The GIP Panel PCR test is an FDA-approved assay designed to detect ten bacterial, four parasitic, and five viral targets commonly associated with gastrointestinal disease. See here for list of targets tested:  [DUHS Biofire GI Panel FAQ](https://prodduke.sharepoint.com/:b:/s/MicrobiologySharepoint/ETjMXINOjvdFrcwRQk2C-koBHTdJ_gY6a2YyTEZsenQZ4A?e=zKRvck)      
  
Testing is available for patients experiencing moderate to severe diarrhea with a suspected infectious cause. It is restricted to patients with a qualifying condition, as listed below. 

Restricted patient population includes:  
- Inpatients admitted <= 3 days  
- Immunocompromised/transplant patients

Immunocompromised status is narrowly defined to be individuals who cannot mount a normal immune response. Some examples include: chemotherapy, immune suppressive therapy, or late stage HIV or AIDS. 

For admitted patients with new hospital onset diarrhea, more than 3 days after admission, consider C. difficile PCR w/ reflex to Toxin EIA - LAB253.
- Click for additional information: [C. difficile PCR w/ reflex to Toxin EIA- https://testcatalog.duke.edu/Home/ProcedureDetails?ProcedureID=dc53e6f1-4ccb-472d-84fa-082b1764db7c

1. The performance of this test has not been established for patients without signs and symptoms of gastrointestinal illness. 
2. The performance of this test has not been established for monitoring treatment of infection with any of the panel organisms.
3. There is a risk of false negative values due to the presence of sequence variants in the gene targets of the assay, procedural errors, amplification inhibitors in specimens, or inadequate numbers of organisms for amplification.
4. Shiga toxin (stx; identical to stx1 of STEC) is found in Shigella dysenteriae; therefore, a BioFire GI Panel report with positive test results for Shiga-like toxin-producing E. coli (STEC) stx1/stx2 and Shigella/Enteroinvasive E. coli (EIEC) in the same sample may indicate the presence of S. dysenteriae.
5. To aid in the identification of STEC of the 0157 serotype, the BioFire GI Panel contains a single assay (Ec0157) to detect a gene target that is specific to this serotype.  Strains of E. coli 0157 that do not carry the Shiga-like toxin genes have also been identified. As the pathogenicity of these non-STEC strains remains undefined, the E. coli 0157 assay result is not reported unless a Shiga-like toxin gene is also detected (STEC detected)
6. Detection of STEC stx1/stx2 and the E. coli 0157 target results in a reporting of E. coli 0157 as a qualifier to the positive STEC result.  If STEC stx1/stx2 is Not Detected, the result for E. coli 0157 is indicated as N/A (Not applicable). The BioFire GI Panel cannot distinguish between infections with a single toxigenic STEC 0157 or rare co-infection of STEC (non-0157) with an stx1/stx2-negative E. coli 0157.
7. The identification of several diarrheagenic E. coli phenotypes has historically relied upon phenotypic characteristics, such as adherence patterns or toxigenicity in certain tissue culture cell lines. The BioFire GI panel targets genetic determinants characteristic of most pathogenic strains of these organisms but may not detect all strains having phenotypic characteristics of a pathotype.  The BioFire GI panel will not detect all strains of Enteroaggregative E. coli (EAEC) exhibiting an aggregative adherence pattern.
8. Target genes associated with the diarrheagenic E. coli/Shigella pathotypes are capable of horizontal transfer between strains, thus Detected result for multiple diarrheagenic E. coli.  Shigella may be due to co-infection with multiple pathotypes. An example of the latter is the 2011 E. coli 0104:H4 outbreak strain that contains determinants of both STEC and EAEC.
9. Enteropathogenic E. coli (EPEC) is detected through targeting of the eae gene, which encodes the adhesion intimin. As some Shiga-like toxin-producing E. coli (STEC) also carry eae, the FilmArray GI Panel cannot distinguish between STEC containing eae and a co-infection of EOEC and STEC. Therefore, the EPEC result is not applicable (N/A) and not reported for specimens in which STEC has also been detected. 
10. Negative test results may occur from sequence variants in the region targeted by the assay, the presence of inhibitors, technical error, sample mix-up, or an infection caused by an organism not detected by the panel.  Test results may also be affected by concurrent antimicrobial therapy or levels of organism in the sample that are below the limit of detection for the test. Negative results should not be used as the sole basis for diagnosis, treatment, or other management decisions. 
11. The performance of the FilmArray has not been established in individuals who received Rotavirus A vaccine. Recent oral administration of a Rotavirus A vaccine may cause positive results for Rotavirus A fi the virus is passed in the stool.
12. V. cholerae isolates with highly divergent toxR genes will be non-reactive with the BioFire GI Panel V. cholerae assay. Very rare strains of V. cholera that do not carry the toxR gene will also not be detected by the V. cholerae assay.
13. Not all Salmonella serotypes were tested in validation studies; however, representatives of the 20 most prevalent serotypes recently circulating in the US were evaluated. In silico sequence analysis supports detection of all subspecies and serotypes of Salmonella.  Refer to package insert.
14. Several organisms were shown to have the potential to cross-react with BioFire GI panel assays:  
	a. Entamoeba dispar when present at high levels (E. histolytica target on the GIP Panel PCR)  
	b. Bifidobacterium spp. And Ruminococcus spp (Giardia lamblia target on the GIP Panel PCR)  
	c. Certain strains of C. koseri, C. sedlakii, Hafnia alvei, and C.davisae containing variants of a flagellar assembly protein (ETEC 2 target on the GIP Panel PCR)   
	d. E. coli containing a variant type III secretion protein (Salmonella target on the GIP Panel PCR)  
	e. Grimontia hollisae, formerly a Vibrio sp. (Vibrio target on the GIP Panel PCR)  
	f. Y. frederiksenii and Y. kristensenii, which are members of the Y. enterocolitica group (Y. enterocolitca target on the GIP Panel PCR)  
	g. Refer to the package insert for additional details on cross-reactivity.  
15. Positive and negative predictive values are highly dependent on prevalence. False negative results are more likely during peak activity when prevalence of disease is high.  False positive results are more likely during periods when prevalence is moderate to low.

The GIP Panel PCR test is intended to be used in conjunction with other clinical, epidemiological, and laboratory data. 

**Acceptable Specimen:** This assay is designed and approved for stool/fecal specimen. All other specimen type/source, including rectal swab, gastric aspirates, abdominal fluid or tissue, as some examples, will be rejected. 

**Acceptable Collection Kit: **Stool must be collected and immediately transferred in a Cary-Blair containing transport media, which includes PARA-PAK C&S. All other collection devices, including sterile container or other PARA-PAK containers, will be rejected.

 ***Note: unpreserved, fresh stool will be rejected***

  ***Note:  A separate collection container must be submitted for this test; no sharing is allowed between the GI Panel PCR and any other stool tests***

**Ordering and Specimen Collection:** For additional ordering information and instructions on collection for the GIP Panel PCR, please visit the DUHS Clinical Microbiology Laboratory video links for: [DUHS Clinical Microbiology Educational video for Gastrointestinal (GIP) Panel](https://duke.app.box.com/s/uhqt2y3df2325ydjiffhfcnwpv992q29) 

**Collection Kit Information:**  
•	Para-Pak C&S [Cary Blair- Orange cap]-- SAP#41272  
•	Vendor--Meridian  
•	Catalog#--960012  


**Patients who do not meet any of these criteria:** For patients without a qualifying condition, as listed above, and do not meet the criteria for restricted patient population for testing, please consider the following send out tests:  
•	[Stool Culture – SENDOUT LABCORP:  https://testcatalog.duke.edu/Home/ProcedureDetails?ProcedureID=62ac793b-a3f5-4b1e-a84f-757e647c5d24
•	[Stool Culture, Vibrio Only SENDOUT LABCORP:  https://testcatalog.duke.edu/Home/ProcedureDetails?ProcedureID=e5798bb4-303a-490d-b250-8c40688dc9b6
•	[Stool Culture, Yersinia Only – SENDOUT LABCORP:  https://testcatalog.duke.edu/Home/ProcedureDetails?ProcedureID=4e9a919a-4a3c-4fa5-9458-8cf73308adb8
•	[Aeromonas/Plesiomonas Culture – SENDOUT LABCORP:  https://testcatalog.duke.edu/Home/ProcedureDetails?ProcedureID=afa8e6b0-bf2e-43bc-ac5f-ba3871387cd0
•	[Giardia lamblia & Cryptosporidium, Direct Detection EIA – SENDOUT LABCORP: https://testcatalog.duke.edu/Home/ProcedureDetails?ProcedureID=4259c0cb-aba0-4260-ac39-2d6279ab90f8