Isolation and genomic characterization of multi-drug resistant Morganella morganii strain from Chinese Soft-Shell Turtle Pelodiscus sinensis

Abstract

An outbreak of granulomatous disease in the visceral organs was observed at a Chinese Soft-Shell Turtle (CSST, Pelodiscus sinensis) aquaculture facility in Changde, Hunan Province, China. The pathology was primarily characterized by the presence of opalescent nodules in vital organs such as the liver, spleen, and heart. The study involved the isolation and identification of the pathogen responsible for the disease, and analyzed its pathogenicity, drug resistance, and genomic characteristics. Results showed the isolation of a dominant strain, HD0531g, from the liver and spleen of affected CSSTs, identified as Morganella morganii through physiological and biochemical tests. Phylogenetic analysis based on 16S rRNA sequences revealed that HD0531g clusters with M. morganii strains M11, JCM1672, and NBRC3848. Experimental infection models demonstrated that the median lethal dose (LD₅₀) of strain HD0531g in CSSTs was 1.05 × 10⁶ CFU/mL. Antimicrobial susceptibility testing revealed pronounced antibiotic resistance in HD0531g, except for its susceptibility to gentamicin. Pathological observation revealed numerous nodular lesions in the liver and spleen of CSSTs, accompanied by severe hemorrhage and inflammation. Whole-genome sequencing revealed that the HD0531g strain has a total genomic length of about 3.90 Mb, including a 2311 bp plasmid and encoding 3653 genes. Phylogenetic analysis of the entire genome placed HD0531g in the same cluster as the M. morganii strain NBRC3848. A virulence factor database query identified the presence of 136 virulence genes in strain HD0531g, representing 47 species across 15 categories and encoding an array of pathogenic proteins including secretion systems, adhesins, and lipooligosaccharides (LOS). Drug resistance gene mapping indicated that HD0531g contains 16 distinct antibiotic resistance genes, most of which are related to antibiotic inactivation and antibiotic efflux. In summary, this study isolated a highly pathogenic, multi-drug resistant strain of M. morganii from CSSTs affected by visceral white spot disease. It detailed the distribution of antibiotic resistance and virulence genes in the strain, offering valuable insights for treatment and the rational use of drugs in HD0531g infections in CSSTs.