Tests performed by nucleic acid amplified probe techniques uses a microorganism’s DNA or RNA to directly identify specific bacteria, viruses, and/or protozoa rather than standard microorganism detection techniques such as bacterial culture, microscopy with and without stains, direct fluorescent antibody testing, rapid antigen testing, qualitative and quantitative immunoassay for identification of antigens or toxins from stool and single-plex PCR assays.

• American College of Gastroenterology 2016 Clinical Guidelines include two relevant sections pertaining to GIPP:
  
  
  
  • “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).”
  
  
  • “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 non-pathogenic 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.”
  
  
  
  


• Infectious Diseases Society of America 2017 Clinical Practice Guidelines for the Diagnosis and Management of Infectious Diarrhea make the following recommendations:
  
  
  
  • “A broad differential diagnosis is recommended in immunocompromised people with diarrhea, especially those with moderate and severe primary or secondary immune deficiencies… Some experts have proposed that these assays may be particularly well suited for making an organism-specific diagnosis in immunocompromised patients.”
  
  
  • “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 or diarrhea with bacteremia (strong, moderate).”
  
  
  • “Multipathogen nucleic acid amplification tests can simultaneously detect viral, parasitic, and bacterial agents, including some pathogens that previously could not be easily detected in the clinical setting such as norovirus, and enterotoxigenic E. coli (ETEC), enteropathogenic E. coli (EPEC), and enteroaggregative E. coli (EAEC) in less time than traditional methods. The short time to results could reduce inappropriate use of antimicrobial agents to treat infections that do not require antimicrobial therapy and could shorten the time to targeted management and isolation measures for certain infections such as STEC O157. With these assays, it is common to detect the presence of greater than one (1) pathogen that may differ with regard to clinical management.”
  
  
  • “Even a positive result for one (1) pathogen should be interpreted in the context of the patient’s clinical presentation, because less is known about the clinical significance of tests that detect nucleic acid as compared with traditional assays that generally detect viable organisms. The importance of detection of multiple pathogens in the same specimen is often unclear; it is unknown if all pathogens detected in the specimen are clinically relevant or if one is more strongly associated with the illness.”
  
  
  
  


• Acute diarrhea, often called gastroenteritis, can be defined as the passage of a greater number of stools of decreased form from the normal lasting less than 14 days. Acute diarrhea is generally associated with clinical features of nausea, vomiting, abdominal pain and cramps, bloating, flatulence, fever, passage of bloody stools, tenesmus and fecal urgency. It is the leading cause of outpatient visits, hospitalizations, and lost quality of life occurring domestically and those traveling abroad.


• Many episodes of acute diarrhea are self-limited and require fluid replacement and supportive care. Oral rehydration is indicated for patients who are mildly to moderately dehydrated. IV fluids may be required for more severe dehydration. Routine use of antidiarrheal agents is not recommended because many of these agents have potentially serious adverse effects, particularly in infants and young children. Antimicrobial therapy is typically warranted for adult and pediatric patients with immune systems which are severely weakened from medications, age and other primary/secondary immunocompromising illnesses/conditions.


• Laboratory testing algorithms for infectious causes of diarrhea generally agree that testing is NOT warranted for community-acquired diarrhea of less than seven (7) days duration without signs or symptoms of severe (fever, bloody diarrhea, dysentery, severe abdominal pain, dehydration, hospitalization and immunocompromised state) disease. In general, when community-acquired diarrhea persists for greater than or equal to seven (7) days, or the diarrhea is travel-related, or there are signs/symptoms of severe disease, GIPP testing may be warranted. Additional directed testing may be indicated if the GIPP results are negative and diarrhea persists. No additional testing is indicated for GIPP-positive result unless the clinical pictures changes. Clostridium difficile molecular testing is warranted on health-care associated diarrhea with onset after the third inpatient day or after recent antibiotic use.


• Whereas a majority of microorganisms can be identified with up to five (5) targets, typically including Salmonella, Campylobacter, Shigella, Cryptosporidium, and Shiga toxin producing E.coli, additional agents may be in the working differential diagnosis, such as (but not limited to) Clostridium difficile, additional E. coli variants, Yersinia enterocolitica, Vibrio parahaemolyticus, Giardia, Cryptosporidium, and viruses including norovius, rotavirus, and enteric adenoviruses.


• Salient illustrations of the literature have annotated a diverse set of offending infectious agents (bacterial, parasitic and viral) in patients presenting with acute diarrhea. However, it must be emphasized that such original study recruitment criteria were not designed to stratify probability/incidence distributions of causative organisms, according to more carefully specified patient presentation categories. Furthermore, the molecular predilection for mixed infectious agent identification is a confounding factor when clinicians are trying to pinpoint the precise etiology of acute diarrhea, given the dilemma between pathogenicity and non-pathogenicity, which was briefly cited above.


• As a result, when the patient history, clinical presentation and symptoms, etc. suggest a specific microbial etiology and/or therapy, a broad GIPP consisting of greater than five (5) infectious targets is not indicated. However, broader GIPP molecular panels (e.g. 6-25 targets) might occasionally be indicated when a patient presents with a clinical scenario and overlapping symptoms consistent with multiple possible microbiological etiologies, where both diagnosis and treatment are particularly challenging (e.g., as noted above for immunocompromised patients).