The new way to test poop! The GI PCR or FilmArray Gastrointestinal Panel

 

Deborah Bloch, MD
deborah.bloch@emory.edu

Mark Gonzalez, MD
mark.gonzalez@choa.org

Craig Shapiro, MD
cshapi2@emory.ed

FilmArrayTM Gastrointestinal Panel?

The FilmArrayTM Gastrointestinal Panel is a rapid test (~2 hr turnaround time) offered by the CHOA microbiology lab for detection of common gastrointestinal pathogens (see Figure 1), which includes bacteria, viruses and parasites. Because of the comprehensiveness of the panel, in most cases stool culture, ova and parasite (O&P) examination, and antigen testing for Adenovirus 40/41, Rotavirus, Cryptosporidium spp. and Giardia lamblia no longer need to be ordered (see Figure 1 for additional information)

 

When should I order the FilmArrayTM Gastrointestinal Panel?

The panel should be ordered for a patient of any age with diarrhea (> 3 unformed stools in a 24 hour period who is not on a laxative) for whom you are worried about infection with a GI pathogen that may impact patient management or isolation practices. Testing should not be performed on formed stool. Please contact the microbiology lab (404-785-6426) or the ID consult service (404-785-DOCS) with any additional questions.

WHEN TO CONSIDER SENDING GI PCR PANEL FOR A PATIENT WITH DIARRHEA:

  • Fever and frankly bloody/mucusy diarrhea (if concern for C diff, also send stool for C diff toxin – not included in GI PCR panel)
  • Prolonged diarrhea>7 days (or before referral to GI for evaluation)
  • Travel-related diarrhea (if persistent or red flags; if concern for worms, also send stool for ova/parasites)
  • Immunocompromised patient – if concern for non-viral etiology
  • IBD patients- newly suspected or unusual change in stools in established IBD pt

What do the results mean?

For non-severe or prolonged (<7 days) illnesses caused by many of the pathogens detected (e.g. EAEC, EPEC, STEC, non-typhoidal Salmonella, all viral pathogens, Giardia lamblia and Cryptosporidium species), treatment is supportive; however, for patients in certain age groups, and patients with certain comorbidities or immunocompromising conditions, antimicrobial treatment may be indicated.

Because the FilmArrayTM Gastrointestinal Panel detects nucleic acids, it cannot differentiate active infection from treated infection or colonization; this must be done by correlating clinical symptoms. Results can remain positive for weeks or months after an infection especially in young children and immunocompromised patients.

Figure 1. Reported pathogens on the FilmArrayTM Gastrointestinal Panel at CHOA and which reflex to culture.

Should I also order a stool culture to get antimicrobial susceptibility results?

When testing is performed in the CHOA microbiology laboratory, a stool culture order is not necessary as positive panels will automatically reflex to culture, and if the isolate is recovered antimicrobial susceptibility testing will be performed when appropriate (Figure 1).

Should I order an O&P examination? What about for patients who drink and use well water?

O&P examinations should be ordered if you suspect a parasite other than those listed on the panel (e.g., for patients who returned from travel abroad). It should be noted that the top parasitic causes of well water contamination are Giardia and Cryptosporidium, which are tested for on the panel. Maximal sensitivity for parasite detection by O&P examination requires up to three stool specimens collected over a 7-10 day period.\

Should I order C. difficile toxin testing separately?

Yes, but it is not typically recommended for children under 2 year of age due to high rates of colonization. 

Should I reorder the FilmArrayTM Gastrointestinal Panel to test for cure?

No. Nucleic acids detected on the panel may remain positive for an indeterminate amount of time, and the FilmArrayTM Gastrointestinal Panel should only be ordered on unformed stool.

 

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