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Both the Infectious Disease Society of American (IDSA) and the American College of Gastroenterology ACG) have published clinical guidelines addressing the use of GPPs.

The Infectious Diseases Society of America guidelines on the Diagnosis and Management of Infectious Diarrhea (Shane, 2017) include the following recommendations:

Clinical consideration should be included in the interpretation of results of multiple-pathogen nucleic acid amplification tests because these assays detect DNA and not necessarily viable organisms (strong, low).
A broad differential diagnosis is recommended in immunocompromised people with diarrhea, especially those with moderate and severe primary or secondary immune deficiencies, for evaluation of stool specimens by culture, viral studies, and examination for parasites (strong, moderate). People with acquired immune deficiency syndrome (AIDS) with persistent diarrhea should undergo additional testing for other organisms including, but not limited to, Cryptosporidium, Cyclospora, Cystoisospora, microsporidia, Mycobacterium avium complex, and cytomegalovirus (strong, moderate).
Diagnostic testing is not recommended in most cases of uncomplicated traveler’s diarrhea unless treatment is indicated. Travelers with diarrhea lasting 14 days or longer should be evaluated for intestinal parasitic infections (strong, moderate). Testing for C. difficile should be performed in travelers treated with antimicrobial agent(s) within the preceding 8-12 weeks. In addition, gastrointestinal tract disease including inflammatory bowel disease (IBD) and postinfectious irritable bowel syndrome (IBS) should be considered for evaluation (strong, moderate).
Clinical consideration should be included in the interpretation of results of multiple-pathogen nucleic acid amplification tests because these assays detect DNA and not necessarily viable organisms (strong, low).
All specimens that test positive for bacterial pathogens by culture-independent diagnostic testing such as antigen-based molecular assays (gastrointestinal tract panels), and for which isolate submission is requested or required under public health reporting rules, should be cultured in the clinical laboratory or at a public health laboratory to ensure that outbreaks of similar organisms are detected and investigated (strong, low). Also, a culture may be required in situations where antimicrobial susceptibility testing results would affect care or public health responses (strong, low).
Culture-independent, including panel-based multiplex molecular diagnostics from stool and blood specimens, and, when indicated, culture-dependent diagnostic testing should be performed when there is a clinical suspicion of enteric fever (diarrhea uncommon) or diarrhea with bacteremia (strong, moderate). Additionally, cultures of bone marrow (particularly valuable if antimicrobial agents have been administered), stool, duodenal fluid, and urine may be beneficial to detect enteric fever (weak, moderate). Serologic tests should not be used to diagnose enteric fever (strong, moderate).
The American College of Gastroenterology Clinical Guideline on acute diarrheal infections in adults (Riddle, 2016) provides a discussion of the benefits and limitations of GI pathogen panels. According to the ACG:

Diarrheal disease by definition has a broad range of potential pathogens particularly well suited for multiplex molecular testing. Several well-designed studies show that molecular testing now surpasses all other approaches for the routine diagnosis of diarrhea. Molecular diagnostic tests can provide a more comprehensive assessment of disease etiology by increasing the diagnostic yield compared with conventional diagnostic tests). They are also faster, providing results in hours rather than days). The new diagnostics’ best applicability is for the clinician in practice, seeing one patient at a time rather than in the public health setting, e.g., in outbreak investigations. One potential drawback of molecular technologies is the need to predefine the particular microbes being sought. In addition the significance of an identified organism may not be clear as these molecular technologies, which involve nucleic acid amplification, are limited to our existing knowledge of a microbes’ genome and do not discriminate between viable and non-viable organisms. As a result they can detect microbes at nonpathogenic levels. Given the high rates of asymptomatic carriage of enteropathogens, this can be a considerable problem. To confound matters, further multiplex techniques are more commonly associated with increased detection of mixed infections and the relative importance of each pathogen may be unclear.
Before bacterial culture is discarded entirely, it is important to acknowledge that multiplex molecular diagnostics do not yield isolates that can be forwarded to public health laboratories. Specimens collected for culture-independent testing may, in some cases, be incompatible with culture because of the collection methods or media that are used for collection. And, a strict reliance on culture-independent diagnostics would limit our ability to detect new causes of diarrheal disease.
Conventional diagnostic approaches to diarrheal disease require multiple procedures: bacterial culture, microscopy with and without stains or immunofluorescence and stool antigen tests for detection of protozoa, and for detecting viral agents, electron microscopy, or antigen-based tests. Routine clinical laboratory detection of bacterial pathogens requires the use of differential culture media, which select for the growth of certain bacteria but may fail to detect other bacteria, especially in the setting of antibiotic use. Culture methods are laborious and time consuming, with results often not available for 48 to 72 h. Historically, a decision to obtain a stool culture in an individual with diarrhea has often been guided by the finding of fecal leukocytes or the presence of stool lactoferrin. Although the latter is a more sensitive predictor of a positive stool culture, using these markers to guide further diagnostic studies has been proven to be imprecise and probably unnecessary.
Stool diagnostic studies may be used if available in cases of dysentery, moderate-to-severe disease, and symptoms lasting >7 days to clarify the etiology of the patient’s illness and enable specific directed therapy. (Strong recommendation, very low level of evidence).
Traditional methods of diagnosis (bacterial culture, microscopy with and without special stains and immunofluorescence, and antigen testing) fail to reveal the etiology of the majority of cases of acute diarrheal infection. If available, the use of Food and Drug Administration-approved culture independent methods of diagnosis can be recommended at least as an adjunct to traditional methods. (Strong recommendation, low level of evidence).
Molecular diagnostic tests can provide a more comprehensive assessment of disease etiology by increasing the diagnostic yield compared with conventional diagnostic tests. They are also faster, providing results in hours rather than days. The new diagnostics’ best applicability is for the clinician in practice, seeing one patient at a time rather than in the public health setting, e.g., in outbreak investigations. One potential drawback of molecular technologies is the need to predefine the particular microbes being sought. In addition the significance of an identified organism may not be clear as these molecular technologies, which involve nucleic acid amplification, are limited to our existing knowledge of a microbes’ genome and do not discriminate between viable and non-viable organisms. As a result they can detect microbes at nonpathogenic levels.

Infections in Adults. Am J Gastroenterol. 2016; 111(5):602-622.

Amjad M. An overview of the molecular methods in the diagnosis of gastrointestinal infectious diseases. Int J Microbiol. 2020; 2020:8135724.

Shane AL, Mody RK, Crump JA, et al. 2017 Infectious Diseases Society of America Clinical Practice Guidelines for the Diagnosis and Management of Infectious Diarrhea. Clin Infect Dis. 2017; 65(12):e45-e80.U