Nature Communications· 2026Q1
Phylogenomics of captured Cryptosporidium sequenced directly from patient samples identifies clade-specific genomic architecture and host-adapted lineages
- 0citations
- Q1SCImago
- 2026year
Short summary
A new RNA bait capture method (CryptoCap_75K) enables whole-genome sequencing of Cryptosporidium from as few as 25 oocysts in patient stool, revealing host-specific genomic regions linked to adaptation.
AI-generated from the title and abstract; the full text is not read.
Key points
- A new RNA bait capture method (CryptoCap_75K) enriches Cryptosporidium genomic DNA from stool, enabling sequencing from as few as 25 oocysts.
- Dual-mapping strategy using C. parvum and C. ubiquitum references minimizes bias and captures lineage-specific variation.
- Phylogenetic analyses identified three C. ubiquitum groups, with human-exclusive groups A and B (B showing admixture) and a zoonotic group C.
- Group-specific polymorphisms cluster in discrete genomic regions, suggesting conserved haploblocks are linked to host adaptation.
AI-generated from the title and abstract; the full text is not read.
Abstract
Abstract Cryptosporidium causes diarrhea and high mortality in young children in Africa and southern Asia. Low oocyst counts in stool often limit whole-genome sequencing from clinical samples. Here, we enrich for Cryptosporidium genomic DNA directly from stool samples using 74,973 RNA baits (CryptoCap_75K; 8.2 Mb) derived from gene-rich areas (100% coding capacity) within the Cryptosporidium parvum genome. This method produces genome-wide sequence data with sufficient depth and breadth of coverage using as few as 25 oocysts, including divergent species such as Cryptosporidium ubiquitum . To minimize reference bias, we utilize a dual-mapping strategy that integrates reads aligned to both C. parvum and C. ubiquitum to capture lineage-specific variation. Phylogenetic networks, haplotypes, and admixture analyses identify three C. ubiquitum groups, A and B exclusive to humans, with B showing evidence of admixture, whereas C is zoonotic. Group-specific polymorphisms cluster within discrete genomic regions, suggesting conserved haploblocks associate with host adaptation. This capture-based genomics approach provides high-resolution insights into Cryptosporidium population genetics and lays the groundwork for studies of zoonotic transmission, anthroponosis, and GWAS directly from clinical material.
The authors' abstract, as published at the source. Nature Communications, 2026 · DOI ↗
Continue with a free account
Ask the paper: 3 free questions a day about this paper; save it, get its citation, new summaries every day for your field. Takeaways are Premium.
Continue free on the webSign in with Google or Apple; no card needed. You come back to this paper.
On your phone:
ParasitologyImmunology and Microbiology