Variable fitness effects of bacteriophage resistance mutations in Escherichia coli: implications for phage therapy

• Published in: Journal of virology 2024-10, Vol.98 (10), p.e0111324
• Main Authors: Gaborieau, Baptiste, Delattre, Raphaëlle, Adiba, Sandrine, Clermont, Olivier, Denamur, Erick, Ricard, Jean-Damien, Debarbieux, Laurent
• Format: Article
• Language: English
• Subjects: Animals; Bacterial Capsules - genetics; Bacterial Capsules - metabolism; Bacteriology; Bacteriophages; Bacteriophages - genetics; Bacteriophages - physiology; Cellular Response to Infection; Coliphages - genetics; Coliphages - physiology; Escherichia coli - genetics; Escherichia coli - virology; Escherichia coli Infections - microbiology; Escherichia coli Infections - therapy; Female; Genetic Fitness; Life Sciences; Lipopolysaccharides - metabolism; Mice; Microbiology and Parasitology; Mutation; Phage Therapy; Virulence
• ISSN: 0022-538X; 1098-5514; 1098-5514
• DOI: 10.1128/jvi.01113-24

Bacteria exposed to bactericidal treatment, such as antibiotics or bacteriophages (phages), often develop resistance. While phage therapy is proposed as a solution to the antibiotic resistance crisis, the bacterial resistance emerging during phage therapy remains poorly characterized. In this study, we examined a large population of phage-resistant extra-intestinal pathogenic 536 clones that emerged from both (non-limited liquid medium) and (murine pneumonia) conditions. Genome sequencing uncovered a convergent mutational pattern in phage resistance mechanisms under both conditions, particularly targeting two cell-wall components, the K15 capsule and the lipopolysaccharide (LPS). This suggests that their identification could be predicted from assays. Phage-resistant clones exhibited a wide range of fitness according to tests, growth rate, and resistance to amoeba grazing, which could not distinguish between the K15 capsule and LPS mutants. In contrast, K15 capsule mutants retained virulence comparable to the wild-type strain, whereas LPS mutants showed significant attenuation in the murine pneumonia model. Additionally, we observed that resistance to the therapeutic phage through a nonspecific mechanism, such as capsule overproduction, did not systematically lead to co-resistance to other phages that were initially capable or incapable of infecting the wild-type strain. Our findings highlight the importance of incorporating a diverse range of phages in the design of therapeutic cocktails to target potential future phage-resistant clones effectively. This study isolated more than 50 phage-resistant mutants from both and conditions, exposing an extra-intestinal pathogenic strain to a single virulent phage. The characterization of these clones revealed several key findings: (1) mutations occurring during phage treatment affect the same pathways as those identified ; (2) the resistance mechanisms are associated with the modification of two cell-wall components, with one involving receptor deletion (phage-specific mechanism) and the other, less frequent, involving receptor masking (phage-nonspecific mechanism); (3) an virulence assay demonstrated that the absence of the receptor abolishes virulence while masking the receptor preserves it; and (4) clones with a resistance mechanism nonspecific to a particular phage can remain susceptible to other phages. This supports the idea of incorporating diverse phages into therapeutic cocktails designed to collectively ta