Fig. 5

Genomic alterations detected in B. caccae isolates support selection throughout treatment. The detected proportions of IS614 and large-scale genomic island integrations (columns) in 41 B. caccae isolates (rows) are shown (filled squares indicate presence). Hierarchical clustering of the 41 isolates by their IS614 integrations within each timepoint reveals four distinct subpopulations of B. caccae strains, three of which appear to shift in relative abundance between timepoints C and D. The IS614 integration upstream of norM is the only one that is absent from all isolates from timepoint A (before ciprofloxacin exposure), but appears in all isolates from timepoint C and D (after ciprofloxacin exposure). The IS614 integration upstream of per1 is present in all of the B. caccae isolates we obtained. Initial analysis of the isolate sequencing data was unable to detect IS614 integrations in front of per1 for two isolates, but manual inspection of the assembly graphs of these confirmed this integration to be present in these two as well (open squares in the per1 column). The IS614 integration upstream of thyA2 appears in a minority of strains in timepoint C (prior to trimethoprim exposure) and appears in the majority of strains in timepoint D (after trimethoprim exposure). The IS614 integration upstream of susC, which was detected in isolate sequence data, also appears to be under selection in timepoint C. Unlike the IS614 integrations, none of the large-scale genomic islands appear to be under selection between timepoints as they are broadly distributed across all subpopulations