Complete Genome Analysis of Lytic Phages and Identification of Hypothetical Phage Proteins Targeting Major Protein Complexes of Staphylococcus Aureus

Abstract

Background: Bacteriophages (phages) are obligate parasites of bacteria. Phages are grouped according to their life cycle as lytic, temperate (lysogenic), pseudo-lysogenic and chronic phages. Lytic phages have been applied efficiently (phage therapy) against human infections caused by pathogens such as Staphylococcus aureus or Escherichia coli. In addition, the viruses destroy antibiotic-resistant bacteria. Genome analysis of phages is significant since it helps in selection of safe phages from harmful ones. The analysis further facilitates the identification of phage genes with unknown functions from ones whose purpose are yet to be unravelled. These strange genes are also known as hypothetical genes and they encode hypothetical proteins. Some of these hypothetical genes have homologs in the GenBank. However, others are non-identical with the GenBank deposited genes and consequently referred as novel genes. Objective: To explore novel lytic phages and compare them with the current known phages. Thereafter, establish functions of their hypothetical proteins against multi-drug resistant S. aureus complex target proteins such as wall teichoic acid (WTA), lipoteichoic acid (LTA) and multidrug resistant efflux pumps associated with quinolones and linezolids. Methods: Highly potent Staphylococcus lytic phages were isolated using S. xylosus sausage fermentor isolate. Thereafter, characterized through morphological, genomical and proteomic means. The phages’ host range were determined by spot and double layer agar assays against numerous clinical samples of S. aureus that are MSSA or MDRSA (including MRSA). Results: Four lytic phages; Stab20, Stab21, Stab22 and Stab23, were identified as Kayviruses. In addition, genomic analysis showed that these viruses are possessed numerous hypothetical proteins. Genome work further indicated inability of the Stabs to shuttle lethal genes like antibiotic resistance encoding genes and chromosomal point mutations associated with drug resistance or virulence. Proteomic outcome displayed the close similarity of the phages. Genomic and proteomic analysis showed that the Stabs are closely related with other phages such as Sb-1 and ISP which are useful therapeutic agents. Stab20 and Stab21 phages had broad host range with high relative EOP. However, two other isolates were active against a few isolates. Conclusion: Efficacy of these phages against human and livestock Staphylococcus bacteria isolates depicts their capability as good candidates for therapeutic and bio-control phage cocktails.