Cryptosporidium Genomics — Current Understanding, Advances, and Applications

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English ED, Guerin A, Tandel J, Striepen B. Live imaging of the Cryptosporidium parvum life cycle reveals direct development of male and female gametes from type I meronts. PLoS Biol. 2022;20(4):e3001604. https://doi.org/10.1371/journal.pbio.3001604.

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Tandel J, English ED, Sateriale A, Gullicksrud JA, Beiting DP, Sullivan MC, et al. Life cycle progression and sexual development of the apicomplexan parasite Cryptosporidium parvum. Nat Microbiol. 2019;4(12):2226–36. https://doi.org/10.1038/s41564-019-0539-x.

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Huang W, Guo Y, Lysen C, Wang Y, Tang K, Seabolt MH, et al. Multiple introductions and recombination events underlie the emergence of a hyper-transmissible Cryptosporidium hominis subtype in the USA. Cell Host Microbe. 2023;31(1):112-23 e4. https://doi.org/10.1016/j.chom.2022.11.013. This work demonstrates how multiple different recobmination events involving C. hominis isolates from within the USA and other countries generated the hyper-transmissiable C. hominis IfA12G1R5 subtype that is increasing in incidence in the USA.

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Ming Z, Gong AY, Wang Y, Zhang XT, Li M, Li Y, et al. Trans-suppression of host CDH3 and LOXL4 genes during Cryptosporidium parvum infection involves nuclear delivery of parasite Cdg7_FLc_1000 RNA. Int J Parasitol. 2018;48(6):423–31. https://doi.org/10.1016/j.ijpara.2017.10.008.

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Dumaine JE, Sateriale A, Gibson AR, Reddy AG, Gullicksrud JA, Hunter EN, et al. The enteric pathogen Cryptosporidium parvum exports proteins into the cytosol of the infected host cell. Elife. 2021;10. https://doi.org/10.7554/eLife.70451.

Graham ML, Li M, Gong AY, Deng S, Jin K, Wang S, et al. Cryptosporidium parvum hijacks a host’s long noncoding RNA U90926 to evade intestinal epithelial cell-autonomous antiparasitic defense. Front Immunol. 2023;14:1205468. https://doi.org/10.3389/fimmu.2023.1205468. This work demonstrates the role that the Cryptosporidium virus plays in affecting regulation of a host lncRNA to epigenetically alter the host cell anti-parastitic response.

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Fan Y, Feng Y, Xiao L. Comparative genomics: how has it advanced our knowledge of cryptosporidiosis epidemiology? Parasitol Res. 2019;118(12):3195–204. https://doi.org/10.1007/s00436-019-06537-x.

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Abrahamsen MS, Templeton TJ, Enomoto S, Abrahante JE, Zhu G, Lancto CA, et al. Complete genome sequence of the apicomplexan Cryptosporidium parvum. Science. 2004;304(5669):441–5. https://doi.org/10.1126/science.1094786.

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Corsi GI, Tichkule S, Sannella AR, Vatta P, Asnicar F, Segata N, et al. Recent genetic exchanges and admixture shape the genome and population structure of the zoonotic pathogen Cryptosporidium parvum. Mol Ecol. 2023;32(10):2633–45. https://doi.org/10.1111/mec.16556. This work identifies and traces the gene flow that resulted from several recombination events in C. parvum between ruminant and human isolates. They also age the recomination events and show that 50% have occurred in the last ~200 years.

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Tichkule S, Caccio SM, Robinson G, Chalmers RM, Mueller I, Emery-Corbin SJ, et al. Global population genomics of two subspecies of Cryptosporidium hominis during 500 years of evolution. Mol Biol Evol. 2022;39(4). https://doi.org/10.1093/molbev/msac056. This work demonstrates the evolution of two proposed subspecies of C. hominis that differ by environment and transmission, i.e., between low-income and high-income countries. These subtypes differ in putative resistance genes, effective population sizes, and there is a bias in the direciton of gene flow between them.

Tichkule S, Jex AR, van Oosterhout C, Sannella AR, Krumkamp R, Aldrich C, et al. Comparative genomics revealed adaptive admixture in Cryptosporidium hominis in Africa. Microb Genom. 2021;7(1). https://doi.org/10.1099/mgen.0.000493.

Troell K, Hallstrom B, Divne AM, Alsmark C, Arrighi R, Huss M, et al. Cryptosporidium as a testbed for single cell genome characterization of unicellular eukaryotes. BMC Genomics. 2016;17:471. https://doi.org/10.1186/s12864-016-2815-y.

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Shaw S, Cohn IS, Baptista RP, Xia G, Melillo B, Agyabeng-Dadzie F, et al. Genetic crosses within and between species of Cryptosporidium. Proc Natl Acad Sci U S A. 2024;121(1):e2313210120. https://doi.org/10.1073/pnas.2313210120. This work highlights the development of a new selectable marker for genetic studies in Cryptosporidium. They use this and an existing marker to perfrom genetic crosses between C. parvum parasites and between C. parvum and C. tyzzeri. This work also reports on the successful use of genome apmplification and long-read sequencing of single oocysts.

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Gaudin M, Desnues C. Hybrid capture-based next generation sequencing and its application to human infectious diseases. Front Microbiol. 2018;9:2924. https://doi.org/10.3389/fmicb.2018.02924.

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Gilchrist CA, Cotton JA, Burkey C, Arju T, Gilmartin A, Lin Y, et al. Genetic diversity of Cryptosporidium hominis in a Bangladeshi community as revealed by whole-genome sequencing. J Infect Dis. 2018;218(2):259–64. https://doi.org/10.1093/infdis/jiy121.

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Baptista RP, Li Y, Sateriale A, Sanders MJ, Brooks KL, Tracey A, et al. Long-read assembly and comparative evidence-based reanalysis of Cryptosporidium genome sequences reveal expanded transporter repertoire and duplication of entire chromosome ends including subtelomeric regions. Genome Res. 2022;32(1):203–13. https://doi.org/10.1101/gr.275325.121.

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Widmer G, Koster PC, Carmena D. Cryptosporidium hominis infections in non-human animal species: revisiting the concept of host specificity. Int J Parasitol. 2020;50(4):253–62. https://doi.org/10.1016/j.ijpara.2020.01.005.

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Baptista RP, Xiao R, Li Y, Glenn TC, Kissinger JC. New T2T assembly of Cryptosporidium parvum IOWA annotated with reference genome gene identifiers. bioRxiv. 2023. https://doi.org/10.1101/2023.06.13.544219. This pre-print reports on the first telomer to telomere genomic assembly for C. parvum that contains all 16 telomeres. This genome sequence is annotated using gene IDs from the current reference IOWA genome assembly when possible and extensive annotation of non-coding RNAs.

Penumarthi LR, Baptista RP, Beaudry MS, Glenn TC, Kissinger JC. A new chromosome-level genome assembly and annotation of Cryptosporidium meleagridis bioRxiv. 2024. https://doi.org/10.1101/2024.02.16.580748

Arias-Agudelo LM, Garcia-Montoya G, Cabarcas F, Galvan-Diaz AL, Alzate JF. Comparative genomic analysis of the principal Cryptosporidium species that infect humans. PeerJ. 2020;8:e10478. https://doi.org/10.7717/peerj.10478.

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Xu Z, Li N, Guo Y, Feng Y, Xiao L. Comparative genomic analysis of three intestinal species reveals reductions in secreted pathogenesis determinants in bovine-specific and non-pathogenic Cryptosporidium species. Microb Genom. 2020;6(6). https://doi.org/10.1099/mgen.0.000379.

Otto TD, Bohme U, Sanders M, Reid A, Bruske EI, Duffy CW, et al. Long read assemblies of geographically dispersed Plasmodium falciparum isolates reveal highly structured subtelomeres. Wellcome Open Res. 2018;3:52. https://doi.org/10.12688/wellcomeopenres.14571.1.

Dunn MJ, Shazib SUA, Simonton E, Slot JC, Anderson MZ. Architectural groups of a subtelomeric gene family evolve along distinct paths in Candida albicans. G3 (Bethesda). 2022;12(12). https://doi.org/10.1093/g3journal/jkac283.

Fei J, Wu H, Su J, Jin C, Li N, Guo Y, et al. Characterization of MEDLE-1, a protein in early development of Cryptosporidium parvum. Parasit Vectors. 2018;11(1):312. https://doi.org/10.1186/s13071-018-2889-2.

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Xu Z, Guo Y, Roellig DM, Feng Y, Xiao L. Comparative analysis reveals conservation in genome organization among intestinal Cryptosporidium species and sequence divergence in potential secreted pathogenesis determinants among major human-infecting species. BMC Genomics. 2019;20(1):406. https://doi.org/10.1186/s12864-019-5788-9.

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Baptista RP, Cooper GW, Kissinger JC. Challenges for Cryptosporidium population studies. Genes (Basel). 2021;12(6). https://doi.org/10.3390/genes12060894.

Wang T, Guo Y, Roellig DM, Li N, Santin M, Lombard J, et al. Sympatric recombination in zoonotic Cryptosporidium leads to emergence of populations with modified host preference. Mol Biol Evol. 2022;39(7). https://doi.org/10.1093/molbev/msac150. This comparative genomic analysis reveals how past and ongoing recombination events, especially between parasite strains isolated from humans and animals, have affected the population structure of C. parvum and affected host preference.

Li Y, Baptista RP, Mei X, Kissinger JC. Small and intermediate size structural RNAs in the unicellular parasite Cryptosporidium parvum as revealed by sRNA-seq and comparative genomics. Microb Genom. 2022;8(5). https://doi.org/10.1099/mgen.0.000821.

Li Y, Baptista RP, Sateriale A, Striepen B, Kissinger JC. Analysis of long non-coding RNA in Cryptosporidium parvum reveals significant stage-specific antisense transcription. Front Cell Infect Microbiol. 2020;10:608298. https://doi.org/10.3389/fcimb.2020.608298.

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Temesgen TT, Tysnes KR, Robertson LJ. Use of oxidative stress responses to determine the efficacy of inactivation treatments on Cryptosporidium oocysts. Microorganisms. 2021;9(7). https://doi.org/10.3390/microorganisms9071463.

Sun L, Li J, Xie F, Wu S, Shao T, Li X, et al. Whole transcriptome analysis of HCT-8 cells infected by Cryptosporidium parvum. Parasit Vectors. 2022;15(1):441. https://doi.org/10.1186/s13071-022-05565-4. This work examines host gene expression 3 and 12 h post-infection and highlights a number of coding and non-coding gene expression differences.

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Greigert V, Saraav I, Son J, Zhu Y, Dayao D, Antia A, et al. Cryptosporidium infection of human small intestinal epithelial cells induces type III interferon and impairs infectivity of Rotavirus. Gut Microbes. 2024;16(1):2297897. https://doi.org/10.1080/19490976.2023.2297897.

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Tandel J, Walzer KA, Byerly JH, Pinkston B, Beiting DP, Striepen B. Genetic ablation of a female-specific apetala 2 transcription factor blocks oocyst shedding in Cryptosporidium parvum. mBio. 2023;14(2):e0326122.

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