<b>Underlying data for '</b><b>Computational prediction of a phage cocktail active against multidrug-resistant bacteria'</b>

Antibiotic misuse and overuse have led to emergence of multi-drug resistant (MDR) bacteria, creating a significant health concern for global population. Phage cocktails combine multiple phages, providing an efficient method to combat multidrug-resistant bacterial infections. In this study, a computational pipeline was used to design a phage cocktail against the MDR bacterial strains Acinetobacter baumannii AB0057, Klebsiella pneumoniae subsp. pneumoniae HS11286, and Pseudomonas aeruginosa UCBPP-PA14. Prophage sequences were identified from whole genome sequences of selected bacterial strains. Prophages were annotated for open reading frames (ORFs), putative promoters, virulence factors, transcriptional terminators, ribosomal RNAs, and transfer RNAs. Dot-plot similarity analyses and phylogenetic analysis were also conducted.
A total of 11 prophages were predicted from the bacterial genomic sequences. About 472 ORFs were identified along having 3 transfer RNAs. Additionally, 754 putative promoter sequences and 281 transcription terminator sequences were also detected. Comparative genomic and phylogenetic analyses revealed the diversity, similarities, and lysis potential of phages. The final designed phage cocktail consisted of five prophages including Acinetobacter baumannii prophages (2759376-2809756) and (3311844-3364667), and Klebsiella pneumoniae prophages (1288317-1338719), (1778306-1808606), and (2280703-2325555). The phage cocktail designed after rigorous validations might be useful against MDR Acinetobacter baumannii and Klebsiella pneumoniae, especially when conventional antibiotics fail to treat. Sequence similarity analyses suggested that this phage cocktail may also be effective against other carbapenemase-producing strains of Klebsiella pneumoniae.