Environmental Enteropathy Research Articles

Intestinal Biopsies for the Evaluation of Environmental Enteropathy and Environmental Enteric Dysfunction.

Environmental enteric dysfunction (EED) is a syndrome characterized by impairments of digestion and absorption and intestinal barrier failure in people living in insanitary or tropical environments. There is substantial evidence that it contributes to impaired linear growth of millions of children in low- and middle-income countries, to slowed neurocognitive development, and to diminished responses to oral vaccines. It represents the functional consequences of environmental enteropathy, an asymptomatic inflammatory disorder of the mucosa, and there is considerable overlap with the enteropathy observed in severe clinical malnutrition. The majority of studies of EED have employed functional tests based on lactulose permeation to define the presence of abnormal leak in the gut. However, where intestinal biopsies can safely be collected the opportunity then arises to study the underlying enteropathy in cellular and molecular detail, as well as to measure important functional elements such as enzyme expression. The purpose of this narrative review is to summarize the current understanding of environmental enteropathy obtained from small intestinal biopsies, and prospects for future work. We review histology, electron microscopy, transcription and protein expression, physiological measures, and the microbiome. We conclude that while noninvasive biomarkers of enteropathy and intestinal dysfunction permit large-scale studies of unquestionable value, intestinal biopsies are still required to investigate pathophysiology in depth.

Gut integrity and duodenal enteropathogen burden in undernourished children with environmental enteric dysfunction.

Environmental enteric dysfunction (EED) is a subclinical condition of intestinal inflammation, barrier dysfunction and malabsorption associated with growth faltering in children living in poverty. This study explores association of altered duodenal permeability (lactulose, rhamnose and their ratio) with higher burden of enteropathogen in the duodenal aspirate, altered histopathological findings and higher morbidity (diarrhea) that is collectively associated with linear growth faltering in children living in EED endemic setting. In a longitudinal birth cohort, 51 controls (WHZ > 0, HAZ > −1.0) and 63 cases (WHZ< -2.0, refractory to nutritional intervention) were recruited. Anthropometry and morbidity were recorded on monthly bases up to 24 months of age. Dual sugar assay of urine collected after oral administration of lactulose and rhamnose was assessed in 96 children from both the groups. Duodenal histopathology (n = 63) and enteropathogen analysis of aspirate via Taqman array card (n = 60) was assessed in only cases. Giardia was the most frequent pathogen and was associated with raised L:R ratio (p = 0.068). Gastric microscopy was more sensitive than duodenal aspirate in H. pylori detection. Microscopically confirmed H. pylori negatively correlated with HAZ at 24 months (r = −0.313, p = 0.013). Regarding histopathological parameters, goblet cell reduction significantly correlated with decline in dual sugar excretion (p< 0.05). Between cases and controls, there were no significant differences in the median (25th, 75th percentile) of urinary concentrations (μg/ml) of lactulose [27.0 (11.50, 59.50) for cases vs. 38.0 (12.0, 61.0) for controls], rhamnose [66.0 (28.0, 178.0) vs. 86.5 (29.5, 190.5)] and L:R ratio [0.47 (0.24, 0.90) vs. 0.51 (0.31, 0.71)] respectively. In multivariable regression model, 31% of variability in HAZ at 24 months of age among cases and controls was explained by final model including dual sugars. In conclusion, enteropathogen burden is associated with altered histopathological features and intestinal permeability. In cases and controls living in settings of endemic enteropathy, intestinal permeability test may predict linear growth. However, for adoption as a screening tool for EED, further validation is required due to its complex intestinal pathophysiology.

Environmental enteric dysfunction, soil transmitted helminthiasis and stunting among 36- to 59-month-old children in Quezon Province, Philippines

Introduction: Environmental enteric dysfunction (EED) is relevant in public health as it is a potential cause of child stunting. In the Philippines, stunting affects 33.4% of children in 2015. As of date, no local studies on EED exist. This study primarily aimed to determine the prevalence of EED, soil transmitted helminthiasis (STH) and stunting; and their relationships. Methods: A cross-sectional study was conducted among 120 children aged 36-59 months old in Quezon Province, Philippines. EED was assessed via glucose hydrogen breath test with a cut-off of &gt;20 ppm over baseline by 90 minutes suggestive of small intestinal bacterial overgrowth (SIBO), a biomarker of EED. Kato Katz Technique was used to determine STH. Stunting was determined using the 2006 World Health Organization Child Growth Standards. Descriptive and correlation analyses of data were done at 10% level of significance. The study received approval from the National Ethics Committee of PCHRD-DOST, Philippines. Results: Data on expired hydrogen level of &lt;20ppm were documented. The prevalence of STH among children were 38.1% for Ascaris lumbricodes, 15.3% for Trichuris trichiura, and 1.7% for hookworm infections. A high rate of stunting at 40.0% was observed. There was a significant positive association between stunting and the presence of Ascaris (p=0.01). Conclusion: There was no case of EED detected in the study. The severity of stunting was high at 40.0%. Among the STH, the prevalence of 38.1% children having Ascaris lumbricodes was alarming in terms of morbidity control. Nutrition interventions including WASH practices and the use of anthelminthic drugs need to be intensified to address stunting and STH.

Implementation challenges from a prospective, interventional biopsy-based study of Environmental Enteropathy in rural Pakistan

The Study of Environmental Enteropathy (EE) and Malnutrition in Pakistan (SEEM) is a community intervention trial designed to understand the pathophysiology of EE and its associated clinical phenotypes in children less than two years of age. Undernutrition is the underlying cause of three million deaths annually, accounting for 45% of all deaths among children under five years of age. Linear growth stunting affects a further 165 million. In Pakistan, where our study is focused, an estimated one in three children are underweight and nearly half are stunted. This manuscript summarizes the challenges faced by the field team and the solutions employed for achieving our research objectives at the rural field site, Matiari. Our study design involved a longitudinal collection of field data and biological samples which required constant engagement of field staff with the participating families. Challenges faced in SEEM included: 1) quality assurance parameters of anthropometry data; 2) 24-hour food recall data collection; 3) clinical management of acutely sick children enrolled in our study; 4) obtaining informed consent for upper gastrointestinal endoscopy (an invasive procedure); and 5) biological sample collection (blood, urine, stool) from malnourished children at the community level. We accomplished our goal of enrolling 350 malnourished children and 50 well-nourished children with a more than 95% success rate of collecting blood, urine and stool specimens. We collected 72% microbiome stool samples within 30 minutes of the child passing stool. We conducted an upper gastrointestinal biopsy in 63 children. Broadly, solutions to these challenges included good governance, the establishment of credibility, and the development of a longitudinal bidirectional relationship embedded in trust and effective communication with the caretakers of the children enrolled in our study. Continuous monitoring, regular training of staff, and effective teamwork were key factors that led to the successful execution of our study.

COVID-19 Testing Experience in a Resource-Limited Setting: The Use of Existing Facilities in Public Health Emergency Management.

Introduction: Coronavirus disease 2019 (COVID-19) is a public health emergency with little testing and treatment experiences at its occurrence. Diagnostic and treatment rapidly changed in the world including Ethiopia. Haramaya University has strived to change its diagnostic capacity using existing facilities in response to the national call to the pandemic.Objective: This summary aims to detail experiences of setting up COVID-19 testing in Haramaya University laboratories, Eastern Ethiopia.Methods: Desktop exercise was conducted to understand the start-up and implementations of COVID-19 testing in two Haramaya University laboratories, Hararghe Health Research Partnership and Campylobacter Genomics and Environmental Enteric Dysfunction laboratories. Communication, formats, guidelines, and standards were reviewed and summarized. Discussion with those involved in the start-up and implementation of the testing were also held. Ideas were summarized to learn the experiences the COVID-19 testing exercises.Lesson Learned: This is a huge experience for Haramaya University to participate in the national call to increase the testing platform in the management of COVID19. Close work relationship with the public health authorities at all levels demonstrated the university's commitment to public service. The university has used the opportunity to advance its molecular testing capability by training its staff and students. The University has also contributed to the capacity development for laboratories in the surrounding areas of Harar, Somali, Oromia, and Dire Dawa. The pandemic has been an opportunity in harnessing existing resource for the benefit of the public during such times of dire needs to provide critical public health laboratory interventions.

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

ABSTRACTBackgroundEnvironmental enteric dysfunction (EED) may influence growth during and recovery from moderate acute malnutrition (MAM), however, biomarkers to assess these relations have yet to be identified.ObjectivesThe objectives of this study were to: 1) develop a score for EED based on host fecal mRNA transcripts, 2) compare biomarkers of EED with each other, and 3) examine associations between the EED biomarkers and recovery from MAM and growth outcomes.MethodsIn a cohort of 520 Sierra Leonean MAM children, biomarkers of EED included the lactulose: mannitol (L: M) test, 15 host fecal mRNA transcripts, and host fecal proteins [α-1-antitrypsin (AAT), myeloperoxidase (MPO), neopterin (NEO)]. Anthropometry data were also collected and z scores were computed for length-for-age (LAZ) and weight-for-length (WLZ). Recovery from MAM was defined as midupper arm circumference ≥12.5 cm. Factor analysis was used to identify EED scores using the mRNA transcripts, and mixed effects regression was conducted to test for associations.ResultsThe 15 host fecal mRNA transcripts were clustered into 3 scores: gut inflammation (GI) score, gut structure (GS) score, and gut defense (GD) score. We found agreement between certain inflammation markers (GI score and MPO), and permeability markers (GS score and AAT; AAT and the L: M excretion ratio). Antimicrobial gut defense (GD score) was inversely associated with percent lactulose excreted, a measure of intestinal permeability. LAZ (β: –0.08; 95% CI: –0.14, –0.02) and WLZ (β: –0.03; 95% CI: –0.06, –0.01) were negatively associated with GI score. A high GD score (β: 0.36; 95% CI: 0.08, 0.64) and low AAT (β: –1.35; 95% CI: –2.35, –0.36) were associated with recovery from MAM.ConclusionsScores derived from host fecal mRNA transcript variably correlated with the L: M test and host fecal proteins. Markers of intestinal inflammation, permeability, and defense were associated with growth outcomes and recovery from MAM.

Key Food Hygiene Behaviors to Reduce Microbial Food Contamination in Rural Bangladesh

ObjectivesMicrobial contamination of complementary foods, which puts young children at risk of developing intestinal infections, could be reduced by improved handwashing and food hygiene practices. We quantify the effect of maternal food hygiene practices on complementary food contamination in order to identify food hygiene behaviors with the greatest impact in our study population. MethodsWe analyzed cross-sectional data on food hygiene practices and measured Escherichia coli counts as an indicator of microbial contamination in complementary food samples from 342 households of the Food and Agricultural Approaches to Reducing Malnutrition (FAARM) trial in Sylhet, Bangladesh. We used multivariable logistic regression to examine associations of maternal food hygiene behaviors with food contamination. ResultsAbout 46% of complementary food samples had detectable levels of Escherichia coli. Handwashing with soap at five critical times (OR: 0.7, 95% CI: 0.6 – 0.9), cleanliness of feeding utensils (OR: 0.4, 95% CI: 0.2 – 0.9), and fresh preparation of food before feeding (OR: 0.1, 95% CI: 0.08 – 0.3) were strongly associated with reduced food contamination, while there was no or only weak evidence that reheating of stored food and safe storage of food reduced contamination. The reduction in food contamination was larger when food hygiene behaviors were practiced in combination. ConclusionsAdoption of single food hygiene practices showed limited potential and a combined practice of multiple food hygiene behaviors is needed to achieve a substantial reduction of complementary food contamination. Funding SourcesThe German Ministry for Education and Research (BMBF) is the primary funder for the FAARM trial. FAARM’s Food Hygiene to reduce Environmental Enteric Dysfunction (FHEED) work was financially supported by Deutsche Forschungsgemeinschaft (DFG) and Foundation Fiat Panis.

P017 Small bowel transcriptomics define similarities and divergent pathways between Crohn, environmental enteric dysfunction (EED), and celiac diseases, implicating role for the microbiome in the pathogenesis

Abstract Background Crohn disease (CD), environmental enteric dysfunction (EED) and celiac disease are prevalent enteropathies linked to chronic gut inflammation. However, unlike celiac and Crohn that are prevalent in westernized countries, EED is seen in only in low- and middle-income countries of the developing world. Recent work has defined specific EED duodenal microbiota associated with stunting, and transmission of EED histologic changes and weight loss by microbial transfer to germ free mice. Methods We performed high throughput transcriptomics of 94 duodenal samples from the SEEM cohort:52 undernourished EED participants, 17 celiac and 25 healthy North American controls. We compared those to our previously reported transcriptomics of 248 newly diagnosed ileal CD from RISK. Comparison were performed between cases and controls within each cohort. Results Above 90% of the expressed protein coding genes are shared between duodenum samples within SEEM, and Crohn ileal within RISK enabling the anticipated comparison. A substantial number of the down-regulated genes in undernourished EED participants overlapped with celiac (212/481, 44%) and with Crohn Disease (249/481, 52%). Shared reduced signatures and functions included decrease in epithelial lipid metabolism, vitamins, and brush border transport signatures. Relative to celiac disease, suppression of antioxidant and detoxification genes were EED- and Crohn-specific, which include the reduction of metallothioneins (MT family) that buffer against toxic metals, and aldo-keto NADPH- genes (AKR1C family) involved in detoxification of environmental compounds. A smaller proportion of the EED up-regulated signal overlapped with celiac (85/781), and we noted a more significant overlap with Crohn disease (248/781, Chi squares p&amp;lt;0.05). Relative to celiac disease, up-regulation of an innate anti-microbial DUOX2 and LCN2 gene, and of myeloid response signals, several CCL chemokines, and extracellular matrix signature were EED- and Crohn-specific. Consistent with this, greater level of DUOX2 protein was detected in duodenal biopsies from EED subjects vs. celiac and controls and in ileal CD vs. ileal controls. As opposed to the robust dysbiosis previously characterized in Crohn disease, we were unable to identify significant microbial signal in celiac patients in comparison to controls, while recent studies identified microbial patterns linked with EED. Conclusion We highlight important biologic signals widely overlapping between Crohn Disease (CD) and EED transcriptome in the small intestine, suggesting mechanisms involving altered gut microbiota. Inhibiting innate immune activation or reverting Crohn dysbiosis may be beneficial future therapy for Crohn Disease and EED.

Insight into the Stunting vis a vis Salmonella and Shigella Species among Children of Pakistan

Pakistan is one of the leading countries where the high childhood mortality (under the age of 5 years) as well as is a country where &gt;33% of children are underweight and 38% show stunted growth. The current study investigated the presence or absence of Salmonella and Shigella sp. in stunted children under five years of age from the lower socioeconomic background of Pakistan. Besides, the antibiotics susceptibility patterns were studied along with the sociodemographic and clinical information demographic factors using a questionnaire. The stool samples from stunted children have processed following standard bacteriological protocols and presumptive colonies of Salmonella and Shigella species were identified and sub-cultured on selective media and confirmed by using the standard biochemical test as well as molecular tests. Antibiotics susceptibility of the isolates to 10 antibiotics was tested using disk diffusion assay. The results suggested that 10.5% and 5.7% of the stool samples were positive for Salmonella and Shigella sp. respectively. Moreover, the antibiotics susceptibility test results of the isolates showed that Salmonella sp., were showing higher resistance to amoxicillin whereas Shigella sp. were more resistant to gentamycin. All Salmonella and Shigella isolates were resistant to Rifampicin and 80% of isolates of both were susceptible to ciprofloxacin and cefotaxime. The study suggested that environmental enteric dysfunction (EED), is widespread among malnourished children and may result in stunted growth. The contributory factors such as unsafe farming practices or close association to poultry or livestock animals and prevailing sanitation &amp; hygiene conditions are the potential source of entero-pathogens.

Biomarkers of environmental enteric dysfunction are not consistently associated with linear growth velocity in rural Zimbabwean infants

ABSTRACTBackgroundChild stunting remains a poorly understood, prevalent public health problem. Environmental enteric dysfunction (EED) is hypothesized to be an important underlying cause.ObjectivesWithin a subgroup of 1169 children enrolled in the SHINE (Sanitation Hygiene Infant Nutrition Efficacy) trial in rural Zimbabwe, followed longitudinally from birth to 18 mo of age, we evaluated associations between the concentration of 11 EED biomarkers and linear growth velocity.MethodsAt infant ages 1, 3, 6, 12, and 18 mo, nurses measured child length and collected stool and blood; the lactulose-mannitol urine test was also conducted at all visits except at 1 mo. Stool neopterin, α-1 antitrypsin, myeloperoxidase, and regenerating gene 1β protein; urinary lactulose and mannitol; and plasma kynurenine, tryptophan, C-reactive protein, insulin-like growth factor-1 (IGF-1), soluble CD14, intestinal fatty acid binding protein, and citrulline were measured. We analyzed the change in relative [∆ length-for-age z score (LAZ)/mo] and absolute (∆ length/mo) growth velocity during 4 age intervals (1–3 mo; 3–6 mo; 6–12 mo; and 12–18 mo) per SD increase in biomarker concentration at the start of each age interval.ResultsIn fully adjusted models, we observed only 3 small, statistically significant associations: kynurenine:tryptophan ratio at 12 mo was associated with decreased mean LAZ velocity during the 12–18 mo interval (−0.015 LAZ/mo; 95% CI: −0.029, −0.001 LAZ/mo); mannitol excretion at 6 mo was associated with increased LAZ velocity during the 6–12 mo interval (0.013 LAZ/mo; 95% CI: 0.001, 0.025 LAZ/mo), and plasma IGF-1 at 1 mo was associated with increased LAZ velocity during the 1–3 mo interval (0.118 LAZ/mo; 95% CI: 0.024, 0.211 LAZ/mo). Results for absolute growth velocity were similar, except IGF-1 was also associated with growth during the 12–18 mo interval. We found no other associations between any EED biomarker and linear growth velocity.ConclusionsNone of 11 biomarkers of EED were consistently associated with linear growth among Zimbabwean children.This trial was registered at clinicaltrials.gov as NCT01824940.

Effects of a combined water and sanitation intervention on biomarkers of child environmental enteric dysfunction and associations with height-for-age z-score: A matched cohort study in rural Odisha, India

Poor water, sanitation and hygiene (WaSH) conditions are hypothesized to contribute to environmental enteric dysfunction (EED), a subclinical condition that may be associated with chronic undernutrition and impaired linear growth. We evaluated the effect of a combined water and sanitation intervention on biomarkers of EED, and then assessed associations of biomarkers of EED with height-for-age z-scores (HAZ), in children under five. We conducted a sub-study within a matched cohort study of a household-level water and sanitation infrastructure intervention in rural Odisha, India, in which we had observed an effect of the intervention on HAZ. We collected stool samples (N = 471) and anthropometry data (N = 209) for children under age 5. We analyzed stool samples for three biomarkers of EED: myeloperoxidase (MPO), neopterin (NEO), and α1-anti-trypsin (AAT). We used linear mixed models to estimate associations between the intervention and each biomarker of EED and between each biomarker and HAZ. The intervention was inversely associated with AAT (-0.25 log μg/ml, p = 0.025), suggesting a protective effect on EED, but was not associated with MPO or NEO. We observed an inverse association between MPO and HAZ (-0.031 per 1000 ng/ml MPO, p = 0.0090) but no association between either NEO or AAT and HAZ. Our results contribute evidence that a transformative WaSH infrastructure intervention may reduce intestinal permeability, but not intestinal inflammation and immune activation, in young children. Our study also adds to observational evidence of associations between intestinal inflammation and nutritional status, as measured by HAZ, in young children.Trial Registration: ClinicalTrials.gov (NCT02441699).

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

Sometimes referred to as hidden hunger, micronutrient deficiencies persist on a global scale. For some micronutrients this appears to be due to inadequate intake, for others intake may not match increased requirements. However, for most micronutrient deficiencies there is uncertainty as to the dominant driver, and the question about the contribution of malabsorption is open. Environmental enteropathy (EE), formerly referred to as tropical enteropathy and also referred to as environmental enteric dysfunction, is an asymptomatic disorder of small intestinal structure and function which is very highly prevalent in many disadvantaged populations. Recent studies of the pathology and microbiology of this disorder suggest that it is driven by very high pathogen burdens in children and adults living in insanitary environments and is characterised by major derangements of the epithelial cells of the intestinal mucosa. Transcriptomic data suggest that it may lead to impaired digestion and absorption of macronutrients. Given the very high prevalence of EE, marginal malabsorption could have large impacts at population scales. However, the relative contributions of inadequate soil and crop micronutrient contents, inadequate intake, malabsorption and increased requirements are unknown. Malabsorption may compromise attempts to improve micronutrient status, but with the exception of zinc there is currently little evidence to confirm that malabsorption contributes to micronutrient deficiency. Much further research is required to understand the role of malabsorption in hidden hunger, especially in very disadvantaged populations where these deficiencies are most prevalent.

Automated Enteropathy: Discovering the Potential of Machine Learning in Environmental Enteropathy.

Automated Enteropathy: Discovering the Potential of Machine Learning in Environmental Enteropathy.

Adaptation of the small intestine to microbial enteropathogens in Zambian children with stunting

Environmental enteropathy is a major contributor to growth faltering in millions of children in Africa and South Asia. We carried out a longitudinal, observational and interventional study in Lusaka, Zambia, of 297 children with stunting (aged 2–17 months at recruitment) and 46 control children who had good growth (aged 1–5 months at recruitment). Control children contributed data only at baseline. Children were provided with nutritional supplementation of daily cornmeal-soy blend, an egg and a micronutrient sprinkle, and were followed up to 24 months of age. Children whose growth did not improve over 4–6 months of nutritional supplementation were classified as having non-responsive stunting. We monitored microbial translocation from the gut lumen to the bloodstream in the cohort with non-responsive stunting (n = 108) by measuring circulating lipopolysaccharide (LPS), LPS-binding protein and soluble CD14 at baseline and when non-response was declared. We found that microbial translocation decreased with increasing age, such that LPS declined in 81 (75%) of 108 children with non-responsive stunting, despite sustained pathogen pressure and ongoing intestinal epithelial damage. We used confocal laser endomicroscopy and found that mucosal leakiness also declined with age. However, expression of brush border enzyme, nutrient transporter and mucosal barrier genes in intestinal biopsies did not change with age or correlate with biomarkers of microbial translocation. We propose that environmental enteropathy arises through adaptation to pathogen-mediated epithelial damage. Although environmental enteropathy reduces microbial translocation, it does so at the cost of impaired growth. The reduced epithelial surface area imposed by villus blunting may explain these findings.

The effect of bovine colostrum/egg supplementation compared with corn/soy flour in young Malawian children: a randomized, controlled clinical trial

Bovine colostrum with egg powder (BC/egg) is rich in essential amino acids and immunoactive compounds. This trial tested the hypothesis that a daily supplement of BC/egg would reduce linear growth faltering and environmental enteric dysfunction (EED) in Malawian infants when compared with an isoenergetic ration of corn/soy flour used as a control. EED was defined by a lactulose permeability test. This was a prospective, randomized, blinded, placebo-controlled clinical trial in which 9-mo-old infants received BC/egg or a control for 3 mo. The primary outcomes were change in length-for-age z-score (ΔLAZ) and urinary lactulose excretion (%L) at 12-mo-old. Secondary outcomes included episodes of diarrhea, stunting, EED, and the 16S configuration of the fecal microbiota. Of the 277 children enrolled, 267 completed the intervention phase of the study. LAZ decreased in all children from 9 to 17 mo, although ΔLAZ was less in children receiving BC/egg from 9 to 12 mo (difference=0.12 z-scores; P=0.0011). This difference persisted after feeding was completed, with less ΔLAZ (difference=0.09 z-scores). A lower prevalence of stunting was seen in the intervention group (n=47/137) than the control group (n=62/127) at 17 mo (RR = 0.70; 95% CI: 0.52, 0.94).The median %L at 12 mo of age in the children receiving BC/egg was 0.14%, compared with 0.17% in the control group (P=0.74). In children with %L>0.45% at enrollment (severe EED), the BC/egg group had more children with normal %L at 12 mo of age (10/20, 50%) than was seen in controls (2/15, 13%; P=0.024). Episodes of diarrhea and β-diversity of the 16S configuration of fecal microbiota did not differ between the 2 groups. Addition of BC/egg to complementary feeding in Malawian infants resulted in less linear growth faltering. This trial was registered at clinicaltrials.gov as NCT03801317.

Mucosal Genomics Implicate Lymphocyte Activation and Lipid Metabolism in Refractory Environmental Enteric Dysfunction

Background & AimsEnvironmental enteric dysfunction (EED) limits the Sustainable Development Goals of improved childhood growth and survival. We applied mucosal genomics to advance our understanding of EED.MethodsThe Study of Environmental Enteropathy and Malnutrition (SEEM) followed 416 children from birth to 24 months in a rural district in Pakistan. Biomarkers were measured at 9 months and tested for association with growth at 24 months. The duodenal methylome and transcriptome were determined in 52 undernourished SEEM participants and 42 North American controls and patients with celiac disease.ResultsAfter accounting for growth at study entry, circulating insulin-like growth factor-1 (IGF-1) and ferritin predicted linear growth, whereas leptin correlated with future weight gain. The EED transcriptome exhibited suppression of antioxidant, detoxification, and lipid metabolism genes, and induction of anti-microbial response, interferon, and lymphocyte activation genes. Relative to celiac disease, suppression of antioxidant and detoxification genes and induction of antimicrobial response genes were EED-specific. At the epigenetic level, EED showed hyper-methylation of epithelial metabolism and barrier function genes, and hypo-methylation of immune response and cell proliferation genes. Duodenal coexpression modules showed association between lymphocyte proliferation and epithelial metabolic genes and histologic severity, fecal energy loss, and wasting (weight-for-length/height Z < -2.0). Leptin was associated with expression of epithelial carbohydrate metabolism and stem cell renewal genes. Immune response genes were attenuated by giardia colonization.ConclusionsChildren with reduced circulating IGF-1 are more likely to experience stunting. Leptin and a gene signature for lymphocyte activation and dysregulated lipid metabolism are implicated in wasting, suggesting new approaches for EED refractory to nutritional intervention.ClinicalTrials.gov, Number: NCT03588013. (https://clinicaltrials.gov/ct2/show/NCT03588013)

Artificial Intelligence-based Analytics for Diagnosis of Small Bowel Enteropathies and Black Box Feature Detection.

Striking histopathological overlap between distinct but related conditions poses a disease diagnostic challenge. There is a major clinical need to develop computational methods enabling clinicians to translate heterogeneous biomedical images into accurate and quantitative diagnostics. This need is particularly salient with small bowel enteropathies; environmental enteropathy (EE) and celiac disease (CD). We built upon our preliminary analysis by developing an artificial intelligence (AI)-based image analysis platform utilizing deep learning convolutional neural networks (CNNs) for these enteropathies. Data for the secondary analysis was obtained from three primary studies at different sites. The image analysis platform for EE and CD was developed using CNNs including one with multizoom architecture. Gradient-weighted class activation mappings (Grad-CAMs) were used to visualize the models' decision-making process for classifying each disease. A team of medical experts simultaneously reviewed the stain color normalized images done for bias reduction and Grad-CAMs to confirm structural preservation and biomedical relevance, respectively. Four hundred and sixty-one high-resolution biopsy images from 150 children were acquired. Median age (interquartile range) was 37.5 (19.0-121.5) months with a roughly equal sex distribution; 77 males (51.3%). ResNet50 and shallow CNN demonstrated 98% and 96% case-detection accuracy, respectively, which increased to 98.3% with an ensemble. Grad-CAMs demonstrated models' ability to learn different microscopic morphological features for EE, CD, and controls. Our AI-based image analysis platform demonstrated high classification accuracy for small bowel enteropathies which was capable of identifying biologically relevant microscopic features and emulating human pathologist decision-making process. Grad-CAMs illuminated the otherwise "black box" of deep learning in medicine, allowing for increased physician confidence in adopting these new technologies in clinical practice.

Alterations in the histological features of the intestinal mucosa in malnourished adults of Bangladesh

There is paucity of knowledge on the histological features of the intestinal mucosa in malnourished adults of Bangladesh. The purpose of the study was to explore the histological features of the intestinal mucosa in malnourished adults of Bangladesh and to compare the findings with their well-nourished counterparts. 64 adults (37 malnourished with body mass index, BMI < 18.5 kg/m2 and 27 controls with BMI > 18.5 kg/m2) from the Bangladesh Environmental Enteric Dysfunction (BEED) study, who underwent upper-gastrointestinal endoscopy, were selected for this study. With a view to address the association of environmental enteric dysfunction (EED) with malnutrition, upper-gastrointestinal endoscopy was performed and mucosal biopsies from the distal duodenum were studied for histopathology. Villous height, crypt depth, and presence of inflammatory infiltrates in lamina propria were investigated. Bivariate analysis was performed to quantify the relation between malnutrition and the histological features. About 95% adults, irrespective of nutritional status, were diagnosed to have chronic non-specific duodenitis on histopathology. Malnourished adults suffered significantly more from chronic active duodenitis compared to their well-nourished counterparts (p = 0.003). Malnourished adults also had significantly higher frequency of subtotal villous atrophy, crypt hyperplasia and marked cellular infiltration in the lamina propria than the healthy controls (p < 0.05).

Campylobacter Colonization, Environmental Enteric Dysfunction, Stunting, and Associated Risk Factors Among Young Children in Rural Ethiopia: A Cross-Sectional Study From the Campylobacter Genomics and Environmental Enteric Dysfunction (CAGED) Project.

Livestock farming provides a possible mechanism by which smallholder farmers can meet their household need for animal source foods (ASF), which may reduce the risk of stunting. However, direct/indirect contacts with domestic animals may increase colonization by Campylobacter spp., which has been associated with Environmental Enteric Dysfunction (EED) and stunting. A cross-sectional study involving 102 randomly selected children between 12 and 16 months of age was conducted in rural eastern Ethiopia to establish prevalence rates of Campylobacter colonization, EED, and stunting, and evaluate potential risk factors. Data were collected between September and December 2018. The prevalence of EED and stunting was 50% (95% CI: 40–60%) and 41% (95% CI: 32–51%), respectively. Among enrolled children, 56% had consumed some ASF in the previous 24 h; 47% had diarrhea and 50% had fever in the past 15 days. 54, 63, 71 or 43% of households owned at least one chicken, cow/bull, goat, or sheep; 54 (53%) households kept chickens indoors overnight and only half of these confined the animals. Sanitation was poor, with high levels of unimproved latrines and open defecation. Most households had access to an improved source of drinking water. The prevalence of Campylobacter colonization was 50% (95% CI: 41–60%) by PCR. In addition to the thermotolerant species Campylobacter jejuni, Campylobacter coli and Campylobacter upsaliensis, non-thermotolerant species related to Campylobacter hyointestinalis and Campylobacter fetus were frequently detected by Meta-total RNA sequencing (MeTRS). Current breastfeeding and ASF consumption increased the odds of Campylobacter detection by PCR, while improved drinking water supply decreased the odds of EED. No risk factors were significantly associated with stunting. Further studies are necessary to better understand reservoirs and transmission pathways of Campylobacter spp. and their potential impact on child health.

Associations Between Biomarkers of Environmental Enteric Dysfunction and Oral Rotavirus Vaccine Immunogenicity in Rural Zimbabwean Infants

Abstract Background Oral rotavirus vaccines (RVV) are poorly immunogenic in low-income countries. Environmental enteric dysfunction (EED) resulting from poor water, sanitation and hygiene (WASH) may contribute. We therefore tested associations between EED and RVV immunogenicity, and evaluated the effect of improved WASH on EED. Methods We measured nine biomarkers of EED among Zimbabwean infants born to mothers enrolled in a cluster-randomised 2 × 2 factorial trial of improved WASH and improved feeding between November 2012 and March 2015 (NCT01824940). We used multivariable regression to determine associations between EED biomarkers and RVV seroconversion, seropositivity and geometric mean titer. Log-binomial regression was used to evaluate the effect of improved WASH on EED. Findings Among 303 infants with EED biomarkers and immunogenicity data, plasma intestinal fatty-acid binding protein and stool myeloperoxidase were positively associated with RVV seroconversion; adjusted RR 1.63 (95%CI 1.04, 2.57) and 1.29 (95%CI 1.01, 1.65), respectively. There were no other associations between RVV immunogenicity and either individual biomarkers or EED domains (intestinal permeability, intestinal damage, intestinal inflammation and microbial translocation). EED biomarkers did not differ between randomised WASH and non-WASH groups. Interpretation We found no evidence that EED was associated with poor RVV immunogenicity. Contrary to our hypothesis, there was weak evidence that EED was associated with increased seroconversion. EED biomarkers were not affected by a package of household-level WASH interventions. Funding This work was supported by the Wellcome Trust. The SHINE trial was funded by the Bill & Melinda Gates Foundation; UK Department for International Development (UK Aid); Swiss Agency for Developmentand Cooperation and US National Institutes of Health.