The Struggle to Fish Out the Dreadful Streptococcus
Author: Vipin Chandra Kalia


In diseases plagued by high morbidity and mortality rates, there is a tremendous pressure to quickly identify the causal organism. Diseases in this category range from Pneumonia, Otitis Media, Meningitis, Bacteremia, etc. One of the most common reasons for visiting a pediatrician is the inflammation of the middle ear and tympanostomy tube placement surgery. These pathogenic situations are associated with multidrug resistant bacteria: Streptococcus pneumoniae, Moraxella catarrhalis, and Haemophilus influenzae.

Meningitis is a health issue, which is caused by the inflammation of the meninges, the membranes which cover the spinal cord and brain. Meningitis occurs if the fluid surrounding the meninges gets infected with bacteria. The disease is contagious in nature and Streptococcus is responsible for it.

All hell may break loose, if bacteria such as Streptococcus infect the blood stream. It may happen through wounds, injection or via surgical operations. Under these scenarios, if blood pressure declines drastically, it may indicate the up coming septic shock. The deprivation of oxygen in tissues and organs allow the accumulation of waste products. It can lead to serious damage to the body or in extreme cases " death.

In scenario, where no control measures could be taken in time, a few among these diseases had assumed epidemic dimension. Medical practitioners, Clinicians and Microbiologists have always been looking for means to identify such pathogens in a rapid manner.

The journey of identifying Streptococcus

In view of the lethality of this bacterium, different strategies to identify them have been developed. A universal technique to target Streptococcus is still not in place. The basic reasons for this persisting problem are: i) very close genetic resemblance among different species, and ii) high rate of transfer of genetic material through horizontal gene transfer. This phenomenon complicates the sensitivity and specificity of the assay system. A few sophisticated and costly procedures like MALDI-TOF mass spectrometry have proved helpful.

The limitations of phylogenetically conserved 16S rDNA ( rrs ) gene

The use of nucleotide sequences of phylogenetically conserved 16S rDNA (rrs) gene resulted in revealing that different Streptococcus species: S. pseudopneumoniae, S. mitis, S. pneumoniae, and S. oralis show more than 99% resemblance among themselves. The problem is compounded by the presence of 4-7 copies of rrs per genome. More recent work based on around 200 copies of rrs representing 50 sequenced genomes of 16 species of Streptococcus, revealed that there is high similarity between different species. Out of these 50 genomes, only 12 genomes representing 9 species could be distinguished in an unambiguous manner, based on the unique Restriction Endonuclease (RE) digestion patterns. Thus, rrs is not proving very effective in this case.

The potential alternatives to rrs

Comparison of all the genes of 50 completely sequenced genomes of Streptococcus enabled segregation of 27 genes, which were to all of them. A thorough analysis of patterns (Fragment number, order and size) generated in different genes purH, pyrH, dnaA, facbG, dnaK, mraY (up to 2500 nucleotides in length) with REs - CviAII, BfaI, AluI, RsaI, BfuCI, TaqI, Tru9I and HpyCH4V, demonstrated that a few combinations can be used for identifying Streptococcus. In certain cases, where a unique gene " RE combination could not be identified, an alternative was deduced, where by 2-3 genes " RE proved helpful.

Previous works had recommended recA as a representative gene to overcome the problem encountered in the use of rrs gene sequence. However, the study (detailed above) involving a battery of REs and genes indicated that this gene (recA) may not be the best candidate for identifying Streptococcus.

Thus, once a disease is diagnosed, treatment can be initiated at the earliest.

Unique selling points

• A unique selling point of this novel strategy was that although purH was present in Staphylococcus species as well, however, there were clear cut differences between the two genera.

• The genes with unique RE digestion patterns were present in all the species.

• The gene(s) can be employed for rapid diagnosis of the disease.


1. Agarwala M, Choudhury B, Yadav RNS (2014) Comparative study of antibiofilm activity of copper oxide and iron oxide nanoparticles against multidrug resistant biofilm forming uropathogens. Indian J Microbiol 54:365"368. doi:10.1007/s12088-014-0462-z

2. Alipiah NM, Shamsudin MN, Yusoff FM, Arshad A (2015) Membrane biosynthesis gene disruption in methicillin-resistant Staphylococcus aureus (MRSA) as potential mechanism for reducing antibiotic resistance. Indian J Microbiol 54:41-49. doi:10.1007/s12088-014-0488-2

3. 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

4. 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

5. 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

6. 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

7. Kalia VC, Kumar R, Kumar P, Koul S (2016) A genome-wide profiling strategy as an aid for searching unique identification biomarkers for Streptococcus. Indian J Microbiol 56:46-58. doi:10.1007/s12088-015-0561-5

8. 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

9. Koul S, Kalia VC (2016) Comparative genomics reveals biomarkers to identify Lactobacillus species. Indian J Microbiol 56:253"263. doi:10.1007/s12088-016-0605-5

10. Koul S, Kumar P, Kalia VC (2015) A unique genome wide approach to search novel markers for rapid identification of bacterial pathogens. J Mol Genet Med 9:194. doi: 10.4172/1747-0862.1000194

11. Koul S, Prakash J, Mishra A, Kalia VC (2016) Potential emergence of multi-quorum sensing inhibitor resistant (MQSIR) bacteria. Indian J Microbiol 56:1-18. doi:10.1007/s12088-015-0558-0

12. Kumar R, Koul S, Kumar P, Kalia VC (2016) Searching biomarkers in the sequenced genomes of Staphylococcus for their rapid identification. Indian J Microbiol 56:64-71.doi:10.1007/s12088-016-0565-9

13. Liu Q, Wang S, Zhi J-F, Ming H, Teng D (2013) Efficient production of lactic acid from sweet sorghum juice by a newly isolated Lactobacillus salivarius CGMCC 7.75. Indian J Microbiol 53:332-336. doi: 10.1007/s12088-013-0377-0

14. Mahale KN, Paranjape PS, Marathe NP, Dhotre DP, Chowdhury S, Shetty SA, Sharma A, Sharma K, Tuteja U, Batra HV, Shouche YS (2014) Draft genome sequences of Yersinia pestis strains from the 1994 plague epidemic of Surat and 2002 Shimla outbreak in India. Indian J Microbiol 54:480-482. doi: 10.1007/s12088-014-0475-7

15. Moroeanu VI, Vamanu E, Paun G, Neagu E, Ungureanu OR, Eremia SAV, Radu GL, Ionescu R, Pelinescu DR (2015) Probiotic strains influence on infant microbiota in the in vitro colonic fermentation model GIS1. Indian J Microbiol 55:423-429. doi: 10.1007/s12088-015-0542-8

16. Prakash O, Pandey PK, Kulkarni GJ, Mahale KN, Shouche YS (2014) Technicalities and glitches of terminal restriction fragment length polymorphism (T-RFLP). Indian J Microiobiol 54:255-261. doi:10.1007/s12088-014-0461-0

17. Prakasham RS, Kumar BS, Kumar YS, Kumar KP (2014) Production and characterization of protein encapsulated silver nanoparticles by marine isolate Streptomyces parvulus SSNP11. Indian J Microbiol 54:329-336. doi: 10.1007/s12088-014-0452-1

18. Saxena A, Mukherjee M, Kumari R, Singh P, Lal R (2014) Synthetic biology in action: Developing a drug against MDR-TB. Indian J Microbiol 54:369-375. doi: 10.1007/s12088-014-0498-0

19. Shang Z, Wang H, Zhou S, Chu W (2014) Characterization of N-acyl-homoserine lactones (AHLs)-deficient clinical isolates of Pseudomonas aeruginosa. Indian J Microbiol 54:158-162. doi:10.1007/s12088-014-0449-9

20. Wang R, Fang S, Xiang S, Ling S, Yuan J, Wang S (2014) Generation and characterization of a scFv antibody against T3SS needle of Vibrio parahaemolyticus. Indian J Microbiol 54:143-150. doi: 10.1007/s12088-013-0428-6

21. Yu S, Peng Y, Chen W, Deng Y, Zheng Y (2014) Comparative genomic analysis of two-component signal transduction systems in probiotic Lactobacillus casei. Indian J Microbiol 54:293-301. doi: 10.1007/s12088-014-0456-x

22. Yu S, Peng Y, Zheng Y, Chen W (2015) Comparative genome analysis of Lactobacillus casei: Insights into genomic diversification for niche expansion. Indian J Microbiol 55:102-107. doi: 10.1007/s12088-014-0496-2

About Author / Additional Info:
Researcher in Microbial Biotechnology and Genomics at CSIR-IGIB, Delhi