Clinical and genomic features of Chryseobacterium species isolated from clinical cultures

ABSTRACT Chryseobacterium species are environmental bacteria occasionally implicated in human infections; however, their clinical and genomic features are not fully characterized. This study investigated the clinical, genotypic, and phenotypic characteristics of Chryseobacterium strains collected through the MultiDrug-Resistant Organisms Clinical Research Network, a multicenter prospective study of patients with carbapenem-resistant gram-negative bacilli isolated at tertiary care hospitals in Japan between April 2019 and March 2024. Among 18 patients with Chryseobacterium spp. confirmed by whole-genome sequencing (WGS), 5 had infection, and 13 were colonized. Bacteremia and pneumonia were the common types of infection. The isolates comprised five species, with Chryseobacterium indologenes and Chryseobacterium culicis being the most frequently detected. Compared with WGS, 16S rRNA gene sequencing demonstrated the highest species-level identification accuracy (93.8%), followed by MALDI Biotyper (50.0%), VITEK-MS (31.3%), and VITEK 2 Blue (31.3%). All systems correctly identified C. indologenes , but other species were frequently misidentified or remained unidentified because of limited database coverage. All isolates exhibited broad β-lactam resistance, including resistance to carbapenems, which was associated with species-specific combinations of metallo-β-lactamase and extended-spectrum β-lactamase genes. Minocycline, trimethoprim-sulfamethoxazole, and cefiderocol retained activity across all species. These findings highlight that diverse Chryseobacterium species, including uncommon ones, can be associated with human infections. Incorporating genomic approaches such as WGS or 16S rRNA gene analysis can improve species-level identification, especially for rare or emerging species. IMPORTANCE Chryseobacterium species are emerging opportunistic pathogens that pose a diagnostic and therapeutic challenge as they are intrinsically resistant to most β-lactams, including carbapenems, and are often misidentified by routine clinical laboratory systems. In this multicenter study, we show that clinical Chryseobacterium isolates represent greater species diversity than is typically recognized, extending beyond Chryseobacterium indologenes to include uncommon species associated with both infection and colonization. Whole-genome sequencing clarified species assignments, revealed species-specific β-lactamase profiles, and highlighted the limitations of commonly used identification platforms, particularly for species absent from commercial databases. Despite broad β-lactam resistance, cefiderocol, minocycline, and trimethoprim-sulfamethoxazole retained in vitro activity across species. These findings emphasize the need for genomic or sequence-based identification to accurately define the clinical spectrum of Chryseobacterium species, guide interpretation of antimicrobial susceptibility, and improve recognition of these organisms as emerging healthcare-associated pathogens.