The Need for Molecular Testing for Gastrointestinal Parasites

In the United States (US), gastrointestinal (GI) parasites are a significant healthcare burden, with more than 350 million cases of acute GI infections annually. Globally, parasite infections are the leading cause of mortality of children under five years old.1,2 Hence, the importance of rapid and accurate diagnosis and treatment is essential for decreasing the significant burden of GI infections.

The Center for Disease Control and Prevention (CDC) recorded a steady increase in reported GI parasite outbreaks in the US over the past 12 years until 2020 (refer to the chart below). At this point, COVID-19 restrictions significantly decreased outbreaks due to reduced mobility, and decreased local and international travel. However, now that restrictions have lifted, reported weekly parasite infections from the National Notifiable Diseases Surveillance System (NNDS) indicate a lift in reported cases in early 2022.


The Need for 'Molecular Ova and Parasite' Testing - A Giardia Case Study

Jason had a misdiagnosed Giardiasis for 60+ days from the onset of his symptoms which led to prolonged illness, inappropriate and ineffective antibiotic treatment, and financial burden. Learn about Jason's journey and how complimentary molecular diagnostic techniques support rapid and accurate detection of GI protozoa.

GI Protozoan Outbreaks in the US

Data sourced from the Center for Disease Control and Prevention (CDC)


As shown in the chart above, reported outbreaks of key infections caused by Entamoeba, Cryptosporidium, Cyclospora, Blastocystis and Giardia had climbed up until 2020, before falling dramatically in line with decreased mobility and travel due to COVID-19 pandemic restrictions.

An outbreak is defined as the occurrence of two or more cases of similar illness epidemiology linked to a common exposure. NORS data are collected from voluntary reporting only. Thus, outbreaks and illness will be underrepresented.

Data includes voluntary reported outbreaks diagnosed as Entamoeba, Cryptosporidium, Cyclospora, Blastocystis and Giardia.

Clinically Relevant Gastrointestinal Protozoa

There is increasing evidence and recognition of numerous parasites that cause symptoms of gastroenteritis.3,4,5 Whilst some are more common, there are other emerging protozoan infections that are becoming of more interest to clinicians. The table below summarises 8 clinically relevant GI protozoa that have significant infection rates in the US, and which can be screened efficiently by molecular ova and parasite methodology and compliment traditional methods, such as stool ova and parasite microscopic exams.


Giardia lamblia/intestinalis

Giardiasis is one of the leading GI parasitic infections, regularly associated with waterborne parasite outbreaks in summer months. Infection is underreported at 20.000 cases in the US each year, with real cases estimated at 1-2 million cases in the US alone.8,7 Giardia infection rarely cause death in the US, however, 4,600 people are hospitalized with giardiasis each year.8


Cryptosporidium spp.

There are more than 2.9 million cases of cryptosporidiosis recorded each year in children aged < 24 months in sub-Saharan Africa alone.9 In the US, an estimated 748,000 cryptosporidiosis cases occur each year. Higher transmission is recorded in summer months with increased recreational water use.10


Entamoeba histolytica

Amebiasis results in 100,000 human deaths annually on a global scale.9 In the US, incidence of amebiasis is low and mostly seen in returning travelers or immigrants from developing countries. In the US, amebiasis-related deaths still occur occasionally, at around five deaths per year. 11


Cyclospora cayetanensis

Between 2018 to 2021 there have been roughly 6,000 domestically-acquired cases of cyclosporiasis in the US, though like other GI parasitic infections, cases are thought to be underreported.12 Outbreaks in the US have been linked to ingestion of contaminated food and water. Infection is also associated with foreign travel.


Dientamoeba fragilis

D. fragilis was identified in 0.5% of all stool samples examined in a large US study, and the prevalence is as high as 20% to 50% in selected populations,12 In some areas of the world, the prevalence of dientamoebiasis exceeds giardiasis. 13


Blastocystis hominis

B. hominis is the predominant parasite found in human stool samples, with a higher prevalence in developing countries (50-60%) than developed countries (about 10% or less).14 It has been suggested that B. hominis may be a commensal organism that becomes pathogenic when the host is immunosuppressed, malnourished or has other infections.15



(Enterocytozoon bieneusil
Encephalitozoon intestinalis)

Microsporidia are increasingly recognized as opportunistic infectious agents worldwide.16 In developed countries prevalence rates for enteric microsporidiosis in HIV-seropositive persons with diarrhea has been seen to range from 2% to 78%.17,18


Other gastrointestinal infections

Genetic Signatures real-time PCR assays provide detection for over 30 bacterial, viral and protozoan targets. For more information about other targets in our GI product range, click here.

For more information on the regulatory status in your region, contact our team at [email protected]

The Benefits of Molecular Ova and Parasite (O&P) Testing

Multiplex PCR assays for detecting ova and parasites have many advantages compared to traditional testing, such as stool ova and parasite microscopic exams

  • Provides a faster, automated process to improve laboratory throughput
    • Rapid high throughput screening for the majority of the clinically relevant parasites in the one sample
    • Allows experienced FTEs to be redeployed to support other laboratory testing needs
  • Increased sensitivity and specificity to support improved positive detection rate21,22,23
    • Supports the detection of parasites not easily detected by traditional methods (e.g. Cyclospora spp.)
    • Molecular solutions are more accurate compared to stool ova and parasite microscopic exams which requires highly trained staff and human judgment
    • Molecular solutions are easy to use and require minimal technical experience
  • Improves reporting and surveillance for epidemiological studies
  • Improves turn around time (TAT) to support clinicians to provide rapid and appropriate administration of anti-protozoal therapies to improve patient management
  • Reduced downstream costs associated with pathology services or hospitalisation24,25

Hear Dr Marc Couturier discuss how molecular ova and parasite testing has supported his laboratory in the on-demand webinar: The burden of gastrointestinal parasites and advances in ova and parasite diagnostic screening. Click here

How Does Molecular Ova and Parasite (O&P) Testing Work?

Molecular ova and parasite testing is an application of real-time multiplex PCR developed exclusively by Genetic Signatures, driven by our proprietary 3baseTM technology. This technology improves the efficiency, sensitivity and specificity of multiplex PCR. Learn more about the advantages of 3baseTM here.

The EasyScreen™ Gastrointestinal Parasite Detection Kit allows patient samples to be tested for 8 clinically relevant gastrointestinal protozoa pathogens at one time. Using the process of PCR, unique target genes for each organism are detected, outlined in the diagram below.


Note: Genetic Signatures’ EasyScreenTM Gastrointestinal Parasite Detection Kit is currently for Investigational Use Only in the United States. Analytical and performance characteristics are not established for Analyte Specific Reagents (ASRs). Contact us for more information on the regulatory status of our products in your region. When using our products always use the label and follow the directions for use.

Educational Webinars: Molecular Testing for Parasites

Free 3-part molecular O&P webinar

Hear from industry experts in the field of parasitology

This webinar series highlights the prevalence of gastrointestinal (GI) protozoan infection, the significant health and economic burden, and the recent advances in rapid and accurate testing techniques. Traditional screening methods for detecting ova and parasites (O&P) (such as stool O&P microscopic exams) have many challenges including longer sample-to-result time and the potential for missed diagnosis. Recent advances in molecular diagnostics can complement traditional methods, while reducing the time in detecting GI protozoa and coinfection.

Webinar 1: The burden of gastrointestinal parasites and advances in ova and parasite diagnostic screening

The first webinar is now available on demand and features two key specialists in parasitology, Professor David Bruckner and Dr Marc Couturier. Rohan Baker, Senior Principal Scientist at Genetic Signatures also introduces the benefits of 3baseTM technology for molecular diagnostics.

Download here

Webinar 2: Molecular O&P - A streamlined workflow for ova and parasite testing and patient management

In this second live webinar held on July 26, two leading experts in medical diagnostics, Lynne Garcia and Damien Stark, will further discuss the advantages of the molecular detection of gastrointestinal parasites and provide an overview of the molecular diagnostic workflow for pathology laboratories. This will include describing the workflow from sample to result and reporting, and the subsequent clinical support for improved patient management. Eight clinically relevant protozoan pathogens that cause significant disease and negative health outcomes will be discussed including:

  • Giardia spp.
  • Cryptosporidium spp.
  • Cyclospora cayetanensis
  • Entamoeba histolytica
  • Dientamoeba fragilis 
  • Blastocystis spp.
  • Enterocytozoon bieneusi
  • Encephalitozoon intestinalis

Download here

Webinar 3: Syndromic PCR testing for gastrointestinal parasites, including Dientamoeba fragilis and microsporidia, and their role in gastrointestinal disease

While there are several real-time multiplex PCR panels available to detect parasites, many only test for Giardia spp., Cryptosporidium spp., and Entamoeba histolytica.

In this webinar, three experts in medical diagnostics, Susan Madison-Antenucci, Damien Stark, and Marc Couturier, will describe the benefits of employing a broader syndromic panel to include the detection of other leading pathogenic parasites causing gastrointestinal diseases, with a focus on Dientamoeba fragilis and microsporidia.

D. fragilis and microsporidia, despite their frequent association with human gastrointestinal (GI) disorders and disease, are often overlooked in their role as pathogens, and subsequently excluded from routine testing for suspected GI infections. The speakers will discuss the clinical significance of D. fragilis, and microsporidia, and the benefits of including these targets in the broader syndromic molecular detection of GI parasites.

Download here


White paper - Learn more about the benefits of Molecular O&P testing

Request to download our 28-page white paper to learn more about molecular ova and parasite testing and to hear from 5 leading clinicians and pathologists within gastrointestinal diagnostics - Dr Bobbi Pritt, Dr Marc Couturier, Dr Glen Hansen, Lexi Bracken and Dr Damien Stark. 

White Paper Contributors

Dr Bobbi Pritt

Dr Bobbi Pritt

Mayo Clinic

Dr Marc R Couturier

Dr Marc R Couturier

ARUP Laboratories

Dr Glen Hansen

Dr Glen Hansen

Hennepin Healthcare

Lexi Bracken

Lexi Bracken

ARUP Laboratories

Dr Damien Stark

Dr Damien Stark

St Vincents Sydney

Genetic Signatures' solution

EasyScreen™ Gastrointestinal Parasite Detection Kit

Genetic Signatures EasyScreenTM Gastrointestinal Parasite Detection Kit* provides a multiplex real-time PCR solution for the detection of 8 clinically relevant GI protozoan pathogens. This assay is supported by our unique 3baseTM technology and is designed to be run on Genetic Signatures’ automated system, the GS1 (see below), which streamlines sample processing, extraction, and PCR setup.

*Currently for Investigational Use Only in the United States, for in vitro diagnostic use in Canada (Health Canada), and CE-IVD in Europe.

Contact our team for kit configuration and regulatory status of our products in your region.

When using our products always read the label and follow the directions for use.


The GS1 Automated System

Watch our workflow video to learn more about how the GS1 can provide medium and high throughput molecular solutions for diagnostics. Contact our sales team below for more information on our products and ordering.


Benefits of the GS1:

  • Performs sample extraction and PCR setup
  • Fast sample processing of up to 61 samples
  • 96-well PCR setup on one platform
  • Significant walk-away-time and improved laboratory workflow
  • Wizard-driven interface enables on-board sample and reagent traceability, and supports minimal wastage
  • Automated data analysis with integration to Laboratory Information System (LIS)
  • Small footprint allows improved use of space

Contact Us

Our Sales and Technical Support team work closely with customers to provide superior testing solutions, training and support.


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  2. Sattar SBA & Singh S. (2020), Bacterial gastroenteritis. StatPearls Publishing. 
  3. Benedict KM et al. (2019), Case-case analyses of cryptosporidiosis and giardiasis using routine national surveillance data in the United States, 2005. Epidemiol Infect, 147: e178. 
  4. Casillas SM et al. (2018), Notes from the Field: Multiple Cyclosporiasis Outbreaks — United States, 2018. Morb Mortal Wkly Rep, 67: 1101–1102. 
  5. Shirley DT et al. (2018), A Review of the Global Burden, New Diagnostics, and Current Therapeutics for Amebiasis. Open Forum Infect Dis, 5(7): ofy161. 
  6. Coffey CM et al. (2021), Evolving Epidemiology of Reported Giardiasis Cases in the United States, 1995–2016. Clin Infect Dis, ciaa128. 
  7. Cama VA & Mathison BA (2015), Infections by Intestinal Coccidia and Giardia duodenalis. Clin Lab Med, 35(2): 423–444 
  8. Giardia Factsheet  
  9. Ryan U et al. (2017), New Technologies for Detection of Enteric Parasites. Trends Parasitol, 33(7): 532– 546. 
  10. Benedict KM et al. (2019), Case-case analyses of cryptosporidiosis and giardiasis using routine national surveillance data in the United States, 2005. Epidemiol Infect, 147: e178. 
  11. Shirley DT et al. (2018), A Review of the Global Burden, New Diagnostics, and Current Therapeutics for Amebiasis. Open Forum Infect Dis, 5(7): ofy161. 
  12. U.S. Food & Drug Administration (FDA), 2021, FDA Releases Cyclospora Prevention, Response and Research Action Plan, [online] Accessed on 31/03/2022. 
  13. Science Direct, [online] Accessed on 31/03/2022. 
  14. Duda, A., et al. (2015), The prevalence of Blastocystis hominis and other protozoan parasites in soldiers returning from peacekeeping missions, Am J Trop Med Hyg, 92(4), 805–806. 
  15. World Health Organisation (WHO), Blastocystis, [online] Accessed on 31/03/2022.  
  16. Stark, D., et al. (2009). Clinical significance of enteric protozoa in the immunosuppressed human population. Clinical Microbiology Reviews. 
  17. Didier, E.S., et al. (2004). Epidemiology of microsporidiosis: sources and modes of transmission. Veterinary Parasitology. 126, pp. 145–166. 
  18. Matos, O., et al. (2012). Epidemiology of Enterocytozoon bieneusi Infection in Humans. Journal of Parasitology Research. 2012, pp. 981424. 
  19. Garcia LS et al. (2017), Practical Guidance for Clinical Microbiology Laboratories: Laboratory Diagnosis of Parasites from the Gastrointestinal Tract. Clin Microbiol Rev, 15; 31(1). 
  20. McHardy IH et al. (2014), Detection of intestinal protozoa in the clinical laboratory. J Clin Microbiol, 52: 712–720. 
  21. Stark D et al. (2014) Evaluation of the EasyScreen™ enteric parasite detection kit for the detection of Blastocystis spp., Cryptosporidium spp., Dientamoeba fragilis, Entamoeba complex, and Giardia intestinalis from clinical stool samples. Diagn Microbiol Infect Dis, 78(2): 149–52. 
  22. Dirani G et al. (2019), EasyScreen™ Enteric Protozoa Assay For the Detection of Intestinal Parasites: A Retrospective Bi-Center Study. J Parasitol, 105(1): 58–63 
  23. Siah SP et al. (2014), Improved detection of gastrointestinal pathogens using generalised sample processing and amplification panels. Pathology, 46(1): 53–9. 
  24. Golan Y et al. (2005), Empirical anti-Candida therapy among selected patients in the intensive care unit: a cost-effectiveness analysis. Ann Intern Med, 143: 857–869. 
  25. Dasta JF et al. (2005), Daily cost of an intensive care unit day: the contribution of mechanical ventilation. Crit Care Med, 33: 1266–1271.