1887

Abstract

Distinuishing the species of mitis group streptococci is challenging due to ambiguous phenotypic characteristics and high degree of genetic similarity. This has been particularly true for resolving atypical Streptococcus pneumoniae and Streptococcus pseudopneumoniae. We used phylogenetic clustering to demonstrate specific and separate clades for both S. pneumoniae and S. pseudopneumoniae genomes. The genomes that clustered within these defined clades were used to extract species-specific genes from the pan-genome. The S. pneumoniae marker was detected in 8027 out of 8051 (>99.7 %) S. pneumoniae genomes. The S. pseudopneumoniae marker was specific for all genomes that clustered in the S. pseudopneumoniae clade, including unresolved species of the genus Streptococcus sequenced by the BC Centre for Disease Control Public Health Laboratory that previously could not be distinguished by other methods. Other than the presence of the S. pseudopneumoniae marker in six of 8051 (<0.08 %) S. pneumoniae genomes, both the S. pneumoniae and S. pseudopneumoniae markers showed little to no detectable cross-reactivity to the genomes of any other species of the genus Streptococcus or to a panel of over 46 000 genomes from viral, fungal, bacterial pathogens and microbiota commonly found in the respiratory tract. A real-time PCR assay was designed targeting these two markers. Genomics provides a useful technique for PCR assay design and development.

  • This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Loading

Article metrics loading...

/content/journal/mgen/10.1099/mgen.0.000175
2018-04-09
2024-03-19
Loading full text...

Full text loading...

/deliver/fulltext/mgen/4/7/mgen000175.html?itemId=/content/journal/mgen/10.1099/mgen.0.000175&mimeType=html&fmt=ahah

References

  1. Arbique JC, Poyart C, Trieu-Cuot P, Quesne G, Carvalho MG et al. Accuracy of phenotypic and genotypic testing for identification of Streptococcus pneumoniae and description of Streptococcus pseudopneumoniae sp. nov. J Clin Microbiol 2004; 42:4686–4696 [View Article][PubMed]
    [Google Scholar]
  2. Kawamura Y, Hou XG, Sultana F, Miura H, Ezaki T. Determination of 16S rRNA sequences of Streptococcus mitis and Streptococcus gordonii and phylogenetic relationships among members of the genus Streptococcus . Int J Syst Bacteriol 1995; 45:406–408 [View Article][PubMed]
    [Google Scholar]
  3. Wessels E, Schelfaut JJ, Bernards AT, Claas EC. Evaluation of several biochemical and molecular techniques for identification of Streptococcus pneumoniae and Streptococcus pseudopneumoniae and their detection in respiratory samples. J Clin Microbiol 2012; 50:1171–1177 [View Article][PubMed]
    [Google Scholar]
  4. Harf-Monteil C, Granello C, Le Brun C, Monteil H, Riegel P. Incidence and pathogenic effect of Streptococcus pseudopneumoniae . J Clin Microbiol 2006; 44:2240–2241 [View Article][PubMed]
    [Google Scholar]
  5. Keith ER, Podmore RG, Anderson TP, Murdoch DR. Characteristics of Streptococcus pseudopneumoniae isolated from purulent sputum samples. J Clin Microbiol 2006; 44:923–927 [View Article][PubMed]
    [Google Scholar]
  6. Laurens C, Michon AL, Marchandin H, Bayette J, Didelot MN et al. Clinical and antimicrobial susceptibility data of 140 Streptococcus pseudopneumoniae isolates in France. Antimicrob Agents Chemother 2012; 56:4504–4507 [View Article][PubMed]
    [Google Scholar]
  7. Keith ER, Murdoch DR. Antimicrobial susceptibility profile of Streptococcus pseudopneumoniae isolated from sputum. Antimicrob Agents Chemother 2008; 52:2998 [View Article][PubMed]
    [Google Scholar]
  8. Rolo D, S Simões A, Domenech A, Fenoll A, Liñares J et al. Disease isolates of Streptococcus pseudopneumoniae and non-typeable S. pneumoniae presumptively identified as atypical S. pneumoniae in Spain. PLoS One 2013; 8:e57047 [View Article][PubMed]
    [Google Scholar]
  9. Shahinas D, Thornton CS, Tamber GS, Arya G, Wong A et al. Comparative genomic analyses of Streptococcus pseudopneumoniae provide insight into virulence and commensalism dynamics. PLoS One 2013; 8:e65670 [View Article][PubMed]
    [Google Scholar]
  10. Leegaard TM, Bootsma HJ, Caugant DA, Eleveld MJ, Mannsåker T et al. Phenotypic and genomic characterization of pneumococcus-like streptococci isolated from HIV-seropositive patients. Microbiology 2010; 156:838–848 [View Article][PubMed]
    [Google Scholar]
  11. van der Linden M, Otten J, Bergmann C, Latorre C, Liñares J et al. Insight into the diversity of penicillin-binding protein 2x alleles and mutations in viridans streptococci. Antimicrob Agents Chemother 2017; 61:e02646-16 [View Article][PubMed]
    [Google Scholar]
  12. Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics 2016; 32:3047–3048 [View Article][PubMed]
    [Google Scholar]
  13. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014; 30:2114–2120 [View Article][PubMed]
    [Google Scholar]
  14. Coil D, Jospin G, Darling AE. A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data. Bioinformatics 2015; 31:587–589 [View Article][PubMed]
    [Google Scholar]
  15. 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 [View Article][PubMed]
    [Google Scholar]
  16. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article][PubMed]
    [Google Scholar]
  17. Cabrera-Rubio R, Garcia-Núñez M, Setó L, Antó JM, Moya A et al. Microbiome diversity in the bronchial tracts of patients with chronic obstructive pulmonary disease. J Clin Microbiol 2012; 50:3562–3568 [View Article][PubMed]
    [Google Scholar]
  18. Darling AE, Jospin G, Lowe E, Matsen FA, Bik HM et al. PhyloSift: phylogenetic analysis of genomes and metagenomes. PeerJ 2014; 2:e243 [View Article][PubMed]
    [Google Scholar]
  19. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312–1313 [View Article][PubMed]
    [Google Scholar]
  20. Huerta-Cepas J, Dopazo J, Gabaldón T. ETE: a python environment for tree exploration. BMC Bioinformatics 2010; 11:24 [View Article][PubMed]
    [Google Scholar]
  21. Sahl JW, Caporaso JG, Rasko DA, Keim P. The large-scale blast score ratio (LS-BSR) pipeline: a method to rapidly compare genetic content between bacterial genomes. PeerJ 2014; 2:e332 [View Article][PubMed]
    [Google Scholar]
  22. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119 [View Article]
    [Google Scholar]
  23. Rognes T, Flouri T, Nichols B, Quince C, Mahé F. VSEARCH: a versatile open source tool for metagenomics. PeerJ 2016; 4:e2584 [View Article][PubMed]
    [Google Scholar]
  24. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403–410 [View Article][PubMed]
    [Google Scholar]
  25. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article][PubMed]
    [Google Scholar]
  26. Kapatai G, Sheppard CL, Al-Shahib A, Litt DJ, Underwood AP et al. Whole genome sequencing of Streptococcus pneumoniae: development, evaluation and verification of targets for serogroup and serotype prediction using an automated pipeline. PeerJ 2016; 4:e2477 [View Article][PubMed]
    [Google Scholar]
  27. Wood DE, Salzberg SL. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol 2014; 15:R46 [View Article][PubMed]
    [Google Scholar]
  28. Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M et al. Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 2012; 28:1647–1649 [View Article][PubMed]
    [Google Scholar]
  29. Roach DJ, Burton JN, Lee C, Stackhouse B, Butler-Wu SM et al. A year of infection in the intensive care unit: Prospective whole genome sequencing of bacterial clinical isolates reveals cryptic transmissions and novel microbiota. PLoS Genet 2015; 11:e1005413 [View Article][PubMed]
    [Google Scholar]
  30. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article][PubMed]
    [Google Scholar]
  31. Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High-throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. bioRxiv 2017; 27:225342
    [Google Scholar]
  32. Konstantinidis KT, Tiedje JM. Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci USA 2005; 102:2567–2572 [View Article][PubMed]
    [Google Scholar]
  33. Chewapreecha C, Harris SR, Croucher NJ, Turner C, Marttinen P et al. Dense genomic sampling identifies highways of pneumococcal recombination. Nat Genet 2014; 46:305–309 [View Article][PubMed]
    [Google Scholar]
  34. Sheppard CL, Kapatai G, Broughton K, Schaefer U, Hannah M et al. Clinical streptococcal isolates, distinct fromStreptococcus pneumoniae, but containing the β-glucosyl transferase tts gene and expressing serotype 37 capsular polysaccharide. PeerJ 2017; 5:e3571 [View Article][PubMed]
    [Google Scholar]
  35. Bowers JR, Lemmer D, Sahl JW, Pearson T, Driebe EM et al. KlebSeq, a diagnostic tool for surveillance, detection, and monitoring of Klebsiella pneumoniae . J Clin Microbiol 2016; 54:2582–2596 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/mgen/10.1099/mgen.0.000175
Loading
/content/journal/mgen/10.1099/mgen.0.000175
Loading

Data & Media loading...

Supplements

Supplementary File 1

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error