Fig 1.
Core genome phylogeny of E. faecalis endophthalmitis isolates.
Single-copy core genome phylogeny of 15 UPMC Campbell Lab isolates plus two additional genomes from NCBI (WGS406 and WGS410), all isolated from endophthalmitis. The RAxML tree is built from single nucleotide polymorphisms (SNPs) in 2024 single copy core genes identified with Roary. Tips are annotated with isolate name, multi-locus sequence type (ST), drug resistance-associated genes, plasmid rep genes, cytolysin operon presence, CRISPR-cas loci presence, and prophage abundance in each genome. CRISR-cas-positive isolates had Class 1 and/or Class 2 Cas proteins associated with their CRISPR loci. Intact or questionable prophages were identified with PHASTER. erm(B) = erythromycin resistance, tet(M) and tet(S) = tetracycline resistance, ant(6)-Ia, aph(3′)-III and aac(6’)-aph(2″) = aminoglycoside resistance.
Fig 2.
Variable biofilm production among endophthalmitis isolates.
In vitro biofilm production of 15 E. faecalis endophthalmitis isolates. Biofilm formation was measured as the optical density (OD) at 550nm using a standard crystal violet-based assay. Isolates are arranged according to their sequence type (ST), and STs with more than one isolate are labeled. Bars shown mean crystal violet absorbance values, and error bars show standard deviation of triplicate experiments, each with eight technical replicates. NC = negative control; ****P<0.0001 by two-tailed t test; ns = not significant.
Table 1.
Minimum Inhibitory concentration (MIC) profiles of E. faecalis endophthalmitis isolates.
Table 2.
Amino acid substitutions in gyrA and parC identified in fluoroquinolone-resistant E. faecalis endophthalmitis isolates.
Fig 3.
An isolate from recurrent endophthalmitis with a mutation in the mismatch repair gene mutS has a higher spontaneous mutation rate compared to earlier isolates from the same patient.
Spontaneous mutation rate, measured with a rifampin mutagenicity assay, in isolates E616, E623 and E633, which were all sampled from a patient with recurrent endophthalmitis. Horizontal lines mark median values for results from 6 biological replicate experiments (each with 2–4 technical replicates).