Phenotypic and genomic characterization of Castellaniella ginsengisoli, an emerging pathogen associated with disease in birds

ABSTRACT The environmental bacterium Castellaniella revealed its clinical relevance from case reports, causing fatal infections in animals. The lack of phenotypic and genomic characterization may have historically contributed to the scattered identification of Castellaniella in the field and in the laboratory. This pioneer study addressed this knowledge gap by performing phenotypic and genomic characterization of C. ginsengisoli isolated from 22 clinical cases of chickens. We observed that C. ginsengisoli isolates exhibited three colony morphologies on blood agar and presented flagella under transmission electron microscopy (TEM) examination. Antimicrobial susceptibility testing showed high minimum inhibitory concentrations (MICs) for penicillins, indicating a potential intrinsic mechanism of resistance to ß-lactams. Efflux pump genes (adeF, qacG) and β-lactamase genes were identified in the whole genomes of all isolates, which could be linked to the high MICs observed for β-lactams. Low MICs for sulfonamides and tetracyclines, among other antimicrobials, were observed for most of the isolates, suggesting a potential treatment option for birds and other affected animals. We further confirmed that all isolates belong to the species C. ginsengisoli through the average nucleotide identity analysis. Additional genomic analysis revealed several putative virulence genes, including superoxide dismutase (sodB), adhesin (tadB), outer membrane (ompA), iron scavenging gene (fur), and secretion systems. This study documented, for the first time, the phenotypic features, in vitro activity of antimicrobials, and provided a comprehensive genomic characterization of clinical isolates of C. ginsengisoli. IMPORTANCE The perception of Castellaniella ginsengisoli as an environmental bacterium has led to a lack of specific diagnostic tools, hindering the characterization of clinically associated isolates. With the increasing number of cases of Castellaniella in birds, there is a need to define characteristics to assist identification, therapeutic guidance, and understanding its potential pathogenicity mechanism. This study provided a comprehensive characterization of 22 C. ginsengisoli clinical isolates from chickens, which included colony morphology features, the in vitro activity of antimicrobials, and the resistant genetic markers identified through genomic characterization. We further provided a list of putative virulence genes and suggested how these genes may participate in the process of pathogenicity. This novel, comprehensive study laid the foundation for future research into C. ginsengisoli, which is likely an emerging pathogen in chickens as well as other animals. The perception of Castellaniella ginsengisoli as an environmental bacterium has led to a lack of specific diagnostic tools, hindering the characterization of clinically associated isolates. With the increasing number of cases of Castellaniella in birds, there is a need to define characteristics to assist identification, therapeutic guidance, and understanding its potential pathogenicity mechanism. This study provided a comprehensive characterization of 22 C. ginsengisoli clinical isolates from chickens, which included colony morphology features, the in vitro activity of antimicrobials, and the resistant genetic markers identified through genomic characterization. We further provided a list of putative virulence genes and suggested how these genes may participate in the process of pathogenicity. This novel, comprehensive study laid the foundation for future research into C. ginsengisoli, which is likely an emerging pathogen in chickens as well as other animals.