Genome-driven elucidation of phage-host interplay and impact of phage resistance evolution on bacterial fitness

• Published in: The ISME Journal 2022-02, Vol.16 (2), p.533-542
• Main Authors: Markwitz, Pawel, Lood, Cédric, Olszak, Tomasz, van Noort, Vera, Lavigne, Rob, Drulis-Kawa, Zuzanna
• Format: Article
• Language: English
• Subjects: 45; 45/23; 45/43; 45/47; 631/158/670; 631/326/1321; Anti-Bacterial Agents; Antibiotic resistance; Antibiotics; Bacteria; Bacteriophages - genetics; Biofilms; Biological Evolution; Biology; Biomedical and Life Sciences; Cloning; Cross-resistance; Defense; Ecology; Evolutionary Biology; Fitness; Genes; Genome; Genomes; Growth rate; Laboratories; Life Sciences; Microbial Ecology; Microbial Genetics and Genomics; Microbiology; Mutation; Nosocomial infections; Pathogens; Phages; Phenotype; Population; Prophages; Prophages - genetics; Pseudomonas aeruginosa; Pseudomonas aeruginosa - genetics; Reproductive fitness; Strains (organisms); Viral infections
• ISSN: 1751-7362; 1751-7370
• DOI: 10.1038/s41396-021-01096-5

When considering the interactions between bacteriophages and their host, the issue of phage-resistance emergence is a key element in understanding the ecological impact of phages on the bacterial population. It is also an essential parameter for the implementation of phage therapy to combat antibiotic-resistant pathogens. This study investigates the phenotypic and genetic responses of five Pseudomonas aeruginosa strains (PAO1, A5803, AA43, CHA, and PAK) to the infection by seven phages with distinct evolutionary backgrounds and recognised receptors (LPS/T4P). Emerging phage-insensitivity was generally accompanied by self and cross-resistance mechanisms. Significant differences were observed between the reference PAO1 responses compared to other clinical representatives. LPS-dependent phage infections in clinical strains selected for mutations in the “global regulatory” and “other” genes, rather than in the LPS-synthesis clusters detected in PAO1 clones. Reduced fitness, as proxied by the growth rate, was correlated with large deletion (20–500 kbp) and phage carrier state. Multi-phage resistance was significantly correlated with a reduced growth rate but only in the PAO1 population. In addition, we observed that the presence of prophages decreased the lytic phage maintenance seemingly protecting the host against carrier state and occasional lytic phage propagation, thus preventing a significant reduction in bacterial growth rate.