They give the impression that they will become the new stars of infectious diseases. But they are already old stars: bacteriophages. A century after their discovery, their properties are being valued again in light of global antibiotic resistance in bacterial pathogens. This is partly because, thanks to modern technologies, it has become possible to raise the antibacterial qualities of bacteriophages to a level that could be described as “supernatural”.
ESKAPE is the acronym for a group of highly virulent bacteria that the World Health Organization has classified as a priority for the development of new antimicrobial drugs because they often evade antibiotics: Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp. Some of these are among the most common pathogens of urinary tract infections: Klebsiella, Enterococcus spp. and Escherichia coli. And because urinary tract infections (UTIs), with an estimated 400 million cases worldwide each year, are one of the most common reasons for starting antibiotic therapy and are therefore a major driver of resistance, many research groups around the world are now concentrating on their natural and ubiquitous enemies, namely bacteriophages.
High specificity
Bacteriophages are viruses that specialize in bacteria. Used as a therapeutic tool, they offer several advantages over antibiotics: low environmental impact, the microbiota is preserved, isolation is simple and inexpensive, there is no cross-resistance, and the therapeutic application is well tolerated according to current knowledge. Above all, phages also infect those bacteria that are already resistant to antibiotics. In some cases, it has also been observed that they increase the sensitivity of bacteria to antibiotics. However, the pronounced specificity of phages is also a problem: phages bind to specific receptors on the surface of their bacterial victims, but the host range is sometimes very narrow. Then, for example, different strains of the same bacterial species cannot be infected. And: phages have “no interest” in completely eliminating their host, as Dr. Samuel Kilcher, a researcher at ETH Zurich, put it. It is also assumed that bacteria can also become resistant to highly specialized phages.
Although phages have been used continuously in the former Soviet Union to treat gastrointestinal infections or gas gangrene, for example, and although there is also a long history of phage research in Poland, phage therapy is still considered to be empirical medicine, at least in western industrialized countries. Randomized controlled clinical trials are rare. However, research into bacteriophages has gained significant momentum in the past decade, as can be seen from the quadrupling of annual publications on the subject.
For example, a working group from Portugal has focused on a phage that is able to infect a carbapenemase-producing Klebsiella pneumoniae strain. In in vitro tests, the phage KP1LMA was able to inactivate the Klebsiella in human urine. KP1LMA is safe to use because the virus has purely lytic properties and does not contain any virulent genes or genes for antibiotic resistance.
“However, its narrow host range suggests that this phage is not capable of infecting another strain,” report João Duarte and Carolina Máximo from the University of Aveiro, Portugal, and colleagues (Antibiotics 2024; 13:195). The phage is therefore particularly suitable for experimental procedures that can be used to create new phages with a broad host spectrum. Phage cocktails could help solve the problem of bacterial phage resistance, say the scientists. To do this, phages with different infection mechanisms would have to be used.
Positive study review
In a review of 55 scientific articles on the study of bacteriophages in animals and humans, biological and clinical improvements in UTI were found in 78 percent of the studies: The bacterial load decreased, clinical symptoms improved, and the frequency of annual UTI recurrences decreased, report Amany Al-Anany of McMaster University in Hamilton, Canada, and her colleagues (Phage (New Rochelle) 2023; 4(3):112–127). It should be noted that phages were often applied in combination with other therapies such as antibiotics.
The phages are introduced in very different ways: via instillation, bladder injection, bladder flushing or lavage. The dosing frequency and duration of therapy also varied greatly in the studies. Individual phages as well as multi-phage cocktails were used. There are currently no standardized treatment protocols. “In most cases, microbiological healing was observed around two weeks after the start of therapy,” said Al-Anany and co-authors. However, effectiveness was not found in all randomized controlled studies.
Another result of the literature review is that the drug appears to be well tolerated. Adverse effects are apparently rare and were probably often due to the accompanying therapies. Strangely, however, in almost 60 percent of the studies evaluated, there was no information at all on whether or not side effects had occurred. Standardized treatment, monitoring and reporting protocols are therefore desirable. This information should ideally be included in a phage register, according to the Canadian scientists.
Glowing phages
If wild-type bacteriophages are so highly specialized, it is important to know exactly which bacterial pathogens caused the urinary tract infection. Researchers at ETH Zurich have developed a rapid diagnostic test for E. coli, Enterococcus spp. and Klebsiella spp., the pathogens most commonly found in UTIs. To do this, two virulent phages were modified in such a way that bioluminescence is induced in the presence of bacteriuria (Nature Communications 2023; 14:4336This would allow targeted antibiotic treatment – within a few hours, whereas conventional microbiological diagnostics take days.
Another advantage of the test is that it is easy to determine which patients would particularly benefit from a tailored phage therapy: the stronger the light signal, the more likely it is. The working group has therefore genetically modified phages so that they can destroy the pathogenic bacteria even more efficiently than before. They have incorporated the genetic information for synthetic antimicrobial peptides and specific cell wall hydrolases into the phages. The bacterial victim must produce these killer molecules itself before it dies. This is also important because the bacteria can develop defense mechanisms against phages, such as the production of extracellular matrix or a reduced expression of phage receptors.
The genetically optimized phages are called heterologous effector phage therapeutics (HEPTs). According to the Swiss researchers, HEPTs or HEPT cocktails should enable the cross-genus fight against bacterial pathogens – the genomic plasticity of the phages makes this possible. In addition to antimicrobial enhancement, HEPTs could also be provided with immunomodulators or biofilm-dissolving enzymes. This personalized treatment approach can be achieved with a minimal number of phage components, which reduces the effort, costs and complexity of the treatment, they say. And of course not only for UTIs, but also for other infectious diseases.
AI support for phage therapy
Artificial intelligence (AI) may also be able to help with future phage selection for antimicrobial therapy: Marianne Keith from The Roslin Institute at the University of Edinburgh and colleagues have developed a genomics-based approach to predict the ideal phage cocktail using machine learning, initially for E. coli infections. The AI was trained using thousands of interactions between a group of phages and sequenced bacterial isolates and the activity of 31 phages was measured on 314 bacterial isolates in artificial urine (PNAS2024;121: e2313574121).
The potential of naturally occurring and genetically optimized phages is currently being investigated in many clinical trials worldwide. Although decades of experience with bacteriophage-based therapies already exist in some regions of Europe, scientists estimate that there is still some way to go before routine use in western industrialized countries.
An important step towards more evidence will be the standardization of phage production and the creation of legal and logistical conditions. To this end, the German Society for Infectious Diseases the S2k guideline “Personalized bacteriophage therapy in Germany” The recommendations of national and international experts are expected to be completed by summer 2024.