Fig. 6

Antibiotic susceptibility testing of B. caccae isolates. Fifteen B. caccae isolates (3 isolates from timepoint A and 4 from each subpopulation present in timepoints C and D) were tested for their susceptibility to ciprofloxacin and trimethoprim, the two antibiotics that the patient was administered during treatment. The minimum inhibitory concentrations (MICs) of the two drugs against each isolate were determined as described in the “Methods”. a The presence (filled square) of different IS614 integrations within tested isolate strains that are upstream of annotated genes norM and thyA2, which are known to contribute to resistance to ciprofloxacin and trimethoprim. NorM is a known multidrug efflux pump that can confer resistance to ciprofloxacin. Upregulation of thyA2/dhfrIII has been shown to affect resistance to trimethoprim [61]. These IS integrations result in the potential introduction of likely bacterial promoters upstream of these genes likely leading to their upregulation increased expression and consequently as a result, increased antibiotic resistance. b MICs of ciprofloxacin against B. caccae strains. Strains from timepoints C and D with IS614 integrations upstream of norM and thyA2/dhfrIII predicted to increase resistance to ciprofloxacin (shaded) have a two- to fourfold increase in their MICs relative to strains from timepoint A. c MICs of trimethoprim against B. caccae strains. Overall, strains from all subpopulations showed high resistance to trimethoprim. Strains from the third subpopulation in timepoints C and D with IS614 integrations predicted to increase resistance to trimethoprim (shaded) show a twofold increase in resistance to trimethoprim compared to other subpopulations