J 2017

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

BRHELOVÁ, Eva, Mariya ANTONOVA, Filip PARDY, Iva KOCMANOVÁ, Jiří MAYER et. al.

Basic information

Original name

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

Authors

BRHELOVÁ, Eva (203 Czech Republic, belonging to the institution), Mariya ANTONOVA (804 Ukraine, belonging to the institution), Filip PARDY (203 Czech Republic, belonging to the institution), Iva KOCMANOVÁ (203 Czech Republic), Jiří MAYER (203 Czech Republic, belonging to the institution), Zdeněk RÁČIL (203 Czech Republic, belonging to the institution) and Martina LENGEROVÁ (203 Czech Republic, guarantor, belonging to the institution)

Edition

Journal of Medical Microbiology, Reading, Society for General Microbiology, 2017, 0022-2615

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10606 Microbiology

Country of publisher

United Kingdom of Great Britain and Northern Ireland

Confidentiality degree

není předmětem státního či obchodního tajemství

Impact factor

Impact factor: 2.112

RIV identification code

RIV/00216224:14110/17:00094427

Organization unit

Faculty of Medicine

DOI

UT WoS

000414369800022

Keywords in English

next generation sequencing; Klebsiella pneumoniae; MLST; ResFinder; PlasmidFinder; BIGSdb-Kp

Tags

Tags

International impact, Reviewed
Změněno: 18/3/2018 16:53, Soňa Böhmová

Abstract

V originále

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.

Links

MUNI/A/1106/2016, interní kód MU
Name: Nové přístupy ve výzkumu, diagnostice a terapii hematologických malignit IV (Acronym: VýDiTeHeMA IV)
Investor: Masaryk University, Category A
TE02000058, research and development project
Name: Centrum kompetence pro molekulární diagnostiku a personalizovanou medicínu (Acronym: MOLDIMED)
Investor: Technology Agency of the Czech Republic