Rational Design of Frontline Institutional Phage Cocktail for the Treatment of Nosocomial Enterobacter cloacae Complex Infections

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Rational Design of Frontline Institutional Phage Cocktail for the Treatment of Nosocomial Enterobacter cloacae Complex Infections

Authors

Subedi, D.; Gordillo Altamirano, F. L.; Deehan, R.; Perera, A.; Patwa, R.; Kostoulias, X.; Korneev, D.; Blakeway, L.; Wiesnewski, J.; Macesic, N.; Peleg, A. Y. L.; Barr, J. J.

Abstract

Phage therapy is a promising strategy to treat antimicrobial-resistant infections. Currently, phage therapy applications span personalised treatments that are tailored for a given patients infection, through to the use of pre-established cocktails of virulent phages against clinically relevant pathogens. However, both approaches face challenges, with personalised phage therapy being time-consuming and requiring a phage match to a patients infection, while phage cocktails may not be effective against a patients specific strain. The Alfred Hospital in Melbourne, Australia has reported an ongoing outbreak of infections by the Enterobacter cloacae complex (ECC), a group of emerging multidrug-resistant pathogens responsible for considerable morbidity and mortality. Utilising the hospitals strain collection, built over the last decade, we established an initial three-phage product with 54% ECC coverage that effectively reduced bacterial loads (>99%) in septicaemic mice. We then iteratively improved this product by enhancing phage killing efficiency using phage training and expanded host range through targeted phage isolation against low-coverage ECC strains. This iterative optimisation led to the creation of the product Entelli-02, containing five well characterised virulent phages that target clinical ECC strains through distinct bacterial cell surface receptors. Importantly, Entelli-02 exhibits broad host coverage (99%) and efficacy (92%) against The Alfred Hospital ECC strain collection (n = 156). We produced this as a therapeutic-grade product, verified and endotoxin unit compliant, ready for use. This approach integrated academic phage research with clinical insights to produce the phage product Entelli-02 as an institution-specific phage cocktail with frontline efficacy and on-demand availability.

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