Skip to main content
SpringerLink
Log in

A Genome-Wide Profiling Strategy as an Aid for Searching Unique Identification Biomarkers for Streptococcus

  • Original Article
  • Published:
Indian Journal of Microbiology Aims and scope Submit manuscript

Abstract

The use of rrs (16S rRNA) gene is widely regarded as the “gold standard” for identifying bacteria and determining their phylogenetic relationships. Nevertheless, multiple copies of this gene in a genome is likely to give an overestimation of the bacterial diversity. In each of the 50 Streptococcus genomes (16 species, 50 strains), 4–7 copies of rrs are present. The nucleotide sequences of these rrs genes show high similarity within and among genomes, which did not allow unambiguous identification. A genome-wide search revealed the presence of 27 gene sequences common to all the Streptococcus species. Digestion of these 27 gene sequences with 10 type II restriction endonucleases (REs) showed that unique RE digestion in purH gene is sufficient for clear cut identification of 30 genomes belonging to 16 species. Additional gene-RE combinations allowed identification of another 15 strains belonging to S. pneumoniae, S. pyogenes, and S. suis. For the rest 5 strains, a combination of 2 genes was required for identifying them. The proposed strategy is likely to prove helpful in proper detection of pathogens like Streptococcus.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  1. Blaschke AJ (2011) Interpreting assays for the detection of Streptococcus pneumoniae. Clin Infect Dis 52:S331–S337. doi:10.1093/cid/cir048

    Article  PubMed Central  PubMed  Google Scholar 

  2. Spellerberg B, Brandt C (2011) Streptococcus. In: Versalovic J, Carroll KC, Funke G, Jorgensen JH, Landry ML, Warnock DW (eds) Manual of clinical microbiology, 10th edn. ASM Press, Washington, pp 331–349

    Google Scholar 

  3. Dubois D, Segonds C, Prere MF, Marty N, Oswald E (2013) Identification of clinical Streptococcus pneumoniae isolates among other alpha and nonhemolytic streptococci by use of the Vitek MS matrix-assisted laser desorption ionization-time of flight mass spectrometry system. J Clin Microbiol 51:1861–1867. doi:10.1128/JCM.03069-12

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  4. Scholz CFP, Poulsen K, Kilian M (2012) Novel molecular method for identification of Streptococcus pneumoniae applicable to clinical microbiology and 16S rRNA sequence-based microbiome studies. J Clin Microbiol 50:1968–1973. doi:10.1128/JCM.00365-12

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  5. Chi F, Nolte O, Bergmann C, Ip M, Hakenbeck R (2007) Crossing the barrier: evolution and spread of a major class of mosaic pbp2x in Streptococcus pneumoniae, S. mitis and S. oralis. Int J Med Microbiol 297:503–512. doi:10.1016/j.ijmm.2007.02.009

    Article  CAS  PubMed  Google Scholar 

  6. Kellogg JA, Bankert DA, Elder CJ, Gibbs JL, Smith MC (2001) Identification of Streptococcus pneumoniae revisited. J Clin Microbiol 39:3373–3375. doi:10.1128/JCM.39.9.3373-3375.2001

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  7. Ferroni A, Suarez S, Beretti JL, Dauphin B, Bille E, Meyer J, Bougnoux M-E, Alanio A, Berche P, Nassif X (2010) Real-time identification of bacteria and Candida species in positive blood culture broths by matrix-assisted laser desorption ionization–time of flight mass spectrometry. J Clin Microbiol 48:1542–1548. doi:10.1128/JCM.02485-09

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  8. Stevenson LG, Drake SK, Murray PR (2010) Rapid identification of bacteria in positive blood culture broths by matrix-assisted laser desorption ionization-time of flight mass spectrometry. J Clin Microbiol 48:444–447. doi:10.1128/JCM.01541-09

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  9. Foster AGW (2013) Rapid identification of microbes in positive blood cultures by use of the Vitek MS matrix-assisted laser desorption ionization-time of flight mass spectrometry system. J Clin Microbiol 51:3717–3719. doi:10.1128/JCM.01679-13

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  10. Kawamura Y, Hou Sultana X-GF, Miura H, Ezaki T (1995) Determination of 16S rRNA sequences of Streptococcus mitisand Streptococcus gordonii and phylogenetic relationships among members of the genus Streptococcus. Int J Syst Bacteriol 45:406–408. doi:10.1099/00207713-45-2-406

    Article  CAS  PubMed  Google Scholar 

  11. Abdeldaim G, Herrmann B, Mölling P, Holmberg H, Blomberg J, Olcén P, Strålin K (2010) Usefulness of real-time PCR for lytA, ply, and Spn9802 on plasma samples for the diagnosis of pneumococcal pneumonia. Clin Microbiol Infect 16:1135–1141. doi:10.1111/j.1469-0691.2009.03069.x

    Article  CAS  PubMed  Google Scholar 

  12. Bhushan A, Joshi J, Shankar P, Kushwah J, Raju SC, Purohit HJ, Kalia VC (2013) Development of genomic tools for the identification of certain Pseudomonas up to species level. Indian J Microbiol 53:253–263. doi:10.1007/s12088-013-0412-1

    Article  PubMed Central  PubMed  Google Scholar 

  13. Bhushan A, Mukherjee T, Joshi J, Shankar P, Kalia VC (2015) Insights into the origin of Clostridium botulinum strains: evolution of distinct restriction endonuclease sites in rrs (16S rRNA gene). Indian J Microbiol 55:140–150. doi:10.1007/s12088-015-0514-z

    Article  PubMed  Google Scholar 

  14. Kalia VC, Mukherjee T, Bhushan A, Joshi J, Shankar P, Huma N (2011) Analysis of the unexplored features of rrs (16S rDNA) of the genus Clostridium. BMC Genom 12:18. doi:10.1186/1471-2164-12-18

    Article  CAS  Google Scholar 

  15. Lal D, Verma M, Lal R (2011) Exploring internal features of 16S rRNA gene for identification of clinically relevant species of the genus Streptococcus. Ann Clin Microbiol Antimicrob 10:28. doi:10.1186/1476-0711-10-28

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  16. Porwal S, Lal S, Cheema S, Kalia VC (2009) Phylogeny in aid of the present and novel microbial lineages: diversity in Bacillus. PLoS ONE 4:e4438. doi:10.1371/journal.pone.0004438

    Article  PubMed Central  PubMed  Google Scholar 

  17. Kalia VC (2015) Let’s explore the latent features of genes to identify bacteria. J Mol Genet Med 9:e105. doi:10.4172/1747-0862.1000E105

    Google Scholar 

  18. Kalia VC, Kumar P (2015) Genome wide search for biomarkers to diagnose Yersinia infections. Indian J Microbiol 55:366–374. doi:10.1007/s12088-015-0552-6

    Article  CAS  PubMed  Google Scholar 

  19. Kalia VC, Kumar P, Kumar R, Mishra A, Koul S (2015) Genome wide analysis for rapid identification of Vibrio species. Indian J Microbiol 55:375–383. doi:10.1007/s12088-015-0553-5

    Article  PubMed  Google Scholar 

  20. Kekre A, Bhushan A, Kumar P, Kalia VC (2015) Genome wide analysis for searching novel markers to rapidly identify Clostridium strains. Indian J Microbiol 55:250–257. doi:10.1007/s12088-015-0535-7

    Article  CAS  PubMed  Google Scholar 

  21. Bishop CJ, Aanensen DM, Jordan GE, Kilian M, Hanage WP, Spratt BG (2009) Assigning strains to bacterial species via the Internet. BMC Biol 7:3. doi:10.1186/1741-7007-7-3

    Article  PubMed Central  PubMed  Google Scholar 

  22. Carvalho MG, Tondella ML, McCaustland K, Weidlich L, McGee L, Mayer LW, Steigerwalt A, Whaley M, Facklam RR, Fields B, Carlone G, Ades GW, Dagan R, Sampson JS (2007) Evaluation and improvement of real-time PCR assays targeting lytA, ply, and psaA genes for detection of pneumococcal DNA. J Clin Microbiol 45:2460–2466. doi:10.1128/JCM.02498-06

    Article  PubMed Central  CAS  Google Scholar 

  23. Chen CC, Teng LJ, Chang TC (2004) Identification of clinically relevant viridans group streptococci by sequence analysis of the 16S-23S ribosomal DNA spacer region. J Clin Microbiol 42:2651–2657. doi:10.1128/JCM.42.6.2651-2657.2004

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  24. Drancourt M, Roux V, Fournier PE, Raoult D (2004) rpoB gene sequence-based identification of aerobic Gram-positive cocci of the genera Streptococcus, Enterococcus, Gemella, Abiotrophia, and Granulicatella. J Clin Microbiol 42:497–504. doi:10.1128/JCM.42.2.497-504.2004

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  25. Picard FJ, Ke D, Boudreau DK, Boissinot M, Huletsky A, Richard D, Ouellette M, Roy PH, Bergeron MG (2004) Use of tuf sequences for genus-specific PCR detection and phylogenetic analysis of 28 streptococcal species. J Clin Microbiol 42:3686–3695. doi:10.1128/JCM.42.8.3686-3695.2004

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  26. Teng LJ, Hsueh PR, Tsai JC, Chen PW, Hsu JC, Lai HC, Lee CN, Ho SW (2002) groESL sequence determination, phylogenetic analysis, and species differentiation for viridans group streptococci. J Clin Microbiol 40:3172–3178. doi:10.1128/JCM.40.9.3172-3178.2002

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  27. Zbinden A, Kohler N, Bloemberg GV (2011) recA-based PCR assay for accurate differentiation of Streptococcus pneumoniae from other viridans streptococci. J Clin Microbiol 49:523–527. doi:10.1128/JCM.01450-10

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  28. Glazunova OO, Raoult D, Roux V (2010) Partial recN gene sequencing: a new tool for identification and phylogeny within the genus Streptococcus. Int J Syst Evol Microbiol 60:2140–2148. doi:10.1099/ijs.0.018176-0

    Article  CAS  PubMed  Google Scholar 

  29. Nielsen XC, Justesen US, Dargis R, Kemp M, Christensen JJ (2009) Identification of clinically relevant nonhemolytic streptococci on the basis of sequence analysis of 16S-23S intergenic spacer region and partial gdh gene. J Clin Microbiol 47:932–939. doi:10.1128/JCM.01449-08

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  30. Park HK, Yoon JW, Shin JW, Kim JY, Kim W (2010) rpoA is a useful gene for identification and classification of Streptococcus pneumoniae from the closely related viridans group streptococci. FEMS Microbiol Lett 305:58–64. doi:10.1111/j.1574-6968.2010.01913.x

    Article  CAS  PubMed  Google Scholar 

  31. Poyart C, Quesne G, Coulon S, Berche P, Trieu-Cuot P (1998) Identification of streptococci to species level by sequencing the gene encoding the manganese-dependent superoxide dismutase. J Clin Microbiol 36:41–47

    PubMed Central  CAS  PubMed  Google Scholar 

  32. Wessels E, Schelfaut JJG, Bernards AT, Claas ECJ (2012) Evaluation of several biochemical and molecular techniques for identification of Streptococcus pneumoniae and Streptococcus pseudopneumoniae and their detection in respiratory samples. J Clin Microbiol 50:1171–1177. doi:10.1128/JCM.06609-11

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  33. Hanage WP, Kaijalainen T, Herva E, Saukkoriipi A, Syrjänen R, Spratt BG (2005) Using multilocus sequence data to define the pneumococcus. J Bacteriol 187:6223–6230. doi:10.1128/JB.187.17.6223-6230.2005

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  34. Innings Å, Krabbe M, Ullberg M, Herrmann B (2005) Identification of 43 Streptococcus species by pyrosequencing analysis of the rnpB gene. J Clin Microbiol 43:5983–5991. doi:10.1128/JCM.43.12.5983-5991.2005

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  35. Kilian M, Poulsen K, Blomqvist T, Havarstein LS, Bek-Thomsen M, Tettelin H, Sorensen UB (2008) Evolution of Streptococcus pneumoniae and its close commensal relatives. PLoS ONE 3:7. doi:10.1371/journal.pone.0002683

    Article  Google Scholar 

  36. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98

    CAS  Google Scholar 

  37. Sajid A, Arora G, Singhal A, Kalia VC, Singh Y (2015) Protein phosphatases of pathogenic bacteria: role in physiology and virulence. Annu Rev Microbiol 69:527–547. doi:10.1146/annurev-micro-020415-111342

    Article  CAS  PubMed  Google Scholar 

  38. Koul S, Prakash J, Mishra A, Kalia VC (2015) Potential emergence of multi-quorum sensing inhibitor resistant (MQSIR) bacteria. Indian J Microbiol. doi:10.1007/s12088-015-0558-0

    PubMed  Google Scholar 

Download references

Acknowledgments

We are thankful to the Director of CSIR-Institute of Genomics and Integrative Biology (IGIB), and CSIR projects—GENESIS (BSC0121) and INDEPTH (BSC0111) for providing the necessary funds, facilities and moral support. Authors are also thankful to the Academy of Scientific & Innovative Research (AcSIR), New Delhi.

Author information

Authors and Affiliations

  1. Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007, India

    Vipin Chandra Kalia, Ravi Kumar, Prasun Kumar & Shikha Koul

  2. Academy of Scientific and Innovative Research (AcSIR), 2, Rafi Marg, Anusandhan Bhawan, New Delhi, 110001, India

    Vipin Chandra Kalia & Shikha Koul

Authors
  1. Vipin Chandra Kalia
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ravi Kumar
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Prasun Kumar
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Shikha Koul
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Vipin Chandra Kalia.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOCX 29 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Kalia, V.C., Kumar, R., Kumar, P. et al. A Genome-Wide Profiling Strategy as an Aid for Searching Unique Identification Biomarkers for Streptococcus . Indian J Microbiol 56, 46–58 (2016). https://doi.org/10.1007/s12088-015-0561-5

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12088-015-0561-5

Keywords

Search

Navigation