Skip to main content

Searching Biomarkers in the Sequenced Genomes of Staphylococcus for their Rapid Identification

Abstract

Bacterial identification using rrs (16S rRNA) gene is widely reported. Bacteria possessing multiple copies of rrs lead to overestimation of its diversity. Staphylococcus genomes carries 5–6 copies of rrs showing high similarity in their nucleotide sequences, which lead to ambiguous results. The genomes of 31 strains of Staphylococcus representing 7 species were searched for the presence of common genes. In silico digestion of 34 common genes using 10 restriction endonucleases (REs) lead to select gene-RE combinations, which could be used as biomarkers. RE digestion of recA allowed unambiguous identification of 13 genomes representing all the 7 species. In addition, a few more genes (argH, argR, cysS, gyrB, purH, and pyrE) and RE combinations permitted further identification of 12 strains. By employing additional RE and genes unique to a particular strain, it was possible to identify the rest 6 Staphylococcus aureus strains. This approach has the potential to be utilized for rapid detection of Staphylococcus strains.

This is a preview of subscription content, access via your institution.

References

  1. Iwg SCC (2009) Classification of staphylococcal cassette chromosome mec (SCCmec): guidelines for reporting novel SCCmec elements. Antimicrob Agents Chemother 53:4961–4967. doi:10.1128/AAC.00579-09

    Article  Google Scholar 

  2. Vuong C, Gerke C, Somerville GA, Fischer ER, Otto M (2003) Quorum-sensing control of biofilm factors in Staphylococcus epidermidis. J Infect Dis 188:706–718. doi:10.1086/377239

    Article  CAS  PubMed  Google Scholar 

  3. Liu GY (2009) Molecular pathogenesis of Staphylococcus aureus infection. Pediatr Res 65:71R–77R. doi:10.1203/PDR.0b013e31819dc44d

    PubMed Central  Article  PubMed  Google Scholar 

  4. Plata K, Rosato AE, Węgrzyn G (2009) Staphylococcus aureus as an infectious agent: overview of biochemistry and molecular genetics of its pathogenicity. Acta Biochim Pol 56:597–612

    CAS  PubMed  Google Scholar 

  5. Kateete DP, Kimani CN, Katabazi FA, Okeng A, Okee MS, Nanteza A, Joloba ML, Najjuka FC (2010) Identification of Staphylococcus aureus: DNase and Mannitol salt agar improve the efficiency of the tube coagulase test. Ann Clin Microbiol Antimicrob 9:23. doi:10.1186/1476-0711-9-23

    PubMed Central  Article  PubMed  Google Scholar 

  6. Gray B, Hall P, Gresham H (2013) Targeting agr- and agr-like quorum sensing systems for development of common therapeutics to treat multiple gram-positive bacterial infections. Sensors 13:5130–5166. doi:10.3390/s130405130

    PubMed Central  Article  CAS  PubMed  Google Scholar 

  7. Kalia VC (2013) Quorum sensing inhibitors: an overview. Biotechnol Adv 31:224–245. doi:10.1016/j.biotechadv.2012.10.004

    Article  CAS  PubMed  Google Scholar 

  8. Kalia VC (2014) Microbes, antimicrobials and resistance: the battle goes on. Indian J Microbiol 54:1–2. doi:10.1007/s12088-013-0443-7

    PubMed Central  Article  CAS  PubMed  Google Scholar 

  9. Kalia VC (2015) Microbes: the most friendly beings? In: Kalia VC (ed) Quorum sensing vs quorum quenching: a battle with no end in sight, Springer India, pp 1–5. ISBN 978-81-322-1981-1. doi: 10.1007/978-81-322-1982-8_1

  10. 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 

  11. Kalia VC, Purohit HJ (2011) Quenching the quorum sensing system: potential antibacterial drug targets. Crit Rev Microbiol 37:121–140. doi:10.3109/1040841X.2010.532479

    Article  CAS  PubMed  Google Scholar 

  12. 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 

  13. Iorio NL, Ferreira RB, Schuenck RP, Malvar KL, Brilhante AP, Nunes AP, Bastos CC, Dos Santos KR (2007) Simplified and reliable scheme for species-level identification of Staphylococcus clinical isolates. J Clin Microbiol 45:2564–2569. doi:10.1128/JCM.00679-07

    PubMed Central  Article  CAS  PubMed  Google Scholar 

  14. Bennett RW, Lancette GA (2001) Bacteriological analytical manual. Chapter 12 Staphylococcus aureus. BAM: Staphylococcusaureus—Food and Drug Administration

  15. Brown DF, Edwards DI, Hawkey PM, Morrison D, Ridgway GL, Towner KJ, Wren MW; Joint Working Party of the British Society for Antimicrobial Chemotherapy; Hospital Infection Society; Infection Control Nurses Association (2005) Guidelines for the laboratory diagnosis and susceptibility testing of methicillin-resistant Staphylococcus aureus (MRSA). J Antimicrob Chemother 56:1000–1018. doi:10.1093/jac/dki372

  16. Francois P, Pittet D, Bento M, Pepey B, Vaudaux P, Lew D, Schrenzel J (2003) Rapid detection of methicillin-resistant Staphylococcus aureus directly from sterile or nonsterile clinical samples by a new molecular assay. J Clin Microbiol 41:254–260. doi:10.1128/JCM.41.1.254-260.2003

    PubMed Central  Article  CAS  PubMed  Google Scholar 

  17. Gröbner S, Kempf VA (2007) Rapid detection of methicillin-resistant staphylococci by real-time PCR directly from positive blood culture bottles. Eur J Clin Microbiol Infect Dis 26:751. doi:10.1007/s10096-007-0368-3

    Article  PubMed  Google Scholar 

  18. Schuenck RP, Em Pereira, Iorio NLP, dos Santos KRN (2008) Multiplex PCR assay to identify methicillin-resistant Staphylococcus heamolyticus. FEMS Immunol Med Microbiol 52:431–435. doi:10.1111/j.1574-695X.2008.00387.x

    Article  CAS  PubMed  Google Scholar 

  19. Pichon B, Hill R, Laurent F, Larsen AR, Skov RL, Holmes M, Edwards GF, Teale C, Kearns AM (2012) Development of a real-time quadruplex PCR assay for simultaneous detection of nuc, Panton-Valentine leucocidin (PVL), mecA and homologue mecALGA251. J Antimicrob Chemother 67:2338–2341. doi:10.1093/jac/dks221

    Article  CAS  PubMed  Google Scholar 

  20. Roberts AL (2014) Identification of Staphylococcus epidermidis in the clinical microbiology laboratory by molecular methods. Methods Mol Biol 1106:33–53. doi:10.1007/978-1-62703-736-5_3

    Article  CAS  PubMed  Google Scholar 

  21. Thomas LC, Gidding HF, Ginn AN, Olma T, Iredell J (2007) Development of a real-time Staphylococcus aureus and MRSA (SAM-) PCR for routine blood culture. J Microbiol Methods 68:296–302. doi:10.1016/j.mimet.2006.09.003

    Article  CAS  PubMed  Google Scholar 

  22. Francois P, Bento M, Renzi G, Harbarth S, Pittet D, Schrenzel J (2007) Evaluation of three molecular assays for rapid identification of methicillin-resistant Staphylococcus aureus. J Clin Microbiol 45:2011–2013. doi:10.1128/JCM.00232-07

    PubMed Central  Article  CAS  PubMed  Google Scholar 

  23. Malhotra-Kumar S, Haccuria K, Michiels M, Ieven M, Poyart C, Hryniewicz W, Goossens H (2008) Current trends in rapid diagnostics for methicillin-resistant Staphylococcus aureus and glycopeptide-resistant Enterococcus species. J Clin Microbiol 46:1577–1587. doi:10.1128/JCM.00326-08

    PubMed Central  Article  PubMed  Google Scholar 

  24. Malhotra-Kumar S, Van Heirstraeten L, Lee A, Abrahantes JC, Lammens C, Vanhommerig E, Molenberghs G, Aerts M, Harbarth S, Goossens H, MOSAR WP2 Study Team (2010) Evaluation of molecular assays for rapid detection of methicillin-resistant Staphylococcus aureus. J Clin Microbiol 48:4598–4601. doi:10.1128/JCM.00004-10

    PubMed Central  Article  PubMed  Google Scholar 

  25. Shore AC, Deasy EC, Slickers P, Brennan G, O’Connell B, Monecke S, Ehricht R, Coleman DC (2011) Detection of staphylococcal cassette chromosome mec type XI carrying highly divergent mecA, mecI, mecR1, blaZ, and ccr genes in human clinical isolates of clonal complex methicillin-resistant Staphylococcus aureus. Antimicrob Agents Chemother 55:3765. doi:10.1128/AAC.00187-11

    PubMed Central  Article  CAS  PubMed  Google Scholar 

  26. 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

    PubMed Central  Article  PubMed  Google Scholar 

  27. 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 

  28. 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

    PubMed Central  Article  PubMed  Google Scholar 

  29. 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 

  30. 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 

  31. 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 

  32. 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 

  33. 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 

  34. Kalia VC, Kumar R, Kumar P, Koul S (2015) A genome-wide profiling strategy as an aid for searching unique identification biomarkers for Streptococcus. Indian J Microbiol. doi:10.1007/s12088-015-0561-5

    Google Scholar 

  35. Koul S, Kumar P, Kalia VC (2016) A unique genome wide approach to search novel markers for rapid identification of bacterial pathogens. J Mol Genet Med (in Press)

  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 

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

Authors

Corresponding author

Correspondence to Vipin Chandra Kalia.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOCX 26 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Kumar, R., Koul, S., Kumar, P. et al. Searching Biomarkers in the Sequenced Genomes of Staphylococcus for their Rapid Identification. Indian J Microbiol 56, 64–71 (2016). https://doi.org/10.1007/s12088-016-0565-9

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12088-016-0565-9

Keywords

  • Biomarkers
  • Diagnosis
  • Genome
  • In silico
  • Restriction endonuclease
  • Staphylococcus