ABSTRACT
We report here 1 near-complete genome sequence and 12 complete genome sequences for clinical Capnocytophaga isolates. Total read coverages ranged from 211× to 737×, and genome sizes ranged from 2.41 Mb to 3.10 Mb. These genomes will enable a more comprehensive taxonomic evaluation of the Capnocytophaga genus.
GENOME ANNOUNCEMENT
Species of the Capnocytophaga genus are commensal organisms that are most commonly found as naturally occurring microbiota in human, dog, and cat oral cavities (1–3). Six of the nine recognized species are associated with periodontal disease in humans (1, 4–7). C. canis, C. canimorsus, and C. cynodegmi are opportunistic zoonotic pathogens that inhabit the oral cavities of cats (Felis catus) and dogs (Canis familiaris) (8, 9). Severe complications from cat and dog bite wound infections in humans can include sepsis, meningitis, and endocarditis, which are often fatal to immunocompromised individuals. We sequenced 13 clinical Capnocytophaga isolates from infections associated with bite wounds to generate clinically relevant reference genome sequences of the Capnocytophaga genus.
All isolates were grown on heart infusion agar with 5% rabbit blood at 35°C with 5% CO2 for 48 h. Genomic DNA was extracted using the MasterPure DNA purification kit (Epicentre, Madison, WI, USA), and quality was assessed with a Qubit fluorometer (Invitrogen, Carlsbad, CA, USA). Either 10-kb or 20-kb libraries were generated with the SMRTbell template prep kit version 1.0. The libraries were bound to polymerase using the DNA/polymerase P6v2 binding kit (Pacific Biosciences, Menlo Park, CA, USA) and then loaded on single-molecule real-time cells and sequenced with C4v2 chemistry (Pacific Biosciences) for movie times of 270 min (10-kb libraries) or 360 min (20-kb libraries) on the RSII instrument (Pacific Biosciences). All 20-kb libraries were size selected with Blue Pippin (Sage Science, Beverly, MA, USA). Paired-end sequencing (2 × 250 bp) was performed on NEBNext ultra DNA libraries with the Illumina MiSeq platform.
The PacBio reads were assembled in Canu version 1.4 with “errorRate=0.013,” “minReadLength=5000,” “corMinCoverage=3,” and “corOutCoverage=500” options, and circularization was attempted for each chromosome with Circlator version 1.4.0, which relied on MUMmer version 3.1 and SPAdes version 3.9.0 (10–13). Illumina read sets were cleaned with BBDUK version 37.02 and Trimmomatic version 0.36 before they were mapped onto their corresponding assemblies with BWA-MEM version 0.7.15-r1140 with the “-x intractg” option (14, 15). Both indel and single-nucleotide polymorphism errors were corrected with Pilon version 1.21 using the “--mindepth 0.5” option (16). For a subset of isolates, the resulting assemblies were verified, and in some cases corrected, by comparing their predicted AflII maps with AflII whole-genome optical maps and with contigs generated by CLC Genomics Workbench version 10.1. Reads were trimmed within CLC Genomics Workbench using a quality limit of 0.02 prior to assembly; contigs were then corrected by mapping PacBio reads to them with a mismatch cost of two, and they were further polished by remapping the Illumina reads with a mismatch cost of 3. Discrepancies between the Canu assemblies and the whole-genome optical maps were detected using MapSolver version 3.2 (OpGen, Inc., Gaithersburg, MD, USA) and corrected using the BioEdit version 7.1.9 sequence-editing tool (17). All final assemblies were submitted to NCBI for archiving and annotation with Prokaryotic Genome Annotation Pipeline (PGAP) version 4.2.
Accession number(s).
The genome sequences of the Capnocytophaga isolates reported here have been deposited in DDBJ/ENA/GenBank under the accession numbers listed in Table 1.
TABLE 1 .
Features of the 13 sequenced genomes of Capnocytophaga strains
| Species | Strain | GenBank accession no. | Total no. of genes | Sequencing depth (×) | Genome size (bp) |
Sequencing technologies |
|---|---|---|---|---|---|---|
| C. canimorsus | 7120 | CP022382 | 2,136 | 531.8 | 2,414,275 | PacBio, Illumina, OpGen |
| C. canimorsus | H3936 | CP022389 | 2,173 | 422.9 | 2,455,405 | PacBio, Illumina, OpGen |
| C. canimorsus | H5594 | CP022388 | 2,269 | 731.6 | 2,493,828 | PacBio, Illumina, OpGen |
| C. canis | H2931 | CP022381 | 2,231 | 523.3 | 2,632,967 | PacBio, Illumina, OpGen |
| C. canis | H4358 | CP022380 | 2,224 | 452.9 | 2,633,192 | PacBio, Illumina |
| C. cynodegmi | G7591 | CP022378 | 2,329 | 422.2 | 2,640,475 | PacBio, Illumina |
| C. gingivalis | H1496 | CP022386 | 2,724 | 211.3 | 2,838,633 | PacBio, Illumina, OpGen |
| C. leadbetteri | H6253 | CP022384 | 2,243 | 643.3 | 2,504,023 | PacBio, Illumina, OpGen |
| C. sputigena | D1179 | CP022379 | 2,563 | 737.4 | 2,855,148 | PacBio, Illumina |
| C. sputigena | H4486 | CP022383 | 2,821 | 503.7 | 3,098,616 | PacBio, Illumina, OpGen |
| C. sputigena | H6490 | NIBW00000000 | 2,671 | 343.5 | 2,963,948 | PacBio, Illumina |
| C. sputigena | KC1668 | CP022385 | 2,822 | 263.6 | 3,074,746 | PacBio, Illumina, OpGen |
| C. stomatis | H2177 | CP022387 | 2,519 | 449.3 | 2,831,350 | PacBio, Illumina, OpGen |
ACKNOWLEDGMENTS
The findings and conclusions in this report are those of the authors and do not necessarily represent the official position of the Centers for Disease Control and Prevention (CDC). Mention of company names or products does not constitute endorsement by the CDC.
Footnotes
Citation Villarma A, Gulvik CA, Rowe LA, Sheth M, Juieng P, Nicholson AC, Loparev VN, McQuiston JR. 2017. Twelve complete reference genomes of clinical isolates in the Capnocytophaga genus. Genome Announc 5:e01186-17. https://doi.org/10.1128/genomeA.01186-17.
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