Genetic modification of the diarrhoeal pathogen Cryptosporidium parvum

Article metrics

Abstract

Recent studies into the global causes of severe diarrhoea in young children have identified the protozoan parasite Cryptosporidium as the second most important diarrhoeal pathogen after rotavirus1,2,3. Diarrhoeal disease is estimated to be responsible for 10.5% of overall child mortality4. Cryptosporidium is also an opportunistic pathogen in the contexts of human immunodeficiency virus (HIV)-caused AIDS and organ transplantation5,6. There is no vaccine and only a single approved drug that provides no benefit for those in gravest danger: malnourished children and immunocompromised patients7,8. Cryptosporidiosis drug and vaccine development is limited by the poor tractability of the parasite, which includes a lack of systems for continuous culture, facile animal models, and molecular genetic tools3,9. Here we describe an experimental framework to genetically modify this important human pathogen. We established and optimized transfection of C. parvum sporozoites in tissue culture. To isolate stable transgenics we developed a mouse model that delivers sporozoites directly into the intestine, a Cryptosporidium clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 system, and in vivo selection for aminoglycoside resistance. We derived reporter parasites suitable for in vitro and in vivo drug screening, and we evaluated the basis of drug susceptibility by gene knockout. We anticipate that the ability to genetically engineer this parasite will be transformative for Cryptosporidium research. Genetic reporters will provide quantitative correlates for disease, cure and protection, and the role of parasite genes in these processes is now open to rigorous investigation.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Figure 1: Transfection of C. parvum.
Figure 2: Luciferase assays for C. parvum drug resistance and CRISPR/Cas9 activity.
Figure 3: Mouse model for selection of stable C. parvum transgenics.
Figure 4: Targeted deletion of C. parvum TK.

References

  1. 1

    Kotloff, K. L. et al. Burden and aetiology of diarrhoeal disease in infants and young children in developing countries (the Global Enteric Multicenter Study, GEMS): a prospective, case-control study. Lancet 382, 209–222 (2013)

  2. 2

    Mondal, D. et al. Contribution of enteric infection, altered intestinal barrier function, and maternal malnutrition to infant malnutrition in Bangladesh. Clin. Infect. Dis. 54, 185–192 (2012)

  3. 3

    Checkley, W. et al. A review of the global burden, novel diagnostics, therapeutics, and vaccine targets for cryptosporidium. Lancet Infect. Dis. 15, 85–94 (2015)

  4. 4

    Liu, L. et al. Global, regional, and national causes of child mortality: an updated systematic analysis for 2010 with time trends since 2000. Lancet 379, 2151–2161 (2012)

  5. 5

    Raja, K. et al. Prevalence of cryptosporidiosis in renal transplant recipients presenting with acute diarrhea at a single center in Pakistan. J. Nephropathol. 3, 127–131 (2014)

  6. 6

    Hunter, P. R. & Nichols, G. Epidemiology and clinical features of Cryptosporidium infection in immunocompromised patients. Clin. Microbiol. Rev. 15, 145–154 (2002)

  7. 7

    Amadi, B. et al. Effect of nitazoxanide on morbidity and mortality in Zambian children with cryptosporidiosis: a randomised controlled trial. Lancet 360, 1375–1380 (2002)

  8. 8

    Amadi, B. et al. High dose prolonged treatment with nitazoxanide is not effective for cryptosporidiosis in HIV positive Zambian children: a randomised controlled trial. BMC Infect. Dis. 9, 195 (2009)

  9. 9

    Striepen, B. Parasitic infections: time to tackle cryptosporidiosis. Nature 503, 189–191 (2013)

  10. 10

    Upton, S. J., Tilley, M. & Brillhart, D. B. Comparative development of Cryptosporidium parvum (Apicomplexa) in 11 continuous host cell lines. FEMS Microbiol. Lett. 118, 233–236 (1994)

  11. 11

    Gut, J. & Nelson, R. G. Cryptosporidium parvum: synchronized excystation in vitro and evaluation of sporozoite infectivity with a new lectin-based assay. J. Eukaryot. Microbiol. 46, 56S–57S (1999)

  12. 12

    Hall, M. P. et al. Engineered luciferase reporter from a deep sea shrimp utilizing a novel imidazopyrazinone substrate. ACS Chem. Biol. 7, 1848–1857 (2012)

  13. 13

    Abrahamsen, M. S. et al. Complete genome sequence of the apicomplexan, Cryptosporidium parvum. Science 304, 441–445 (2004)

  14. 14

    Theodos, C. M., Griffiths, J. K., D'Onfro, J., Fairfield, A. & Tzipori, S. Efficacy of nitazoxanide against Cryptosporidium parvum in cell culture and in animal models. Antimicrob. Agents Chemother. 42, 1959–1965 (1998)

  15. 15

    Mochizuki, K. High efficiency transformation of Tetrahymena using a codon-optimized neomycin resistance gene. Gene 425, 79–83 (2008)

  16. 16

    Gueiros-Filho, F. J. & Beverley, S. M. On the introduction of genetically-modified Leishmania outside the laboratory. Exp. Parasitol. 78, 425–428 (1994)

  17. 17

    Fox, B. A., Ristuccia, J. G., Gigley, J. P. & Bzik, D. J. Efficient gene replacements in Toxoplasma gondii strains deficient for nonhomologous end-joining. Eukaryot. Cell 8, 520–529 (2009)

  18. 18

    Lee, A. H., Symington, L. S. & Fidock, D. A. DNA repair mechanisms and their biological roles in the malaria parasite Plasmodium falciparum. Microbiol. Mol. Biol. Rev. 78, 469–486 (2014)

  19. 19

    Brooks, C. F. et al. The Toxoplasma apicoplast phosphate translocator links cytosolic and apicoplast metabolism and is essential for parasite survival. Cell Host Microbe 7, 62–73 (2010)

  20. 20

    Jinek, M. et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816–821 (2012)

  21. 21

    Sidik, S. M., Hackett, C. G., Tran, F., Westwood, N. J. & Lourido, S. Efficient genome engineering of Toxoplasma gondii using CRISPR/Cas9. PLoS ONE 9, e100450 (2014)

  22. 22

    Griffiths, J. K., Theodos, C., Paris, M. & Tzipori, S. The gamma interferon gene knockout mouse: a highly sensitive model for evaluation of therapeutic agents against Cryptosporidium parvum. J. Clin. Microbiol. 36, 2503–2508 (1998)

  23. 23

    Fayer, R., Nerad, T., Rall, W., Lindsay, D. S. & Blagburn, B. L. Studies on cryopreservation of Cryptosporidium parvum. J. Parasitol. 77, 357–361 (1991)

  24. 24

    Liu, J., Bolstad, D. B., Bolstad, E. S. D., Wright, D. L. & Anderson, A. C. Towards new antifolates targeting eukaryotic opportunistic infections. Eukaryot. Cell 8, 483–486 (2009)

  25. 25

    Striepen, B. et al. Gene transfer in the evolution of parasite nucleotide biosynthesis. Proc. Natl Acad. Sci. USA 101, 3154–3159 (2004)

  26. 26

    Salic, A. & Mitchison, T. J. A chemical method for fast and sensitive detection of DNA synthesis in vivo. Proc. Natl Acad. Sci. USA 105, 2415–2420 (2008)

  27. 27

    Striepen, B. in Antimicrobial Drug Resistance Vol. 1 (eds Mayers, D. L., Lerner, S. A., Ouellette, M. & Sobel, J. D. ) 605–621 (Springer, 2009)

  28. 28

    Sheoran, A., Wiffin, A., Widmer, G., Singh, P. & Tzipori, S. Infection with Cryptosporidium hominis provides incomplete protection of the host against Cryptosporidium parvum. J. Infect. Dis. 205, 1019–1023 (2012)

  29. 29

    McDonald, V., Deer, R., Uni, S., Iseki, M. & Bancroft, G. J. Immune responses to Cryptosporidium muris and Cryptosporidium parvum in adult immunocompetent or immunocompromised (nude and SCID) mice. Infect. Immun. 60, 3325–3331 (1992)

  30. 30

    Jiang, L., Lee, P. C., White, J. & Rathod, P. K. Potent and selective activity of a combination of thymidine and 1843U89, a folate-based thymidylate synthase inhibitor, against Plasmodium falciparum. Antimicrob. Agents Chemother. 44, 1047–1050 (2000)

  31. 31

    Harb, O. S. & Roos, D. S. The Eukaryotic Pathogen Databases: a functional genomic resource integrating data from human and veterinary parasites. Methods Mol. Biol. 1201, 1–18 (2015)

  32. 32

    van Dooren, G. G., Tomova, C., Agrawal, S., Humbel, B. M. & Striepen, B. Toxoplasma gondii Tic20 is essential for apicoplast protein import. Proc. Natl Acad. Sci. USA 105, 13574–13579 (2008)

  33. 33

    Gubbels, M. J., Li, C. & Striepen, B. High-throughput growth assay for Toxoplasma gondii using yellow fluorescent protein. Antimicrob. Agents Chemother. 47, 309–316 (2003)

  34. 34

    Saeij, J. P., Boyle, J. P., Grigg, M. E., Arrizabalaga, G. & Boothroyd, J. C. Bioluminescence imaging of Toxoplasma gondii infection in living mice reveals dramatic differences between strains. Infect. Immun. 73, 695–702 (2005)

  35. 35

    Cong, L. et al. Multiplex genome engineering using CRISPR/Cas systems. Science 339, 819–823 (2013)

  36. 36

    Chakrabarti, K. et al. Structural RNAs of known and unknown function identified in malaria parasites by comparative genomics and RNA analysis. RNA 13, 1923–1939 (2007)

  37. 37

    Striepen, B. & Soldati, D. in Toxoplasma gondii: The Model Apicomplexan — Perspective and Methods (eds Weiss, L. M. & Kim, K. ) 391–415 (Elsevier, 2007)

  38. 38

    Sharling, L. et al. A screening pipeline for antiparasitic agents targeting cryptosporidium inosine monophosphate dehydrogenase. PLoS Negl. Trop. Dis. 4, e794 (2010)

  39. 39

    Bessoff, K., Sateriale, A., Lee, K. K. & Huston, C. D. Drug repurposing screen reveals FDA-approved inhibitors of human HMG-CoA reductase and isoprenoid synthesis that block Cryptosporidium parvum growth. Antimicrob. Agents Chemother. 57, 1804–1814 (2013)

  40. 40

    Mary, C. et al. Multicentric evaluation of a new real-time PCR assay for quantification of Cryptosporidium spp. and identification of Cryptosporidium parvum and Cryptosporidium hominis. J. Clin. Microbiol. 51, 2556–2563 (2013)

  41. 41

    Upton, S. J. in Cryptosporidium and Cryptosporidiosis (ed. Fayer, R. ) 181–207 (CRC, 1997)

Download references

Acknowledgements

We thank L. Sharling for initial contributions and L. Hedstrom, J. Mead, S. Vaishnava, L. Xiao and Y. Belkaid for discussion. This work was funded in part by the National Institutes of Health (NIH; R01AI112427) to B.S. and by a pilot grant from the Centers for Disease Control and the University of Georgia Research Foundation to B.S. and L. Xiao. M.J.C. was supported by training grant NIH T32AI060546 and B.S. is a Georgia Research Alliance Distinguished Investigator.

Author information

S.V. developed the transfection and luciferase assay; M.C.P. optimized transfection and developed the Cas9 system; S.V., M.C.P., A.S. and C.F.B. developed the mouse infection protocol and A.S. developed selection assays; C.F.B. developed surgery; C.J.S. and Y.B.-P. constructed some of the plasmids; and M.J.C. provided bioinformatics support. S.V., M.C.P., A.S. and C.F.B. conducted animal experiments and genotypic and phenotypic characterization. S.V., M.C.P., A.S., C.F.B. and B.S. conceived the study and B.S. wrote the manuscript with contributions from S.V., M.C.P. and A.S.

Correspondence to Boris Striepen.

Ethics declarations

Competing interests

Competing interests: S.V., C.F.B. and B.S. are listed as inventors on the Patent Cooperation Treaty (PCT) application entitled “Cryptosporidium transfection methods and transfected Cryptosporidium cells”, filed by the University of Georgia Research Foundation.

Extended data figures and tables

Extended Data Figure 1 Optimization of sporozoite transfection.

a, Ten-million sporozoites prepared in either cytomix (BTX) or Lonza Buffers SE, SF or SG (4D Nucleofection) were combined with 10 μg DNA (Eno_Nluc-GS-Nluc_Eno). Samples were electroporated using previously determined settings for BTX (1,500 V, 25 Ω, 25 μF) or various program settings for 4D Nucleofection as indicated. Parasites were added to cultures of HCT-8 cells and luciferase activity was read after 48 h. Bars represent average of two technical replicates. b, Transfection was further optimized by comparing the best preliminary settings (buffers SF and SG; programs EH 100 and EO 100) with additional pulse programs as indicated. Transfection was carried out as in a. Bars represent average of two technical replicates. c, Electroporation systems (BTX and 4D Nucleofection) were compared using the same number of C. parvum sporozoites and quantities of DNA using buffers and conditions optimized in a and b. Bars represent average of three technical replicates. Note about tenfold enhancement of transient transfection using 4D Nucleofection. The impact of electroporation on stable transformation cannot be assessed in this setup and may be higher. Experiments in a and b were done once for the purpose of optimization, while c was repeated three times; a single representative experiment is shown.

Extended Data Figure 2 Direct surgical injection of transfected C. parvum sporozoites into the small intestine.

Mice are shaved and anaesthetized with isofluorane (3% initially, then maintained at 1.5% for the surgery). The abdominal skin is disinfected with Betadine and a small incision is made into the peritoneum. Forceps are used to grasp the small intestine and 100 µl of PBS containing 107 transfected C. parvum sporozoites is injected into the lumen. The peritoneum and the abdominal skin are each sutured with 4-0 polydioxanone and mice are injected with meloxicam (1 mg kg−1) subcutaneously. Each procedure takes around 15 min, and mice recover rapidly.

Extended Data Figure 3 Optimization of paromomycin treatment of infected mice.

a, Dosing of mice accounting for drug concentration, animal weight, and measured daily water consumption. At 16 mg ml−1 each mouse received 40 mg paromomycin daily (dotted line). b, This dose was found to be sufficient to decrease oocyst shedding in treated mice to background. By day 7 mice without paromomycin treatment shed large amounts of oocysts when compared to untreated mice. Treated mice showed no shedding above background. Oocysts were enumerated by high-throughput imaging assay. Five mice were analysed individually with two technical replicates.

Extended Data Figure 4 Mouse model for selection of stable C. parvum transgenics.

Repeat of the experiment described in Fig. 3b. a, Measurement of C. parvum infection using faecal PCR. b, Luminescence measurements. Note increasing luminescence from day 6 in parasites that received resistance and Cas9 plasmids. Mice were infected in groups of four per cage and pooled faeces was analysed for each cage (each measurement represents three technical replicates).

Extended Data Figure 5 C. parvum maintains the stable transgene when passed serially in mice without paromomycin treatment.

a, Mice were infected orally with 100,000 transgenic oocysts. b, c, Infected mice were then treated with paromomycin (b) or left untreated (c). Oocysts were purified from faecal collections by sucrose flotation and CsCl centrifugation, and used to infect a second cohort of mice. Again, each mouse received 100,000 transgenic oocysts and mice were treated or not. Faeces were tested for luminescence every 3 days. Each reading represents the pooled faecal sample from five mice with three technical replicates.

Supplementary information

Supplementary Information

This file contains Supplementary Table 1, a list of sequences of primer and other oligonucleotides used in the study. (PDF 67 kb)

PowerPoint slides

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Vinayak, S., Pawlowic, M., Sateriale, A. et al. Genetic modification of the diarrhoeal pathogen Cryptosporidium parvum. Nature 523, 477–480 (2015) doi:10.1038/nature14651

Download citation

Further reading

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.