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It is also a cause of congenital malformation and abortion in both animals and humans and is considered one of the most important foodborne pathogens worldwide with different strains showing variable distribution and differing pathogenicity. Thus, strain-level differentiation of <jats:italic>T. gondii<\/jats:italic> isolates is an essential asset in the understanding of parasite\u2019s diversity, geographical distribution, epidemiology and health risk. Here, we designed and implemented an Oxford Nanopore MinION protocol to analyse genomic sequence variation including single nucleotide polymorphisms (SNPs) and insertion\/deletion polymorphisms (InDel\u2019s) of four different genomic loci, part of protein coding genes <jats:italic>SAG2, SAG3, ROP17<\/jats:italic> and <jats:italic>ROP21<\/jats:italic>. This method provided results with the sequencing depth necessary for accurate differentiation of <jats:italic>T. gondii<\/jats:italic> strains and represents a rapid approach compared to conventional techniques which we further validated against environmental samples isolated from wild wood mice. In summary, multi-locus sequence typing (MLST) of both highly conserved and more polymorphic areas of the genome, provided robust data for strain classification in a platform ready for further adaption for other strains and pathogens.<\/jats:p>","DOI":"10.1186\/s13568-024-01728-x","type":"journal-article","created":{"date-parts":[[2024,6,6]],"date-time":"2024-06-06T16:01:35Z","timestamp":1717689695000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["Rapid genotyping of Toxoplasma gondii isolates via Nanopore-based multi-locus sequencing"],"prefix":"10.1186","volume":"14","author":[{"given":"Zisis","family":"Koutsogiannis","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5051-1613","authenticated-orcid":false,"given":"Paul W.","family":"Denny","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,6,6]]},"reference":[{"key":"1728_CR1","doi-asserted-by":"publisher","first-page":"4641","DOI":"10.1128\/JCM.01152-10","volume":"48","author":"D Ajzenberg","year":"2010","unstructured":"Ajzenberg D, Collinet F, Mercier A, Vignoles P, Darde ML (2010) Genotyping of Toxoplasma Gondii isolates with 15 microsatellite markers in a single multiplex PCR assay. 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