Unravelling the genomes of multidrug-resistant Klebsiella quasipneumoniae: A study of clinical and environmental isolates

Klebsiella quasipneumoniae is an opportunistic pathogen that predominantly resides in the human gut posing a significant risk of severe infections in individuals with compromised immune systems. In this study, whole genome sequencing of two multi-drug-resistant clinical and freshwater K. quasipneumoniae subsp. similipneumoniae isolates was performed and compared using Illumina sequencing technology. The genome size of the clinical isolate and freshwater isolate was 5.23 Mbp and 5.22 Mbp, respectively, with a Guanine-cytosine (GC) content of 57.77 % and 57.21 %. Genomic analyses identified 29 genes associated with antimicrobial resistance, mainly related to efflux pumps. CRISPR sequences were also predicted, of which 4 were identified in the freshwater isolate and 1 in the clinical isolate. Genomic islets (GIts) and genomic islands (GIs) were also delineated using IslandViewer4. The freshwater isolate contained 13 GIs and 16 GIts, while the clinical isolate contained 14 GIs and 19 GIts, harbouring important virulence and antimicrobial resistance genes (such as acr, bdcA, fim and norB). PHASTEST analysis revealed six intact phage regions in the freshwater isolate and five in the clinical isolate. Finally, a Maximum Likelihood tree was constructed based on the amino acid sequences of 440 orthologous genes from the 98 K. quasipneumoniae genomes, showing that the isolates were positioned within distinct internal clades.