A New Method for Universal Parasite Detection by Targeted Deep Amplicon Sequencing

Diseases caused by parasites are notoriously difficult to diagnose and the morphologic skills required to diagnose less common parasitic infections are becoming rarer. But in a journal article published recently in BMC Microbiome, scientists at the U.S. Centers for Disease Control and Prevention (CDC) have developed a new laboratory method that has the potential to detect all blood parasites using a single targeted deep amplicon sequencing test.

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The method, called Universal Parasite Diagnostic test, or UPDx, improves parasitic diagnosis by selectively detecting parasite DNA in a clinical blood sample without interference from human DNA. CDC scientists believe UPDx may be applied in the future to other pathogens. Because of this potential, CDC has applied for a patent on this method with plans to make it available to other researchers at no charge.

Universal Detection of Blood Parasites

The paper, entitled Restriction enzyme digestion of host DNA enhances universal detection of parasitic pathogens in blood via targeted amplicon deep sequencing, describes the universal detection of blood parasites by targeted amplicon next generation sequencing. The researchers used an 18s rRNA PCR to detect parasitic agents in human blood. To avoid problems encountered previously with selective amplification of host DNA, the researchers used restriction enzymes to preferentially cut host sequences downstream of the PCR primer binding sites, thus selectively reducing amplification of background host DNA.  While a prototype at present, the team is progressing towards optimization and improvement of the assay to reduce time, costs and improve sensitivity in order to allow its application to diagnostic testing and pathogen discovery research. While only available for blood at present, alteration and optimization of the assay for use in the detection of all parasites from feces and tissue is currently being performed.

AMD Program Supports Open Science

CDC’s Advance Molecular Detection (AMD) Program provided funding for development of UPDx. Scientists from CDC’s Division of Parasitic Diseases and Malaria used two important AMD tools—next generation genomic sequencing and bioinformatics—to create this parasite detection test. The AMD program and CDC feel it is important to make this testing process available to researchers and other laboratories. Patenting the process will keep UPDx in an open forum where it can be shared for other public health applications. Integration of this AMD technology into our arsenal of public health diagnostic tools will give us the ability to rapidly and effectively diagnose parasitic diseases and ensure American’s health and safety.

Richard Bradbury

Team Lead, Parasite Diagnostic Reference Laboratory, Centers for Disease Control and Prevention