Guided by nature learning from bacteriophages to uncover new biology

The study of bacteriophages, the viruses infecting bacteria, has greatly transformed fundamental and translational biosciences. For example, the study of bacteriophages was crucial in establishing the central dogma of molecular biology and the nature of the genetic code. However, our understanding of fundamental mechanisms that govern phage-host interactions is mostly limited to the study of few traditional models and was outpaced by the massive expansion of the field in recent years. It is therefore likely that the true potential of the molecular biology of phages is still largely untapped. Beyond their use as model systems, phages also hold exciting potential for the treatment of antibiotic-resistant infections and other applications due to their astonishing diversity and recent breakthroughs in their genetic engineering. Despite the early recognition of their therapeutic potential and the growing threat of bacterial multidrug resistance, phages have so far failed to become an established treatment option in clinical practice. Among other factors, this failure has been linked to occasional discrepancies between the potency of phages in vitro and in vivo. In our research group we have therefore set out to investigate the nature of phage-host interactions under conditions that are more representative to those that they face in the nature.
We sought to promote a more systematic investigation of phage-host interactions by composing a library of 68 newly isolated phages infecting Escherichia coli that we shared with the community as the BASEL (BActeriophage Selection for your Laboratory) collection (Section 4.1). We determined host receptors of all phages, characterized their sensitivity to various classes of immunity systems, and determined their host-range across a representative selection of strains. We highlighted systematic patterns in the distribution of phage phenotypes in relationship to their genomic features and suggested the molecular basis of receptor specificity in several phage groups. Furthermore, we also uncovered strong trade-offs between fitness traits like host recognition and sensitivity to immunity systems that might be representative of the ecological niches occupied by different phage groups.
In the environment, bacteria are thought to be mostly in a slowly- or non-growing state. In a clinical context, bacterial dormancy has been linked to persistence inside patients and the failure to effectively eradicate chronic, relapsing infections. Given the environmental abundance of non-growing bacteria, we wondered whether some phages exist that can directly infect and kill dormant bacteria. After establishing rigorous conditions to study bacterial dormancy (Section 4.2), we have indeed found, that most bacteriophages fail to replicate on dormant hosts and instead enter a state of hibernation. (Sections 4.3 and 5.1). However, we have isolated two novel phages of Pseudomonas aeruginosa named Paride and Ercole that show remarkable potency in killing dormant, antibiotic-tolerant hosts by direct lytic replication. Intriguingly, both phages depend on the host stress response that drives antibiotic-tolerance for efficient replication on dormant hosts.
In our studies we have uncovered several new aspects of the molecular biology governing phage-host interactions. Through the construction of the BASEL collection, we want to inspire future work that will explore the fundamental biology of phages and their hosts, including bacterial immunity, phage therapy and biotechnology (Section 6.1). Similarly, our studies of bacterial dormancy, have provided the basis to how phages overcome and exploit the dormant physiology of bacteria (Section 6.2). Through the continued study of the infection of dormant bacteria, we anticipate that novel Achille’s heels of the dormant, antibiotic-tolerant physiology of bacteria will be uncovered that might provide the basis for the development of new treatments targeting resilient bacterial infections (Section 6.3).