Whole genome enrichment approach for genomic surveillance of Toxoplasma gondii

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...

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Bibliographic Details
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
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Summary: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.
ISSN:0740-0020
1095-9998
DOI:10.1016/j.fm.2023.104403