Contribution of PCR Denaturing Gradient Gel Electrophoresis
Combined with Mixed Chromatogram Software Separation for
Complex Urinary Sample Analysis

J 2017

Contribution of PCR Denaturing Gradient Gel Electrophoresis Combined with Mixed Chromatogram Software Separation for Complex Urinary Sample Analysis

KOTÁSKOVÁ, Iva, Barbora MALIŠOVÁ, Hana OBRUČOVÁ, Veronika HOLÁ, Tereza PEROUTKOVÁ et. al.

Basic information

Original name

Contribution of PCR Denaturing Gradient Gel Electrophoresis Combined with Mixed Chromatogram Software Separation for Complex Urinary Sample Analysis

Authors

KOTÁSKOVÁ, Iva (203 Czech Republic, belonging to the institution), Barbora MALIŠOVÁ (203 Czech Republic, belonging to the institution), Hana OBRUČOVÁ (203 Czech Republic, belonging to the institution), Veronika HOLÁ (203 Czech Republic, belonging to the institution), Tereza PEROUTKOVÁ (203 Czech Republic, belonging to the institution), Filip RŮŽIČKA (203 Czech Republic, belonging to the institution) and Tomáš FREIBERGER (203 Czech Republic, guarantor, belonging to the institution)

Edition

Journal of Molecular Microbiology and Biotechnology, Basel, Karger, 2017, 1464-1801

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10606 Microbiology

Country of publisher

Switzerland

Confidentiality degree

není předmětem státního či obchodního tajemství

Impact factor

Impact factor: 1.462

RIV identification code

RIV/00216224:14110/17:00095700

Organization unit

Faculty of Medicine

DOI

http://dx.doi.org/10.1159/000484524

UT WoS

000426010400003

Keywords in English

Catheter; Complex sample; Mixed chromatogram; PCR denaturing gradient gel electrophoresis; RipSeq Mixed

Abstract

V originále

Complex samples are a challenge for sequencing-based broad-range diagnostics. We analysed 19 urinary catheter, ureteral Double-J catheter, and urine samples using 3 methodological approaches. Out of the total 84 operational taxonomic units, 37, 61, and 88% were identified by culture, PCR-DGGE-SS (PCR denaturing gradient gel electrophoresis followed by Sanger sequencing), and PCR-DGGE-RM (PCR- DGGE combined with software chromatogram separation by RipSeq Mixed tool), respectively. The latter approach was shown to be an efficient tool to complement culture in complex sample assessment.

Links

MUNI/A/1183/2015, interní kód MU

Name: Patogeneze a léčba humorální imunodeficiencí

Investor: Masaryk University, Category A

NT13242, research and development project

Name: Polymikrobiální biofilm jako příčina chronických močových infekcí a selhávání terapie: kultivační a PCR-DGGE diagnostika, význam a možnosti řešení

Investor: Ministry of Health of the CR

NV16-31593A, research and development project

Name: Polymikrobiální biofilm jako komplexní mikrobiom v rámci léčby nozokomiálních infekcí

Citovat

KOTÁSKOVÁ, Iva, Barbora MALIŠOVÁ, Hana OBRUČOVÁ, Veronika HOLÁ, Tereza PEROUTKOVÁ, Filip RŮŽIČKA and Tomáš FREIBERGER. Contribution of PCR Denaturing Gradient Gel Electrophoresis Combined with Mixed Chromatogram Software Separation for Complex Urinary Sample Analysis. Journal of Molecular Microbiology and Biotechnology. Basel: Karger, 2017, vol. 27, No 6, p. 350-355. ISSN 1464-1801. Available from: https://dx.doi.org/10.1159/000484524.

@article{1404252,
   author = {Kotásková, Iva and Mališová, Barbora and Obručová, Hana and Holá, Veronika and Peroutková, Tereza and Růžička, Filip and Freiberger, Tomáš},
   article_location = {Basel},
   article_number = {6},
   doi = {http://dx.doi.org/10.1159/000484524},
   keywords = {Catheter; Complex sample; Mixed chromatogram; PCR denaturing gradient gel electrophoresis; RipSeq Mixed},
   language = {eng},
   issn = {1464-1801},
   journal = {Journal of Molecular Microbiology and Biotechnology},
   title = {Contribution of PCR Denaturing Gradient Gel Electrophoresis Combined with Mixed Chromatogram Software Separation for Complex Urinary Sample Analysis},
   volume = {27},
   year = {2017}
}

TY  - JOUR
ID  - 1404252
AU  - Kotásková, Iva - Mališová, Barbora - Obručová, Hana - Holá, Veronika - Peroutková, Tereza - Růžička, Filip - Freiberger, Tomáš
PY  - 2017
TI  - Contribution of PCR Denaturing Gradient Gel Electrophoresis Combined with Mixed Chromatogram Software Separation for Complex Urinary Sample Analysis
JF  - Journal of Molecular Microbiology and Biotechnology
VL  - 27
IS  - 6
SP  - 350-355
EP  - 350-355
PB  - Karger
SN  - 14641801
KW  - Catheter
KW  - Complex sample
KW  - Mixed chromatogram
KW  - PCR denaturing gradient gel electrophoresis
KW  - RipSeq Mixed
N2  - Complex samples are a challenge for sequencing-based broad-range diagnostics. We analysed 19 urinary catheter, ureteral Double-J catheter, and urine samples using 3 methodological approaches. Out of the total 84 operational taxonomic units, 37, 61, and 88% were identified by culture, PCR-DGGE-SS (PCR denaturing gradient gel electrophoresis followed by Sanger sequencing), and PCR-DGGE-RM (PCR- DGGE combined with software chromatogram separation by RipSeq Mixed tool), respectively. The latter approach was shown to be an efficient tool to complement culture in complex sample assessment.
ER  -

KOTÁSKOVÁ, Iva, Barbora MALIŠOVÁ, Hana OBRUČOVÁ, Veronika HOLÁ, Tereza PEROUTKOVÁ, Filip RŮŽIČKA and Tomáš FREIBERGER. Contribution of PCR Denaturing Gradient Gel Electrophoresis Combined with Mixed Chromatogram Software Separation for Complex Urinary Sample Analysis. \textit{Journal of Molecular Microbiology and Biotechnology}. Basel: Karger, 2017, vol.~27, No~6, p.~350-355. ISSN~1464-1801. Available from: https://dx.doi.org/10.1159/000484524.

Detailed Information on Publication Record