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

Discriminatory power Highly polymorphic regions Intra-genotype variability Multilocus sequence typing Toxoplasmosis Typing

Journal

European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology

ISSN: 1435-4373

Titre abrégé: Eur J Clin Microbiol Infect Dis

Pays: Germany

ID NLM: 8804297

Informations de publication

Date de publication:
15 Dec 2023

Historique:

received: 27 09 2023

accepted: 16 11 2023

medline: 15 12 2023

pubmed: 15 12 2023

entrez: 15 12 2023

Statut: aheadofprint

Résumé

A new high-resolution next-generation sequencing (NGS)-based method was established to type closely related European type II Toxoplasma gondii strains. 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. 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. 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.

Identifiants

DOI: 10.1007/s10096-023-04721-7 PMID: 38099986

pubmed: 38099986

doi: 10.1007/s10096-023-04721-7

pii: 10.1007/s10096-023-04721-7

doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

Informations de copyright

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