Detail
Článek
Článek online
FT
Medvik - BMČ
  • Je něco špatně v tomto záznamu ?

Rapid high-resolution melting genotyping scheme for Escherichia coli based on MLST derived single nucleotide polymorphisms

M. Bezdicek, M. Nykrynova, K. Sedlar, S. Kralova, J. Hanslikova, A. Komprdova, H. Skutkova, I. Kocmanova, J. Mayer, M. Lengerova

. 2021 ; 11 (1) : 16572. [pub] 20210816

Jazyk angličtina Země Velká Británie

Typ dokumentu časopisecké články, práce podpořená grantem

Perzistentní odkaz   https://www.medvik.cz/link/bmc22003924

Routinely used typing methods including MLST, rep-PCR and whole genome sequencing (WGS) are time-consuming, costly, and often low throughput. Here, we describe a novel mini-MLST scheme for Eschericha coli as an alternative method for rapid genotyping. Using the proposed mini-MLST scheme, 10,946 existing STs were converted into 1,038 Melting Types (MelTs). To validate the new mini-MLST scheme, in silico analysis was performed on 73,704 strains retrieved from EnteroBase resulting in discriminatory power D = 0.9465 (CI 95% 0.9726-0.9736) for mini-MLST and D = 0.9731 (CI 95% 0.9726-0.9736) for MLST. Moreover, validation on clinical isolates was conducted with a significant concordance between MLST, rep-PCR and WGS. To conclude, the great portability, efficient processing, cost-effectiveness, and high throughput of mini-MLST represents immense benefits, even when accompanied with a slightly lower discriminatory power than other typing methods. This study proved mini-MLST is an ideal method to screen and subgroup large sets of isolates and/or quick strain typing during outbreaks. In addition, our results clearly showed its suitability for prospective surveillance monitoring of emergent and high-risk E. coli clones'.

Citace poskytuje Crossref.org

000      
00000naa a2200000 a 4500
001      
bmc22003924
003      
CZ-PrNML
005      
20230530133646.0
007      
ta
008      
220113s2021 xxk f 000 0|eng||
009      
AR
024    7_
$a 10.1038/s41598-021-96148-3 $2 doi
035    __
$a (PubMed)34400722
040    __
$a ABA008 $b cze $d ABA008 $e AACR2
041    0_
$a eng
044    __
$a xxk
100    1_
$a Bezdíček, Matěj, $u Department of Internal Medicine, Hematology and Oncology, University Hospital Brno, Brno, Czech Republic $u Department of Internal Medicine, Hematology and Oncology, Masaryk University, Brno, Czech Republic $d 1989- $7 mub20231180867
245    10
$a Rapid high-resolution melting genotyping scheme for Escherichia coli based on MLST derived single nucleotide polymorphisms / $c M. Bezdicek, M. Nykrynova, K. Sedlar, S. Kralova, J. Hanslikova, A. Komprdova, H. Skutkova, I. Kocmanova, J. Mayer, M. Lengerova
520    9_
$a Routinely used typing methods including MLST, rep-PCR and whole genome sequencing (WGS) are time-consuming, costly, and often low throughput. Here, we describe a novel mini-MLST scheme for Eschericha coli as an alternative method for rapid genotyping. Using the proposed mini-MLST scheme, 10,946 existing STs were converted into 1,038 Melting Types (MelTs). To validate the new mini-MLST scheme, in silico analysis was performed on 73,704 strains retrieved from EnteroBase resulting in discriminatory power D = 0.9465 (CI 95% 0.9726-0.9736) for mini-MLST and D = 0.9731 (CI 95% 0.9726-0.9736) for MLST. Moreover, validation on clinical isolates was conducted with a significant concordance between MLST, rep-PCR and WGS. To conclude, the great portability, efficient processing, cost-effectiveness, and high throughput of mini-MLST represents immense benefits, even when accompanied with a slightly lower discriminatory power than other typing methods. This study proved mini-MLST is an ideal method to screen and subgroup large sets of isolates and/or quick strain typing during outbreaks. In addition, our results clearly showed its suitability for prospective surveillance monitoring of emergent and high-risk E. coli clones'.
650    12
$a techniky typizace bakterií $7 D015373
650    _2
$a zastoupení bazí $7 D001482
650    _2
$a počítačová simulace $7 D003198
650    _2
$a DNA primery $7 D017931
650    _2
$a DNA bakterií $x chemie $x genetika $7 D004269
650    _2
$a epidemický výskyt choroby $7 D004196
650    _2
$a Escherichia coli $x klasifikace $x genetika $x izolace a purifikace $7 D004926
650    _2
$a infekce vyvolané Escherichia coli $x mikrobiologie $7 D004927
650    12
$a bakteriální geny $7 D005798
650    _2
$a genom bakteriální $7 D016680
650    12
$a genotypizační techniky $7 D060005
650    _2
$a multilokusová sekvenční typizace $x metody $7 D058885
650    _2
$a denaturace nukleových kyselin $7 D009691
650    _2
$a polymerázová řetězová reakce $x metody $7 D016133
650    12
$a jednonukleotidový polymorfismus $7 D020641
650    _2
$a surveillance populace $7 D011159
650    _2
$a repetitivní sekvence nukleových kyselin $7 D012091
650    _2
$a sekvenování celého genomu $7 D000073336
651    _2
$a Česká republika $x epidemiologie $7 D018153
655    _2
$a časopisecké články $7 D016428
655    _2
$a práce podpořená grantem $7 D013485
700    1_
$a Nykrýnová, Markéta, $u Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic $d 1994- $7 xx0302014
700    1_
$a Sedlar, Karel $u Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
700    1_
$a Kralova, Stanislava $u Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Brno, Czech Republic
700    1_
$a Hansliková, Jana $u Department of Internal Medicine, Hematology and Oncology, University Hospital Brno, Brno, Czech Republic $7 xx0302018
700    1_
$a Komprdova, Aja $u Department of Internal Medicine, Hematology and Oncology, University Hospital Brno, Brno, Czech Republic
700    1_
$a Skutkova, Helena $u Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
700    1_
$a Kocmanova, Iva $u Department of Clinical Microbiology and Immunology, University Hospital Brno, Brno, Czech Republic
700    1_
$a Mayer, Jiri $u Department of Internal Medicine, Hematology and Oncology, University Hospital Brno, Brno, Czech Republic
700    1_
$a Lengerova, Martina $u Department of Internal Medicine, Hematology and Oncology, University Hospital Brno, Brno, Czech Republic. Lengerova.Martina@fnbrno.cz $u Department of Internal Medicine, Hematology and Oncology, Masaryk University, Brno, Czech Republic. Lengerova.Martina@fnbrno.cz
773    0_
$w MED00182195 $t Scientific reports $x 2045-2322 $g Roč. 11, č. 1 (2021), s. 16572
856    41
$u https://pubmed.ncbi.nlm.nih.gov/34400722 $y Pubmed
910    __
$a ABA008 $b sig $c sign $y p $z 0
990    __
$a 20220113 $b ABA008
991    __
$a 20230530133641 $b ABA008
999    __
$a ok $b bmc $g 1751400 $s 1155073
BAS    __
$a 3
BAS    __
$a PreBMC
BMC    __
$a 2021 $b 11 $c 1 $d 16572 $e 20210816 $i 2045-2322 $m Scientific reports $n Sci Rep $x MED00182195
LZP    __
$a Pubmed-20220113

Najít záznam

Citační ukazatele

Možnosti archivace