Variable effects on virulence of bacteriophage resistance mechanisms in extraintestinal pathogenic Escherichia coli

AO_SCPLOWBSTRACTC_SCPLOWBacteria exposed to killing agents such as antibiotics or viruses develop resistance. While phage therapy, the use of bacteriophages (phages) for treating bacterial infections, is proposed to answer the antibiotic resistance crisis, bacterial resistance to phages remains poorly characterized during phage treatment. We studied a large population of phage-resistant extra-intestinal pathogenic Escherichia coli 536 clones emerging from both in vitro (non-limited liquid medium) and in vivo (murine pneumonia) conditions. Genome sequencing revealed a mutational convergence of phage resistance mechanisms towards the modification of two cell-wall components, the K15 capsule and the LPS, whatever the condition, showing that their identification could be predicted from the in vitro conditions. The fitness cost of all phage resistant clones was broad in terms of growth rate and resistance to grazing by amoeba and could not discriminate K15 capsule to LPS mutants. By contrast, the virulence of the clones tested in mice showed that K15 capsule mutants were as virulent as the wildtype strain while LPS mutants were strongly attenuated. We also found that resistance to one phage led to the sensitization to other phages. In clinics, to control phage-resistant clones that remains virulent phage cocktail should include phages infecting both phage susceptible and future phage resistant clones. ImportanceEscherichia coli is a leading cause of life-threatening infections, including pneumonia acquired during ventilatory assistance for patients hospitalized in Intensive Care Unit, and a major multidrug resistant pathogen. A century-old concept, phage therapy (i.e. using specific anti-bacterial viruses), is being clinically re-evaluated supported with hundreds of successful compassionate phage treatments. However, along billions of years of coevolution bacteria have developed many ways to resist to phages. Phage resistance occurring during phage therapy remains often overlooked despite its critical role for a successful outcome. During this work we characterized phage resistant mutants in a virulent extra-intestinal pathogenic E coli strain and found that (1) phage resistance taking place during a phage treatment in vivo could be predicted from an in vitro assay; (2) phage resistance has, often but not always, a major fitness cost in terms of virulence; and (3) could be countered by appropriate cocktails of phages.