Detection and interpretation of fecal host mRNA in rural Malawian infants aged 6–12 months at risk for environmental enteric dysfunction

Abstract

Recent studies have suggested that environmental enteric dysfunction can be assessed in rural African children by measuring levels of fecal mRNA transcripts. The field collection of fecal samples is less invasive and cumbersome than administration of the lactulose:mannitol test, which is typically used to assess environmental enteric dysfunction. This study sought to determine if, as in children aged 12-60 months, an array of seven fecal host transcripts (CD53, CDX1, HLA-DRA, TNF, S100A8, MUC12, and REG1A) could predict environmental enteric dysfunction in rural African infants. Host fecal transcript abundance was correlated to the percentage of lactulose (%L) excreted in the urine for 340 samples from Malawian children aged 6-12 months. Permeability was categorized as not severe (%L < 0.45) and severe (%L ≥ 0.45). This study found the prevalence of severe environmental enteric dysfunction to be 114/834 (14%), lower than what was previously reported for 12-60 months old children, 595/1521 (39%, P = 0.001). In linear regression analysis with the seven host transcripts, two were associated with %L: β coefficients of -1.843 ( P = 0.035) and 0.215 ( P = 0.006) for CDX1 and REG1A, respectively. The seven fecal host transcripts in a random forest model did not predict severe environmental enteric dysfunction. Future models utilizing different transcripts identified from an untargeted, agnostic assessment of all potential host transcripts could provide accurate predictions of environmental enteric dysfunction in infants. Impact statement Environmental enteric dysfunction (EED) is associated with reduced linear growth. The dual sugar absorption test has been used as a non-invasive method to determine the gut health of individuals. Alternative methods using fecal host mRNAs as predictors of the gut health are promising. In older children, we have determined that seven transcripts can predict the gut health in a random forest model. Our current study determined that the host fecal mRNA is abundant in infants and toddlers alike. Severe EED in rural Malawian children is less prevalent in infants than in young children. REG1A and CDX1 are associated with gut health. Fecal host mRNA may well be a means to assess gut health in African infants, but the panel of transcripts used to do this will differ from that in older children.

Biomarkers of environmental enteric dysfunction are differently associated with recovery and growth among children with moderate acute malnutrition in Sierra Leone

“…Our study adds to the growing body of literature on field appropriate biomarkers of EED. The clusters of host fecal mRNA transcripts identified by this study have also been reported previously ( 31 ). Agreement between the clusters of inflammation and permeability with other more established EED biomarkers gives us confidence that they are measuring changes to the intestine characteristic of EED.…”

“…Although the biomarkers in our study did not all agree with each other, this may be a sign that they are measuring different aspects and stages of the complex condition that is EED. Similar to our findings, other studies have found conflicting results for associations between the biomarkers examined in this study ( 11 , 18 , 31 ). Differences in age, study design, and selection of biomarkers among studies muddy the evidence for the association between EED and growth outcomes.…”

Effects of improved water, sanitation, and hygiene and improved complementary feeding on environmental enteric dysfunction in children in rural Zimbabwe: A cluster-randomized controlled trial

“…There is no agreed case definition for EED. Differential urinary excretion of two sugars, typically lactulose and mannitol, has most often been used to characterize abnormalities in gut permeability and absorption, but this test has substantial limitations [17,18] and only captures part of the pathology underlying EED [15]. To date, studies have failed to demonstrate reproducible changes in these markers following interventions.…”

The contribution of environmental enteropathy to the global problem of micronutrient deficiency

“…More recent studies have used fluorescein as a marker of the leakiness of the mucosa, either by showing leakage of fluorescein from the systemic circulation into the gut lumen during endoscopy (52,58) , or by showing leakage of oral fluorescein into the systemic circulation (59,60) . In an ingenious approach, transcriptomic analysis of shed enterocytes in stool samples identified mucin and inflammatory genes associated with EE in an entirely non-invasive way (61) .…”