Preparation of Cryptosporidium DNA for Whole Genome Sequencing

Guy Robinson; Rachel M Chalmers

doi:10.1007/978-1-4939-9748-0_9

Preparation of Cryptosporidium DNA for Whole Genome Sequencing

Methods Mol Biol. 2020:2052:129-138. doi: 10.1007/978-1-4939-9748-0_9.

Authors

Guy Robinson¹, Rachel M Chalmers²

Affiliations

¹ Cryptosporidium Reference Unit, Public Health Wales Microbiology and Health Protection, Singleton Hospital, Swansea, UK.
² Cryptosporidium Reference Unit, Public Health Wales Microbiology and Health Protection, Singleton Hospital, Swansea, UK. Rachel.Chalmers@wales.nhs.uk.

PMID: 31452161
DOI: 10.1007/978-1-4939-9748-0_9

Abstract

The application of whole genome sequencing (WGS) to Cryptosporidium has been challenged by the relatively small numbers of oocysts present in feces and lack of suitable culture systems to generate sufficient DNA that is required. Here, we provide a method for the preparation of sufficient, high-quality Cryptosporidium DNA for WGS from feces, incorporating parasite purification stages and an optional whole genome amplification step.

Keywords: Cryptosporidium; DNA extraction; WGS; Whole genome amplification; Whole genome sequencing.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Cryptosporidium / genetics*
Cryptosporidium / isolation & purification
DNA, Protozoan / genetics
DNA, Protozoan / isolation & purification*
Feces / parasitology*
Humans
Oocysts / genetics
Oocysts / isolation & purification*
Whole Genome Sequencing / methods*
Workflow

Substances

DNA, Protozoan