Whole genome enrichment approach for genomic surveillance of Toxoplasma gondii

• Published in: Food microbiology 2024-04, Vol.118, p.104403-104403, Article 104403
• Main Authors: Sundararaman, Balaji, Shapiro, Karen, Packham, Andrea, Camp, Lauren, Meyer, Rachel S., Shapiro, Beth, Green, Richard Ed
• Format: Article
• Language: English
• Subjects: Genomic epidemiology; One health; Pathogen surveillance; Shellfish; Toxoplasmosis; Whole genome enrichment
• ISSN: 0740-0020; 1095-9998
• DOI: 10.1016/j.fm.2023.104403

Pathogenic bacteria, viruses, fungi, and protozoa can cause food and waterborne diseases. Surveillance methods must therefore screen for these pathogens at various stages of water distribution and of food from production to consumption. Detection using nucleic acid amplification methods offer rapid identification, but such methods have limited utility for characterizing populations, variant types or virulence traits of pathogens. Whole genome sequencing (WGS) can be used to determine this information. However, pathogens must be isolated and cultured to yield sufficient DNA for WGS, which is laborious or not feasible for certain stages of parasites like oocysts of Toxoplasma gondii. We previously developed the Circular Nucleic acid Enrichment Reagent (CNER) method to make whole genome enrichment (WGE) baits for difficult-to-grow bacterial pathogens. WGE using CNERs facilitates direct sequencing of pathogens from samples without the need to isolate and grow them. Here, we made WGE-CNERs for T. gondii to demonstrate the use of the CNER method to make baits to enrich the large genomes of water and foodborne protozoan pathogens. By sequencing, we detected as few as 50 parasites spiked in an oyster hemolymph matrix. We discuss the use of WGE-CNERs for genomic surveillance of food and waterborne pathogens. •Whole genome enrichment allows direct sequencing of pathogens from samples.•We describe a method to make probes for whole genome enrichment of Toxoplasma.•We enriched Toxoplasma gondii DNA from as few as 50 parasites in oysters.•Our probes are specific to enrich T. gondii, but not related Sarcocystidae species.