Study Uses Metagenomics to Diagnose Diarrheal Infections

November 21, 2019

Rollins researchers were part of a research team that investigated the effectiveness of using advanced metagenomics techniques to diagnose microbial causes of diarrheal diseases in children. The study, which found that traditional lab tests misdiagnosed the cause in roughly half of E. coli-attributed diarrheal cases, focused on unearthing the source of these diseases as well as understanding the related consequences for childhood development.

Levy joined researchers from the Georgia Institute of Technology and Universidad San Francisco de Quito for the project, which is part of a study funded by the National Institute of Allergy and Infectious Diseases (NIAID) that integrates epidemiological, molecular, and metagenomic data to understand how enteric (food and waterborne) pathogens and the gut microbiome vary across an urban-rural gradient in Ecuador. Frequent illness can affect the growth and development of children during their critical early years.

The findings were reported October 4 in the journal Applied and Environmental Microbiology and included researchers from Georgia Institute of Technology, Universidad San Francisco de Quito and the Universidad Central del Ecuador. Karen Levy, PhD, MPH, associate professor of environmental health at Rollins, was an author on the study.  

In the study, the investigators collected over 1,000 stool samples from infected Ecuadorian children and analyzed the samples using conventional lab methods to determine which causative E. coli pathogens were present. A subset of 30 of these samples was also sent to the Konstantinidis lab at Georgia Tech, where researchers used new genomic techniques to identify the disease-causing pathogens, as well as the degree of their effects on the microbiome.

One major finding from this research is that the results from the metagenomics technique significantly disagreed with the conventional analysis. “In 50 percent of the cases where the lab suggested E. coli was the agent, we didn’t see evidence from metagenomics that this was the case,” said Kostas Konstantinidis, professor in the School of Civil and Environmental Engineering at Georgia Tech.

The results of this study also raised questions about the long-standing definitions of pathogenic E. coli infections, many of which are actually asymptomatic. “The approach we used in this analysis helps to not only detect whether or not the pathogenic E. coli is present in the stool, but also if it is the likely cause of diarrhea experienced by study subjects,” said Levy. “This holds promise that, in the future, we could use metagenomic approaches to diagnose not just the presence of the so-called ‘pathogenic E. coli,’ but also of the actual pathogenicity of these organisms.”

The researchers’ novel approach uses detection of virulence factors (ability of an organism to infect a host and cause disease) as one of its diagnostic lines of evidence, so the study was also able to determine that the common diffuse adherent E. coli (DAEC) strain may be more virulent than previously thought based on previously unnoticed symptoms.

Based on these results, the researchers believe that their new metagenomics technique could ultimately serve as the foundation for a shift toward personalized medicine based on pathogen identification.

Through another NIAID award, the next step for this team will be to examine how environmental factors— such as water quality, presence of animals in the home, and the chemical environment—affect the microbiomes of small children. In this cohort of children from different geographic areas, the investigators will examine additional enteric pathogens and follow children for their first two years of life. This will offer the opportunity to understand whether infections are cleared from the body or if they continue to lurk in low levels.