Experience of Klebsiella pneumoniae genome sequencing using the short read method on the Illumina platform
A. S. Shaforost,
A. A. Ziatskov,
E. V. Voropaev,
O. V. Osipkina,
A. V. Voropaeva,
N. A. Bonda,
I. O. Stoma https://doi.org/10.51523/2708-6011.2023-20-1-19
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.
About the Authors
A. S. Shaforost
Gomel State Medical University
Belarus
Belarus
Alexander S. Shaforost, Senior Researcher at the Research Laboratory
Gomel
A. A. Ziatskov
Gomel State Medical University
Belarus
Belarus
Alexey A. Ziatskov, Senior Researcher at the Research Laboratory
Gomel
E. V. Voropaev
Gomel State Medical University
Belarus
Belarus
Evgenii V. Voropaev, Candidate of Medical Sciences, Associate Professor, Vice-Rector for Scientific Work
Gomel
O. V. Osipkina
Gomel State Medical University
Belarus
Belarus
Olga V. Osipkina, Head of the Research Laboratory
Gomel
A. V. Voropaeva
Republican scientific and practical center for radiation medicine and human ecology
Belarus
Belarus
Alla V. Voropaeva, Candidate of Biological Sciences, Associate Professor, Physician at Clinical Laboratory Diagnostics
Gomel
N. A. Bonda
Gomel Regional Center for Hygiene, Epidemiology and Public Health
Belarus
Belarus
Nadezhda A. Bonda, Head of the Microbiology Laboratory
Gomel
I. O. Stoma
Gomel State Medical University
Belarus
Belarus
Igor O. Stoma, Doctor of Medical Sciences, Associate Professor, Rector
Gomel
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Review
For citations:
Shaforost A.S., Ziatskov A.A., Voropaev E.V., Osipkina O.V., Voropaeva A.V., Bonda N.A., Stoma I.O. Experience of Klebsiella pneumoniae genome sequencing using the short read method on the Illumina platform. Health and Ecology Issues. 2023;20(1):152-159. (In Russ.) https://doi.org/10.51523/2708-6011.2023-20-1-19
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