The aim of this project is to set up a phage therapy laboratory in Finland. We are collecting and analysing phages that infect ESKAPEE bacterial species: Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter sp, Pseudomonas aeruginosa, Escherichia coli and Enterobacter cloacae. Our goal is to obtain phages that infect 50 – 70% of clinical ESKAPEE strains. Our current ESKAPEE phage collection contains 72 phages, out of which 5 infect E. faecium, 2 S. aureus, 17 K. pneumoniae, 2 Acinetobacter, 9 P. aeruginosa, 23 E. coli, and 14 E. cloacae. The phages have mostly been isolated from Finnish waste water samples. The EM analysis of phage morphology shows that 23.9% of phages belong to Myoviridae, 41.8% to Podoviridae and 34.3% to Siphoviridae.
The strain infection coverage has been tested with 149 clinical E. coli strains and 50 strains for other ESKAPEE species. The infection coverage was found to vary from 100% of S. aureus to 16% of Acinetobacter. We have sequenced most phage genomes by NGS, and the genome sizes vary from ~18 kb to ~180 kb. Based on the sequence data, ~65% of the phages seem lytic, but this varies significantly between phages infecting different host species.
We are also developing methods for rapid host specificity screening and phage purification. For host specificity screening, we have set up a method in which we dry phages onto 96-well plates, add bacterial suspension at low C.F.U./ml, and follow bacterial growth by monitoring A600. This method gave a similar host specificity profile as the traditional spot test, and the dried phages were stable for at least 8 weeks. For the phage purification, ion exchange chromatography gave 100% recovery of the model phage fHo-Eco02, and efficiently eliminated bacterial DNA and 95% of endotoxin from the phage preparation.