About Medical Parasitology

New Infections

Ova & Parasite (O&P) Exams

CPT Codes

Quizzes, General

Quizzes, Histology

Quizzes, Blood

Review Tests


Information Tables

Organism Index (A-Z)

Informational Tables

- Parasite Classification | - Parasite, Body Site |
- Stool Testing Order Recommendations | - STAT Testing |
- Fecal Fixatives | - Stool Collection Options | - Report Comments |
- Tips for Fecal ImmunoAssay | - Malaria (5 Species) |
- Malaria (5 Species) Images | - Rapid Malaria Testing |
- Malaria Parasitemia Method | - Malaria Parasitemia Interpretation |

- HELMINTH PARASITES ASSOCIATED WITH EOSINOPHILIA | - Histology: Staining Characteristics - Table 1 | - Histological Identification of Parasites - Table 2 | - Microscope Calibration | - Figures for Histology Identification Table 2

References for Section 7

Stool Collection and Testing Options






Rejection of stools from inpatients who have been in-house for >3 daysa


Data suggests that patients who begin to have diarrhea after they have been inpatients for a few days are not symptomatic from parasitic infections, but generally other causes.



There is always the chance that the problem is related to a healthcare-associated (nosocomial) parasitic infection (rare), but Cryptosporidium and microsporidia may be possible considerations.


Examination of a single stool (O&P examination)

Data suggest that 40-50% of organisms present will be found with only a single stool exam.


Two O&P exams (concentration, permanent stained smear) are acceptable, but not always as good as three specimens (may be relatively cost-effective approach); any patient remaining symptomatic would require additional testing.



Some feel that most intestinal parasitic infections can be diagnosed from examination of a single stool. However, this is not really the best clinical approach, and limited diagnostic information is obtained from this approach.


With the examination of 3 specimens, the yield of protozoa increases (Entamoeba histolytica, 22.7%; Giardia lamblia, 11.3%; and Dientamoeba fragilis, 31.1%)



Diagnosis from a single stool examination depends primarily on the parasite load in the specimen. In a series of 3 stool specimens, frequently not all 3 specimens are positive and/or may be positive for different organisms. Thus, the examination of a single specimen provides very limited information.


Examination of a single stool and an immunoassay (EIA, FA, lateral or vertical flow cartridge) This approach is a mix: one immunoassay may be acceptable; however, immunoassay testing of two separate specimens may be required to confirm the presence of Giardia antigen. One O&P exam is not the best approach (review options above) Very few laboratories use this approach – SEE ORDERING RECOMMENDATIONS TABLE


If the examinations are negative and the patient’s symptoms subside, then probably no further testing is required



Patients may exhibit symptoms (off and on), so it may be difficult to “rule out” parasitic infections with only a single stool and one fecal immunoassay. If the patient remains symptomatic, then even if two Giardia immunoassays are negative, other protozoa may be missed (the Entamoeba histolytica/E. dispar group, Entamoeba histolytica, Dientamoeba fragilis, Cryptosporidium spp., the microsporidia). Normally, there are specific situations where fecal immunoassays OR O&P exams should be ordered. It is not recommended to automatically perform both the O&P and fecal immunoassay as a stool exam for parasites. Specific ordering options apply to either the O&P or a fecal immunoassay (which detects only limited organisms)



Pool three specimens for examination; perform one concentration and one permanent stain (the laboratory would pool the specimens).


Three specimens are collected by the patient (three separate collection vials) over 7-10 days and pooling by the laboratory may save time and expense.



Organisms present in low numbers may be missed due to the dilution factor once the specimens are pooled.   This is not a recommended approach.



Pool three specimens for examination; perform a single concentrate and three permanent stained smears on each of the collection vial contents (the laboratory would pool the specimens).


Three specimens are collected by the patient (three separate collection vials) over 7-10 days; pooling by the laboratory for the concentration would probably be sufficient for the identification of helminth eggs.  Examination of the three separate permanent stained smears (one from each vial) would maximize recovery of intestinal protozoa in areas of the country where these organisms are most common.




Might miss light helminth infection (eggs, larvae) due to the pooling of the three specimens for the concentration; however, with a permanent stain performed on each of the three specimens, this approach would probably be the next best option in lieu of the standard approach (concentration and permanent stained smear performed on every stool).  Coding and billing would have to match the work performed.


The patient collects three stools, but puts a sample of stool from all three specimens into a single vial (patient given a single vial only) (the patient would pool the specimens).



Pooling of the specimens would require only a single vial.


This would complicate patient collection and very likely result in poorly preserved specimens, especially regarding the recommended ratio of stool to preservative and the lack of proper mixing of specimen and fixative. The vials would tend to be overfilled.



Perform immunoassays on selected patientsb using methods for Giardia lamblia, Cryptosporidium spp. and/or the Entamoeba histolytica/E. dispar group or Entamoeba histolytica.(true pathogen)




Would be more cost-effective than performing immunoassay procedures on all specimens; however, information required to group patients is often not received with specimens.  This approach assumes the physicians have guidance in terms of correct ordering options. Ordering Recommendations:  Routine O&P Examinations OR Fecal Immunoassays




Labs rarely receive information that would allow them to place a patient in a particular risk group:  children <5 yrs old, children from day-care centers (may or may not be symptomatic), patients with immunodeficiencies, and patients from outbreaks. 

Performance of immunoassay procedures on every stool is not cost-effective and the positive rate will be low unless an outbreak situation is involved.  Education for the physicians is critical for proper test ordering.



Perform immunoassays and O&P examinations ON REQUEST*  Giardia lamblia, Cryptosporidium spp. and/or Entamoeba histolytica/E. dispar group or Entamoeba histolytica


A number of variables will determine the approach to immunoassay testing and the O&P examination (geography, organisms recovered, positive rate, physician requests).  Immunoassays and/or O&P examinations should be separately ordered, reported, and billed.





Using this approach, will limit number of stools on which immunoassay procedures are performed for parasites.  Immunoassay results do not have to be confirmed by any other testing (such as O&P examinations or modified acid-fast stains).  If specific kit performance problems have been identified, individual laboratories may prefer to do additional testing.  HOWEVER, the fecal immunoassays are more sensitive than the O&P examination and special stains (modified acid-fast stains).  Also, this may be considered duplicate testing and may not be approved for reimbursement unless specifically ordered by the physician.



Will require education of the physician clients regarding appropriate times and patients for whom fecal immunoassays should be ordered.  Educational initiatives must also include information on the test report indicating the pathogenic parasites that will NOT be detected using these methods.  It is critical to make sure clients know that if patients have become asymptomatic, further testing may not be required.  HOWEVER, if the patient remains symptomatic, then further testing (O&P exams) is required.  Remember, a single O&P may not reveal all organisms present.


Present plan to physicians for approval:  Immunoassays or O&P examinations, procedure discussion, report formats, clinical relevance, and limitations on each approach.



Perform molecular panels on request as an overall screening approachc .


It is important to remember that using any algorithm must include the option for additional testing if the panel tests are negative but the patient remains symptomatic


This approach will also depend on the parasites included in the panel


Using this approach, some of the intestinal protozoa will be targeted for identification (Giardia, Entamoeba histolytica or the Entamoeba histolytica/E. dispar group, Cryptosporidium, or Cyclospora). Not all panels contain all relevant protozoan targets


Some of the most numerous/important organisms are not widely available as molecular panel targets (Dientamoeba fragilis, Blastocystis spp., microsporidia including Enterocytozoon bieneusi and Encephalitozoon intestinalis). If the panel results are negative and the patient remains symptomatic, additional testing is recommended.


a O&P, ova and parasite examination; EIA, enzyme-linked immunoassay; FA, fluorescent antibody immunoassay.

b See Ordering Recommendations:  Routine O&P Examinations or Fecal Immunoassays. It’s difficult to know when you may be in an early outbreak situation where testing of all specimens for either Giardia lamblia, Cryptosporidium spp., or both, may be relevant.  Extensive efforts are underway to encourage communication among laboratories, water companies, pharmacies, and public health officials regarding the identification of potential or actual outbreaks.  If it appears that an outbreak is in the early stages, then performing the immunoassays on request can be changed to screening all stools.

c One of the molecular automated parasite panels will include Blastocystis, Cryptosporidium, Cyclospora, Dientamoeba, E. histolytica, Giardia, microsporidia (Enterocytozoon bieneusi, Encephalitozoon intestinalis), and Strongyloides. FDA clearance for this panel is pending and is anticipated in 2021 (VERIGENE II GI panel).



Garcia LS. Diagnostic Medical Parasitology, 6 th ed. Washington, D.C.: ASM Press; 2015

Garcia LS. Practical Guide to Diagnostic Parasitology, 3rd ed. Washington, D.C.: ASM Press; 2021

Hiatt RA, Markell EK, and Ng E.  How many stool examinations are necessary to detect pathogenic intestinal protozoa?  Am. J. Trop. Med. Hyg.


Kehl KSC.  Screening stools for Giardia and Cryptosporidium: are antigen tests enough? Clin. Micro. News. 1996;18:133-135.

Morris AJ, Wilson ML, and Reller LB. Application of rejection criteria for stool ovum and parasite examinations.  J. Clin. Microbiol. 1992;30:3213-3216.

Siegel, DL, Edelstein PH, and Nachamkin, I. Inappropriate testing for diarrheal diseases in the hospital.  JAMA 1990;263:979-982.