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Dig out to Fight out Staphylococcus: The Genomic Route

BY: Vipin Chandra Kalia | Category: Environmental-Biotechnology | Submitted: 2017-01-30 12:19:00
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Article Summary: "Staphylococcus is the route cause of diseases such as cellulitis, boils, food poisoning, impetigo, toxic shock syndrome. In general, these bacteria don't cause disease. Physically the infection can be seen as collection of pus, tender, painful reddened and swollen skin area. The most notorious of this group is known as MRSA (Met.."


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Dig out to Fight out Staphylococcus: The Genomic Route
Author: Vipin Chandra Kalia

Introduction

Staphylococcus can cause quite a few diseases such as cellulitis, boils, food poisoning, impetigo, toxic shock syndrome. These can be either due to direct infections or through production of toxins. In general, these bacteria don’t cause disease. Physically the infection can be seen as collection of pus, tender, painful reddened and swollen skin area. In damaged skin or injuries, bacteria are able to overcome the natural mechanism of the human body, which leads to infection. The most notorious of this group is known as MRSA (Methicillin-resistant Staphylococcus aureus). Treatments depend upon the type of infections, which varies from topical, oral, or intravenous antibiotics.

Among the various kinds of scenarios being encountered, the following are more susceptible to infections are: newborn infants, breastfeeding women, and patients who have lung diseases and chronic diseases - diabetes, cancer, vascular disease. Others with a weak immune system also are at a risk of developing staphylococcus infections. The contagious nature is a common mechanism of transmission, such as through use of razors, bandages, etc., or through direct contact with a wound. Interestingly, casual contacts through kissing or hugging are not worrisome until there is a direct contact with the infected area.

Diagnosis and identification of Staphylococcal infections
Skin infections are diagnosed by their physical appearance. In case of infection having reached the bloodstream, pneumonia, and endocarditis, bacterial culturing is done. Identification of Staphylococcus through enzyme assays are based on alkaline phosphatase, urease, coagulase and amono acid decarboxylases. Other assays include utilization of sugars like glucose and mannitol, etc.

Genomic makers for Staphylococcus species

Molecular techniques involve amplification of genes such as 16S rRNA (rrs), gyrA, ileS, spa, femA, coa, etc. The most widely used gene is atlE which encodes autolysin. The MRSA detection kit targets the combination of the following genes: lukPVL mecA, femA and rrs. In general, rrs gene is used for identifying bacteria up to species level. However, the presence of 5-6 copies ofrrs per genome in almost all the strains of Staphylococcus, and further high similarity among them, complicates the identification process. To circumvent this problem, most researchers resort to use of 6-8 housekeeping genes. However, so far there has been no consensus on the additional genes, which must be present in all the strains. A novel approach has been devised, where genes which are common to all the Staphylococcus strains. This step was clubbed with the Restriction Endonuclease enzymes: Tru9I, RsaI, HpyCH4V, BfaI, TaqI, and BfuCI, which could provide unique digestion pattern, among recA, gyrB, pyrE, argR, argH, cysS, and purH.

Treatment of Staphylococcal infections

For treating skin infections, ointments based on antibiotics are applied. In contrast, life-threatening infections are treated using oral or intravenous antibiotics. The antibiotics used for such treatments are cefazolin, nafcillin (Nallpen), clindamycin (Cleocin), cefuroxime, rifampin, cephalexin, oxacillin (Bactocill), dicloxacillin, telavancin (Vibativ), vancomycin, etc. alone or in various combinations. MRSA strains are highly resistant to many antibiotics.

This novel genomic approach allows correct identification and diagnosis, which are a must for proper treatment.

References:

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. 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

14. 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/annurevmicro-020415-111342

15. 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.

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