Synonymous codon usage in forty staphylococcal phages identifies the factors controlling codon usage variation and the phages suitable for phage therapy

The immergence and dissemination of multidrug-resistant strains of Staphylococcus aureus in recent years have expedited theresearch on the discovery of novel anti-staphylococcal agents promptly. Bacteriophages have long been showing tremendouspotentialities in curing the infections caused by various pathogenic bacteria including S. aureus. Thus far, only a few virulentbacteriophages, which do not carry any toxin-encoding gene but are capable of eradicating staphylococcal infections, werereported. Based on the codon usage analysis of sixteen S. aureus phages, previously three phages were suggested to be useful as theanti-staphylococcal agents. To search for additional S. aureus phages suitable for phage therapy, relative synonymous codon usagebias has been investigated in the protein-coding genes of forty new staphylococcal phages. All phages appeared to carry A and Tending codons. Several factors such as mutational pressure, translational selection and gene length seemed to be responsible for thecodon usage variation in the phages. Codon usage indeed varied phage to phage. Of the phages, phages G1, Twort, 66 and Sap-2may be extremely lytic in nature as majority of their genes possess high translational efficiency, indicating that these phages may beemployed in curing staphylococcal infections.