Fig 1.
Identification of patients meeting the daptomycin exposure and control study definitions.
Fig 2.
Proportion of different Enterococcus types within each patient sample.
Each bar represents all the isolates from the patient’s index sample divided by the percentage of isolates that were identified as E. faecium, E. faecalis, E. casseliflavus, E. gallinarum, or other Enterococcus. Other Enterococcus is used for clones that were morphologically Enterococcus but did not contain any of the sequences used for PCR identification. Patients to the left of the dotted line are in the control cohort and to the right are in the daptomycin-treated cohort. The underlying data for this figure can be found in S1 Data.
Fig 3.
Daptomycin resistance of each clone by patient and exposure group. Blue circles are the control patients and red circles are from daptomycin-exposed patients. Each circle is the mean of 2 independent estimates of the MICC for a single clone. Clones above the dashed line are daptomycin resistant (due to the continuous nature of the computed MIC (MICC), an MICC of >4μg/ml is equivalent to the clinical 2-fold MIC cutoff of ≥8μg/ml (see Methods for a more detailed discussion of the MICC method)). The underlying data for this figure can be found in S1 Data.
Table 1.
Summary of Models and DIC analysis results.
Fig 4.
Posterior distribution of random and fixed effects from the Bayesian mixed effects model.
(Main panel) Posterior distributions for standard deviations of the clones within patients and the error. Blue markers indicate control patients, red indicate daptomycin-treated patients, and black is the error (circle: mean; thick lines: 50% credibility interval; thin lines: 95% credibility interval). The 95% credibility interval of the error falls within the error marker. (Insert) Posterior distribution of fixed effect for prior daptomycin exposure. The underlying data for this figure can be found in S1 Data.
Fig 5.
Within-patient resistance over time.
Each plot shows patient admission periods, drug doses, and resistance of E. faecium clones isolated from screening swabs and blood stream infections for an individual patient. Time 0 is the index sample included in the previous analysis. Patient admission periods are shown as gray blocks, and individual doses of vancomycin (purple), linezolid (yellow), and daptomycin (red) are detailed in the bars at the top of the plot. Circles show daptomycin resistance (MICC) for 10 clones per sample. Each circle is the mean of 2 replicates with black circles denoting VR E. faecium and blue circles denoting VS E. faecium. Pink diamonds are isolates from VR E. faecium blood stream infections. The underlying data for this figure can be found in S1 Data.
Fig 6.
Phylogeny for E. faecium strains isolated from 4 patients.
Midpoint rooted tree of 89 isolates. Six sequenced isolates were excluded that had core genomes identical to other samples in the alignment. The panel on the right shows the mean daptomycin MICC (ug/mL) for each sample. Many isolates were closely related, resulting in very short branch lengths. See Fig 7 for more detailed visualization of phylogenetic structure within hosts. Sequence data is available at NCBI GenBank under the study accession number PRJNA673360.
Fig 7.
Individual phylogenies for E. faecium strains isolated from 4 patients.
A midpoint-rooted phylogeny was created based on the core genome alignment of all isolates using RAxML. Here, subsets of the full tree (Fig 6) are shown, including only the isolates from each patient (i.e., other tips are masked). Scale bars for branch length (mean number of substitutions per site) are included for each tree and insert. Rectangle inserts show detailed structure of indicated groups. Daptomycin MICCs are listed for each tip. For tips representing 2 isolates with identical core genomes, the daptomycin MICCs for both isolates are listed. Asterisks indicate mutations in genes known to be associated with variation in daptomycin susceptibility. For each patient, one assembled genome (two for the 2 clades in Patient 150) was used as a reference genome for variant calling (see Methods). (A) Patient 4 (B) Patient 86 (C) Patient 150 (D) Patient 87. Sequence data is available at NCBI GenBank under the study accession number PRJNA673360.