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Epic Test Code LAB101011 Gastrointestinal Pathogen Panel, PCR, Feces

Important Note

Required Container


 

Additional Codes

MML: GIP

LIS:RCMISCT

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

Method Name

Multiplex Polymerase Chain Reaction (PCR)

Reporting Name

GI Pathogen Panel, PCR, F

Specimen Type

Fecal


Advisory Information


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

-VIBC / Vibrio Culture, Stool

-ROTA / Rotavirus Antigen, Feces

-LADV / Adenovirus, Molecular Detection, PCR

-GIAR / Giardia Antigen, Feces

-CRYPS / Cryptosporidium Antigen, Feces

-CYCL / Cyclospora Stain

-STL / Enteric Pathogens Culture, Stool

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

-CDFRP / Clostridioides (Clostridium) difficile Toxin, Molecular Detection, PCR, Feces



Additional Testing Requirements


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 that 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.



Shipping Instructions


Specimen must arrive within 96 hours of collection. 



Necessary Information


 



Specimen Required


Supplies: C and S Vial (T058)

Specimen Type: Preserved stool

Container/Tube: Cary-Blair transport system is required. Specific for recovery of enteric pathogens from fecal specimens (15 mL of non-nutritive transport medium containing phenol red as a pH indicator, either Cary-Blair or Para-Pak C and S [T058]). Submit sample in original Cary Blair medium container (not an aliquot).

Specimen Volume: 1 gram or 5 mL

Collection Instructions:

1. Collect fresh stool and place in preservative within 2 hours of collection.

2. Submit a representative portion of stool in container with transport medium.


Specimen Minimum Volume

1 mL

Specimen Stability Information

Specimen Type Temperature Time
Fecal Ambient (preferred) 4 days
  Refrigerated  4 days

Reject Due To

Hemolysis

NA

Lipemia

NA

Icterus

NA

Other

Specimen older than 96 hours, frozen specimen, commercial transport media other than liquid Cary Blair (eg, ETM, Para-Pak Enteric Plus; Copan FecalSwab/ESwab), Cary Blair gel swabs, products containing formalin, SAF, PVA fixative, EcoFix preservative, rectal swabs, stool swab, gel swabs, endoscopy specimens, unpreserved stool

Clinical Information

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 number of infections, by pathogen, were as follows: Salmonella species (7,800), Campylobacter species (6,793), Shigella species (2,138), Cryptosporidium species (1,234), 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.

 

See Parasitic Investigation of Stool Specimens Algorithm and Laboratory Testing for Infectious Causes of Diarrhea in Special Instructions for other diagnostic tests that may be of value in evaluating patients with diarrhea.

Reference Values

Negative (for all targets)

Interpretation

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.

 

Positive results do not distinguish between a viable or replicating organism and the presence of a nonviable organism or nucleic acid, nor do they exclude the potential for coinfection by organisms not contained within the panel.

 

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.

 

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 that 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 MCL within 96 hours of specimen collection to request supplemental testing for positive GIP test results:

 

Gastrointestinal Pathogen Panel Positive for

Client Action

Campylobacter species

Salmonella species

Shigella/Enteroinvasive E coli

Yersinia species

Request add on test: STL / Enteric Pathogens Culture, Stool

(for the Shigella/Enteroinvasive E coli target, the culture will assess for Shigella species only)

Vibrio species

Request add on test: VIBC / Vibrio Culture, Stool

Shiga toxin-producing E coli

E coli O157

Request aliquot of stool be returned to client for submission to their state or city department of health

 

MCL will report such culture results to the client for STL / Enteric Pathogens Culture or VIBC / Vibrio Culture when ordered. If cultures are positive and the client is in need of the isolated organism (eg, Campylobacter, Salmonella, Shigella, Yersinia, or Vibrio species) for submission to a public health laboratory, the client needs to call MCL and request that the isolates be returned to them (the client). The client will be responsible for submitting the isolates to the appropriate public health department. Positive culture results will also be reported via the Electronic Clinical Laboratory Reporting System (ECLRS).

 

Alternatively (not preferred), clients who want a patient specimen returned from MCL should call MCL as soon as possible and at the latest within 96 hours of specimen collection to request that MCL return an aliquot of the submitted specimen to them. Clients will be responsible for submitting specimens to appropriate public health departments.

Cautions

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.

 

This test is not recommended as a test of cure.

 

Repeat testing should not be performed on samples collected less than 7 days apart.

 

The presence of blood or mucous in the sample may interfere with testing.

 

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 C jejuni, C coli, and C upsaliensis. Other species will not be detected. Helicobacter pullorum may cross react.

Clostridioides (Clostridium) 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 S enterica and S bongori. Cross-reactivity 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 Y enterocolitica but does not differentiate known serotypes or biotypes. Y kristensenii, Y frederiksenii, and Y intermedia cross-react at high levels with Y enterocolitica; detection is reported to genus level only.

Diarrheagenic Escherichia 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 Escherichia 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 Escherichia 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 Escherichia 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, E 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 Escherichia 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 Shiga toxin-producing Escherichia coli. 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).

Escherichia coli O157: The Escherichia 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 (non-O157) with an 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, C hominis and C parvum), as well as less common species (eg, C meleagridis, C felis, C canis, C cuniculus, C muris, and C suis), but is not expected to detect the very rare species C bovis, C ryanae, and C xiaoi.

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

Giardia: Detects G lamblia (also known as G intestinalis, G 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 cross-react 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 CE IVD, BioFire Diagnostics, LLC, Salt Lake City, Utah)

 

Supportive Data

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),  Clostridium 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.

Day(s) and Time(s) Performed

Monday through Sunday; Continuously

Analytic Time

1 day

Specimen Retention Time

7 days

Performing Laboratory

Mayo Clinic Laboratories in Rochester

CPT Code Information

87507

NY State Approved

Yes

Testing Algorithm

The following algorithms are available in Special Instructions:

-Parasitic Investigation of Stool Specimens Algorithm

-Laboratory Testing for Infectious Causes of Diarrhea

Forms

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

-Microbiology Test Request (T244)

-Gastroenterology and Hepatology Client Test Request (T728)