Complete genome sequence analysis of Rhodococcus equi Phage E3 and Insight into R. equi Phage Diversity.

Salifu, Samson Pandam

Abstract

Rhodococcus equi (R. equi) is a Gram positive, facultative and weakly acid-fast bacterium, which causes respiratory disease in foals worldwide resulting in pneumonia, often with fatal consequences. Human infections of R. equi that are resistant to antibiotics are increasingly reported. A novel approach of treating R. equi infections is needed. While phage/phage-derived proteins have been demonstrated for effective treatment and diagnoses of major pathogenic bacteria such as Staphylococcus aureus and Mycobacterium tuberculosis, little is known about the diversity and genomics of phages infecting R. equi.
The objectives of this study were to isolate and characterise the diversity of phages infecting R. equi, to sequence a single R. equi phage genome and, based on detailed bioinformatic analysis, to identify and characterise the in vitro activity of selected R. equi phage proteins with potential lytic activity.
The diversity of 26 lytic R. equi phages isolated from Scottish soil was assessed, resulting in a designation of 16 distinct groups by genome restriction profiles and with host range analysis. All belong to the Siphoviridae, with the exception of phage E3, the first Myoviridae known to infect Rhodococcus and capable of lysing 8 R. equi strains tested. Analysis of the genome termini of representatives of the 12 phage groups revealed the presence of cohesive ends in phages V6, V15, GV10, GV11, GV12 and GV22, while 6 phage genome terminal cohesive ends could not be established.
The genome sequence of E3 was determined, revealing a dsDNA genome of 142,563 bp, encoding 221 ORFs. The E3 genome is globally similar to that of the Myoviridae of mycobacteriophages. Interestingly, a holin, 2 putative endolysins (lysA) and 3 putative lipolytic (lysB) genes were identified in the E3 genome. One putative lysA and lysB, encoding gp98 and gp84 respectively, were cloned and the in vitro activity investigated, revealing lytic activity against R. equi for gp98 while the activity of gp84 could not be established.
The findings presented in this thesis represent a significant advance in R. equi and mycolata phage biology and provide interesting insight to the evolutionary context of mycolata-infecting Myoviridae, supporting the argument for taxonomy classification based on comparative genomics.

Citation

Salifu, S. P. Complete genome sequence analysis of Rhodococcus equi Phage E3 and Insight into R. equi Phage Diversity. (Thesis). Edinburgh Napier University. Retrieved from http://researchrepository.napier.ac.uk/id/eprint/4841

• Thesis Type: Thesis
• Deposit Date: Dec 21, 2011
• Peer Reviewed: Not Peer Reviewed
• Keywords: Rhodococcus equi; pneumonia; pathogenic bacteria; phage; genomics; bioinformatic analysis
• Public URL: http://researchrepository.napier.ac.uk/id/eprint/4841
• Award Date: Dec 19, 2011