Genomic determinants of fluoroquinolone resistance and delafloxacin activity in Staphylococcus epidermidis isolates causing implant-associated bone and joint infections

Implant-associated bone and joint infections (IA-BJIs) due to Staphylococcus epidermidis are increasingly problematic because of biofilm formation and rising fluoroquinolone resistance. Delafloxacin is a recently approved fluoroquinolone with promising activity against resistant staphylococci; however, genomic determinants of susceptibility in S. epidermidis from IA-BJI remain insufficiently characterized. The aim of this study was to characterize delafloxacin in vitro activity against S. epidermidis clinical isolates from IA-BJI and to define the genomic determinants underlying reduced susceptibility to delafloxacin. This retrospective multicenter study (2022–2026) including 47 S. epidermidis isolates recovered from IA-BJI. Antimicrobial susceptibility was determined by broth microdilution/MIC strips. Multilocus sequence typing, QRDR substitutions ( gyrA , gyrB , parC , parE ), efflux pump genes, and the presence of the biofilm-associated ica operon were characterized by whole-genome sequencing (MiSeq, Illumina). Thirty-five isolates were levofloxacin-resistant. Among these, delafloxacin MIC _50/90 were 0.38 and 1.5 mg/L; 49% (17/35) met the Staphylococcus aureus MIC ≤ 0.25 mg/L susceptibility breakpoint. All levofloxacin-resistant strains carried GyrA-S84 and ParC-S80 substitutions. Cumulative QRDR substitutions were associated with higher delafloxacin MICs ( P = 0.0012). ParE substitutions were present in 14/35 isolates. The distribution of efflux pump genes did not differ between groups, whereas the ica operon was strongly associated with quinolone resistance (74% vs 8%; P < 0.001). We also report three osteosynthesis-associated infection cases caused by a levofloxacin-resistant S. epidermidis that achieved clinical cure after 6 weeks of delafloxacin. Delafloxacin retains in vitro activity against a substantial fraction of levofloxacin-resistant S. epidermidis , although higher MICs were associated with greater cumulative QRDR burden. Rapid PCR assays targeting key QRDR substitutions could facilitate genotype-guided therapy and surveillance.

IMPORTANCE

The objective of this multicenter study is to assess the in vitro activity of delafloxacin against Staphylococcus epidermidis isolates from implant-associated osteoarticular infections. We identified genomic mutations associated with reduced in vitro susceptibility, which have potential as an actionable diagnostic strategy, for example, in the form of targeted molecular assays. In addition, three cases of osteosynthesis-associated infections caused by levofloxacin-resistant S. epidermidis isolates are reported. These cases were successfully treated with a 6-week course of delafloxacin, with favorable follow-ups. These strains have been the subject of extensive genomic study, and the resulting data will doubtless prove to be of significant benefit in future research and treatment decision-making. The manuscript is considered to be of significance, as it addresses a clear knowledge gap concerning a clinically important device-associated pathogen that has the potential to guide antimicrobial therapy and surveillance.