1887

Abstract

(SDSE) is a β-hemolytic streptococcus that causes severe invasive streptococcal infections, especially in the elderly and people with underlying diseases. SDSE strains are primarily characterized by Lancefield group G or C antigens.

We have previously reported the prevalence of Lancefield group A SDSE (GA-SDSE) strains in Japan and have analysed the draft genome sequences of these strains. As GA-SDSE is a rare type of SDSE, only one complete genome has been sequenced to date.

The present study is focused on genetic characteristics of GA-SDSE strains. In order to examine molecular characteristics, we also tested growth inhibition of other streptococci by GA-SDSE.

We determined the complete genome sequences of three GA-SDSE strains by two new generation sequencing systems (short-read and long-read sequencing data). Using the sequences, we also conducted a comparative analysis of GA-SDSE and group C/G SDSE strains. In addition, we tested multiplex and quantitative PCRs targeting the GA-SDSE, group G SDSE, and .

We found a group-specific conserved region in GA-SDSE strains that is composed of genes encoding predicted anti-bacteriocin and streptococcal lantibiotic (Sal) proteins. Multiplex and quantitative PCRs targeting the GA-SDSE-specific region were able to distinguish between GA-SDSE, other SDSE, and strains. The growth of GA-SDSE was suppressed in the presence of group G SDSE, indicating a possible explanation for the low frequency of isolation of GA-SDSE.

The comparative genome analysis shows that the genome of GA-SDSE has a distinct arrangement, enabling the differentiation between , GA-SDSE, and other SDSE strains using our PCR methods.

Funding
This study was supported by the:
  • KoheiOgura , Takeda Science Foundation , (Award 2018)
  • KoheiOgura , Japan Society for the Promotion of Science , (Award 18K07133)
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2021-02-03
2021-02-26
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References

  1. Rantala S. Streptococcus dysgalactiae subsp. equisimilis bacteremia: an emerging infection. Eur J Clin Microbiol Infect Dis 2014; 33: 1303 1310 [CrossRef] [PubMed]
    [Google Scholar]
  2. Brandt CM, Spellerberg B. Human infections due to Streptococcus dysgalactiae subspecies equisimilis . Clin Infect Dis 2009; 49: 766 772 [CrossRef] [PubMed]
    [Google Scholar]
  3. Wajima T, Morozumi M, Hanada S, Sunaoshi K, Chiba N et al. Molecular Characterization of Invasive Streptococcus dysgalactiae subsp. equisimilis, Japan. Emerg Infect Dis 2016; 22: 247 254 [CrossRef] [PubMed]
    [Google Scholar]
  4. Cohen-Poradosu R, Jaffe J, Lavi D, Grisariu-Greenzaid S, Nir-Paz R et al. Group G streptococcal bacteremia in Jerusalem. Emerg Infect Dis 2004; 10: 1455 1460 [CrossRef] [PubMed]
    [Google Scholar]
  5. Bert F, Lambert-Zechovsky N. Analysis of a case of recurrent bacteraemia due to Group A Streptococcus equisimilis by pulsed-field gel electrophoresis. Infection 1997; 25: 250 251 [CrossRef] [PubMed]
    [Google Scholar]
  6. Chochua S, Rivers J, Mathis S, Li Z, Velusamy S et al. Emergent invasive Group A Streptococcus dysgalactiae subsp. equisimilis, United States, 2015-2018. Emerg Infect Dis 2019; 25: 1543 1547 [CrossRef] [PubMed]
    [Google Scholar]
  7. Ishihara H, Ogura K, Miyoshi-Akiyama T, Nakamura M, Kaya H et al. Prevalence and genomic characterization of Group A Streptococcus dysgalactiae subsp. equisimilis isolated from patients with invasive infections in Toyama prefecture, Japan. Microbiol Immunol 2020; 64: 113 122 [CrossRef] [PubMed]
    [Google Scholar]
  8. Jolley KA, Maiden MCJ. BIGSdb: scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics 2010; 11: 595 [CrossRef] [PubMed]
    [Google Scholar]
  9. McMillan DJ, Bessen DE, Pinho M, Ford C, Hall GS et al. Population genetics of Streptococcus dysgalactiae subspecies equisimilis reveals widely dispersed clones and extensive recombination. PLoS One 2010; 5: e11741 [CrossRef] [PubMed]
    [Google Scholar]
  10. Brandt CM, Haase G, Schnitzler N, Zbinden R, Lütticken R. Characterization of blood culture isolates of Streptococcus dysgalactiae subsp. equisimilis possessing Lancefield's group A antigen. J Clin Microbiol 1999; 37: 4194 4197 [CrossRef] [PubMed]
    [Google Scholar]
  11. Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 2017; 13: e1005595 [CrossRef] [PubMed]
    [Google Scholar]
  12. Tanizawa Y, Fujisawa T, Nakamura Y. DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication. Bioinformatics 2018; 34: 1037 1039 [CrossRef] [PubMed]
    [Google Scholar]
  13. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32: 929 931 [CrossRef] [PubMed]
    [Google Scholar]
  14. Darling ACE, Mau B, Blattner FR, Perna NT. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res 2004; 14: 1394 1403 [CrossRef] [PubMed]
    [Google Scholar]
  15. Hsiao W, Wan I, Jones SJ, Brinkman FSL. IslandPath: aiding detection of genomic islands in prokaryotes. Bioinformatics 2003; 19: 418 420 [CrossRef] [PubMed]
    [Google Scholar]
  16. Waack S, Keller O, Asper R, Brodag T, Damm C et al. Score-Based prediction of genomic islands in prokaryotic genomes using hidden Markov models. BMC Bioinformatics 2006; 7: 142 [CrossRef] [PubMed]
    [Google Scholar]
  17. Langille MGI, Hsiao WWL, Brinkman FSL. Evaluation of genomic island predictors using a comparative genomics approach. BMC Bioinformatics 2008; 9: 329 [CrossRef] [PubMed]
    [Google Scholar]
  18. Bertelli C, Laird MR, Williams KP, Lau BY et al. Simon Fraser University Research Computing Group IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets. Nucleic Acids Res 2017; 45: W30 W35 [CrossRef] [PubMed]
    [Google Scholar]
  19. Bland C, Ramsey TL, Sabree F, Lowe M, Brown K et al. Crispr recognition tool (crt): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics 2007; 8: 209 [CrossRef] [PubMed]
    [Google Scholar]
  20. Zhou Y, Liang Y, Lynch KH, Dennis JJ, Wishart DS. PHAST: a fast phage search tool. Nucleic Acids Res 2011; 39: W347 W352 [CrossRef] [PubMed]
    [Google Scholar]
  21. Kerdsin A, Hatrongjit R, Hamada S, Akeda Y, Gottschalk M. Development of a multiplex PCR for identification of β-hemolytic streptococci relevant to human infections and serotype distribution of invasive Streptococcus agalactiae in Thailand. Mol Cell Probes 2017; 36: 10 14 [CrossRef] [PubMed]
    [Google Scholar]
  22. Lowe TM, Chan PP. tRNAscan-SE on-line: integrating search and context for analysis of transfer RNA genes. Nucleic Acids Res 2016; 44: W54 W57 [CrossRef] [PubMed]
    [Google Scholar]
  23. Suzuki H, Lefébure T, Hubisz MJ, Pavinski Bitar P, Lang P et al. Comparative genomic analysis of the Streptococcus dysgalactiae species group: gene content, molecular adaptation, and promoter evolution. Genome Biol Evol 2011; 3: 168 185 [CrossRef] [PubMed]
    [Google Scholar]
  24. Shimomura Y, Okumura K, Murayama SY, Yagi J, Ubukata K et al. Complete genome sequencing and analysis of a Lancefield group G Streptococcus dysgalactiae subsp. equisimilis strain causing streptococcal toxic shock syndrome (STSS). BMC Genomics 2011; 12: 17 [CrossRef] [PubMed]
    [Google Scholar]
  25. Watanabe S, Kirikae T, Miyoshi-Akiyama T. Complete genome sequence of Streptococcus dysgalactiae subsp. equisimilis 167 carrying Lancefield group C antigen and comparative genomics of S. dysgalactiae subsp. equisimilis strains. Genome Biol Evol 2013; 5: 1644 1651 [CrossRef] [PubMed]
    [Google Scholar]
  26. Upton M, Tagg JR, Wescombe P, Jenkinson HF. Intra- and interspecies signaling between Streptococcus salivarius and Streptococcus pyogenes mediated by SalA and SalA1 lantibiotic peptides. J Bacteriol 2001; 183: 3931 3938 [CrossRef] [PubMed]
    [Google Scholar]
  27. Moriconi M, Acke E, Petrelli D, Preziuso S. Multiplex PCR-based identification of Streptococcus canis, Streptococcus zooepidemicus and Streptococcus dysgalactiae subspecies from dogs. Comp Immunol Microbiol Infect Dis 2017; 50: 48 53 [CrossRef] [PubMed]
    [Google Scholar]
  28. Heng NCK, Ragland NL, Swe PM, Baird HJ, Inglis MA et al. Dysgalacticin: a novel, plasmid-encoded antimicrobial protein (bacteriocin) produced by Streptococcus dysgalactiae subsp. equisimilis . Microbiology 2006; 152: 1991 2001 [CrossRef] [PubMed]
    [Google Scholar]
  29. Swe PM, Heng NCK, Cook GM, Tagg JR, Jack RW. Identification of DysI, the immunity factor of the streptococcal bacteriocin dysgalacticin. Appl Environ Microbiol 2010; 76: 7885 7889 [CrossRef] [PubMed]
    [Google Scholar]
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