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Draft genome sequence and analysis of Klebsiella oxytoca strain NK-1 isolated from ureteral stent.

ABSTRACT: Klebsiella oxytoca is a facultative aerobic, gram-negative, rod-shaped bacterium capable of causing nosocomial infections, in particular catheter-associated urinary tract infections (CAUTIs). Data on the possible roles of uncommon pathogens such as K. oxytoca in the pathogenesis of biofilm-associated infections such as CAUTIs have been already reported. Herein, we describe the draft genome sequence of K. oxytoca strain NK-1 isolated from the surface of ureteral stent retrieved from a Russian female. The genome comprises 6,232,464 bp, with a G + C content of 55.60% and an L ₅₀ of 7. A total of 6246 putative protein-encoding genes were predicted, including considerable number of genes responsible for adhesion, invasion, drug resistance, iron acquisition and other genes relevant for virulence. The NK-1 strain was ascribed a sequence type (ST) as ST 216 (4, 6, 19, 10, 46, 24, 31). Data comparison of the recA gene sequences confirmed that the strain belongs to the species K. oxytoca. Minimal inhibitory concentration of different antibiotics have been determined. This whole genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number QPKC00000000.1.

SUBMITTER: Giliazeva AG

PROVIDER: S-EPMC6463764 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BACKGROUND: The giant panda (Ailuropoda melanoleuca) is an endangered species well-known for ingesting bamboo as a major part of their diet despite the fact that it belongs to order Carnivora. However, the giant panda's draft genome shows no direct evidence of enzymatic genes responsible for cellulose digestion. To explore this phenomenon, we study the giant panda's gut microbiota using genomic approaches in order to better understand their physiological processes as well as any potential microbial cellulose digestion processes. RESULTS: A complete genome of isolated Klebsiella oxytoca HKOPL1 of 5.9 Mb has been successfully sequenced, closed and comprehensively annotated against various databases. Genome comparisons within the Klebsiella genus and K. oxytoca species have also been performed. A total of 5,772 genes were predicted, and among them, 211 potential virulence genes, 35 pathogenicity island-like regions, 1,615 potential horizontal transferring genes, 23 potential antibiotics resistant genes, a potential prophage integrated region, 8 genes in 2,3-Butanediol production pathway and 3 genes in the cellulose degradation pathway could be identified and discussed based on the comparative genomic studies between the complete genome sequence of K. oxytoca HKOPL1 and other Klebsiella strains. A functional study shows that K. oxytoca HKOPL1 can degrade cellulose within 72 hours. Phylogenomic studies indicate that K. oxytoca HKOPL1 is clustered with K. oxytoca strains 1686 and E718. CONCLUSIONS: K. oxytoca HKOPL1 is a gram-negative bacterium able to degrade cellulose. We report here the first complete genome sequence of K. oxytoca isolated from giant panda feces. These studies have provided further insight into the role of gut microbiota in giant panda digestive physiology. In addition, K. oxytoca HKOPL1 has the potential for biofuel application in terms of cellulose degradation and potential for the production of 2,3-Butanediol (an important industrial raw material).

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Draft genome sequence and analysis of Klebsiella oxytoca strain NK-1 isolated from ureteral stent.

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