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Cryptosporidium as a testbed for single cell genome characterization of unicellular eukaryotes
Natl Vet Inst, Dept Microbiol, S-75007 Uppsala, Sweden..
Publ Hlth Agcy Sweden, Dept Microbiol, Solna, Sweden..
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Division of Pharmacognosy. Natl Vet Inst, Dept Microbiol, S-75007 Uppsala, Sweden..
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2016 (English)In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 17, 471Article in journal (Refereed) PublishedText
Abstract [en]

Background: Infectious disease involving multiple genetically distinct populations of pathogens is frequently concurrent, but difficult to detect or describe with current routine methodology. Cryptosporidium sp. is a widespread gastrointestinal protozoan of global significance in both animals and humans. It cannot be easily maintained in culture and infections of multiple strains have been reported. To explore the potential use of single cell genomics methodology for revealing genome-level variation in clinical samples from Cryptosporidium-infected hosts, we sorted individual oocysts for subsequent genome amplification and full-genome sequencing. Results: Cells were identified with fluorescent antibodies with an 80 % success rate for the entire single cell genomics workflow, demonstrating that the methodology can be applied directly to purified fecal samples. Ten amplified genomes from sorted single cells were selected for genome sequencing and compared both to the original population and a reference genome in order to evaluate the accuracy and performance of the method. Single cell genome coverage was on average 81 % even with a moderate sequencing effort and by combining the 10 single cell genomes, the full genome was accounted for. By a comparison to the original sample, biological variation could be distinguished and separated from noise introduced in the amplification. Conclusions: As a proof of principle, we have demonstrated the power of applying single cell genomics to dissect infectious disease caused by closely related parasite species or subtypes. The workflow can easily be expanded and adapted to target other protozoans, and potential applications include mapping genome-encoded traits, virulence, pathogenicity, host specificity and resistance at the level of cells as truly meaningful biological units.

Place, publisher, year, edition, pages
2016. Vol. 17, 471
Keyword [en]
Apicomplexa, Single cell genomics, Whole genome amplification, Cryptosporidium, Multiple infection, FACS
National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
URN: urn:nbn:se:uu:diva-299711DOI: 10.1186/s12864-016-2815-yISI: 000378380600001PubMedID: 27338614OAI: diva2:950020
Swedish Civil Contingencies Agency, DNR2012-172 1109-2015-3.4.4Swedish Research Council, 2012-3892 2012-5095
Available from: 2016-07-26 Created: 2016-07-26 Last updated: 2016-07-26Bibliographically approved

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Divne, Anna-MariaAlsmark, CeciliaBertilsson, Stefan
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