Phage Therapy (Biocontrol*): Light and Shade Visit new site : Sellanophagetherapy.blogspot.com: D29, L5, Bxz2 and TM4 mycobacteriophages

"In silico"

From Wikipedia
If the target host* of a phage therapy treatment is not an animal the term "biocontrol" (as in phage-mediated biocontrol of bacteria) is usually employed, rather than "phage therapy".

In silico
From:"Genomics,Proteomics and Clinical Bacteriology",N.Woodford and Alan P.Johnson

Phrase that emphasizes the fact that many molecular biologists spend increasing amounts of their time in front of a computer screen, generating hypotheses that can subsequently be tested and (hopefully) confirmed in the laboratory.

Wednesday 30 September 2009

D29, L5, Bxz2 and TM4 mycobacteriophages

I have investigated the genomes of these phages searching for a relationship of cause and effect (D29,Bxz2,L5 and TM4 phages grow on M.ulcerans and M.smegmatis).
Each time two genomes are compared by BugView software ( Smith Waterman algorithm ).The results obtained are(cds from files .gbk):

D29 on L5:31,39,85/on BXZ2:3,4,38/on TM4:24,27,39

L5 on D29:34,39,82 /on BXZ2:3,4,38/on TM4:24,27,39

BXZ2 on D29:34,39,51/on L5:31,39,85/on TM4:24,27,39

TM4 on D29:34,39,80/on L5:31,39,85/on BXZ2:4,2,38

I have selected ( Sockeye software):

cds 4 from Bxz2 genome

cds 24 from TM4 genome

cds 31 from L5 genome

cds 34 from D29 genome

E	Enterococcus faecium	Third most common cause of HCA BSI. Increasing resistance to vancomycin.
S	Staphylococcus aureus (MRSA)	Emerging resistance to current drugs and significant drug toxicities. Lack of oral agents for step-down therapy
K	Klebsiella Escherichia coli K pneumoniae	ESBL-producing organisms increasing in frequency and severity; associated with increasing mortality. K pneumoniae carbapenemases causing severe infections in LTCF. Few active agents; nothing in development
A	Acinetobacter baumannii	Increasing worldwide, recent surge reported in hospitals. Very high mortality. Carbapenem-resistant.
P	Pseudomonas aeruginosa	Increasing P. aeruginosa infections in US and worldwide. Resistant to carbapenems, quinolones, aminoglycosides
E	Enterobacter species	MDR HCA infections increasing; resistance via ESBLs, carbapenemases, and cephalosporinases

E	Enterococcus faecium
S	Staphylococcus aureus (MRSA)	+
K	Klebsiella Escherichia coli K pneumoniae
A	Acinetobacter baumannii	+
P	Pseudomonas aeruginosa	++
E	Enterobacter species

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"In silico"

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Wednesday 30 September 2009

D29, L5, Bxz2 and TM4 mycobacteriophages