Whole Genome Sequencing and Cyclospora

Posted in Cyclospora,Outbreaks & Recalls on August 28, 2018

We often hear of Cyclospora causing gastrointestinal illness but wonder what in the world is Cyclospora? Simply put, it is a parasite, but it is only a single cell; too small to even be seen with a microscope. The infection that is causes is called Cyclosporiasis and the time that the infection enters the body until symptoms are noticed is usually about a week. Common symptoms include: watery diarrhea, but can also include: loss of appetite, weight loss, stomach pain, bloating, increased gas, nausea, and fatigue according to the CDC.

Recently a study was completed to show that Cyclospora originates from a vast number of geographic locations by doing a whole genome sequencing project.

What is Whole Genome Sequencing?

When learning about new ideas I am always extra curious about the ins and outs of how studies are completed and the methods used and why they are chosen. In doing some internet research I found a lot of information on Whole Genome Sequencing and wanted to share here.

Genes in Life wrote a great article and made whole genome sequencing easy to understand for everyone.

Whole genome sequencing is the mapping out of a person’s unique DNA. Your genome is the unique blueprint for your body. Sometimes, because of new or inherited genetic mutations, your genes can cause a disease or increase your risk for disease. By sequencing your genome, health professionals can look at the unique variations found in your genes. Some of it matters.  Some doesn’t matter. Some is still unknown or uncertain.

It is most often used in medical research and is beginning to be used more in clinical practice. For example, a doctor or genetic counselor could use whole genome sequencing to see if a patient has a genetic disorder or is at risk for a disease.

Whole genome sequencing results can be placed into 3 categories: Single-gene disorders, multi-factorial disorders, and the pharmacogenomic profile.

1. Single-gene disorders (sometimes also called Mendelian disorders) are diseases that are caused by a mutation in the DNA for one gene. An example of these diseases is Sickle Cell Anemia.
2. Multi-factorial disorders are diseases associated with DNA changes in more than one gene. This often includes diseases like obesity and diabetes and often is highly influenced by your environment.
3. Pharmacogenomic profiles use an individual’s genetic code to determine how they will respond to a drug so that a doctor can prescribe the correct amount. This is an example of personalized medicine.

Whole genome sequencing is not your average diagnostic test.  A blood pressure test will give you a straightforward ‘yes’ or ‘no’ answer about your health.  Whole genome sequencing, though, will often give you a ‘maybe.’ Most of the information you get from a genomic test tells you about your risk for disease, not whether you have a disease or will for sure get the disease.

The National Institute of Health found so much great information about whole genome sequencing and Cyclospora and we wanted to share with our readers just a bit of the study and what it means for the United States for future outbreaks including easier detection and investigation as well as ways to keep an eye on Cyclospora.

The Background:

Cyclospora cayetanensis is an emerging coccidian parasite that causes endemic and epidemic diarrheal disease called cyclosporiasis, and this infection is associated with consumption of contaminated produce or water in developed and developing regions. Food-borne outbreaks of cyclosporiasis have occurred almost every year in the USA since the 1990s. Investigations of these outbreaks are currently hampered due to lack of molecular epidemiological tools for trace back analysis. The apicoplast of C. cayetanensis, a relict non-photosynthetic plastid with an independent genome, provides an attractive target to discover sequence polymorphisms useful as genetic markers for detection and trace back analysis of the parasite. Distinct differences in the apicoplast genomes of C. cayetanensis could be useful in designing advanced molecular methods for rapid detection and, subtyping and geographical source attribution, which would aid outbreak investigations and surveillance studies.

What Method was Used?

To obtain the genome sequence of the C. cayetanensis apicoplast, we sequenced the C. cayetanensisgenomic DNA extracted from clinical stool samples, assembled and annotated a 34,146 bp-long circular sequence, and used this sequence as a reference genome in this study. We compared the genome and the predicted proteome to the data available from other apicomplexan parasites. To initialize the search for genetic markers, we mapped the raw sequence reads from an additional 11 distinct clinical stool samples originating from Nepal, New York, Texas, and Indonesia to the apicoplast reference genome.

The Results:

We identified several high-quality single nucleotide polymorphisms (SNPs) and small insertion/deletions spanning the apicoplast genome supported by extensive sequencing reads data, and a 30 bp sequence repeat at the terminal spacer region in a Nepalese sample. The predicted proteome consists of 29 core apicomplexan peptides found in most of the apicomplexans. Cluster analysis of these C. cayetanensisapicoplast genomes revealed a familiar pattern of tight grouping with Eimeria and Toxoplasma, separated from distant species such as Plasmodium and Babesia.

The Conclusion of the Study

This study focused on closing the molecular epidemiology gap to help link clinical cases to each other, and to particular food items. The availability of genomic data and associated sample metadata from across the world should accelerate the profiling of C. cayetanensis isolates or even species of Cyclospora from diverse sources samples, e.g. zoonotic samples possibly leading to development of molecular tools for identification and source-tracking. The WGS-based reference genome reported in this work was completed by high quality, in depth read-mapping and comparative genomics. In the process, we have developed a framework to perform in-depth intra- and inter-species comparisons of apicoplast genomes to study the evolutionary relationship of apicomplexan parasites, and to identify specific variations in C. cayetanensis strains.

Technology and genetics have come so far in just the last several years allowing us to know even more about illnesses than ever before. The advances in ways to detect and isolate certain illnesses make not only diagnosis but treatment better and often easier for both doctors and patients alike.

Got Cyclospora and have questions? Contact our Cyclospora Lawyer for more information.

By: Samantha Cooper, Contributing Writer (Non-Lawyer)