Laboratory Services

Gastrointestinal Pathogen Panel, PCR, Feces

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Updated Test Information:

Test Description
Gastrointestinal Pathogen Panel, PCR, Feces

Campylobacter species (C. jejuni/coli/upsaliensis); Plesiomonas shigelloides; Vibrio cholerae; Enteroaggregative Escherichia coli (EAEC); Enteropathogenic Escherichia coli (EPEC); Enterotoxigenic Escherichia coli (ETEC); Shiga toxin producing E. coli; Escherichia coli O157 serotype; Shigella/Enteroinvasive Escherichia coli (EIEC); Cyclospora cayetanensis; Giardia; Astrovirus; Norovirus GI/GII; Rotavirus A; Gastrointestinal Infections; Cryptosporidium species; Entamoeba histolytica; Multiplex PCR; Sapovirus; Salmonella species; Yersinia species; C difficile toxin A/B; Clostridium difficile toxin; Clostridioides difficile toxin; Vibrio species (V. parahaemolyticus/vulnificus/cholerae); C diff; C. diff; Clostridioides; Adenovirus F 40/41; Clostridioides (Clostridium) difficile toxin

Test ID
General Information

Useful for rapid detection of gastrointestinal infections caused by:

  • Campylobacter species (Campylobacter jejuni/Campylobacter coli/Campylobacter upsaliensis)

  • Clostridioides (Clostridium) difficile toxin A/B

  • Plesiomonas shigelloides

  • Salmonella species

  • Vibrio species (Vibrio parahaemolyticus, Vibrio vulnificus, Vibrio cholerae)

  • Vibrio cholerae

  • Yersinia species

  • Enteroaggregative Escherichia coli (EAEC)

  • Enteropathogenic E coli (EPEC)

  • Enterotoxigenic E coli (ETEC)

  • Shiga toxin

  • E coli O157

  • Shigella/Enteroinvasive E coli (EIEC)

  • Cryptosporidium species

  • Cyclospora cayetanensis

  • Entamoeba histolytica

  • Giardia

  • Adenovirus F 40/41

  • Astrovirus

  • Norovirus GI/GII

  • Rotavirus A

  • Sapovirus

  • See Parasitic Investigation of Stool Specimens Algorithm

  • See Laboratory Testing for Infectious Causes of Diarrhea

Container Type

Cary-Blair transport system is required

Specimen Type


Specimen Requirements

C and S Vial (T058)

Specimen Collection / Processing Instructions

  • Collect representative portion of feces; 1 gram or 5 mL

  • Collect fresh fecal specimen and submit in container with transport medium

  • Place feces in preservative within 2 hours of collection

Minimum Sample Volume

1 mL

Additional Processing Details

  • Samples must be received at Incyte Monday through Friday, and no later than 1:00 pm on Friday or will be rejected due to stability.

  • Specimen must arrive within 96 hours of collection

Required Information

  • In some cases, there may be local public health requirements that impact Mayo Clinic Laboratories (MCL) clients and require additional testing on specimens with positive results from this panel. Clients should familiarize themselves with local requirements. MCL recommends clients retain an aliquot of each specimen submitted for this test to perform additional testing themselves, as needed. If necessary, selected add-on tests can be performed by MCL at an additional charge, as detailed below

  • Call 800-533-1710 within 96 hours of specimen collection to request supplemental testing for positive test results:

  • Campylobacter species: Request add on test: CAMPC / Campylobacter Culture, Feces

  • Salmonella species: Request add on test: SALMC / Salmonella Culture, Feces

  • Shigella/Enteroinvasive E coli: Request add on test: SHIGC / Shigella Culture, Feces (for the Shigella/Enteroinvasive E coli target, the culture will assess for Shigella species only)

  • Yersinia species: Request add on test: YERSC / Yersinia Culture, Feces

  • Vibrio species: Request add on test: VIBC / Vibrio Culture, Feces

  • Shiga toxin-producing E coli  OR E coli O157: Request add on test: E157C / Escherichia coli O157:H7 Culture, Feces


  • Ambient (preferred): 4 days

  • Refrigerated: 4 days

Unacceptable Specimen Conditions

  • Commercial transport media other than liquid Cary Blair (eg, ETM, Para-Pak Enteric Plus; Copan FecalSwab/ESwab)

  • Cary Blair gel swab

  • Products containing formalin

  • SAF

  • PVA fixative

  • EcoFix preservative

  • Rectal swab

  • Stool swab

  • Gel swab

  • Endoscopy specimen

  • Unpreserved stool

  • Frozen specimen


  • The detection of microbial DNA or RNA is dependent upon proper sample collection, handling, transportation, storage, and preparation. There is a risk of false-negative results due to the presence of strains with sequence variability or genetic rearrangements in the target regions of the assays

  • Repeat testing should not be performed on specimens collected less than 7 days apart

  • The presence of blood or mucous in the specimen may interfere with testing

  • Aeromonas species are not detected by this panel, but may be detected by tests STL / Enteric Pathogens Culture, Feces or AERMC / Aeromonas Culture, Feces

  • The following information is provided by the test manufacturer:

  • Cary Blair media, used for dilution and processing of clinical stools, is screened by manufacturers for viable organisms but may not be specifically tested for microbial nucleic acids. The presence of nucleic acids at levels that can be detected by the FilmArray GI Panel may lead to false positive test results. (BioFire Technical Notes FLM1-PRT-0239-01 and QS-339B-01)

  • Campylobacter species: Detects but does not differentiate Campylobacter jejuni, Campylobacter coli, and Campylobacter upsaliensis. Other species will not be detected. Helicobacter pullorum may cross react

  • Clostridioides difficile: Detects but does not differentiate toxin A gene (tcdA) and toxin B gene (tcdB). A positive result may reflect asymptomatic carriage or C difficile-associated diarrhea

  • Salmonella species: Detects but does not differentiate Salmonella enterica and Salmonella bongori. Crossreactivity may occur with some strains of Escherichia coli, which have the cryptic ETT2 type-III secretion system

  • Vibrio species: Detects but does not differentiate Vibrio parahaemolyticus and Vibrio vulnificus. The assay may also react with less common Vibrio species such as, Vibrio alginolyticus, Vibrio fluvialis, and Vibrio mimicus. The assay is not expected to detect rare species of Vibrio such as: Vibrio cincinnatiensis, Vibrio furnissii and Vibrio metschnikovii. Grimontia hollisae may cross react

  • Vibrio cholerae:V cholerae is specifically reported when detected.V cholerae strains that do not carry the toxR gene or which carry highly divergent toxR genes may not be detected.Rare non-cholerae strains of Vibrio that have acquired the toxR gene may cross-react (eg, Vibrio harveyi, Vibrio mimicus, Vibrio alginolyticus, Vibrio vulnificus)

  • Yersinia species: Detects Yersinia enterocolitica but does not differentiate known serotypes or biotypes. Yersinia kristensenii, Yersinia frederiksenii, and Yersinia intermedia cross-react at high levels with Y enterocolitica; detection is reported to genus level only

  • Diarrheagenic E coli: Detects genetic determinants associated with classic diarrheagenic E coli/Shigella pathotypes. Transfer of these genes between organisms has been documented; therefore, detected results for multiple diarrheagenic E coli/Shigella may be due to the presence of multiple pathotypes or a single strain containing the genes characteristic of multiple pathotypes

  • Enteroaggregative E coli (EAEC): Detects but does not differentiate 2 gene targets typically associated with enteroaggregative E coli; the aggR regulatory gene and the putative outer membrane protein, aatA, both located on the partially-conserved pAA plasmid. pAA is not present in all strains phenotypically identified as EAEC, and not all pAA plasmids carry aggR and aatA genes; therefore, the assay will not detect all members of this diverse pathotype, but is likely to detect most pathogenic strains

  • Enterotoxigenic E coli (ETEC): Detects but does not differentiate heat-labile (LT) enterotoxin (ltA) and 2 heat-stable (ST) enterotoxin variants (st1a and st1b). Cross-reactivity may occur with strains of Hafnia alvei, Citrobacter koseri, Citrobacter sedlakii, and Cedecea davisae. LT-II and the STB/ST2 toxins are not detected

  • Enteropathogenic E coli (EPEC): Detects eae gene but does not differentiate typical and atypical EPEC. The LEE pathogenicity island, which includes the eae gene, is also found in some Shiga toxin-producing E coli (STEC; O157 and non-O157 strains). Therefore, the results of the eae assay (positive or negative) are only reported when STEC is not detected. When STEC is detected, EPEC will not be reported, regardless of the EPEC assay result. Consequently, the assay cannot distinguish between STEC containing eae and a coinfection of EPEC and STEC. Rare instances of other organisms carrying eae have been documented (eg, Aeromonas species, Citrobacter species, Escherichia albertii, Shigella boydii). Others assays target bfp to detect EPEC and, if positive, reflex to eae detection to characterize isolates as typical or atypical EPEC. The bfp gene is not used to detect EPEC in this assay. For the reasons described above, EPEC may be missed or overcalled

  • Shiga toxin-producing E coli (STEC): Detects but does not differentiate Shiga toxin 1 (stx1) and Shiga toxin 2 (stx2) sequences. Shiga toxin-positive results indicate the likely presence of STEC. Rare instances of detection of Shiga-like toxin genes in other genera and species have been reported (eg, Aeromonas caviae, Acinetobacter haemolyticus, Shigella sonnei, Enterobacter cloacae, Citrobacter freundii, Klebsiella pneumoniae)

  • E coli O157: The E coli O157 assay is not reported as detected unless a Shiga-like toxin gene is also detected. The assay cannot distinguish between infections with a single toxigenic STEC O157 or rare coinfections of STEC (nonO157) with a stx1/stx2-negative E coli O157

  • Shigella/Enteroinvasive E coli (EIEC): Detects but does not differentiate Shigella species from enteroinvasive E coli

  • Cryptosporidium species: Detects but does not differentiate approximately 23 different Cryptosporidium species, including the most common species (eg, Cryptosporidium hominis and Cryptosporidium parvum), as well as less common species (eg, Cryptosporidium meleagridis, Cryptosporidium felis, Cryptosporidium canis, Cryptosporidium cuniculus, Cryptosporidium muris, and Cryptosporidium suis), but is not expected to detect the very rare species Cryptosporidium bovis, Cryptosporidium ryanae, and Cryptosporidium xiaoi

  • Entamoeba histolytica: Detects E histolytica. Entamoeba dispar present in high levels may cross-react

  • Giardia: Detects Giardia lamblia (also known as Giardia intestinalis, Giardia duodenalis). A very low frequency of cross-reactivity with the commensal microorganisms Bifidobacterium and Ruminococcus species was observed in the clinical evaluation

  • Adenovirus F40/41: Detects but does not differentiate F40 and F41. Does not detect respiratory adenovirus species such as B, C, and E

  • Astrovirus: Detects but does not differentiate 8 subtypes (HAstV1-8)

  • Norovirus GI/GII: Detects but does not differentiate GI and GII. Does not detect genogroup GIV, nonhuman genogroups, or closely related Caliciviruses

  • Rotavirus: Detects all strains of rotavirus A. In silico sequence analysis indicates that these assays will not crossreact with rotavirus B and C, which are less common in human disease, or rotavirus D, E, and F, which have not been found in humans. Recent oral rotavirus A vaccines may result in patients passing the virus in stool and be detectable in stool PCR testing. Contamination of specimens with vaccine can cause false-positive rotavirus PCR results. Specimens should not be collected or processed in areas that are exposed to rotavirus A vaccine material

  • Sapovirus: Detects but does not differentiate genogroups I, II, IV, V. Genogroup III will not be detected.(FilmArray Gastrointestinal [GI] Panel. BioFire Diagnostics, LLC)


Multiplex Polymerase Chain Reaction (PCR)

Estimated TAT

1-2 days

Testing Schedule


Test Includes

7 days

CPT Code(s)


Reference Range

Negative (for all targets)

Performing Lab


LOINC Code(s)

31208-2, 82196-7, 82197-5, 82198-3, 82199-1, 82200-7, 82201-5, 82202-3, 80349-4, 80348-6, 80351-0, 82203-1, 82204-9, 80350-2, 82205-6, 82206-4, 82207-2, 82208-0, 82209-8, 82210-6, 82211-4, 82212-2, 82213-0, 59464-8

Additional Information