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

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.

Základní údaje

Originální název

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

Autoři

BRHELOVÁ, Eva (203 Česká republika, domácí), Mariya ANTONOVA (804 Ukrajina, domácí), Filip PARDY (203 Česká republika, domácí), Iva KOCMANOVÁ (203 Česká republika), Jiří MAYER (203 Česká republika, domácí), Zdeněk RÁČIL (203 Česká republika, domácí) a Martina LENGEROVÁ (203 Česká republika, garant, domácí)

Vydání

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

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10606 Microbiology

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Impakt faktor

Impact factor: 2.112

Kód RIV

RIV/00216224:14110/17:00094427

Organizační jednotka

Lékařská fakulta

DOI

http://dx.doi.org/10.1099/jmm.0.000624

UT WoS

000414369800022

Klíčová slova anglicky

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

Štítky

EL OK, podil

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 18. 3. 2018 16:53, Soňa Böhmová

Anotace

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.

Návaznosti

MUNI/A/1106/2016, interní kód MU

Název: Nové přístupy ve výzkumu, diagnostice a terapii hematologických malignit IV (Akronym: VýDiTeHeMA IV)

Investor: Masarykova univerzita, Nové přístupy ve výzkumu, diagnostice a terapii hematologických malignit IV, DO R. 2020_Kategorie A - Specifický výzkum - Studentské výzkumné projekty

TE02000058, projekt VaV

Název: Centrum kompetence pro molekulární diagnostiku a personalizovanou medicínu (Akronym: MOLDIMED)

Investor: Technologická agentura ČR, Centrum kompetence pro molekulární diagnostiku a personalizovanou medicínu

Citovat

BRHELOVÁ, Eva, Mariya ANTONOVA, Filip PARDY, Iva KOCMANOVÁ, Jiří MAYER, Zdeněk RÁČIL a Martina LENGEROVÁ. Investigation of next-generation sequencing data of Klebsiella pneumoniae using web-based tools. Journal of Medical Microbiology. Reading: Society for General Microbiology, 2017, roč. 66, č. 11, s. 1673-1683. ISSN 0022-2615. Dostupné z: https://dx.doi.org/10.1099/jmm.0.000624.

@article{1405561,
   author = {Brhelová, Eva and Antonova, Mariya and Pardy, Filip and Kocmanová, Iva and Mayer, Jiří and Ráčil, Zdeněk and Lengerová, Martina},
   article_location = {Reading},
   article_number = {11},
   doi = {http://dx.doi.org/10.1099/jmm.0.000624},
   keywords = {next generation sequencing; Klebsiella pneumoniae; MLST; ResFinder; PlasmidFinder; BIGSdb-Kp},
   language = {eng},
   issn = {0022-2615},
   journal = {Journal of Medical Microbiology},
   title = {Investigation of next-generation sequencing data of Klebsiella pneumoniae using web-based tools},
   volume = {66},
   year = {2017}
}

TY  - JOUR
ID  - 1405561
AU  - Brhelová, Eva - Antonova, Mariya - Pardy, Filip - Kocmanová, Iva - Mayer, Jiří - Ráčil, Zdeněk - Lengerová, Martina
PY  - 2017
TI  - Investigation of next-generation sequencing data of Klebsiella pneumoniae using web-based tools
JF  - Journal of Medical Microbiology
VL  - 66
IS  - 11
SP  - 1673-1683
EP  - 1673-1683
PB  - Society for General Microbiology
SN  - 00222615
KW  - next generation sequencing
KW  - Klebsiella pneumoniae
KW  - MLST
KW  - ResFinder
KW  - PlasmidFinder
KW  - BIGSdb-Kp
N2  - 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.
ER  -

BRHELOVÁ, Eva, Mariya ANTONOVA, Filip PARDY, Iva KOCMANOVÁ, Jiří MAYER, Zdeněk RÁČIL a Martina LENGEROVÁ. Investigation of next-generation sequencing data of Klebsiella pneumoniae using web-based tools. \textit{Journal of Medical Microbiology}. Reading: Society for General Microbiology, 2017, roč.~66, č.~11, s.~1673-1683. ISSN~0022-2615. Dostupné z: https://dx.doi.org/10.1099/jmm.0.000624.

Podrobný výpis o publikaci