Sequencing a parasite genome

Draft Genome Assembly of a Potentially Zoonotic Cryptosporidium parvum Isolate, UKP1. Nash JHE*, Robertson J*, Elwin K, Chalmers RA, Kropinski AM, and Guy RA*. Microbiol Resour Announc 2018 Nov 15; 7(19). doi:

This science story details the collaborative work resulting in a publication on the assembly of a draft genome sequence for a zoonotic isolate of Cryptosporidium parvum (C. parvum). As highlighted in this work, important tools are being developing to better study the biology and transmission of this highly prevalent global parasite.

What was known about this area prior to your work, and why was the research done?

Cryptosporidiosis is a reportable disease in Canada that was first identified as a human disease in 1976. It is caused by an enteric parasite transmitted though food and water or direct contact. During the 1980s, cryptosporidiosis was attributed as the major cause of chronic diarrhea in AIDS patients. Today, it is the second most important diarrheal disease and global leading cause of morbidity and mortality in children under 5 years of age. Currently, there are 36 known species of Cryptosporidium and over 60 genotypes, yet human infections in Canada are typically identified only at the genus level of Cryptosporidium. Beyond this, very little is known about the biology or transmission of the parasite, and there is a lack of molecular subtyping tools that could help fully characterize this parasite and assist in outbreak investigations associated with treated recreational water, food, or direct contact of young farm livestock. When we started our research, there were only three whole genome sequences (WGS) of Cryptosporidium publically available (C. parvum, C. hominis and C. muris). Our research was done to help create much needed molecular-based tools that could be developed by comparing Cryptosporidium genomes. These subtyping tools would facilitate improved surveillance and better understanding transmission routes of the parasite.

What are your most significant findings from this work?

Cryptosporidium is challenging to grow in a laboratory setting, thereby making it difficult to extract sufficient DNA for sequencing and analysis. We developed an approach to overcome this limitation through whole genome amplification. We used two sequencing platforms to ensure good genome coverage in developing the draft Cryptosporidium genome assembly. In doing this, we found a high level of sequence similarity between our human isolate and a cattle reference isolate, which supports that this parasite is potentially zoonotic and could be used to inform routes of transmission and infection control procedures.

What are the implications or impact of the research?

We used a new method that allows for whole genome sequencing from limited parasite material. This approach will help public health researchers further explore this often neglected parasite by removing a significant barrier in generating WGS data. The comparison and analysis of different Cryptosporidium genome sequence strains will aid in designing much needed subtyping tools by identifying genomic markers to distinguish isolates and possibly virulence traits. In doing so, this will allow for improved surveillance and outbreak source identification that can help mitigate its spread.

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