The draft genome sequence of the blood-origin Streptococcus canis strain FU149, isolated from a dog with a necrotizing soft tissue infection in Japan, is reported. The genome size was 2.108 Mbp, with a G+C content of 39.5%. Sequences unmapped to the reference genome sequence of NCTC 12191T (GenBank accession number LR134293) were characterized.
ABSTRACT
The draft genome sequence of the blood-origin Streptococcus canis strain FU149, isolated from a dog with a necrotizing soft tissue infection in Japan, is reported. The genome size was 2.108 Mbp, with a G+C content of 39.5%. Sequences unmapped to the reference genome sequence of NCTC 12191T (GenBank accession number LR134293) were characterized.
ANNOUNCEMENT
Streptococcus canis, which was first proposed in 1986 (1), is characterized as having beta-hemolysis activity and as Lancefield carbohydrate antigen group G. This bacterium can cause mild to severe infections in humans and animals (2–5). Here, we report the draft genome sequence of an S. canis strain isolated from the blood of a miniature sausage dog (male, 13 years old, born in Hiroshima City, Japan) with a necrotizing soft tissue infection.
The blood-origin strain FU149 was isolated using the blood culture system VersaTrek (Kohjin-Bio, Japan) (6). Isolates were inoculated onto sheep blood agar plates and incubated in 5% CO2 at 35°C for 24 h (3). Colonies with a gray-white smooth appearance (indicating beta-hemolysis) were further grown overnight in Todd-Hewitt broth supplemented with yeast extract. We picked up a single colony and extracted its genomic DNA using a DNeasy blood and tissue kit (Qiagen, Germany) after pretreating it with lysozyme and proteinase K. DNA samples were stored at −70 to −80°C until used. The DNA sequencing library was generated using a Nextera XT DNA sample prep kit (Illumina, USA). Sequencing was performed on an Illumina MiSeq benchtop sequencer. Paired-end runs were performed with read lengths of 2 × 75 bp.
Sequencing yielded 8,071,438 reads (604,909,372 bases). Reads were trimmed based on the quality trimming tool in CLC Genomics Workbench (v.12.0) with default parameters. De novo assembly was performed using CLC Genomics Workbench with modified parameters, in which the minimum contig length setting was changed from 200 to 500 bp. Draft genome sequences were annotated using the DDBJ Fast Annotation and Submission Tool (DFAST; https://dfast.nig.ac.jp) (7). Assembly metrics and annotated features included the genome size (2,108,133 bp), number of contigs (74), average coverage (284×), N50 value (73,653 bp), numbers of coding DNA sequences (CDSs; 2,049), tRNAs (18), rRNAs (2), and clustered regularly interspaced short palindromic repeats (2), G+C content (39.5%), and coding ratio (84.6%).
Mapping FU149 reads to the reference genome sequence of S. canis NCTC 12191T (GenBank accession number LR134293) was performed using the reference tool with default parameters in the CLC Genomics Workbench. We attempted de novo assembly using the remaining unmapped reads (1,005,451 reads) and yielded 35 contigs. These contigs were uploaded into Web-based applications PathogenFinder v.1.1 (https://cge.cbs.dtu.dk/services/PathogenFinder/; Center for Genomic Epidemiology) (8) and DFAST to identify any pathogenic gene families that were not present in NCTC 12191T. Seven CDSs (position 1164 to 207 bp) were recognized by both applications (Table 1). These CDSs were found to encode DNA integration (contig number 49) and phage/phage-associated proteins (contig numbers 32 and 29) identical to those in pathogenic streptococci (Streptococcus dysgalactiae subsp. equisimilis and Streptococcus pyogenes), suggesting genetic transmission between animal-derived S. canis and other pathogenic streptococci.
TABLE 1.
Characteristics of Streptococcus canis strain FU149a pathogenic gene families that were not present in NCTC 12191T,b identical to other pathogenic streptococci
| Other pathogenic streptococcic | GenBank accession no. | Protein accession no. | Data from PathogenFinder v1.1d
|
Data from DFASTe
|
|||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Product | Contig no. | Nucleotide start | Nucleotide end | Size (bp) | Product | Contig no. | Nucleotide start | Nucleotide end | |||
| Streptococcus dysgalactiae subsp. equisimilis GGS_124 | AP010935.1 | BAH82621 | DNA integration/recombination/inversion protein | 49 | 19755 | 20918 | 1,164 | Site-specific integrase | 49 | 19755 | 20918 |
| Streptococcus pyogenes MGAS10394 | CP000003.1 | AAT86183 | Unknown phage protein | 32 | 6937 | 7824 | 888 | Hypothetical protein | 32 | 6937 | 7824 |
| Streptococcus pyogenes MGAS5005 | CP000017.2 | AAZ52060 | Phage transcriptional activator | 32 | 534 | 950 | 417 | Hypothetical protein | 32 | 534 | 950 |
| Streptococcus pyogenes MGAS5005 | CP000017.2 | AAZ52050 | Phage protein | 32 | 8203 | 8481 | 279 | Hypothetical protein | 32 | 8203 | 8481 |
| Streptococcus pyogenes MGAS6180 | CP000056.2 | AAX72951 | Hypothetical protein | 29 | 2524 | 2751 | 228 | Hypothetical protein | 29 | 2524 | 2751 |
| Streptococcus pyogenes MGAS5005 | CP000017.2 | AAZ52045 | Phage protein | 32 | 10380 | 10613 | 234 | Hypothetical protein | 32 | 10380 | 10613 |
| Streptococcus pyogenes MGAS9429 | CP000259.1 | ABF31726 | Phage protein | 29 | 57517 | 57723 | 207 | Hypothetical protein | 29 | 57517 | 57723 |
| Streptococcus pyogenes MGAS5005 | CP000017.2 | AAZ52055 | Hypothetical protein | 32 | 5814 | 5930 | 117 | Not detected | |||
Accession number BLRR01000000.
GenBank accession number LR134293.1.
We found the data regarding the other pathogenic streptococci, accession numbers, and protein numbers using the PathogenFinder v 1.1.
The PathogenFinder v.1.1 (https://cge.cbs.dtu.dk/services/PathogenFinder/; Center for Genomic Epidemiology) was applied to obtain an overview of the genomic pathogenic gene families.
The DDBJ Fast Annotation and Submission Tool (DFAST; https://dfast.nig.ac.jp/) was used to confirm the products (coding DNA sequences), contig numbers, and nucleotide starts/ends obtained using PathogenFinder.
We also determined the S. canis M-like protein (SCM) allele (9), sequence type (ST) by MLST v.2.0 (https://cge.cbs.dtu.dk/services/MLST/; Center for Genomic Epidemiology) (10), and antimicrobial resistance (AMR) genotype by ResFinder v.3.2 (https://cge.cbs.dtu.dk/services/ResFinder/; Center for Genomic Epidemiology) (11) using contigs. This strain showed a previously described pathogenic ST9 harboring SCM allele 1 without AMR genes (12).
Data availability.
The draft genome sequence of S. canis has been deposited in DDBJ/EMBL/GenBank under accession number BLRR00000000.1, with SRA accession number DRR221832.
ACKNOWLEDGMENTS
We thank Mieko Goto (Laboratory of Infectious Diseases, Graduate School of Infection Control Sciences, Ōmura Satoshi Memorial Institute, Kitasato University, Tokyo, Japan) for her helpful assistance and Editage for English language editing.
This work was supported in part by JSPS KAKENHI (grant number 18K08447 to T.T.).
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Data Availability Statement
The draft genome sequence of S. canis has been deposited in DDBJ/EMBL/GenBank under accession number BLRR00000000.1, with SRA accession number DRR221832.