Genomic and Pathogenic Characterization of Francisella salimarina Associated with Mortality in Fourfinger Threadfin (Eleutheronema tetradactylum) in Taiwan.
Abstract
In 2024, a mortality event affected farmed fourfinger threadfin (Eleutheronema tetradactylum) in Pingtung County, Taiwan, resulting in significant economic losses. Affected fish displayed anorexia and lethargy, with internal lesions characterized by multifocal white nodules. Histopathological examination confirmed systemic granulomatous disease. Two bacterial isolates, designated F5 and F69, were recovered from internal organs and identified as Francisella spp. by PCR. Experimental challenge demonstrated that strain F69 was less virulent than F5, exhibiting a higher LD50 (5.6 × 106 CFU/fish vs. 2.5 × 106 CFU/fish). Whole-genome average nucleotide identity analysis confirmed that both strains share >95% ANI with the Francisella salimarina group, classifying them within this species. Comparative genomic analysis identified two distinct polysaccharide-associated regions in strains F5 and F69. One region comprises a sugar biosynthetic gene cluster that is intact in F5 but contains several disrupted genes in strain F69. A second region encodes surface architecture characteristic of a KpsMT-dependent polysaccharide export system (kpsD, kpsE, kpsM, and kpsS), along with multiple glycosyltransferases and enzymes involved in the biosynthesis of UDP-activated amino sugars. Both strains contained a single copy of the Francisella pathogenicity island; however, key components such as pdpC were absent, and the pdpD gene was disrupted in F69. Genomic analysis identified a class A β-lactamase gene (blaOXY-2) in both strains, while F5 additionally harbored an FPH-family carbapenem-hydrolyzing class A β-lactamase. Consistent with these findings, both strains were phenotypically resistant to penicillins and cephalosporins, whereas only F5 exhibited resistance to imipenem. This study represents the first documented case of F. salimarina infection in Asia, affecting fourfinger threadfin in Taiwan, and provides important insights into its pathogenicity, antimicrobial resistance, and genomic features.