Periodic Reporting for period 3 - PHARMS (Bacteriophage inhibition of antibiotic-resistant pathogenic microbes and founding for novel therapeutic strategies)
Período documentado: 2022-01-01 hasta 2023-06-30
Phage therapy, a promising complement to antibiotics, utilizes viruses of bacteria (bacteriophages) or phage-derived inhibitors as natural ways to fight AMR. The main obstacles in the clinical application of phage-based AMR therapy are the limited number of phage isolates and the unknown molecular mechanisms of phage-delivered bactericidal action. Building on the recent advances of my group in high-throughput, culture-independent but host-targeted methodologies, PHARMS aims to deploy a revolutionary approach: to screen for all possible phages of a resistant bacterial isolate, characterize multiple lines of their bactericidal functions, and use this information for the design of a whole battery of phage-based therapies that employ multifaceted modes of action. By elucidating universal and specific mechanisms of phage-delivered inhibition of AMR pathogens, PHARMS is positioned to provide the rational framework for the design of novel therapeutic strategies aimed at treating common and life-threatening infectious diseases.
Next, we looked into the infection mechanisms of novel phages on A. Baumannii cells to showcase the novel infection strategies those new phages encode. We studied phage-host interaction in different physiological states of the bacteria, and using a multi-omics approach that integrates genomics, transcriptomics, proteomics, and metabolomics. We revealed significant changes in host metabolism co-occurred with a twentyfold increase in phage mRNAs involved in the regulatory, metabolic, and antibacterial activities. Yet, many phage genes upregulated were of unknown functions. In addition, we have identified over a hundred proteins and metabolites specific to phage-infected bacteria, which varied based on the host's physiology and time of infection. Moreover, the network analyses showed dynamic correlations between different omes through the infection period. The strongest correlations were observed for omes involved in fatty acid, nucleotide, and amino acid metabolisms, suggesting significant phage-specific reprogramming of the host's metabolic activities.
In addition, to join the fight against health complications caused by the COVID-19 pandemic, we isolated, characterized, and formulated a combination of phages for treating acute pneumonia caused by co-infection with multiresistant bacteria. The top-notch cocktail that was developed following extensive kinetics analyses consists of highly efficient phages against the most common sources of co-infections in COVID-19 patients: multiresistant Klebsiella pneumonia, Pseudomonas aeruginosa, and Staphylococcus aureus. Our analyses showed high genetic diversity among the selected phages suggesting diverse infection strategies used by them for infecting the target bacteria; this further complicates the development of resistance in host bacteria and holds its potential for further therapeutic development.
To date, we have identified over a hundred major novel viruses and discovered novel phage infection strategies. Multi-omics approaches were tailored to generate a list of novel phage genes which hold potential for further therapeutic development; in vitro and in vivo evaluation are ongoing.