Fig. 3
From: Urinary cell-free DNA is a versatile analyte for monitoring infections of the urinary tract
Estimating bacterial population growth rates from urinary cfDNA. a Normalized bacterial genome coverage for four representative bacterial species. The coverage was binned in 1 kbp tiles and normalized. Each panel represents a single sample (see Supplementary Data 6), with the exception of C. acnes (asterisk (*)) for which the coverage was aggregated across 99 samples (solid line is a LOESS filter smoothing curve, span = 0.70). The non-uniform genome coverage for E. coli and K. pneumoniae, with an overrepresentation of sequences at the origin of replication, is a result of bi-directional replication from a single origin of replication. The initial and final 5% of the genome is removed for display. b The skew in genome coverage reflects the bacterial growth rate, where a stronger skew signals faster growth36. Box plots of growth rates for species in 14 genera grouped by patient groups (at least 2500 alignments, 41 samples, see Methods for definition of pre/post-UTI). Each point indicates a bacterial species in a sample. Triangles indicate culture-confirmed bacteria by genus. Boxplot features are described in Methods. See Supplementary Data 6 and 7
