Test Id : GIP

The following algorithms are available:

-Parasitic Investigation of Stool Specimens Algorithm

-Laboratory Testing for Infectious Causes of Diarrhea

It is not recommended that the following tests be concomitantly ordered if this test is ordered:

-VIBC / Vibrio Culture, Feces

-ROTA / Rotavirus Antigen, Feces

-LADV / Adenovirus, Molecular Detection, PCR, Varies

-GIAR / Giardia Antigen, Feces

-CRYPS / Cryptosporidium Antigen, Feces

-CYCL / Cyclospora Stain, Feces

-STL / Enteric Pathogens Culture, Feces

-CAMPC / Campylobacter Culture, Feces

-SHIGC / Shigella Culture, Feces

-SALMC / Salmonella Culture, Feces

-YERSC / Yersinia Culture, Feces

-E157C / Escherichia coli O157:H7 Culture, Feces

-STFRP / Shiga Toxin, Molecular Detection, PCR, Feces

-CDPCR / Clostridioides difficile Toxin, PCR, Feces

-LNORO / Norovirus PCR, Molecular Detection, Feces

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, see Interpretation for detailed information about how to obtain this testing.

Specimen must arrive within 96 hours of collection.

Do not freeze. Testing will be canceled on specimens received frozen.

Supplies: Culture and Sensitivity Stool Transport Vial (T058)

Container/Tube:

Preferred: Specific modified Cary Blair transport system; see Additional Information for acceptable collection media

Acceptable: Approved Cary Blair transport system (15 mL of non-nutritive transport medium containing phenol red as a pH indicator)

Specimen Volume: Representative portion of feces

Collection Instructions:

1. Collect fresh fecal specimen and submit 1 gram or 5 mL in container with transport medium.

2. Place feces in preservative within 2 hours of collection.

3. Submit preserved feces in original container. Do not aliquot.

4. If unpreserved specimens received, testing will be canceled.

Additional Information:

If collection media other than those listed is utilized, testing may be canceled. Media listed have been verified for use by Mayo Clinic Laboratories.

Modified Cary Blair media:

Preferred: Culture and Sensitivity Stool Transport Vial (T058)

Acceptable: Meridian Para-Pak C and S, Cardinal Health Culture and Sensitivity Stool transport Vial

Cary Blair media: Remel Cary Blair, Remel; Protocol Cary Blair

• Parasitic Investigation of Stool Specimens Algorithm
• Laboratory Testing for Infectious Causes of Diarrhea

If not ordering electronically, complete, print, and send 1 of the following forms with the specimen:

-Gastroenterology and Hepatology Test Request (T728)

-Microbiology Test Request (T244)

1 mL

Rapid detection of gastrointestinal infections caused by:

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

-Clostridioides 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

This test is not recommended as a test of cure.

The following algorithms are available:

-Parasitic Investigation of Stool Specimens Algorithm

-Laboratory Testing for Infectious Causes of Diarrhea

Acute diarrheal syndromes are usually self-limiting but may be complicated by dehydration, vomiting, and fever. Diagnostic testing and treatment may be required in some instances. Many bacterial enteric infections in the United States originate within the food supply chain. According to the CDC, in 2012 there were 19,531 laboratory-confirmed cases of infection with pathogens potentially transmitted through food in the United States. The numbers of infections, by pathogen, were as follows: Salmonella species (7800), Campylobacter species (6793), Shigella species (2138), Cryptosporidium species (1234), Shiga toxin-producing Escherichia coli non-O157 (551), Shiga toxin-producing E coli O157 (531), Vibrio species (193), Yersinia species (155), and Cyclospora cayetanensis (15). Giardia may also be transmitted through ingestion of contaminated food and water. There were 15,178 cases of giardiasis reported to the CDC in 2012. Since the clinical presentation may be very similar to many of these bacterial, viral, and parasitic pathogens, laboratory testing is required for definitive identification of the causative agent.

Rapid multiplex panel detection of the most common agents of bacterial, viral, and parasitic enteric infections directly from stool specimens is sensitive, specific, and provides same-day results, obviating the need for culture, antigen testing, microscopy, or individual nucleic acid amplification tests.

For other diagnostic tests that may be of value in evaluating patients with diarrhea the following are available:

-Parasitic Investigation of Stool Specimens Algorithm

-Laboratory Testing for Infectious Causes of Diarrhea

Negative (for all targets)

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

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.

The BioFire FilmArray Gastrointestinal Panel is an FDA-cleared assay for testing Cary-Blair-preserved stool. A performance verification study of the FilmArray Gastrointestinal Panel was completed at Mayo Clinic (Rochester Minnesota).(1) Five hundred clinical stool specimens (retrospective/stored samples=270; prospective samples=230) were evaluated. Results were compared to a reference standard result, which was defined as an organism identified by routine culture, microscopy, or a consensus (2 out of 3) result obtained by molecular and/or antigen assays. Among 500 clinical stool samples, the assay showed greater than 90% agreement for all targets. Several targets, including Plesiomonas shigelloides, Cyclospora cayetanensis, Entamoeba histolytica, Vibrio species, and enterotoxigenic Escherichia coli did not have an adequate number of positive samples to rigorously assess the sensitivity of these targets.

In order to supplement the data derived from clinical samples, spiking studies were completed to evaluate the accuracy of all targets, including those that could not be analyzed by clinical specimens alone. This group included: Campylobacter species (n=4), Clostridioides difficile (n=4), Plesiomonas shigelloides (n=4), Salmonella species (n=4), Yersinia enterocolitica (n=4), Vibrio cholerae (n=4), enteroaggregative E coli (n=4), enteropathogenic E. coli (n=8), enterotoxigenic E coli (n=4), E coli O157 (n=4), Shigella species (n=8), Cryptosporidium species (n=4), Cyclospora cayetanensis (n=8), Entamoeba histolytica (n=4), Giardia lamblia (n=4), adenovirus 40/41 (n=4), norovirus (n=8), rotavirus A (n=4), sapovirus (n=4), and astrovirus (n=8). All targets demonstrated 100% agreement with the expected result during the spiking studies.

1. Khare R, Espy MJ, Cebelinski E, et al. Comparative evaluation of two commercial multiplex panels for detection of gastrointestinal pathogens by use of clinical stool specimens. J Clin Microbiol. 2014;52(10):3667-3673

2. Centers for Disease Control and Prevention. Incidence and trends of infection with pathogens transmitted commonly through food-foodborne diseases active surveillance network, 10 U.S. sites, 1996-2012. MMWR Morb Mortal Wkly Rep. 2013;62(15):283-287

3. Centers for Disease Control and Prevention. Summary of notifiable diseases-United States, 2012. MMWR Morb Mortal Wkly Rep. 2014;61(53):1-121

4. DuPont HL. Persistent diarrhea: A clinical review. JAMA. 2016;315(24):2712-2723. doi:10.1001/jama.2016.7833

5. Lawson PA, Citron DM, Tyrrell KL, Finegold SM. Reclassification of Clostridium difficile as Clostridioides difficile (Hall and O'Toole 1935) Prevot 1938. Anaerobe. 2016;40:95-99. doi:10.1016/j.anaerobe.2016.06.008

6. Oren A, Garrity GM. Validation List No. 169. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol. 2016;66(6):2456-2458. doi:10.1099/ijsem.0.001181

The FilmArray GastrointestinaI Panel is a closed system that performs the chemistry required for isolation, amplification, and detection of nucleic acid from multiple viral, bacterial, and parasitic gastrointestinal pathogens from a single stool specimen of patients suspected to have a gastrointestinal infection. A panel contains reagents in freeze-dried form and is divided into discrete segments where the required chemical processes are carried out. Patient sample and hydration fluid are drawn by vacuum into the panel and then placed into the FilmArray instrument. The detection process operations are automated (nucleic acid purification, first-stage polymerase chain reaction [PCR], second-stage PCR, and melt analysis) and complete in about an hour in this closed system:

-Nucleic Acid Purification:

The sample is lysed by a combination of chemical and mechanical mechanisms and the liberated nucleic acid is captured, washed, and eluted using magnetic bead technology.

-First-Stage PCR:

A reverse transcription step is performed to convert viral RNA into complementary DNA prior to amplification. The purified nucleic acid solution is combined with a preheated master mix to initiate the reverse transcription step and subsequent thermocycling for multiplex PCR.

-Second-Stage PCR:

Products of first-stage PCR are diluted and mixed with fresh PCR reagents containing an intercalating fluorescent DNA dye (LCGreen Plus), which is distributed over the second-stage PCR array. The individual wells of the array contain primers for different assays (in triplicate) that target specific nucleic acid sequences from each of the pathogens detected, as well as control template material.

-DNA Melting Analysis:

Temperature is slowly increased and fluorescence in each well of the array is monitored and analyzed to generate a melt curve.

-Analysis of Melt Curves:

The software evaluates the DNA melt curve for each well to determine if a PCR product was present in that well. If the melt profile indicates the presence of a PCR product, then the analysis software calculates the melting temperature of the curve, which is then compared against the expected range for the assay. When the software determines that the melt curve is positive and in range, it is called positive. When it determines that the melt curve is negative or is not in the appropriate range, it is called negative.

-Analysis of Replicates:

Melt curves of each of the 3 replicates for each assay are evaluated to determine the assay result. For an assay to be called positive, at least 2 of the 3 associated melt curves must be called positive, and the temperature for at least 2 of the 3 positive melt curves must be similar (within 1 degree C). Assays that do not meet these criteria are called negative.(Instruction manual: FilmArray Gastrointestinal [GI] Panel CE IVD. BioFire Diagnostics, LLC; RFIT-PRT-0143-05, 05/2021)

Monday through Sunday

• Authorized users can sign in to Test Prices for detailed fee information.
• Clients without access to Test Prices can contact Customer Service 24 hours a day, seven days a week.
• Prospective clients should contact their account representative. For assistance, contact Customer Service.

This test has been cleared, approved, or is exempt by the US Food and Drug Administration and is used per manufacturer's instructions. Performance characteristics were verified by Mayo Clinic in a manner consistent with CLIA requirements.

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