Genotyping of European Toxoplasma gondii strains by a new high-resolution next-generation sequencing-based method

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F75010330%3A_____%2F24%3A00014808" target="_blank" >RIV/75010330:_____/24:00014808 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/62157124:16170/24:43880571 RIV/62157124:16810/24:43880571

Výsledek na webu

<a href="https://link.springer.com/article/10.1007/s10096-023-04721-7" target="_blank" >https://link.springer.com/article/10.1007/s10096-023-04721-7</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1007/s10096-023-04721-7" target="_blank" >10.1007/s10096-023-04721-7</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Genotyping of European Toxoplasma gondii strains by a new high-resolution next-generation sequencing-based method

Popis výsledku v původním jazyce

Purpose A new high-resolution next-generation sequencing (NGS)-based method was established to type closely related European type II Toxoplasma gondii strains.Methods T. gondii field isolates were collected from different parts of Europe and assessed by whole genome sequencing (WGS). In comparison to ME49 (a type II reference strain), highly polymorphic regions (HPRs) were identified, showing a considerable number of single nucleotide polymorphisms (SNPs). After confirmation by Sanger sequencing, 18 HPRs were used to design a primer panel for multiplex PCR to establish a multilocus Ion AmpliSeq typing method. Toxoplasma gondii isolates and T. gondii present in clinical samples were typed with the new method. The sensitivity of the method was tested with serially diluted reference DNA samples.Results Among type II specimens, the method could differentiate the same number of haplotypes as the reference standard, microsatellite (MS) typing. Passages of the same isolates and specimens originating from abortion outbreaks were identified as identical. In addition, seven different genotypes, two atypical and two recombinant specimens were clearly distinguished from each other by the method. Furthermore, almost all SNPs detected by the Ion AmpliSeq method corresponded to those expected based on WGS. By testing serially diluted DNA samples, the method exhibited a similar analytical sensitivity as MS typing.Conclusion The new method can distinguish different T. gondii genotypes and detect intra-genotype variability among European type II T. gondii strains. Furthermore, with WGS data additional target regions can be added to the method to potentially increase typing resolution.

Název v anglickém jazyce

Genotyping of European Toxoplasma gondii strains by a new high-resolution next-generation sequencing-based method

Popis výsledku anglicky

Purpose A new high-resolution next-generation sequencing (NGS)-based method was established to type closely related European type II Toxoplasma gondii strains.Methods T. gondii field isolates were collected from different parts of Europe and assessed by whole genome sequencing (WGS). In comparison to ME49 (a type II reference strain), highly polymorphic regions (HPRs) were identified, showing a considerable number of single nucleotide polymorphisms (SNPs). After confirmation by Sanger sequencing, 18 HPRs were used to design a primer panel for multiplex PCR to establish a multilocus Ion AmpliSeq typing method. Toxoplasma gondii isolates and T. gondii present in clinical samples were typed with the new method. The sensitivity of the method was tested with serially diluted reference DNA samples.Results Among type II specimens, the method could differentiate the same number of haplotypes as the reference standard, microsatellite (MS) typing. Passages of the same isolates and specimens originating from abortion outbreaks were identified as identical. In addition, seven different genotypes, two atypical and two recombinant specimens were clearly distinguished from each other by the method. Furthermore, almost all SNPs detected by the Ion AmpliSeq method corresponded to those expected based on WGS. By testing serially diluted DNA samples, the method exhibited a similar analytical sensitivity as MS typing.Conclusion The new method can distinguish different T. gondii genotypes and detect intra-genotype variability among European type II T. gondii strains. Furthermore, with WGS data additional target regions can be added to the method to potentially increase typing resolution.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

30310 - Parasitology

Projekt

—

Návaznosti

R - Projekt Ramcoveho programu EK

Rok uplatnění

2024

Kód důvěrnosti údajů

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

Název periodika

European Journal of Clinical Microbiology and Infectious Diseases

ISSN

0934-9723

e-ISSN

1435-4373

Svazek periodika

43

Číslo periodika v rámci svazku

2

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

17

Strana od-do

355-371

Kód UT WoS článku

001129755400001

EID výsledku v databázi Scopus

2-s2.0-85179934861