Genomic characterization of respiratory Elizabethkingia: antimicrobial resistance and strain relatedness

Elizabethkingia species are emerging multidrug-resistant opportunistic pathogens associated with high mortality in critically ill patients. However, the genomic epidemiology and mechanisms of fluoroquinolone resistance in respiratory Elizabethkingia isolates remain incompletely understood. The objective of this study was to characterize the clinical, genomic, and resistance features of respiratory Elizabethkingia isolates from a tertiary pulmonary hospital and to explore the structural basis of fluoroquinolone non-susceptibility associated with DNA gyrase subunit A (GyrA) S83I substitution. A total of 18 non-duplicate Elizabethkingia isolates from 16 patients with severe pulmonary disease at a tertiary hospital (2024-2025) were included. Whole-genome sequencing was performed for species identification, pangenome analysis, and core-genome SNP-based phylogenetic reconstruction. Antimicrobial susceptibility testing was conducted using the VITEK^® 2 system. Mutations in the quinolone resistance-determining region (QRDR) were analyzed, and the structural impact of the GyrA S83I substitution was evaluated by molecular docking. Among the 18 isolates, 15 were identified as Elizabethkingia anophelis and 3 as Elizabethkingia meningoseptica. Pangenome analysis demonstrated an open genome structure (γ = 0.156). Core-genome phylogeny revealed distinct clade-specific clustering, with seven highly related E. anophelis isolates in Clade B, suggesting potential nosocomial transmission. All isolates exhibited broad resistance to multiple antimicrobial classes, whereas minocycline retained full in vitro activity. Fluoroquinolone non-susceptibility was strongly associated with lineage and significantly correlated with the GyrA S83I substitution. Molecular docking analysis showed that this substitution reduced the binding affinity of ciprofloxacin and levofloxacin to GyrA (ΔΔG ≈ 3-6 kcal/mol). However, because GyrA S83I was largely lineage-restricted, its independent contribution could not be disentangled from clade background, and several non-susceptible isolates lacked S83I, indicating additional mechanisms, our integrated genomic and structural findings underscore the critical interplay between localized clonal expansion and target-site adaptation in driving fluoroquinolone resistance in clinical Elizabethkingia strains.