Table 1.

Efficiency calculation. Time, in hours, indicates hands-on time, transfer time between different institutes, and inevitable waiting periods. Transfer time to the next institute is counted to the respective previous step. Step 1–5a: Steps of the pipeline, see Figure 1. E factor minimum/maximum: efficiency factor, calculated using Equation (1), considering the minimal/maximum cumulative time. E factor mean: mean efficiency factor, calculated using minimum and maximum E factor. Phases I and II focused only on steps requiring optimization, and the results of the standardized steps 4 and 5b of phase I were considered for E factor calculation. Parameters with an asterisk * are integrated into Equation (1).

	Number of Patients	Number of Bacteria	Successful Patient Data Retrieval*	Step 1 (h)	Step 2 (h)	Step 3 (h)	Percentage of Bacteria with High-Titre Phages*	Number of High-Titre Phages/Bacteria*	Step 4 (h)	Percentage of Reliable Genomic Sequences*	Step 5b (h)	Final Titre (PFU/mL)*	Final Volume (mL)*	Cumulative Time (h)*	E Factor Minimum	E Factor Maximum	E Factor Mean
Phase I	25	42	95.5% (42/44)	48–72	48	48–336	87.0% (20/23)	2.4 (55/23)	72	87.3% (48/55)	10	1 × 1010	11.0	226–538	0.39	0.92	0.65
Phase II	30	34	100% (34/34)	48–72	48	24–72	58.8% (20/34)	1.1 (37/34)						202–274	0.25	0.34	0.29
Phase III	6	6	100% (6/6)	48–72	48	24–96	83.3% (5/6)	2.0 (12/6)						202–298	0.64	0.86	0.75