Survival and Genome Evolution Signatures of Klebsiella pneumoniae Isolates Originated in Seven Species of Aquatic Animals

Abstract

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.