Challenges associated with the use of phages as a therapeutic and disinfection tool – ResisPhages

Bacteriophages are currently used in different countries to disinfect instruments, rooms, and food products. They are applied to treat acute and chronic infections in humans, animals and plants, and sometimes for prophylaxis in patients. Bacteriophages are also studied to face highly pathogenic bacteria that could represent a bioterrorism threat.

In France, phage therapy is not presently allowed but some compassionate assays have been performed. Others are ongoing, notably to treat infection by multidrug resistant (MDR) Pseudomonas aeruginosa, although it could be also interesting to use phages early during the evolution of an infection, similarly to what is done in Georgia, Poland and Russia, i.e. before failure of classical treatment is recognized. At least two potential applications could lead to a renewed usage of phage therapy: non-chemical decontamination of instruments or rooms, and fight against MDR germs. An elevated frequency of MDR strains belonging to international clones is observed in the case of P. aeruginosa and Acinetobacter baumannii, two species frequently isolated in burn patients, or during post-surgery infections, particularly in soldiers with war wounds. Members of these clones often carry plasmids or transposons bearing antibiotic resistance genes. In addition some clones show a high capacity to form biofilms.
In this context, it is essential to possess a collection of phages active against a large spectrum of strains, and, for maximal security, to anticipate the risk caused by phages and bacteria co-evolution after infection, in order to eliminate all danger for humans, and to limit the emergence of resistant bacteria. Progress of genome analysis techniques (next generation sequencing and bioinformatics) allows to examine this old approach with a new perspective.

The project intends to constitute, for three bacterial species of interest in military medicine, a collection of strains resisting classical therapy, then to be able to elaborate phage cocktails with a strong efficiency against these strains. The use of cocktails rather than unique phages should lower the risk of emergence of resistant strains. The phage genomes will be sequenced and annotated, and their interactions with bacterial strains will be studied to answer 4 key questions addressing security issues:

(i) is there a risk that the selected phages insert their DNA into the host genome, introducing new toxic genes and contributing to the emergence of more dangerous bacteria?

(ii) during the lytic cycle, is there a risk that phages evolve through gene exchanges, between them or with the bacterial host?

(iii) how frequent will be the emergence of bacteria resistant to different phages and will their resistance to antibiotics be affected? Similarly, will the bacteria accumulating antibiotic resistance see their phage susceptibility changing? Are there bacteria naturally resisting to all phages?

(iv) What is the risk of transferring antibiotic resistance from one strain to another through phage transduction? The problem of DNA transfer by phages is considered unimportant as long as virulent phages are used. This is not proven and it is known that generalized transduction is possible at a low but not insignificant frequency when selection by antibiotics is used.