Engineered reporter phages for rapid detection of Escherichia coli, Klebsiella spp., and Enterococcus spp. in urine

Meile, S.; Du, J.; Staubli, S.; Grossmann, S.; Koliwer-Brandl, H.; Piffaretti, P.; Leitner, L.; Matter, C. I.; Baggenstos, J.; Hunold, L.; Milek, S.; Guebeli, C.; Kozomara-Hocke, M.; Neumeier, V.; Botteon, A.; Klumpp, J.; Marschall, J.; McCallin, S.; Zbinden, R.; Kessler, T. M.; Loessner, M. J.; Dunne, M.; Kilcher, S.

doi:10.1101/2022.11.23.517494

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bioRxiv · 10.1101/2022.11.23.517494

Engineered reporter phages for rapid detection of Escherichia coli, Klebsiella spp., and Enterococcus spp. in urine

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Abstract

The rapid detection and species-level differentiation of bacterial pathogens facilitates antibiotic stewardship and improves disease management. Here, we develop a rapid bacteriophage-based diagnostic assay to detect the most prevalent pathogens causing urinary tract infections: Escherichia coli, Klebsiella spp., and Enterococcus spp. For each uropathogen, two virulent phages were genetically engineered to express a nanoluciferase reporter gene upon host infection. Using 206 patient urine samples, reporter phage-induced bioluminescence was quantified to identify bacteriuria and the assay was benchmarked against conventional urinalysis. Overall, E. coli, Klebsiella spp., and Enterococcus spp. were each detected with high sensitivity (68%, 78%, 85%), specificity (99%, 99%, 99%), and accuracy (90%, 94%, 96%) at a resolution of [>=]103 CFU/ml within 5 h. We further demonstrate how bioluminescence in urine can be used to predict phage antibacterial activity, demonstrating the future potential of reporter phages as companion diagnostics that guide patient-phage matching prior to therapeutic phage application.

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Meile, S., Du, J., Staubli, S., Grossmann, S., Koliwer-Brandl, H., Piffaretti, P., Leitner, L., Matter, C. I., Baggenstos, J., Hunold, L., Milek, S., Guebeli, C., Kozomara-Hocke, M., Neumeier, V., Botteon, A., Klumpp, J., Marschall, J., McCallin, S., Zbinden, R., Kessler, T. M., Loessner, M. J., Dunne, M., Kilcher, S.. 2022-11-23. Engineered reporter phages for rapid detection of Escherichia coli, Klebsiella spp., and Enterococcus spp. in urine. https://doi.org/10.1101/2022.11.23.517494

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