Enteropathogen Testing and Diarrhea Incidence

The burden of moderate-to-severe diarrhea on developing countries has been underestimated by previous research.

Disease burden associated with diarrhea attributable to pathogens may be 2 times higher than previously suggested, according to research published in Lancet.

Eric R. Houpt, MD, division of infectious diseases and international health at the University of Virginia, Charlottesville, and colleagues reanalyzed data from GEMS (the Global Enteric Multicenter Study), a study of moderate-to-severe diarrhea in Asian and African children 5 years of age or younger. Through quantitative molecular diagnostic methods, Dr Houpt and colleagues were able to test stool samples for 32 enteropathogens and calculate revised pathogen-specific burdens of disease.

The researchers tested 11,400 specimens collected from 5700 cases and matched controls; valid results were obtained from 5304 (93.1%) matched, case-control pairs. Using quantitative real-time PCR (qPCR), Dr Houpt and colleagues found that for most pathogens, incidence was greater using qPCR than with original methods—particularly with adenovirus 40/41, Shigella spp or enteroinvasive Escherichia coli (EIEC), Campylobactor jejuni or C coli, and the heat-stable enterotoxin-producing E coli (ST-ETEC; around 5 and 2 times greater, respectively).

At the population level, pathogen-attributable diarrheal burden was 89.3% (95% confidence interval [CI] 83.2-96), compared to 51.5% (95% CI 48-55) in the original GEMS analysis. Shigella spp, rotavius, adenovirus 40/41, ST-ETEC, Cryptosporidium spp, and Campylobacter spp—the 6 top pathogens—accounted for 77.8% (95% CI 74.6-80.9) of all attributable diarrhea. The researchers found that 42.5% of all cases studied had one pathogen detected; 38.9% had 2 or more.

“For most pathogens, the qPCR-derived attributable incidence surpassed the original estimate,” said Dr Houpt. “These 6 pathogen groups were responsible for 77.8% of attributable diarrhea in this study, and therefore, targeted interventions could have large public health benefits than previously projected.”


  • A quantitative approach will inherently “function less well for pathogens that are shed with high frequency, in high quantities, and for an extended duration,” the researchers noted.
  • Heterogeneity of pathogens between sites was noted, despite GEMS being carefully designed to choose study sites that were broadly representative of countries with moderate-to-high diarrhea-related mortality.
  • Molecular assays did not provide the infection speciation and subtyping that vaccine development depends on.

Funding for this study was provided by the Bill & Melinda Gates Foundation.


Liu J, Platts-Mills JA, Juma J, et al. Use of quantitative molecular diagnostic methods to identify causes of diarrhoea in children: a reanalysis of the GEMS case-control study. Lancet. 2016;388:1291-1301.