Expanded Stool Gastrointestinal Panel by PCR

Test Mnemonic


CPT Codes

  • 87507 - QTY (1)


  • adenovirus F40/41
  • astrovirus
  • biofire
  • campylobacter
  • cholerae
  • cryptosporidium
  • cyclospora
  • E. coli
  • EAEC
  • EIEC
  • entamoeba histolytica
  • EPEC
  • ETEC
  • gastrointestinal
  • giardia
  • GIP
  • norovirus
  • O157
  • plesiomonas
  • rotavirus
  • salmonella
  • sapovirus
  • shiga toxin
  • shigella
  • STEC
  • stool
  • stx1
  • stx2
  • vibrio
  • yersinia

Performing Laboratory

Cleveland Clinic Laboratories

Specimen Requirements

Volume Type Container Collect Temperature Transport Temperature Special Instructions
OneStoolCary-Blair kit  The stool must be passed into a clean, dry, wide mouthed container and not contaminated by urine or water. A bed pan is an ideal initial collection container provided it has been thoroughly cleaned and the patient is cautioned against contaminating the specimen with urine. A plastic bag placed over the toilet seat is also acceptable. Select bloody, slimy, or watery portions of the stool using the collection spoon provided in the cap of the container. Place enough stool (~1g) in the Cary-Blair transport vial (Oracle #1124361, or #1570140 as part of STUL kit) to bring the liquid level up to the “fill to here” line. Mash and mix the stool with the spoon along the sides of the container. Tighten the cap and shake the vial until the mixture appears homogeneous.


Environmental Condition Description
Ambient4 days in Cary-Blair transport media
Refrigerated4 days in Cary-Blair transport media

Days Performed

7 days a week

Turnaround Time

24 hours


Name Description
Qualitative Polymerase Chain Reaction 

Reference Range

Clinical Info

The Biofire FilmArray Gastrointestinal (GI) Panel is an FDA-cleared multiplexed nucleic acid test that qualitatively detects and identifies nucleic acids from 21 bacterial, viral, and parasitic targets directly from stool samples in Cary-Blair transport media. This panel does not contain Clostridium difficile, which must be ordered separately (SQCDPCR) if clinically appropriate. This panel contains the following targets: Campylobacter species (C. jejuni/C. coli/C. upsaliensis), Plesiomonas shigelloides, Salmonella species, Vibrio species (V. parahaemolyticus/V. vulnificus/ V. cholerae), Vibrio cholerae, Yersinia enterocolitica, Enteroaggregative E.coli (EAEC), Enteropathogenic E.coli (EPEC), Enterotoxigenic E.coli (ETEC), Shiga-like toxin producing E.coli (STEC), E.coli O157, Shigella/Enteroinvasive E.coli (EIEC), Adenovirus F 40/41, Astrovirus, Norovirus GI/GII, Rotavirus A, Sapovirus (Genogroups I, II, IV, V), Cryptosporidium, Cyclospora cayetanensis, Entamoeba histolytica, and Giardia lamblia. Specimens positive for organisms of public health concern may be reflexed to culture and/or sendout testing at a public health lab as indicated in the result comments. The Infectious Diseases Society of America recommends stool pathogen testing in individuals with diarrhea accompanied by fever, bloody or mucoid stools, severe abdominal cramping or tenderness, or signs of sepsis; in an outbreak setting; and in immunocompromised hosts with diarrhea. Identification of the infectious etiology of diarrheal illness can help guide appropriate therapy, prevent unnecessary or harmful antibiotic exposure, and facilitate further workup. Repeat testing within 14 days of the same episode of diarrhea, or for test of cure, is not recommended. Consider a more limited PCR panel for the most common enteric bacterial pathogens only (SQSTLPCR) for patients who are not immunocompromised or severely-ill. Immunocompromised individuals with persistent diarrhea may benefit from additional testing (ie. SQOVAP: Stool Ova/Parasite Exam, SQCRYSPO: Cryptosporidium/Cyclospora/Cystoisospora Exam, SQMICSPO: Microsporidia Exam, and gastrointestinal biopsy, among others). Individuals with travel history outside the United States with persistent diarrhea lasting >14 days may benefit from additional parasitic testing (ie. SQOVAP: Stool Ova/Parasite exam, SQCRYSPO: Cryptosporidium/Cyclospora/Cystoisospora exam). Individuals with onset of diarrhea after more than 3 days of hospital admission or with prior antibiotic exposure history may benefit from testing for C. difficile (SQCDPCR).

Clinical Limitation

The Biofire FilmArray Gastrointestinal (GI) Panel is indicated as an aid in the diagnosis of specific agents of gastrointestinal illness and results are meant to be used in conjunction with other clinical, laboratory, and epidemiological data. Positive results do not rule out coinfection with organisms not included in the panel. The agent detected may not be the definite cause of the disease. Some targets on this panel have potential for false positives due to contaminated transport media, or non-specific cross reactivity. Some have been associated with asymptomatic colonization/infection. Negative results in the setting of clinical illness compatible with gastroenteritis may be due to infection by pathogens that are not detected by this test or non-infectious causes such as ulcerative colitis, irritable bowel syndrome, or Crohn’s disease. Some patients may experience financial toxicity with this expanded multiplex panel, as it is variably reimbursed by insurance.

Clinical Reference

1. Shane AL, Mody RK, Crump JA, Tarr PI, Steiner TS, Kotloff K, Langley JM, Wanke C, Warren CA, Cheng AC, Cantey J, Pickering LK. 2017 Infectious Diseases Society of America Clinical Practice Guidelines for the Diagnosis and Management of Infectious Diarrhea. Clin Infect Dis. 2017 Nov 29;65(12):e45-e80. doi: 10.1093/cid/cix669. PMID: 29053792. 2. Buss SN, Leber A, Chapin K, Fey PD, Bankowski MJ, Jones MK, Rogatcheva M, Kanack KJ, Bourzac KM. Multicenter evaluation of the BioFire FilmArray gastrointestinal panel for etiologic diagnosis of infectious gastroenteritis. J Clin Microbiol. 2015 Mar;53(3):915-25. doi: 10.1128/JCM.02674-14. Epub 2015 Jan 14. PMID: 25588652. 3. Collins JP, Shah HJ, Weller DL, Ray LC, Smith K, McGuire S, Trevejo RT, Jervis RH, Vugia DJ, Rissman T, Garman KN, Lathrop S, LaClair B, Boyle MM, Harris S, Kufel JZ, Tauxe RV, Bruce BB, Rose EB, Griffin PM, Payne DC. Preliminary Incidence and Trends of Infections Caused by Pathogens Transmitted Commonly Through Food - Foodborne Diseases Active Surveillance Network, 10 U.S. Sites, 2016-2021. MMWR Morb Mortal Wkly Rep. 2022 Oct 7;71(40):1260-1264. doi: 10.15585/mmwr.mm7140a2. PMID: 36201372.