Experience of Klebsiella pneumoniae genome sequencing using the short read method on the Illumina platform

Abstract

Objective. To review the main stages of Klebsiella pneumoniae genome sequencing using the Illumina short-read method and describe the peculiarities of sample library preparation and analysis of the obtained data.Materials and methods. Deoxyribonucleic acid (DNA) for high-throughput sequencing was isolated from Klebsiella pneumoniae cultures. Sample preparation was performed according to the manufacturer’s instructions for the Nextera XT DNA Library Prep kit. Sequencing was performed on an Illumina MiSeq platform using a 2x151 cartridge. Genome assembly to the contigs was performed using the SPAdes Genome Assembler application on the Illumina BaseSpace Sequence Hub service and a set of programs in a Linux environment. The quality of genome assembly was assessed using the QUAST service.Results. Genome sequencing of K. pneumoniae culture samples was performed, followed by an evaluation of the quality of the launch, assembly of the genome, and determination of its main parameters.Conclusion. The main steps of K. pneumoniae genome sequencing have been considered using the short-read method on the Illumina platform. The main parameters for assessing the quality of sample preparation, launch and genome assembly are described.