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Bayona-Vásquez NJ, Sullivan AH, Beaudry MS, Khan A, Baptista RP, Petersen KN, Bhuiyan M, Brunelle B, Robinson G, Chalmers RM, Alves-Ferreira E, Grigg ME, Kissinger JC, Glenn TC. WHOLE GENOME TARGETED ENRICHMENT AND SEQUENCING OF HUMAN-INFECTING CRYPTOSPORIDIUM spp. RESEARCH SQUARE 2024:rs.3.rs-4294842. [PMID: 38798642 PMCID: PMC11118713 DOI: 10.21203/rs.3.rs-4294842/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
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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Affiliation(s)
- N J Bayona-Vásquez
- Division of Natural Science and Mathematics, Oxford College of Emory University, Oxford, GA, 30054, USA
| | - A H Sullivan
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA, 30602, USA
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
| | - M S Beaudry
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA, 30602, USA
- Daicel Arbor Biosciences, Ann Arbor, MI, 48103, USA
| | - A Khan
- Animal Parasitic Disease Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, MD, 20705, USA
| | - R P Baptista
- Infectious Diseases, Houston Methodist Research Institute, Houston, TX, 77030, USA
| | - K N Petersen
- Odum School of Ecology, University of Georgia, University of Georgia, Athens, GA, 30602, USA
| | - Miu Bhuiyan
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA, 30602, USA
| | - B Brunelle
- Daicel Arbor Biosciences, Ann Arbor, MI, 48103, USA
| | - G Robinson
- Cryptosporidium Reference Unit, Public Health Wales, Microbiology and Health Protection, Singleton Hospital, Swansea SA2 8QA, UK
- Swansea University Medical School, Singleton Park, Swansea, SA2 8PP, UK
| | - R M Chalmers
- Cryptosporidium Reference Unit, Public Health Wales, Microbiology and Health Protection, Singleton Hospital, Swansea SA2 8QA, UK
- Swansea University Medical School, Singleton Park, Swansea, SA2 8PP, UK
| | - Evc Alves-Ferreira
- Laboratory of Parasitic Diseases, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - M E Grigg
- Laboratory of Parasitic Diseases, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - J C Kissinger
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, 30602, USA
| | - T C Glenn
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA, 30602, USA
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
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Bayona-Vásquez NJ, Sullivan AH, Beaudry MS, Khan A, Baptista RP, Petersen KN, Bhuiyan M, Brunelle B, Robinson G, Chalmers RM, Alves-Ferreira E, Grigg ME, AlvesFerreira Kissinger JC, Glenn TC. WHOLE GENOME TARGETED ENRICHMENT AND SEQUENCING OF HUMAN-INFECTING CRYPTOSPORIDIUM spp. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.29.586458. [PMID: 38585809 PMCID: PMC10996700 DOI: 10.1101/2024.03.29.586458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
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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