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

Abstract

The environmental bacteriumrevealed 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 ofin the field and in the laboratory. This pioneer study addressed this knowledge gap by performing phenotypic and genomic characterization ofisolated from 22 clinical cases of chickens. We observed thatisolates 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 () 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 speciesthrough the average nucleotide identity analysis. Additional genomic analysis revealed several putative virulence genes, including superoxide dismutase (), adhesin (), outer membrane (), iron scavenging gene (), and secretion systems. This study documented, for the first time, the phenotypic features,activity of antimicrobials, and provided a comprehensive genomic characterization of clinical isolates of.IMPORTANCEThe perception ofas 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 ofin 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 22clinical isolates from chickens, which included colony morphology features, theactivity 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 intowhich is likely an emerging pathogen in chickens as well as other animals.