Development of computationally-guided workflow for designing therapeutic phage cocktail: targeting multidrug-resistant (MDR) bacteria

Abstract

Background: Antibiotic misuse and overuse have contributed to the emergence of multi-drug resistant bacteria (MDR), a serious public health problem across the globe. Phage cocktails, which combine several phages to destroy various bacterial strains, offer a more thorough and efficient method of battling MDR illnesses. This might revolutionize the looming threat of reemergence of untreatable bacterial diseases. To provide a focused strategy to tackle the rising incidence of MDR bacterial infections, a phage cocktail against Acinetobacter baumannii, Klebsiella pneumoniae, and Pseudomonas aeruginosa was intended to be made computationally. Predicting a group of prophages which can successfully lyse and disrupt these three MDR bacterial strains and might help to lessen the severity and occurrence of illnesses caused by these notorious pathogens. Methods: The genomes of selected MDR bacteria were accessed through NCBI GenBank, and prophages targeting them were selected. The prophages were further annotated for ORFs, putative promotors, virulence factors, transcriptional terminators, and tRNAs. Dot plot was created to investigate the similar phages and phylogenetic analysis was performed. Results: A total of 11 prophages were predicted from three MDR bacterial genomes, the investigation identified 472 ORFs and CDS, rRNA, and tRNA regions in 11 prophage genomes were predicted. The presence of 3 tRNAs encoded by the predicted prophages suggests a possible reliance on the host translation machinery for protein synthesis. The presence of transcription terminators and promotors were detected to understand the transcriptional and translational regulation of prophage genes. The comparative genomic and phylogenetic analyses of predicted prophages provided important insights into diversity and relatedness of the phages. The final selected five prophages included Acinetobacter baumannii prophage (2759376-2809756), Acinetobacter baumannii prophage (3311844-3364667), Klebsiella pneumoniae (1288317-1338719), Klebsiella pneumoniae prophage (1778306-1808606), and Klebsiella pneumoniae prophage (2280703-2325555). Conclusion: In conclusion, our work provides an example of developing a phage cocktail to combat multidrug resistant Acinetobacter baumannii and Klebsiella pneumoniae. Sequence similarity analyses revealed that the cocktail is capable of targeting Enterobacter hormaechei and other carbapenemase-producing K. pneumoniae strains also. The phage cocktail indicates the possibility of being employed as a therapeutic agent for reducing harmful bacterial infections, where conventional antibiotic therapeutics fail.