Investigation of next-generation sequencing data of Klebsiella pneumoniae using web-based tools

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14110%2F17%3A00094427" target="_blank" >RIV/00216224:14110/17:00094427 - isvavai.cz</a>

Alternative codes found

RIV/65269705:_____/17:00067946

Result on the web

<a href="http://dx.doi.org/10.1099/jmm.0.000624" target="_blank" >http://dx.doi.org/10.1099/jmm.0.000624</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1099/jmm.0.000624" target="_blank" >10.1099/jmm.0.000624</a>

Result language

angličtina

Original language name

Investigation of next-generation sequencing data of Klebsiella pneumoniae using web-based tools

Original language description

Purpose. Rapid identification and characterization of multidrug-resistant Klebsiella pneumoniae strains is necessary due to the increasing frequency of severe infections in patients. The decreasing cost of next-generation sequencing enables us to obtain a comprehensive overview of genetic information in one step. The aim of this study is to demonstrate and evaluate the utility and scope of the application of web-based databases to next-generation sequenced (NGS) data. Methodology. The whole genomes of 11 clinical Klebsiella pneumoniae isolates were sequenced using Illumina MiSeq. Selected web-based tools were used to identify a variety of genetic characteristics, such as acquired antimicrobial resistance genes, multilocus sequence types, plasmid replicons, and identify virulence factors, such as virulence genes, cps clusters, urease-nickel clusters and efflux systems. Results. Using web-based tools hosted by the Center for Genomic Epidemiology, we detected resistance to 8 main antimicrobial groups with at least 11 acquired resistance genes. The isolates were divided into eight sequence types (ST11, 23, 37, 323, 433, 495 and 562, and a new one, ST1646). All of the isolates carried replicons of large plasmids. Capsular types, virulence factors and genes coding AcrAB and OqxAB efflux pumps were detected using BIGSdb-Kp, whereas the selected virulence genes, identified in almost all of the isolates, were detected using CLC Genomic Workbench software. Conclusion. Applying appropriate web-based online tools to NGS data enables the rapid extraction of comprehensive information that can be used for more efficient diagnosis and treatment of patients, while data processing is free of charge, easy and time-efficient.

Czech name

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Czech description

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Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

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OECD FORD branch

10606 - Microbiology

Project

<a href="/en/project/TE02000058" target="_blank" >TE02000058: Center of competence for molecular diagnostics and personalized medicine</a><br>

Continuities

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year

2017

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Journal of Medical Microbiology

ISSN

0022-2615

e-ISSN

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Volume of the periodical

66

Issue of the periodical within the volume

11

Country of publishing house

GB - UNITED KINGDOM

Number of pages

11

Pages from-to

1673-1683

UT code for WoS article

000414369800022

EID of the result in the Scopus database

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