Molecular DNA enrichment methods for parasite genomic sequencing in clinical samples: a systematic review.
Catarine Aragone de Albuquerque Mello, Gilberto Silva Nunes Bezerra, Elis Dionísio da Silva et al.
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In 30 seconds
This systematic review assessed molecular strategies for enriching parasite DNA to support whole-genome sequencing (WGS) of clinical samples, where low parasitemia and abundant host DNA can hinder sequencing. Following PRISMA 2020 guidelines, the authors identified 20 eligible studies published in searches through December 2025; most examined protozoa, particularly Plasmodium spp. Methods included hybridization capture, selective whole-genome amplification, host DNA depletion, and adaptive sampling. No single approach was suitable across all parasites: the preferred method depended on the pathogen, sample type, and research objective.
Key findings
- The review included 20 studies, most focused on protozoa, particularly Plasmodium spp.
- Approaches included hybridization capture, selective whole-genome amplification, host DNA depletion, and in silico enrichment through adaptive sampling.
- No single enrichment method was suitable for all parasites; optimal choice depended on pathogen, sample type, and research objective.
Why it matters
Enriching parasite DNA may help overcome low pathogen abundance and host-DNA predominance, barriers to applying WGS to clinical samples. Better access to parasite genomic data could support investigation of genetic variation and drug resistance, as well as genomic surveillance. The review also highlights that methods need to be matched to the intended pathogen and sample rather than treated as interchangeable.
What to keep in mind
The review reports that most included studies focused on protozoa, particularly Plasmodium spp.; evidence may therefore be less representative of other parasite groups.