Environmental Compatibility and Genome Flexibility of Klebsiella oxytoca Isolated from Eight Species of Aquatic Animals

Abstract

Klebsiella oxytoca is an emerging pathogen that can cause life-threatening infectious diseases in humans. Recently, we firstly reported for the first time the presence of K. oxytoca in edible aquatic animals. In this study, we further investigated its bacterial environmental fitness and genome evolution signatures. The results revealed that K. oxytoca isolates (n = 8), originating from eight species of aquatic animals, were capable of growing under a broad spectrum of environmental conditions (pH 4.5–8.5, 0.5–6.5% NaCl), with different biofilm formation and swimming mobility profiles. The genome sequences of the K. oxytoca isolates were determined (5.84–6.02 Mb, 55.07–56.06% GC content). Strikingly, numerous putative mobile genetic elements (MGEs), particularly genomic islands (GIs, n = 105) and prophages (n = 24), were found in the K. oxytoca genomes, which provided the bacterium with specific adaptation traits, such as resistance, virulence, and material metabolism. Interestingly, the identified prophage-related clusters were derived from Burkholderia spp., Enterobacter spp., Klebsiella spp., Pseudomonas spp., and Haemophilus spp., suggesting phage transmission across Klebsiella and the other four genera. Many strain-specific (n = 10–447) genes were present in the K. oxytoca genomes, whereas the CRISPR-Cas protein-encoding gene was absent, indicating likely active horizontal gene transfer (HGT) and considerable genome variation in K. oxytoca evolution. Overall, the results of this study are the first to demonstrate the environmental compatibility and genome flexibility of K. oxytoca of aquatic animal origins.

Growth and Genome Features of Non-O1/O139 Vibrio cholerae Isolated from Three Species of Common Freshwater Fish

“…The V. cholerae strains were cultured in the TSB (2% NaCl, pH 8.0) until reaching the midlogarithmic growth phase (mid-LGP) at 37 • C. The bacterial cells were collected at 2700× g for 10 min at 4 • C. The genomic DNA was extracted using the TIANamp Bacteria DNA Kit (Tiangen Biochemical Technology Co., Ltd., Beijing, China) and analyzed [9,[17][18][19].…”

“…The 16S rRNA gene of V. cholerae strains was individually amplified by the PCR assay, and the PCR products were purified, sequenced, and analyzed [9,[17][18][19].…”

“…Orthologous genes in each of V. cholerae genomes were predicted using OrthoMCL software (version 14-137) [29], with their encoding proteins having at least more than 60% amino acid identity and 80% sequence coverage. Proteins with less than 30% identity or no matches were classified as strain-specific genes at a significance level of E ≤ 1 × 10 −5 [9,[17][18][19].…”

“…The phylogenetic tree of 71 V. cholerae isolates was constructed using the maximum likelihood approach [9,[17][18][19]. The cutoff threshold for bootstrap values was set above 50%.…”

“…Resistance genes (RGs) may mainly be spread through horizontal gene transfer (HGT), which is arguably the most significant driving force of bacterial evolution [8]. This transfer could occur specifically through mobile genomic elements (MGEs), such as integrons (Ins), prophages, genomic islands (GIs), and insertion sequences (ISs) [9]. HGT significantly contributes to microbial adaptation to the environments and to the hosts [10].…”