Comparison of simple sequence repeats in Staphylococcus strains using in-silico approach.

Sunil Thorat,Prashant Thakare

doi:10.6026/97320630081182

Abstract

Staphylococci are Gram-positive bacteria which play an important role in infectious disease and are major causes of communityacquired and hospital-acquired infections. Strains of Staphylococcus aureus are reported as genomically and phenotypically highly heterogeneous; hence in-silico based comparison of genomic data on simple sequence repeats may provide valuable information for understanding the pathogenicity and control measures. This study determined the distribution of a specific group of Simple Sequence Repeats (SSRs), in genome sequences of six Staphylococcus strains (Staphylococcus aureus COL, S.aureus MRSA252, S.aureus MSSA476, S.aureus Mu50, S.aureus MW2, S.aureus N315) and plasmid sequences of four Staphylococcus strains (Staphylococcus aureus COL pT181, Staphylococcus aureus MSSA pSAS, Staphylococcus aureus VRSAp, Staphylococcus aureus, Staphylococcus aureus pN315 DNA) downloaded from the GenBank database for identifying abundance, distribution and composition of SSRs. The data obtained in the present study shows that (i) a large number of tandem repeats are distributed throughout the genome and plasmid sequences. (ii) Number of mononucleotide SSRs decreased rapidly with increase in size of repeat unit. (iii) Total frequency of SSRs in plasmid regions is less than genomic regions. (iv) In all investigated strains, ratios of AT/TA repeats are dominating over GC/CG repeats in genomics as well as plasmid sequences, and (v) Dinucleotide combination of AT is dominated in all the six Staphylococcus genome sequences.

Highlights

Staphylococci are Gram-positive bacteria which play an important role in infectious disease and are major causes of communityacquired and hospital-acquired infections
Being a commensal organism living asymptomatically Mu50, MW2 and N315 were studied along with four in the nasal cavities of a large number of the human population, Staphylococcus aureus plasmids; COL pT181, MSSA pSAS, S.aureus is responsible for a raft of different infections that VRSAp, pN315 DNA which were downloaded from the range in both anatomical site and severity
Tools for analysis of SSRs A tool for Simple Sequence Repeats was developed to find out the short tandem repeats from the input sequences, the SSR tool is hosted on a local webserver i.e. wampserver which has a combination of Apache, MySQL and PHP to run the scripts for analysis

Summary

Introduction

Staphylococci are Gram-positive bacteria which play an important role in infectious disease and are major causes of communityacquired and hospital-acquired infections. Being a commensal organism living asymptomatically Mu50, MW2 and N315 were studied along with four in the nasal cavities of a large number of the human population, Staphylococcus aureus plasmids; COL pT181, MSSA pSAS, S.aureus is responsible for a raft of different infections that VRSAp, pN315 DNA which were downloaded from the range in both anatomical site and severity. Open access genomes has allowed us to identify novel multiple tandem repeats that are similar to MIRUs in M.tuberculosis, and the present study describes the nature and distribution of these repeats, and their potential as a novel tool for understanding the micro-evolution of hospital MRSA.

Results

Conclusion