Enteric Pathogens

Most acute infectious diarrhea is self-limited, caused by bacteria or viruses, and has a duration of illness less than 7 days. When illness is severe or becomes prolonged, laboratory evaluation may be indicated.   

Common bacterial causes of severe acute diarrhea include Campylobacter, Salmonella, Shigella, and enterotoxigenic or shiga toxin-producing E. coli. Less common bacterial pathogens include Yersinia enterocolitica, Aeromonas, Plesiomonas, and Vibrio species.

Parasites are an uncommon cause of acute diarrhea, and many studies have shown that routine comprehensive fecal ova and parasite testing is not cost-effective. Most enteric parasite infections in the United States are caused by Giardia or Cryptosporidium. 

Traditional testing included microscopic examination, culture, and immunoassays. Several multiplex nucleic acid amplification tests (NAATs) for enteric pathogens have been FDA approved. They allow the testing for multiple stool pathogens simultaneously and have higher sensitivity and shorter turnaround time than the traditional tests. 

The following multiplex platforms are commercially available: BioFire FilmArray Gastrointestinal Panel, BD Max System, Great Basin Stool Bacterial Pathogens Panel, Luminex xTAG Gastrointestinal Panel, Verigene Enteric Pathogens Nucleic Acid Test. The FilmArray can simultaneously test for: Campylobacter, Salmonella, Shigella, Enteroaggregative E. Coli, Enteropathogenic E. Coli, Enterotoxigenic E. Coli, Shiga toxin-producing E. Coli, Enteroinvasive E. Coli, Plesiomonas shigelooides, Vibrio, Yersinia, Clostridium difficile toxin A/B, Cryptosporodium, Entamoeba histolytica, Giardia lamblia, Cyclospora cayetanensis, Norovirus, Rotavirus, Adenovirus, Astrovirus, and Sapovirus.

A stool sample can be tested for all of these pathogens within 1 to 2 hours. Even though GI multiplex tests cost more per test than conventional methods, they can reduced the overall heath care costs. Decreased lab turnaround time can reduce the need for isolation procedures and decrease hospital length of stay. 

The high sensitivity of GI multiplex NAATs and a syndromic catch-all approach can potentially lead to finding mixed infections that are difficult to interpret. For example, more than 1 pathogen has been identified in 13.0% to 31.5% of patients with diarrhea. Multiplex NAATs detect DNA or RNA, which might not indicate infection with a viable organism. They can also detect microorganisms at nonpathogenic levels in asymptomatic carriers. 

Stool samples need to be preserved in Cary-Blair media for transportation to the laboratory. Reference values are no organism detected. 

References

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):1963–1973.

Riddle MS, DuPont HL, Connor BA. ACG Clinical Guideline: diagnosis, treatment, and prevention of acute diarrheal infections in adults. Am J Gastroenterol. 2016;111(5):602–622. 

Yalamanchili H, Dandachi D, Okhuysen PC. Use and Interpretation of Enteropathogen Multiplex Nucleic Acid Amplification Tests in Patients With Suspected Infectious Diarrhea. Gastroenterol Hepatol (N Y). 2018;14(11):646-652.