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

The environmental bacterium <i>Castellaniella</i> 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 <i>Castellaniella</i> in the field and in the laboratory. This pioneer study addressed this knowledge gap by performing phenotypic and genomic characterization of <i>C. ginsengisoli</i> isolated from 22 clinical cases of chickens. We observed that <i>C. ginsengisoli</i> 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 (<i>adeF, qacG</i>) 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 <i>C. ginsengisoli</i> through the average nucleotide identity analysis. Additional genomic analysis revealed several putative virulence genes, including superoxide dismutase (<i>sodB</i>), adhesin (<i>tadB</i>), outer membrane (<i>ompA</i>), iron scavenging gene (<i>fur</i>), and secretion systems. This study documented, for the first time, the phenotypic features, <i>in vitro</i> activity of antimicrobials, and provided a comprehensive genomic characterization of clinical isolates of <i>C. ginsengisoli</i>.IMPORTANCEThe perception of <i>Castellaniella ginsengisoli</i> 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 <i>Castellaniella</i> 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 <i>C. ginsengisoli</i> clinical isolates from chickens, which included colony morphology features, the <i>in vitro</i> 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 <i>C. ginsengisoli,</i> which is likely an emerging pathogen in chickens as well as other animals.