ANNOUNCEMENT

Campylobacter helveticus has been isolated from healthy and diarrheic companion animals and is closely related to C. upsaliensis (1). However, C. helveticus has not been isolated from humans with gastroenteritis (2). In a study exploring Campylobacter spp. in companion animals and their food (3) (approved by the Massey University Animal Ethics Committee; application number 09/70), C. helveticus isolates from clinically normal cats (seven isolates, one from each) and a dog (one isolate) were sequenced and analyzed with the genome of C. helveticus strain ATCC 51209T (4).
Bacteria were isolated and identified as described (3) with subculture onto Columbia horse blood agar (Fort Richard Laboratories, New Zealand) in an H2-enriched microaerobic atmosphere at 37°C. Genomic DNA was extracted from the Columbia horse blood agar subcultures using a QIAamp DNA minikit (Qiagen, Germany) and sequenced at New Zealand Genomics Ltd. (Massey University, New Zealand) using a MiSeq instrument (Illumina, Australia) following the manufacturer’s instructions, with paired read lengths of 250 base pairs after library preparation using the Nextera XT library kit (Illumina).
Default parameters and settings were used for all software unless otherwise described. Velvet version 1.2.10 (5) was used for de novo genome assembly. Sequence data were quality processed, analyzed, and assembled using ea-utils (https://bio.tools/ea-utils) within QCtool (https://bio.tools/qctool) and SPAdes version 3.13.0 (6). Assembly statistics for the eight New Zealand isolates were extracted from the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) and are described in Table 1. Geneious version 10.2.6 (7) was used to calculate GC values and to check for the presence of the cdtABC operon. Signal peptides from amino acid predictions were discovered using the SignalP-5.0 server (http://www.cbs.dtu.dk/services/SignalP-5.0/).
TABLE 1
TABLE 1 Assembly information for eight Campylobacter helveticus isolates from New Zealand
ParameterData for strain:
ACP102bACP108aACP110bACP114bACP123bACP141aACP175aACP183a
No. of reads2,619,9322,218,2601,991,0841,821,7601,155,1921,211,8961,386,3722,157,198
No. of contigs149185180175181155149161
Genome length (bp)1,768,0111,881,7421,859,8621,784,8841,899,3211,821,1441,829,3031,755,938
N50 (bp)29,02730,10226,65133,94328,60230,92032,67330,818
Coverage (×)360309277247159168192296
GC content (%)34.4634.2734.3134.3434.2234.434.3934.53
No. of proteins1,7911,9501,9411,8301,9861,8821,8881,814
No. of rRNAs356541196
No. of tRNAs3934343936353339
No. of other RNAs33333333
No. of genes1,8972,0582,0431,9352,0972,0002,0061,923
No. of signal peptides126146148135152139137137
GenBank accession no.VDBW00000000VDBV00000000VDBU00000000VDBT00000000VDBS00000000VDBR00000000VDBQ00000000VDBP00000000
SRA run no.SRR10248249SRR10248248SRR10248247SRR10248246SRR10248244SRR10248243SRR10248242SRR10248245
BioSample no.SAMN11567273SAMN11567274SAMN11567275SAMN11567276SAMN11567277SAMN11567278SAMN11567279SAMN11567280
SRA no.SRX6966295SRX6966296SRX6966297SRX6966298SRX6966299SRX6966300SRX6966301SRX6966302
HostFelis catusFelis catusFelis catusFelis catusFelis catusCanis lupus familiarusFelis catusFelis catus
For functional and core genome analysis, concatenated contigs were annotated with Prokka version 1.11 (8) using the default settings and the predicted amino acid sequences were searched against the Clusters of Orthologous Groups (COGs) database (using COGsoft version 201204) (9). COGs were considered to be core if present in all of the isolates. CRISPRFinder (10) and PHAST (11) were used to identify clustered regularly interspaced short palindromic repeats (CRISPRs) and phage, respectively. Abricate version 0.8.11 (https://github.com/tseemann/abricate) was used via Nullarbor to screen for genes related to antimicrobial resistance.
Aligning the coding DNA sequences (CDSs) to the COGs database gave 1,243 unique COGs in the pangenome of the eight isolates plus the reference genome, with an average 1,169 COGs and 1.34 copies per genome. The C. helveticus core genome contained 1,083 COGs, approximately 87.1% of the pangenome. CRISPRs were detected in one isolate (ACP114b), although the other isolates had 1 to 3 “questionable” CRISPRs detected. No intact bacteriophage insertions were identified. Only two genes associated with antimicrobial resistance were found, both in ACP110b. The cdtABC operon (cytolethal distending toxin) was detected in all eight isolates.

Data availability.

The C. helveticus draft genome sequences have been deposited in GenBank under the BioProject accession number PRJNA541328, with the individual accession numbers shown in Table 1.

ACKNOWLEDGMENTS

This work was funded, in part, by the Institute of Veterinary, Animal and Biomedical Sciences (now the School of Veterinary Science) Postgraduate Research Fund at Massey University and the New Zealand Companion Animal Health Foundation (to K.B. and E.A.). The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
The genome sequence of the C. helveticus strain ATCC 51209T was kindly provided by William Miller.
We declare no conflicts of interest.

REFERENCES

1.
Stanley J, Burnens AP, Linton D, On SLW, Costas M, Owen RJ. 1992. Campylobacter helveticus sp. nov., a new thermophilic species from domestic animals: characterization, and cloning of a species-specific DNA probe. J Gen Microbiol 138:2293–2303.
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Lastovica AJ. 2006. Emerging Campylobacter spp.: the tip of the iceberg. Clin Microbiol Newsl 28:49–56.
3.
Bojanić K, Midwinter AC, Marshall JC, Rogers LE, Biggs PJ, Acke E. 2016. Isolation of Campylobacter spp. from client-owned dogs and cats, and retail raw meat pet food in the Manawatu, New Zealand. Zoonoses Public Health 64:438–449.
4.
Miller WG, Yee E, Bono JL. 2017. Complete genome sequence of the Campylobacter helveticus type strain ATCC 51209. Genome Announc 5:e00398-17.
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Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821–829.
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Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, Thierer T, Ashton B, Meintjes P, Drummond A. 2012. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28:1647–1649.
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Seemann T. 2014. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30:2068–2069.
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Tatusov RL, Koonin EV, Lipman DJ. 1997. A genomic perspective on protein families. Science 278:631–637.
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Grissa I, Vergnaud G, Pourcel C. 2007. CRISPRFinder: a Web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res 35:W52–W57.
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Information & Contributors

Information

Published In

cover image Microbiology Resource Announcements
Microbiology Resource Announcements
Volume 9Number 530 January 2020
eLocator: 10.1128/mra.01244-19
Editor: David Rasko, University of Maryland School of Medicine

History

Received: 12 October 2019
Accepted: 6 January 2020
Published online: 30 January 2020

Contributors

Authors

Krunoslav Bojanić
School of Veterinary Science, Massey University, Palmerston North, New Zealand
Present address: Krunoslav Bojanić, Center of Excellence for Marine Bioprospecting, Ruđer Bošković Institute, Zagreb, Croatia; Els Acke, IDEXX GmbH, Ludwigsburg, Germany.
Anne C. Midwinter
School of Veterinary Science, Massey University, Palmerston North, New Zealand
Els Acke
School of Veterinary Science, Massey University, Palmerston North, New Zealand
Present address: Krunoslav Bojanić, Center of Excellence for Marine Bioprospecting, Ruđer Bošković Institute, Zagreb, Croatia; Els Acke, IDEXX GmbH, Ludwigsburg, Germany.
Jonathan C. Marshall
School of Veterinary Science, Massey University, Palmerston North, New Zealand
School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
Angela J. Cornelius
Institute of Environmental Science and Research Limited, Christchurch, New Zealand
School of Veterinary Science, Massey University, Palmerston North, New Zealand
School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
New Zealand Food Safety Science and Research Centre, Massey University, Palmerston North, New Zealand

Editor

David Rasko
Editor
University of Maryland School of Medicine

Notes

Address correspondence to Patrick J. Biggs, [email protected].

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