Policy: The Scoop on Poop - Number and Timing of Stool Specimen Collection

In order to clarify the appropriate means of stool testing and to provide a clinically relevant, cost-effective approach to
the evaluation of diarrheal illness, the Elliot laboratory has developed a policy for the number and timing of stool
specimen collections submitted for routine bacterial and parasitology testing.

Routine bacterial culture recommendations for diagnostic testing

A routine stool culture will detect the following: Salmonella species, Shigella species, Campylobacter species, Shiga-
toxin producing Escherichia coli, Aeromonas species, and Plesiomonas shigelloides. In addition, by special request, the
Laboratory will perform stool culture for the detection of Yersinia species and Vibrio species.

1. For stool culture, the Laboratory will accept no more than two specimens per patient, collected on consecutive
days (preferably at least 24 hours apart). Multiple stool specimens are rarely indicated for detection of bacterial
stool pathogens causing enterocolitis. In studies of adult and pediatric patients who submitted more than 1
specimen, the enteric pathogen was detected in the first sample 87-94% of the time, with the second specimen
bringing the positive rate up to 98%. If the initial stool culture is negative, then an additional stool sample may
be submitted for testing. Multiple stool samples from the same patient submitted on the same day will not be
cultured. Also, the Lab will reject more than three stools from the same patient in a 3-week period.

2. The Laboratory will not accept stool specimens submitted for culture from inpatients after the third hospital day
without prior consultation from the Microbiology Laboratory or an Infectious Disease physician. The Lab will
reject stool cultures received from adults and older (≥16 yo) pediatric patients hospitalized for >3 days, unless
the patient is known to be HIV positive or in a case of a cluster epidemic within the institution. Diarrheal stool
samples from infants and toddlers should not be rejected after the fourth day of hospitalization since studies
have shown that it may take longer to collect stool samples from pediatric patients admitted with gastroenteritis
that are placed on bowel rest and are not eating a normal diet. For adults, data has shown that entero-
pathogenic bacteria other than Clostridium difficile are grown from 0.5% of cultures obtained more than 3 days
after hospital admission compared with a 10-fold higher yield of tests for Clostridium difficile toxin. Thus, testing
for C.difficile infection and consideration of non-infectious causes such as antibiotic-associated or osmotic
diarrhea should be the first steps in the evaluation of nosocomial diarrhea.

3. At least 1 gram of stool should be collected and submitted for bacterial culture testing on each of 2 consecutive
days. More stool specimen will be required for multiple test requests on the same sample. Stool specimens
should be collected in a clean, wide mouthed plastic container with a tight-fitting lid. The specimens should not
be contaminated with water or urine. It is not appropriate for the Laboratory to process hard, solid, formed
stools for bacterial culture or C.difficile toxin assay testing by PCR. The specimen of choice to diagnose diarrheal
illness is diarrheal stool, not a formed stool or a swab.

4. Stool culture should not be performed for patients being treated with broad-spectrum antimicrobial agents,
because it is likely that the antimicrobial therapy is responsible for the diarrhea. There may be overgrowth with
other bacteria, including Pseudomonas aeruginosa, and Candida species, the role of which in disease production
is not clear. Their presence will be reported along with a statement indicating that the organism was the
predominant organism recovered and that expected enteric organisms were not present, which suggests an
antimicrobial inhibition.
 5. For Clostridium difficile toxin assay (by PCR) testing, a single loose, watery, unformed diarrheal stool specimen is
recommended as sufficient for C. difficile testing. The specimen can be held for up to 24 hours at room
temperature but must be tested within this time frame. Alternately, store the collected specimen at 2-8°C
(refrigerated) for up to 5 days. Repeat testing of patients negative by the C.difficile toxin assay PCR test should
not be performed for 7-14 days. The C.difficile PCR nucleic acid amplification test performed at the Elliot
Hospital is not FDA approved for use on formed stools, stools from ostomy contents, or on patients less than 2
years of age. Only when a physician notes that the patient has ileus, a formed stool specimen submitted for C.
difficile PCR testing will be sent to the reference laboratory for testing. Also, bear in mind, positive test results
for Clostridium difficile do not correlate well with disease in young children. For the testing of pediatric patients
under age two, stool specimens will be sent to the reference laboratory for testing. Please refer to Policy
Manager for the Infection Prevention C.difficile testing policy for testing criteria.

6. The Lab will not accept rectal swabs for bacterial stool culture. It is appropriate, however, to collect swabs from
rectal/anal folds for a VRE screen.

7. It is appropriate to submit stool specimens during the acute stage of infection (usually 5-7 days) because
pathogens decrease in number with time.

8. If fresh stool is submitted for culture that is not preserved in transport medium, the specimen must be
transported to the Laboratory for processing within 2 hours of collection. The Lab is only able to accept stool to
perform a Gram stain for leukocytes on an unpreserved specimen within two hours of collection.

9. If fresh stool is submitted for culture in transport medium, the preserved specimen may be held at room
temperature and transported to the Lab within 24 hours for the best recovery of pathogens. Keep in mind,
refrigeration of the specimen may adversely affect the ability of the Laboratory to recover Shigella species.

Routine parasitology recommendations for diagnostic testing

Full Ova & Parasite stool testing by wet mount and trichrome stain performed at the reference laboratory will detect
intestinal parasites. The reference laboratory requests submission of three separate stool specimens within a 10-day
period with an individual order submitted for each specimen. The full O&P Alcor Parasep device provided by the
laboratory for specimen transport must be used within ONE hour of specimen collection. Please note: full O&P exam
performed at the reference laboratory does not specifically detect Cryptosporidiuim, Cyclospora, Cystoisospora, and
Microsporidia. By special request, the presence of these organisms in stool can be identified by the reference
laboratory. Also, note stool antigen testing for the presence of Entamoeba histolytica antigen, the optimal test method,
can be performed at the reference laboratory.

1. Cost-effective testing includes the examination of a single diarrheal stool specimen. A second specimen for O&P
EIA screen is suggested only when the first is negative for common Giardia and Cryptosporidium parasites and
the patient remains symptomatic. A third specimen can be submitted only if the patient continues to be O&P
negative and symptomatic. At this time it is wise to consider a full O&P examination. For O&P screen, the
Laboratory will not accept more than three specimens per patient collected and submitted preferably on
separate days. Many organisms, particularly the intestinal protozoa, do not appear in the stool in consistent
numbers on a daily basis, and the series of three specimens collected every other day is considered adequate for
 parasitic screening; otherwise the series of three specimens should be submitted within no more than 10 days.
Multiple specimens from the same patient should not be submitted on the same day. One possible exception
would be a patient who has severe, watery diarrhea, in whom any organisms present might be missed because
of a tremendous dilution factor related to fluid loss. These specimens will be accepted only after consultation
with the physician.

2. The Laboratory will not accept specimens for parasitic detection from inpatients after the fourth hospital day,
without prior consultation from the Microbiology Laboratory or an Infectious Disease physician.

3. Stool specimens should be collected in a clean, wide mouthed plastic container with a tight-fitting lid. The
specimens should not be contaminated with water or urine because water may contain free-living organisms
that can be mistaken for human parasites and urine may destroy motile organisms. The presumptive diagnosis
or relevant travel history information is helpful and should accompany the test request. If there are delays
from the time of specimen passage until examination in the laboratory, the use of stool preservative should be
considered. Specimens preserved in stool fixatives should be stored at room temperature. It is also important
to use the correct ratio of stool and fixative to ensure proper fixation. Commercial vials are marked with a ”fill-
to” line for the addition of stool to the container. The stool preservative container should not be over-filled or
under-filled.

4. Collection of stool for parasite detection should always be performed before barium is used for radiological
exam. Intestinal protozoa may be undetectable for 5 to 10 days after barium is given to a patient. The following
substances may also interfere with the detection of intestinal protozoa. These include: mineral oil, bismuth,
antibiotics (metronidazole or tetracycline), antimalarial agents, and non-absorbable antidiarrheal preparations.
After administration of any of these compounds, parasites may not be recovered for a week to several weeks.
Therefore, specimen collection should be delayed for 5-10 days or at least 2 weeks after barium or antibiotics,
respectively, are administered.

5. Three specimens have also been recommended for post-therapy examinations. However, a patient who has
received treatment for a protozoan infection should be checked 3 to 4 weeks after therapy and those treated for
Taenia infections should be checked 5 to 6 weeks after therapy. In many cases, post-therapy specimens are not
collected, often as a cost containment measure. If the patient becomes symptomatic again, additional stool
specimens can be submitted. The probability of detecting clinically relevant parasites in a single stool specimen
may be as low as 50 to 60% but is >95% if three samples are examined.

6. To evaluate patients who are at risk for giardiasis, the negative predictive value of some of the immune-assays
on a single stool specimen is not sufficiently high to exclude the possibility of a Giardia lamblia infection. In
cases where the clinical suspicion for G. lamblia infection is moderate or high and the first assay yields a
negative result, testing of a second specimen is recommended.

Microbiology Department: ext. 3456

Infection Preventionists: ext. 2216 or ext. 2195

Infectious Disease office: (603) 429-1611

July 2017