Spontaneous Phage Resistance in Avian Pathogenic Escherichia coli

Abstract

Avian pathogenic Escherichia coli (APEC) is one of the most important bacterial pathogens affecting poultry worldwide. The emergence of multidrug-resistant pathogens has renewed the interest in the therapeutic use of bacteriophages (phages). However, a major concern for the successful implementation of phage therapy is the emergence of phage-resistant mutants. The understanding of the phage-host interactions, as well as underlying mechanisms of resistance, have shown to be essential for the development of a successful phage therapy. Here, we demonstrate that the strictly lytic Escherichia phage vB_EcoM-P10 rapidly selected for resistance in the APEC ST95 O1 strain AM621. Whole-genome sequence analysis of 109 spontaneous phage-resistant mutant strains revealed 41 mutants with single-nucleotide polymorphisms (SNPs) in their core genome. In 32 of these, a single SNP was detected while two SNPs were identified in a total of nine strains. In total, 34 unique SNPs were detected. In 42 strains, including 18 strains with SNP(s), gene losses spanning 17 different genes were detected. Affected by genetic changes were genes known to be involved in phage resistance (outer membrane protein A, lipopolysaccharide-, O- antigen-, or cell wall-related genes) as well as genes not previously linked to phage resistance, including two hypothetical genes. In several strains, we did not detect any genetic changes. Infecting phages were not able to overcome the phage resistance in host strains. However, interestingly the initial infection was shown to have a great fitness cost for several mutant strains, with up to ∼65% decrease in overall growth. In conclusion, this study provides valuable insights into the phage-host interaction and phage resistance in APEC. Although acquired resistance to phages is frequently observed in pathogenic E. coli, it may be associated with loss of fitness, which could be exploited in phage therapy.

Phage Resistance Evolution Induces the Sensitivity of Specific Antibiotics in Pseudomonas aeruginosa PAO1

“…Specific amino acid substitutions in T4P synthesis-related genes or specific modifications on T4P would significantly decrease the susceptibility of strains to phage infection ( 29 ). This is consistent with a previous report that the majority of detected phage-resistant mutant strains were shown to resist phage infection via blocking phage adsorption ( 30 ). Our data also suggest the reduction of the T4P-mediated adsorption rate is the major strategy for the resistant mutant PAO1-R1 to defend against phage vB_Pae_QDWS and vB_Pae_W3 ( Fig.…”

In ovo administration of a phage cocktail partially prevents colibacillosis in chicks

“…As the K1 capsule and O2 antigen, which are known to be major virulence factors of APEC ( Guabiraba and Schouler, 2015 ), were both detected in REC-resistant clones, others virulence factors are probably affected, as well as the modification of one or more nonvirulence genes being associated with fitness trade-off. Indeed, it was previously shown that an APEC O1 strain resistant to the T4-like phage P10 suffered a significant fitness cost following mutations in genes related to bacterial growth (acetate kinase) or in the beta-oxidation cycle of fatty acid degradation ( Sørensen et al, 2021 ). Clearly, further studies of REC and BEN4358 phage-bacteria interactions would be required to identify the phage target and to improve our understanding of the dynamics during phage therapy.…”