ABSTRACT
We report the draft genome sequence of Streptococcus pyogenes strain AB1 isolated from the blood of a woman with peritonitis—toxic shock syndrome. The genome measured 1.855 Mbp, with a G + C content of 38.3%. Sequences unmapped to the reference genome sequence of M1 SF370 (GenBank accession number AE004092.2) were characterized.
KEYWORDS: Streptococcus pyogenes, woman, peritonitis, toxic shock syndrome
ANNOUNCEMENT
Streptococcus pyogenes strain AB1 harboring emm103/ST1363 was isolated from the standard blood cultures of a 22-year-old woman presenting with primary peritonitis, bilateral empyema, and toxic shock syndrome. The research is carried out in accordance with the Declaration of Helsinki. Informed consent was obtained from the patient and her family for this case presentation. We report the draft genome sequence of AB1, with characteristic sequences unmapped to the reference genome sequence of SF370.
The strain AB1 was inoculated in 5% sheep blood agar plate and aerobically incubated in 5% CO2 at 35°C for 24 h. A colony with a gray-white smooth appearance, indicating β-hemolysis, was picked up from the plate and grown overnight in Todd–Hewitt broth supplemented with yeast extract. DNA was extracted using a DNeasy Blood & Tissue Kit (Qiagen, Germany) after pretreatment with proteinase K (1–3). Whole-genome sequencing was performed on a DNBSEQ-G400RS platform (MGI-Tech, Japan) using DNA Nanoball technology based on circular DNA fragment amplification (4). The sequencing library was generated using MGIEasy FS DNA Library Prep Set (item no. 1000006987, MGI-Tech). Paired-end runs were performed with a read length of 2 × 150 bp.
Sequencing yielded 19,820,691 reads (5.946 Gbp). The reads were trimmed using the quality trimming tool in CLC Genomics Workbench (ver. 23.0.4) with default parameters. De novo assembly was performed using the CLC Genomics Workbench with modified parameters, wherein the minimum contig length was set to 800 bp. Draft genome sequences were annotated using the DDBJ Fast Annotation and Submission Tool (DFAST; https://dfast.nig.ac.jp) (5). The assembly metrics and annotated features included genome size (1,855,299 bp), number of contigs (56), average coverage (3,205×), N50 (149,366 bp), number of coding DNA sequences (CDSs)/tRNAs/rRNAs/clustered regularly interspaced short palindromic repeats (1,758/27/5/1), G + C content (38.3%), and coding ratio (84.8%).
Mapping of AB1 reads to the reference genome sequence (GenBank accession number AE004092.2) of serotype M1 S. pyogenes strain SF370 was performed using the reference tool with default parameters in the CLC Genomics Workbench. The remaining unmapped reads (2,911,962 reads) were assembled de novo, which yielded 47 contigs. These contigs were uploaded to the web-based applications PathogenFinder ver. 1.1 (https://cge.food.dtu.dk/services/PathogenFinder/) (6) and DFAST to identify pathogenic gene families that were not present in SF370. In all, 16 CDSs (length 1,206–144 bp) were recognized by both applications (Table 1). These CDSs encoded a transcriptional regulator (contig number 12) (7), DNA integrase (contig number 1), and phage/phage-associated proteins (main contig number 4) (8, 9), identical to those of S. pyogenes and S. dysgalactiae subsp. equisimilis (SDSE). CDS-encoding DNA integrase from SDSE has been observed previously in the genome sequence of blood-origin S. canis isolated from a dog with necrotizing soft tissue infection (3), suggesting genetic transmission between S. pyogenes and other pathogenic streptococci.
TABLE 1.
Traits of Streptococcus pyogenes strain AB1a pathogenic gene families that were not present in serotype M1 SF370,b identical to pathogenic streptococcus
| Data from PathogenFinder ver. 1.1c | Data from DFASTe and BLASTpf | ||||||||
|---|---|---|---|---|---|---|---|---|---|
| Pathogenic streptococcus d | Accession no. (Protein no.) | Product | Contig no. | Nucleotide start | Nucleotide end | Size (bp) | Product | Product | |
| 1 | S. pyogenes MGAS9429 | CP000259.1 (ABF31304.1) | Transcriptional regulator, AraC family | 12 | 38,071 (reverse) | 36,866 | 1,206 | YSIRK-targeted surface antigen transcriptional regulator | Bacterial regulatory helix-turn-helix, AraC family protein |
| 2 2 |
S. dysgalactiae subsp. equisimilis GGS_124 | AP010935.1 (BAH82621.1) | DNA integration/recombination/inversion protein | 1 | 35,315 | 36,478 | 1,164 | Site-specific integrase | Site-specific integrase |
| 3 | S. pyogenes MGAS9429 | CP000259.1https://www.ncbi.nlm.nih.gov/nuccore/CP000017.2/(ABF31725.1) | Phage protein | 4 | 315,992 | 316,633 | 642 | Hypothetical protein | Hypothetical protein |
| 4 | S. pyogenes MGAS6180 | CP000056.2 (AAX72126.1) | Phage protein | 4 | 311,016 (reverse) | 310,534 | 483 | Hypothetical protein | DUF669 domain-containing protein in phage proteins |
| 5 | S. pyogenes MGAS10394 | CP000003.1 (AAT87334.1) | Holin | 4 | 280,566 (reverse) | 280,111 | 456 | Hypothetical protein | Phage holin family protein |
| 6 | S. pyogenes MGAS9429 | CP000259.1https://www.ncbi.nlm.nih.gov/nuccore/CP000017.2/(ABF31767.1) | Phage protein | 4 | 293,210 (reverse) | 292,785 | 426 | Hypothetical protein | Hypothetical protein |
| 7 | S. pyogenes MGAS6180 | CP000056.2 (AAX72112.1) | Phage protein | 4 | 301,081 | 301,458 | 378 | Type II toxin-antitoxin system HicB family antitoxin | Type II toxin-antitoxin system HicB family antitoxin |
| 8 | S. pyogenes MGAS6180 | CP000056.2 (AAX72904.1) | Phage protein | 27 | 22 | 429 | 408 | Hypothetical protein | Hypothetical protein |
| 9 | S. pyogenes MGAS8232 | AE009949.1 (AAL97901.1) | Hypothetical phage protein | 4 | 313,944 (reverse) | 313,615 | 330 | Hypothetical protein | Hypothetical protein |
| 10 | S. pyogenes MGAS10394 | CP000003.1 (AAT87160.1) | Unknown phage protein | 4 | 318,467 | 318,772 | 306 | Hypothetical protein | Membrane protein |
| 11 | S. pyogenes MGAS8232 | AE009949.1 (AAL97899.1) | Hypothetical phage protein | 4 | 313,424 (reverse) | 313,140 | 285 | Hypothetical protein | Hypothetical protein |
| 12 | S. pyogenes MGAS10394 | CP000003.1 (AAT87144.1) | Unknown phage protein | 4 | 297,702 (reverse) | 297,478 | 225 | Hypothetical protein | Hypothetical protein |
| 13 | S. pyogenes NZ131 | CP000829.1 (ACI60688.1) | Hypothetical protein | 1 | 26,121 (reverse) | 25,978 | 144 | Hypothetical protein | Hypothetical protein |
| 14 | S. pyogenes MGAS10270 | CP000260.1 (ABF33634.1) | Phage protein | 4 | 300,844 | 301,029 | 186 | Hypothetical protein | Toxin-antitoxin system, toxin component, HicA family |
| 15 | S. pyogenes MGAS10394 | CP000003.1 (AAT87133.1) | Unknown phage protein | 4 | 291,758 (reverse) | 291,585 | 174 | Hypothetical protein | Hypothetical protein |
| 16 | S. pyogenes MGAS10394 | CP000003.1 (AAT87145.1) | Unknown phage protein | 4 | 297,865 (reverse) | 297,695 | 171 | Hypothetical protein | Hypothetical protein |
GenBank nucleotide accession number BTGW00000000.1. GenBank assembly accession number GCF_033008475.1.
GenBank nucleotide accession number AE004092.2. GenBank assembly accession number GCF_000006785.2.
The PathogenFinder ver. 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.
We found the data regarding the pathogenic streptococcus, GenBank accession number, and protein number using the PathogenFinder ver. 1.1.
The DDBJ Fast Annotation and Submission Tool (DFAST; https://dfast.nig.ac.jp/) was used to confirm the product (coding DNA sequence) obtained using PathogenFinder ver. 1.1.
The Protein Basic Local Alignment Search Tool (BLASTp; https://blast.ncbi.nlm.nih.gov/Blast.cgi) of the National Center for Biotechnology Information was also applied to confirm the product (coding DNA sequence) obtained using PathogenFinder ver. 1.1.
We determined the phage/phage-associated protein distribution and antimicrobial resistance (AMR) genotypes by the phage detection application PHASTER (https://phaster.ca) (10) and ResFinder ver. 4.1 (https://cge.food.dtu.dk/services/ResFinder/) (11) using whole-contigs. AB1 contained a phage-related region (51.6 kbp) of contig 4 without AMR genes.
ACKNOWLEDGMENTS
The authors wish to thank Ms. Katsuko Okuzumi (Laboratory of Infectious Diseases, Graduate School of Infection Control Sciences, Ōmura Satoshi Memorial Institute, Kitasato University, Minato, Tokyo, Japan) for her direct financial support and the Editage (http://www.editage.jp) for its English proofreading.
T.M.: Conceptualization, Data curation, Formal analysis, Investigation, Writing—review and editing; H.Y.: Data curation, Formal analysis, Methodology, Validation, Writing—review and editing; N.A.: Resources; K.M.: Resources; M.G.: Formal analysis; T.T.: Conceptualization, Writing—original draft, Writing—review and editing.
Contributor Information
Takahiro Maeda, Email: di21005@st.kitasato-u.ac.jp.
Vanja Klepac-Ceraj, Wellesley College Department of Biological Sciences, USA.
DATA AVAILABILITY
The draft genome sequence is deposited in DDBJ/EMBL/GenBank under the accession number BTGW00000000.1, with the SRA accession number DRR493916.
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Data Availability Statement
The draft genome sequence is deposited in DDBJ/EMBL/GenBank under the accession number BTGW00000000.1, with the SRA accession number DRR493916.