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Growing antimicrobial resistance (AMR) infections are among the top contemporary concerns in public healthcare systems which can place considerable burdens on healthcare systems. Phage therapy has long been considered a viable option to help combat AMR infections, including on broad geographic scales. One bottleneck in the application of phage therapy is the accurate matching of host-specific phages to bacterial strains, which is traditionally done using molecular techniques. Here we present an open-access deep learning-based model that shows incredible potential to accurately predict phages for therapeutic use. Our goal is to attenuate the matching process so that specific phages, or a cocktail of phages can be prepared for patients with a high probability of therapeutic success, helping to democratize phage therapy treatments even in low to middle-income countries where genomic resources can be limited, costly, or time prohibitive. We feel this is an important first step towards incorporating and applying bioinformatic practices in promising fields such as phage therapy.
Growing antimicrobial resistance (AMR) infections are among the top contemporary concerns in public healthcare systems which can place considerable burdens on healthcare systems. Phage therapy has long been considered a viable option to help combat AMR infections, including on broad geographic scales. One bottleneck in the application of phage therapy is the accurate matching of host-specific phages to bacterial strains, which is traditionally done using molecular techniques. Here we present an open-access deep learning-based model that shows incredible potential to accurately predict phages for therapeutic use. Our goal is to attenuate the matching process so that specific phages, or a cocktail of phages can be prepared for patients with a high probability of therapeutic success, helping to democratize phage therapy treatments even in low to middle-income countries where genomic resources can be limited, costly, or time prohibitive. We feel this is an important first step towards incorporating and applying bioinformatic practices in promising fields such as phage therapy.
The growing threat of antimicrobial resistance (AMR), exacerbated by the COVID-19 pandemic, highlights the urgent need for alternative treatments such as bacteriophage (phage) therapy. Phage therapy offers a targeted approach to combat bacterial infections, particularly those resistant to conventional antibiotics. This study aimed to standardize an agar plate method for high-mix, low-volume phage production, suitable for personalized phage therapy. Plaque assays were conducted with the double-layer agar method, and plaque sizes were precisely measured using image analysis tools. Regression models developed with Minitab software established correlations between plaque size and phage production, optimizing production while minimizing resistance development. The resulting Plaque Size Calculation (PSC) model accurately correlated plaque size with inoculum concentration and phage yield, establishing specific plaque-forming unit (PFU) thresholds for optimal production. Using phages targeting pathogens such as Escherichia, Salmonella, Staphylococcus, Pseudomonas, Chryseobacterium, Vibrio, Erwinia, and Aeromonas confirmed the model’s accuracy across various conditions. The model’s validation showed a strong inverse correlation between plaque size and minimum-lawn cell clearing PFUs (MCPs; R² = 98.91%) and identified an optimal inoculum density that maximizes yield while minimizing the evolution of resistant mutants. These results highlight that the PSC model offers a standardized and scalable method for efficient phage production, which is crucial for personalized therapy and AMR management. Furthermore, its adaptability across different conditions and phages positions it as a potential standard tool for rapid and precise phage screening and propagation in both clinical and industrial settings.
Bacteriophages are viruses that have the potential to combat bacterial infections caused by antimicrobial-resistant bacterial strains. In this study, we investigated a novel lytic bacteriophage, vB_EcoS_JSSK01, isolated from sewage in Hualien, Taiwan, which effectively combats multidrug-resistant (MDR) Escherichia coli of the K1 capsular type. K1 E. coli is a major cause of severe extraintestinal infections, such as neonatal meningitis and urinary tract infections. Phage JSSK01 was found to have a genome size of 44,509 base pairs, producing approximately 123 particles per infected cell in 35 min, and was highly stable across a range of temperatures and pH. JSSK01 infected 59.3% of the MDR strains tested, and its depolymerase (ORF40) specifically degraded the K1 capsule in these bacteria. In a zebrafish model, JSSK01 treatment after infection significantly improved survival, with survival in the treated group reaching 100%, while that in the untreated group dropped to 10% after three days. The functional activity of depolymerase was validated using zone inhibition and agglutination tests. These results indicate that JSSK01 and its substrate-specific depolymerase have promising therapeutic and diagnostic applications against K1-encapsulated MDR E. coli infections.
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