Phylogenomics of captured Cryptosporidium sequenced directly from patient samples identifies clade-specific genomic architecture and host-adapted lineages
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.
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BibTeX
@article{alvesferreira2026phylogenomics,
title = {{Phylogenomics of captured Cryptosporidium sequenced directly from patient samples identifies clade-specific genomic architecture and host-adapted lineages}},
author = {E. V. C. Alves-Ferreira and A. Khan and M. D. Tettey and F. Ihara and H. Vogel and S. Botchie and I. Ayi and M. C. Pawlowic and G. Robinson and R. M. Chalmers and H. A. Lorenzi and M. E. Grigg},
journal = {Nature Communications},
year = {2026},
month = oct,
doi = {10.1038/s41467-026-78927-6},
url = {https://www.nature.com/articles/s41467-026-78927-6},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Phylogenomics of captured Cryptosporidium sequenced directly from patient samples identifies clade-specific genomic architecture and host-adapted lineages
AU - E. V. C. Alves-Ferreira
AU - A. Khan
AU - M. D. Tettey
AU - F. Ihara
AU - H. Vogel
AU - S. Botchie
AU - I. Ayi
AU - M. C. Pawlowic
AU - G. Robinson
AU - R. M. Chalmers
AU - H. A. Lorenzi
AU - M. E. Grigg
PY - 2026
DA - 2026/10/24
JO - Nature Communications
DO - 10.1038/s41467-026-78927-6
UR - https://www.nature.com/articles/s41467-026-78927-6
AB - 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.
SN - 2041-1723
ER -