Characterization, pathogenicity and complete genome of Klebsiella aerogenes isolated from diseased Macrobrachium rosenbergii larvae.

Macrobrachium rosenbergii is an economically important freshwater aquaculture species in China. In 2025, severe mortality was observed among postlarvae in a commercial hatchery in Gaoyou, Jiangsu Province. In the present study, a dominant bacterial strain, designated MRW3, was isolated from diseased postlarvae and identified as Klebsiella aerogenes through physiological and biochemical characterization, and molecular identification. Experimental challenge tests revealed that the LD50 of strain MRW3 for M. rosenbergii was 2.1 × 105 CFU/mL at 7 dpi. Histopathological analysis demonstrated that MRW3 infection caused severe lesions in the gills, hepatopancreas, and intestine of M. rosenbergii. The virulence gene detection showed the strain MRW3 contained multiple virulence-related genes (ompA, fimA, fliG, acrB, fliA, EcpA, tufA and acrA) identified by the PCR assay. Furthermore, the results of whole genome sequencing revealed that the strain MRW3 genome consisted a circular chromosome of 5,556,689 bp with a GC content of 54.77%. It comprised 5,501 predicted protein-coding sequences (CDS) in addition to 87 tRNA, and 25 rRNA. A total of 72 genes were predicted as virulence-related genes by VFDB database annotation, which could be classified as adherence, motility, invasion and type VI secretion system. There were 29 genes were predicted as antibiotic resistance genes related to tetracyclines, fluoroquinolones, aminoglycosides, macrolides, chloramphenicols and cephalosporins resistance. This study provides valuable insights into the pathogenicity, virulence characteristics, and antibiotic resistance of K. aerogenes, thereby offering a theoretical basis for the prevention and control of K. aerogenes infections in aquaculture.