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
| Parameter | Data for strain: | |||||||
|---|---|---|---|---|---|---|---|---|
| ACP102b | ACP108a | ACP110b | ACP114b | ACP123b | ACP141a | ACP175a | ACP183a | |
| No. of reads | 2,619,932 | 2,218,260 | 1,991,084 | 1,821,760 | 1,155,192 | 1,211,896 | 1,386,372 | 2,157,198 |
| No. of contigs | 149 | 185 | 180 | 175 | 181 | 155 | 149 | 161 |
| Genome length (bp) | 1,768,011 | 1,881,742 | 1,859,862 | 1,784,884 | 1,899,321 | 1,821,144 | 1,829,303 | 1,755,938 |
| N50 (bp) | 29,027 | 30,102 | 26,651 | 33,943 | 28,602 | 30,920 | 32,673 | 30,818 |
| Coverage (×) | 360 | 309 | 277 | 247 | 159 | 168 | 192 | 296 |
| GC content (%) | 34.46 | 34.27 | 34.31 | 34.34 | 34.22 | 34.4 | 34.39 | 34.53 |
| No. of proteins | 1,791 | 1,950 | 1,941 | 1,830 | 1,986 | 1,882 | 1,888 | 1,814 |
| No. of rRNAs | 3 | 5 | 6 | 5 | 4 | 11 | 9 | 6 |
| No. of tRNAs | 39 | 34 | 34 | 39 | 36 | 35 | 33 | 39 |
| No. of other RNAs | 3 | 3 | 3 | 3 | 3 | 3 | 3 | 3 |
| No. of genes | 1,897 | 2,058 | 2,043 | 1,935 | 2,097 | 2,000 | 2,006 | 1,923 |
| No. of signal peptides | 126 | 146 | 148 | 135 | 152 | 139 | 137 | 137 |
| GenBank accession no. | VDBW00000000 | VDBV00000000 | VDBU00000000 | VDBT00000000 | VDBS00000000 | VDBR00000000 | VDBQ00000000 | VDBP00000000 |
| SRA run no. | SRR10248249 | SRR10248248 | SRR10248247 | SRR10248246 | SRR10248244 | SRR10248243 | SRR10248242 | SRR10248245 |
| BioSample no. | SAMN11567273 | SAMN11567274 | SAMN11567275 | SAMN11567276 | SAMN11567277 | SAMN11567278 | SAMN11567279 | SAMN11567280 |
| SRA no. | SRX6966295 | SRX6966296 | SRX6966297 | SRX6966298 | SRX6966299 | SRX6966300 | SRX6966301 | SRX6966302 |
| Host | Felis catus | Felis catus | Felis catus | Felis catus | Felis catus | Canis lupus familiarus | Felis catus | Felis 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
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Information & Contributors
Information
Published In
Microbiology Resource Announcements
Volume 9 • Number 5 • 30 January 2020
eLocator: 10.1128/mra.01244-19
Editor: David Rasko, University of Maryland School of Medicine
PubMed: 32001558
Copyright
© 2020 Bojanić et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.
History
Received: 12 October 2019
Accepted: 6 January 2020
Published online: 30 January 2020
Contributors
Editor
David Rasko
Editor
University of Maryland School of Medicine
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Citation
2020.
Draft Genome Sequences of Eight Strains of Campylobacter helveticus Isolated from Cats and a Dog in New Zealand. Microbiol Resour Announc
9:10.1128/mra.01244-19.
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