Klebsiella pneumoniae can cause serious pneumonitis in humans. The bacterium is also the common causative agent of hospital-acquired multidrug-resistant (MDR) infections. Here we for the first time reported the genetic diversity of K. pneumoniae strains in 14 species of edible aquatic animals sampled in the summer of 2018 and 2019 in Shanghai, China. Virulence-related genes were present in the K. pneumoniae strains (n = 94), including the entB (98.9%), mrkD (85.1%), fimH (50.0%), and ybtA (14.9%) strains. Resistance to sulfamethoxazole-trimethoprim was the most prevalent (52.1%), followed by chloramphenicol (31.9%), and tetracycline (27.7%), among the strains, wherein 34.0% had MDR phenotypes. Meanwhile, most strains were tolerant to heavy metals Cu²⁺ (96.8%), Cr³⁺ (96.8%), Zn²⁺ (91.5%), Pb²⁺ (89.4%), and Hg²⁺ (81.9%). Remarkably, a higher abundance of the bacterium was found in bottom-dwelling aquatic animals, among which mollusk Tegillarca granosa contained K. pneumoniae 8-2-5-4 isolate from serotype K2 (ST-2026). Genome features of the potentially pathogenic isolate were characterized. The enterobacterial repetitive intergenic consensus polymerase chain reaction (ERIC-PCR)–based genome fingerprinting classified the 94 K. pneumoniae strains into 76 ERIC genotypes with 63 singletons, demonstrating considerable genetic diversity in the strains. The findings of this study fill the gap in the risk assessment of K. pneumoniae in edible aquatic animals.

Klebsiella pneumoniae can cause life-threatening pneumonia in humans. The bacterium is also the causative agent of nosocomial infection diseases. In our recent research, we reported, for the first time, the presence of K. pneumoniae in fourteen species of aquatic animals sampled in Shanghai, China. Here, we further investigated the bacterial survival and genome evolution traits. The results revealed that K. pneumoniae isolates (n = 7), recovered from 7 species of commonly consumed aquatic animals, had multiple antibiotic and heavy metal resistance profiles. The isolates were capable of growing vigorously at pH 4.5−7.5 and 0.5−1.0% NaCl in TSB medium at 37 °C. Draft genome sequences of the K. pneumoniae isolates were determined (5,256,522−5,857,823 bp, 56.35–57.81% GC contents), which carried many mobile genetic elements, including genomic islands (n = 87), prophages (n = 14), integrons (n = 4), and insertion sequences (n = 22), indicating possible active horizontal gene transfer during the genome evolution. Meanwhile, numerous strain-specific (n = 199−605) genes, antibiotic resistance (n = 20−35, e.g., β-lactamase) genes, and virulence (n = 43−59, e.g., enterobactin)-related genes, were also identified, demonstrating considerable genome variation in the K. pneumoniae isolates. Overall, the results of this study fill prior gaps in understanding the K. pneumoniae genomes derived from aquatic animals.