Phylogenomics of captured Cryptosporidium sequenced directly from patient samples identifies clade-specific genomic architecture and host-adapted lineages
Authors: Eliza V.C. Alves‐Ferreira (National Institutes of Health, National Institute of Allergy and Infectious Diseases), A. Khan (National Institutes of Health, National Institute of Allergy and Infectious Diseases), M. D. Tettey (National Institutes of Health, National Institute of Allergy and Infectious Diseases), Fumiaki Ihara (National Institutes of Health, National Institute of Allergy and Infectious Diseases), H. Vogel (National Institutes of Health, National Institute of Allergy and Infectious Diseases), S. Botchie (University of Ghana, Noguchi Memorial Institute for Medical Research), I. Ayi (University of Ghana, Noguchi Memorial Institute for Medical Research), Mattie Christine Pawlowic (University of Dundee, Wellcome Centre for Anti-Infectives Research), Guy Robinson (Singleton Hospital, Swansea University), RM Chalmers (Singleton Hospital, Swansea University), Hernán Lorenzi (National Institutes of Health, National Institute of Allergy and Infectious Diseases), Michael E. Grigg (National Institutes of Health, National Institute of Allergy and Infectious Diseases)
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.
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Abstract
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