Genomic analysis and in vitro/in vivo characterization of phage resistant E. coli K1 isolates

E. coli K1 is involved in several types of human infections, including meningitis, urinary tract infections and bloodstream infections. The understanding of the bacterial resistance mechanisms to phages has implications for the development of phage-based therapies. The objective of this study was to investigate the resistance of E. coli K1 isolates to ULINTec4, a K1-dependent bacteriophage. Resistant bacterial colonies were isolated from an avian pathogenic E. coli strain APEC 45 and the human strain C5, both previously exposed to ULINTec4. After confirming their resistance, genomic analysis was carried out and several parameters were evaluated, such as growth capacity, phage adsorption, phenotypic impact at capsular level and virulence in the in vivo Galleria mellonella model. One of the resistant isolates exhibited a significantly slower growth rate suggesting the presence of a resistance mechanism altering its fitness. Comparative genomic analysis revealed insertion sequences at various capsular gene sites. Adsorption of the ULINTec4 phage was reduced on all resistant isolates. In addition, antigenic tests targeting the K1 capsule showed a very low positive reaction compared to the control. Nevertheless, microscopic images revealed the presence of capsules and a clustered organization of resistant strains. In the Galleria model, larvae infected with phage-resistant strains showed better survival rates than larvae infected with phage-sensitive strains. In conclusion, a phage resistance mechanism was detected at the genomic level, have an impact on capsular expression and was able to decrease the virulence of E. coli K1 in-vivo.
The project was financially supported by Wallonia in the framework of the call for projects organised by BioWin competitiveness cluster (Project Inteliphages)