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

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.

doi:10.1101/2024.06.30.601436

bioRxiv · 10.1101/2024.06.30.601436

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

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.

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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 Hospitals 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. SUMMARYO_ST_ABSIn briefC_ST_ABSWe developed a phage product containing five phages with frontline potential to address infections caused by multidrug-resistant Enterobacter cloacae complex.

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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.. 2024-07-01. Rational Design of Frontline Institutional Phage Cocktail for the Treatment of Nosocomial Enterobacter cloacae Complex Infections. https://doi.org/10.1101/2024.06.30.601436

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