title: Whole genome sequencing of Staphylococcus epidermidis isolated from synovial fluid
design: Characterization of S. epidermidis from synovial fluid culturesGenomic characterization of S. epidermidis PJI isolates: S. epidermidis isolated from synovial fluid during surgery were subjected whole genome sequencing employing Illumina and ONT platforms (genomes available at XXX). Isolates were assigned to 7 sequence types, and 5/10 isolates belonged to STs typically associated with hospital-acquired infections (i.e. ST5, ST23, ST87). 9/10 S. epidermidis isolates carried mecA (located on SCCmec type IVa(2B) in 7/10). Most isolates belonged to Agr group II (6/10). Interestingly, S. epidermidis isolate 1 could not be assigned to any agr-type, and further analysis revealed that the isolate carried an uncommon agrD sequence, that did not align to the Agr I-III typing scheme PMID: 25070736. Genome analysis confirmed the presence of qPCR target genes in all isolates; Phenotypic characterization of S. epidermidis PJI isolates: Analysis of growth dymics were tested using TSB and artificial synovial fluid (ASF; PMID: 35967857) found no gross differences between isolates. The ability to form biofilms was variable, with 4/10 isolates forming biofilms, while all others were biofilm negative. Hemolytic activity of culture supernatants was very low and quantitative near to the negative control in 6/10 S. epidermidis isolates, and reached values as high as the positive control in only 2/10 cases (Figure XC). 6/10 S. epidermidis isolates tested phenotypically resistant against oxacillin. Of notice, only 2/10 isolates were resistant against rifampin (Figure X).