Rapid genotyping of Toxoplasma gondii isolates via Nanopore-based multi-locus sequencing

Koutsogiannis, Zisis; Denny, Paul W.

Abstract

Toxoplasma gondii is an obligate intracellular parasite associated with severe disease, especially in the immunosuppressed. 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 T. gondii isolates is an essential asset in the understanding of parasite’s 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’s) of four different genomic loci, part of protein coding genes SAG2, SAG3, ROP17 and ROP21. This method provided results with the sequencing depth necessary for accurate differentiation of T. gondii 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.

Citation

Koutsogiannis, Z., & Denny, P. W. (2024). Rapid genotyping of Toxoplasma gondii isolates via Nanopore-based multi-locus sequencing. AMB Express, 14(1), Article 68. https://doi.org/10.1186/s13568-024-01728-x

• Journal Article Type: Article
• Acceptance Date: May 27, 2024
• Online Publication Date: Jun 6, 2024
• Publication Date: Jun 6, 2024
• Deposit Date: Jun 10, 2024
• Publicly Available Date: Jun 10, 2024
• Journal: AMB Expresss
• Electronic ISSN: 2191-0855
• Publisher: SpringerOpen
• Peer Reviewed: Peer Reviewed
• Volume: 14
• Issue: 1
• Article Number: 68
• DOI: https://doi.org/10.1186/s13568-024-01728-x
• Keywords: Multi-locus sequence typing (MLST), Genotyping, Toxoplasma gondii, Oxford Nanopore MinION
• Public URL: https://durham-repository.worktribe.com/output/2480435