Genome-targeted enrichment and sequencing of human-infecting Cryptosporidium spp.
13 affiliations
- 1Division of Natural Science and Mathematics, Oxford College of Emory University, Oxford, GA, USA. [email protected]
- 2Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA, USA
- 3Institute of Bioinformatics, University of Georgia, Athens, GA, USA
- 4Daicel Arbor Biosciences, Ann Arbor, MI, USA
- 5Animal Parasitic Disease Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, MD, USA
- 6Center for Infectious Diseases, Houston Methodist Research Institute, Houston, TX, USA
- 7Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- 8Odum School of Ecology, University of Georgia, University of Georgia, Athens, GA, USA
- 9Cryptosporidium Reference Unit, Public Health Wales Microbiology and Health Protection, Singleton Hospital, Swansea, UK
- 10Swansea University Medical School, Singleton Park, Swansea, UK
- 11Laboratory of Parasitic Diseases, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- 12Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, USA
- 13Department of Genetics, University of Georgia, Athens, GA, USA
Abstract
Cryptosporidium spp. are protozoan parasites that cause severe illness in vulnerable human populations. Obtaining pure Cryptosporidium DNA from clinical and environmental samples is challenging because the oocysts shed in contaminated feces are limited in quantity, difficult to purify efficiently, may derive from multiple species, and yield limited DNA (<40 fg/oocyst). Here, we develop and validate a set of 100,000 RNA baits (CryptoCap_100k) based on six human-infecting Cryptosporidium spp. ( C. cuniculus , C. hominis , C. meleagridis , C. parvum , C. tyzzeri , and C. viatorum ) to enrich Cryptosporidium spp. DNA from a wide array of samples. We demonstrate that CryptoCap_100k increases the percentage of reads mapping to target Cryptosporidium references in a wide variety of scenarios, increasing the depth and breadth of genome coverage, facilitating increased accuracy of detecting and analyzing species within a given sample, while simultaneously decreasing costs, thereby opening new opportunities to understand the complex biology of these important pathogens.
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BibTeX
@article{bayonavasquez2026genometargeted,
title = {{Genome-targeted enrichment and sequencing of human-infecting Cryptosporidium spp.}},
author = {Natalia J. Bayona‐Vásquez and AH Sullivan and Megan S. Beaudry and A. Khan and Rodrigo P. Baptista and KN Petersen and MIU Bhuiyan and Brian W. Brunelle and Guy Robinson and Rachel M. Chalmers and Eliza V.C. Alves‐Ferreira and Michael E. Grigg and Jessica C. Kissinger and Travis C. Glenn},
journal = {Nature Communications},
year = {2026},
month = aug,
doi = {10.1038/s41467-026-76192-1},
url = {https://doi.org/10.1038/s41467-026-76192-1},
note = {CC BY-NC-ND},
}
RIS
TY - JOUR
TI - Genome-targeted enrichment and sequencing of human-infecting Cryptosporidium spp.
AU - Natalia J. Bayona‐Vásquez
AU - AH Sullivan
AU - Megan S. Beaudry
AU - A. Khan
AU - Rodrigo P. Baptista
AU - KN Petersen
AU - MIU Bhuiyan
AU - Brian W. Brunelle
AU - Guy Robinson
AU - Rachel M. Chalmers
AU - Eliza V.C. Alves‐Ferreira
AU - Michael E. Grigg
AU - Jessica C. Kissinger
AU - Travis C. Glenn
PY - 2026
DA - 2026/08/06
JO - Nature Communications
DO - 10.1038/s41467-026-76192-1
UR - https://doi.org/10.1038/s41467-026-76192-1
AB - Cryptosporidium spp. are protozoan parasites that cause severe illness in vulnerable human populations. Obtaining pure Cryptosporidium DNA from clinical and environmental samples is challenging because the oocysts shed in contaminated feces are limited in quantity, difficult to purify efficiently, may derive from multiple species, and yield limited DNA (<40 fg/oocyst). Here, we develop and validate a set of 100,000 RNA baits (CryptoCap_100k) based on six human-infecting Cryptosporidium spp. ( C. cuniculus , C. hominis , C. meleagridis , C. parvum , C. tyzzeri , and C. viatorum ) to enrich Cryptosporidium spp. DNA from a wide array of samples. We demonstrate that CryptoCap_100k increases the percentage of reads mapping to target Cryptosporidium references in a wide variety of scenarios, increasing the depth and breadth of genome coverage, facilitating increased accuracy of detecting and analyzing species within a given sample, while simultaneously decreasing costs, thereby opening new opportunities to understand the complex biology of these important pathogens.
SN - 2041-1723
ER -