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Fecal Pathogens by PCR (8000101168)
Test Mnemonic:


Specimen Requirements:


Test Included:

Panel for the detection of:

  • Campylobacter (C. jejuni, C. coli, C. upsaliensis)
  • Plesiomonas shigelloides
  • Salmonella
  • Vibrio (V. parahaemolyticus , V. vulnificus , V. cholerae), including specific identification of Vibrio cholerae
  • Yersinia enterocolitica
  • Enteroaggregative Escherichia coli (EAEC)
  • Enteropathogenic Escherichia coli (EPEC)
  • Enterotoxigenic Escherichia coli (ETEC) lt/st
  • Shiga-like toxin-producing Escherichia coli (STEC) stx1/stx2 (including specific identification of the E. coli O157 serogroup within STEC)
  • Shigella / Enteroinvasive Escherichia coli (EIEC)
  • Cryptosporidium
  • Cyclospora cayetanensis
  • Entamoeba histolytica
  • Giardia lamblia (also known as G. intestinalis and G. duodenalis)
  • Adenovirus F 40/41
  • Astrovirus
  • Norovirus GI/GII
  • Rotavirus A
  • Sapovirus (Genogroups I, II, IV, and V)

Collect feces into a clean, dry container. 


Clean, dry container

Cary-Blair preservative container (e.g., FecalSwab® collection system)

Minimum Volume:

1 mL


Feces should be transported to the lab within 2 hours of collection.  Otherwise, submit in Cary-Blair preservative (FecalSwab® tube) refrigerated or at room temperature.


Specimen Preparation:

Feces not transported to the lab immediately after collection should be transferred to a Cary-Blair transport container such as FecalSwab®.

FecalSwab® Instructions:

  1. Carefully open the pouch containing the swab and tube.
  2. Remove swab.  Do not touch the swab tip.  Handle the shaft of the swab above the marked breakpoint.
  3. Remove the cap from the tube and insert the entire tip of the swab into the feces.  Rotate swab insuring there is visible material on it.  Swab can be reinserted into the feces if necessary.  Note: Bloody, slimy, or watery area of feces should be sampled.
  4. Transfer the swab into the FecalSwab™ tube.  Insure the maximum fill line (“MAX FILL”) on the label is not exceeded.
  5. Holding the swab shaft between thumb and finger, mash and mix, the specimen against the side of the tube to evenly disperse and suspend the specimen in the liquid.
  6. Hold the tube with the inserted swab away from your face, bend the swab shaft at a 180° angle to break at the marked breakpoint.  If necessary, gently twist the shaft between thumb and forefinger to completely remove it.  Discard the shaft.
  7. Replace and tighten the cap onto the tube.
  8. Shake the tube until the sample appears homogenous.
  9. Label the tube with the sample’s identification and transport to the laboratory either refrigerated or at room temperature.

Specimens in Cary-Blair are stable up to 4 days refrigerated or at room temperature.

Causes for Rejection:

Specimens must meet criteria set forth in the Laboratory Services Specimen Labeling and Requests for Testing policy.

Formed stool specimens are not acceptable for testing.

Testing is not performed on patients that have been hospitalized > 3 days.

Specimens are canceled as duplicates if collected within 14 days.

Frozen specimen, commercial transport media other than liquid Cary Blair, Cary Blair gel swabs, products containing formalin, SAF, PVA fixative, EcoFix preservative, rectal swabs, stool swab, gel swabs, endoscopy specimens

Reference Range:


Turnaround Time:

1 - 2 days


Multiplex Polymerase Chain Reaction (PCR)


Clinical Microbiology


GI Pathogens, BioFire FilmArray, Stool Pathogens, Astrovirus, Adenovirus, Campylobacter, Cryptosporidium, Cyclospora, E. coli, O157, Entamoeba histolytica, Giardia, Norovirus, Plesiomonas, Rotavirus, Salmonella, Sapovirus, Shigella, Vibrio, Cholera, Yersinia, diarrhea

Clinical Indication:

This test is used to detect fecal pathogens in patients with severe diarrhea, diarrhea of 7 or more days, and diarrhea associated with travel outside of the United States - Campylobacter species, Plesiomonas shigelloides, Salmonella species, Vibrio species, V cholerae, Yersinia entercolitica, enteroaggregative Escherichia coli, enteropathogenic E coli, enterotoxigenic E coli, Shiga toxin-producing E coli, E coli O157, Shigella/Enteroinvasive E coli, Cryptosporidium species, Cyclospora cayetanensis, Entamoeba histolytica, Giardia lamblia, adenovirus F 40/41, astrovirus, norovirus, rotavirus, and sapovirus.

CPT 4 Code:



A negative result should not rule-out infection in patients with a high pre-test probability for gastrointestinal infection.  The assay does not test for all potential infectious agents of diarrheal disease.

Positive results do not distinguish between a viable organism and the presence of a nonviable organism or nucleic acid.

Results of the panel are intended to aid in the diagnosis of illness and are meant to be used in conjunction with other clinical and epidemiological findings.

There may be public health requirements that requires reporting as a notifiable condition and additional testing.

FecalSwab® available through Laboratory Client Services.

When ordering tests for which Medicare or Medicaid reimbursement will be sought, physicians should only order tests that are medically necessary for the diagnosis or treatment of the patient. Components of the organ or disease panels may be ordered individually. The diagnostic information must substantiate all tests ordered and must be in the form of an ICD-10 code or its verbal equivalent.
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