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Diebold PJ, Rhee MW, Shi Q, Trung NV, Umrani F, Ahmed S, Kulkarni V, Deshpande P, Alexander M, Thi Hoa N, Christakis NA, Iqbal NT, Ali SA, Mathad JS, Brito IL. Clinically relevant antibiotic resistance genes are linked to a limited set of taxa within gut microbiome worldwide. Nat Commun 2023; 14:7366. [PMID: 37963868 PMCID: PMC10645880 DOI: 10.1038/s41467-023-42998-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 10/27/2023] [Indexed: 11/16/2023] Open
Abstract
The acquisition of antimicrobial resistance (AR) genes has rendered important pathogens nearly or fully unresponsive to antibiotics. It has been suggested that pathogens acquire AR traits from the gut microbiota, which collectively serve as a global reservoir for AR genes conferring resistance to all classes of antibiotics. However, only a subset of AR genes confers resistance to clinically relevant antibiotics, and, although these AR gene profiles are well-characterized for common pathogens, less is known about their taxonomic associations and transfer potential within diverse members of the gut microbiota. We examined a collection of 14,850 human metagenomes and 1666 environmental metagenomes from 33 countries, in addition to nearly 600,000 isolate genomes, to gain insight into the global prevalence and taxonomic range of clinically relevant AR genes. We find that several of the most concerning AR genes, such as those encoding the cephalosporinase CTX-M and carbapenemases KPC, IMP, NDM, and VIM, remain taxonomically restricted to Proteobacteria. Even cfiA, the most common carbapenemase gene within the human gut microbiome, remains tightly restricted to Bacteroides, despite being found on a mobilizable plasmid. We confirmed these findings in gut microbiome samples from India, Honduras, Pakistan, and Vietnam, using a high-sensitivity single-cell fusion PCR approach. Focusing on a set of genes encoding carbapenemases and cephalosporinases, thus far restricted to Bacteroides species, we find that few mutations are required for efficacy in a different phylum, raising the question of why these genes have not spread more widely. Overall, these data suggest that globally prevalent, clinically relevant AR genes have not yet established themselves across diverse commensal gut microbiota.
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Affiliation(s)
- Peter J Diebold
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Matthew W Rhee
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Qiaojuan Shi
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Nguyen Vinh Trung
- Oxford University Clinical Research Unit (OUCRU) in Ho Chi Minh City, Ho Chi Minh city, Viet Nam
| | | | | | - Vandana Kulkarni
- Johns Hopkins University Clinical Trials Unit, Byramjee Jeejeebhoy Government Medical College, Pune, Maharashtra, India
| | - Prasad Deshpande
- Johns Hopkins University Clinical Trials Unit, Byramjee Jeejeebhoy Government Medical College, Pune, Maharashtra, India
| | - Mallika Alexander
- Johns Hopkins University Clinical Trials Unit, Byramjee Jeejeebhoy Government Medical College, Pune, Maharashtra, India
| | - Ngo Thi Hoa
- Oxford University Clinical Research Unit (OUCRU) in Ho Chi Minh City, Ho Chi Minh city, Viet Nam
- Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Microbiology Department and Center for Tropical Medicine Research, Ngoc Thach University of Medicine, Ho Chi Minh city, Vietnam
| | | | | | | | | | - Ilana L Brito
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA.
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2
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Sarfraz A, Jamil Z, Ahmed S, Umrani F, Qureshi AK, Jakhro S, Sajid M, Rahman N, Rizvi A, Ma JZ, Mallawaarachchi I, Iqbal NT, Syed S, Iqbal J, Sadiq K, Moore SR, Ali SA. Impact of diarrhoea and acute respiratory infection on environmental enteric dysfunction and growth of malnourished children in Pakistan: a longitudinal cohort study. Lancet Reg Health Southeast Asia 2023; 15:100212. [PMID: 37614352 PMCID: PMC10442970 DOI: 10.1016/j.lansea.2023.100212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 01/04/2023] [Accepted: 04/26/2023] [Indexed: 08/25/2023]
Abstract
Background Diarrhoea and acute respiratory infections (ARI) are assumed to be major drivers of growth and likely contribute to environmental enteric dysfunction (EED), which is a precursor to childhood malnutrition. In the present study, we checked the correlation between diarrhoeal/ARI burden and EED using a novel duodenal histological index. Methods Between November 2017 and July 2019, a total of 365 infants with weight-for-height Z scores (WHZ score) of <-2 were enrolled, and 51 infants with WHZ scores of >0 and height-for-age Z scores (HAZ scores) of >-1 were selected as age-matched healthy controls. Morbidity was assessed weekly and categorised as the total number of days with diarrhoea and acute respiratory infection (ARI) from enrolment until two years of age and was further divided into four quartiles in ascending order. Findings The HAZ declined until two years of age regardless of morbidity burden, and WHZ and weight-for-age Z scores (WAZ scores) were at their lowest at six months. Sixty-three subjects who had a WHZ score <-2 and failed to respond to nutritional and educational interventions were further selected at 15 months to investigate their EED histological scores with endoscopy further. EED histological scores of the subjects were higher with increasing diarrhoeal frequency yet remained statistically insignificant (p = 0.810). Interpretation There was not a clear correlation between diarrhoea and ARI frequency with growth faltering, however, children with the highest frequency of diarrhoea had the highest EED histological scores and growth faltering. Funding Bill and Melinda Gates Foundation and The National Institutes of Health.
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Affiliation(s)
- Azza Sarfraz
- Department of Pediatrics and Child Health, The Aga Khan University, Pakistan
| | - Zehra Jamil
- Department of Biological & Biomedical Sciences, The Aga Khan University, Pakistan
| | - Sheraz Ahmed
- Department of Pediatrics and Child Health, The Aga Khan University, Pakistan
| | - Fayaz Umrani
- Department of Pediatrics and Child Health, The Aga Khan University, Pakistan
| | | | - Sadaf Jakhro
- Department of Pediatrics and Child Health, The Aga Khan University, Pakistan
| | - Muhammad Sajid
- Department of Pediatrics and Child Health, The Aga Khan University, Pakistan
| | - Najeeb Rahman
- Department of Pediatrics and Child Health, The Aga Khan University, Pakistan
| | - Arjumand Rizvi
- Department of Pediatrics and Child Health, The Aga Khan University, Pakistan
| | - Jennie Z. Ma
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | | | - Najeeha T. Iqbal
- Department of Pediatrics and Child Health, The Aga Khan University, Pakistan
- Department of Biological & Biomedical Sciences, The Aga Khan University, Pakistan
| | - Sana Syed
- Department of Pediatrics and Child Health, The Aga Khan University, Pakistan
- Department of Pediatrics, University of Virginia, Charlottesville, VA, USA
| | - Junaid Iqbal
- Department of Pediatrics and Child Health, The Aga Khan University, Pakistan
- Department of Biological & Biomedical Sciences, The Aga Khan University, Pakistan
| | - Kamran Sadiq
- Department of Pediatrics and Child Health, The Aga Khan University, Pakistan
| | - Sean R. Moore
- Department of Pediatrics, University of Virginia, Charlottesville, VA, USA
| | - Syed Asad Ali
- Department of Pediatrics and Child Health, The Aga Khan University, Pakistan
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Sarfraz A, Ahmed S, Muhammad S, Rehman N, Soomro SI, Qureshi K, Jakhro S, Umrani F, Greene A, Syed S, Moore SR, Ali SA. Standard RUTF vs. locally-made RUSF for acutely malnourished children: A quasi-experimental comparison of the impact on growth and compliance in a rural community of Pakistan. PLoS One 2023; 18:e0287962. [PMID: 37437065 PMCID: PMC10337979 DOI: 10.1371/journal.pone.0287962] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 06/14/2023] [Indexed: 07/14/2023] Open
Abstract
BACKGROUND The reduction in severe and moderate acute malnutrition (SAM and MAM) rates in Pakistan has been sub-optimal compared to other low-and middle-income countries (LMICs). Specially-formulated products have been designed globally to manage SAM and MAM, such as ready-to-use therapeutic food (RUTF) and ready-to-use supplementary food (RUSF), with variable efficacies. RUTF is primarily produced and patented in industrialized countries, raising supply challenges in resource-constrained regions with a high burden of acute malnutrition. RUSF minimizes costs by using locally-available ingredients while providing similar nutritional value. In this study, we compared the efficacy, side effects, and compliance of two months of supplementation with either RUTF or RUSF. METHODS Children aged nine months in the rural district of Matiari, Pakistan, with a weight-for-height z-score (WHZ) <-2 received either RUTF (500 kcal sachet) for two months in 2015 or RUSF (520 kcal sachet) for two months in 2018. RESULTS The RUSF group had a higher height gain and mid-upper arm circumferences (MUAC) score. Higher compliance was noted with lower side effects in the RUSF group. A higher compliance rate did correlate with the growth parameters in respective groups. CONCLUSION Our study found that both RUTF and RUSF partially improve the anthropometric status of acutely malnourished children, with neither being superior to the other.
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Affiliation(s)
- Azza Sarfraz
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Sheraz Ahmed
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Sajid Muhammad
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Najeeb Rehman
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Sanam Iram Soomro
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Khaliq Qureshi
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Sadaf Jakhro
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Fayaz Umrani
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Adam Greene
- Department of Pediatrics, University of Virginia, Charlottesville, VA, United States of America
| | - Sana Syed
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
- Department of Pediatrics, University of Virginia, Charlottesville, VA, United States of America
| | - Sean R. Moore
- Department of Pediatrics, University of Virginia, Charlottesville, VA, United States of America
| | - Syed Asad Ali
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
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Khan M, Jamil Z, Ehsan L, Zulqarnain F, Srivastava S, Siddiqui S, Fernandes P, Raghib M, Sengupta S, Mujahid Z, Ahmed Z, Idrees R, Ahmed S, Umrani F, Iqbal N, Moskaluk C, Raghavan S, Cheng L, Moore S, Ali SA, Iqbal J, Syed S. Quantitative Morphometry and Machine Learning Model to Explore Duodenal and Rectal Mucosal Tissue of Children with Environmental Enteric Dysfunction. Am J Trop Med Hyg 2023; 108:672-683. [PMID: 36913924 PMCID: PMC10077000 DOI: 10.4269/ajtmh.22-0063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 12/21/2022] [Indexed: 03/15/2023] Open
Abstract
Environmental enteric dysfunction (EED) is a subclinical enteropathy prevalent in resource-limited settings, hypothesized to be a consequence of chronic exposure to environmental enteropathogens, resulting in malnutrition, growth failure, neurocognitive delays, and oral vaccine failure. This study explored the duodenal and colonic tissues of children with EED, celiac disease, and other enteropathies using quantitative mucosal morphometry, histopathologic scoring indices, and machine learning-based image analysis from archival and prospective cohorts of children from Pakistan and the United States. We observed villus blunting as being more prominent in celiac disease than in EED, as shorter lengths of villi were observed in patients with celiac disease from Pakistan than in those from the United States, with median (interquartile range) lengths of 81 (73, 127) µm and 209 (188, 266) µm, respectively. Additionally, per the Marsh scoring method, celiac disease histologic severity was increased in the cohorts from Pakistan. Goblet cell depletion and increased intraepithelial lymphocytes were features of EED and celiac disease. Interestingly, the rectal tissue from cases with EED showed increased mononuclear inflammatory cells and intraepithelial lymphocytes in the crypts compared with controls. Increased neutrophils in the rectal crypt epithelium were also significantly associated with increased EED histologic severity scores in duodenal tissue. We observed an overlap between diseased and healthy duodenal tissue upon leveraging machine learning image analysis. We conclude that EED comprises a spectrum of inflammation in the duodenum, as previously described, and the rectal mucosa, warranting the examination of both anatomic regions in our efforts to understand and manage EED.
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Affiliation(s)
- Marium Khan
- Department of Pediatrics, School of Medicine, University of Virginia, Charlottesville, Virginia
| | - Zehra Jamil
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
| | - Lubaina Ehsan
- Department of Pediatrics, School of Medicine, University of Virginia, Charlottesville, Virginia
| | - Fatima Zulqarnain
- Department of Pediatrics, School of Medicine, University of Virginia, Charlottesville, Virginia
| | - Sanjana Srivastava
- Department of Pediatrics, School of Medicine, University of Virginia, Charlottesville, Virginia
| | - Saman Siddiqui
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Philip Fernandes
- Department of Pediatrics, School of Medicine, University of Virginia, Charlottesville, Virginia
| | - Muhammad Raghib
- Department of Pediatrics, School of Medicine, University of Virginia, Charlottesville, Virginia
| | - Saurav Sengupta
- School of Data Science, University of Virginia, Charlottesville, Virginia
| | - Zia Mujahid
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Zubair Ahmed
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Romana Idrees
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Sheraz Ahmed
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
| | - Fayaz Umrani
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
| | - Najeeha Iqbal
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | | | - Shyam Raghavan
- Department of Pathology, University of Virginia, Charlottesville, Virginia
| | - Lin Cheng
- Department of Pathology, Rush University, Chicago, Illinois
| | - Sean Moore
- Department of Pediatrics, School of Medicine, University of Virginia, Charlottesville, Virginia
| | - Syed Asad Ali
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Junaid Iqbal
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan.,Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Sana Syed
- Department of Pediatrics, School of Medicine, University of Virginia, Charlottesville, Virginia.,Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan.,School of Data Science, University of Virginia, Charlottesville, Virginia.,Department of Public Health Sciences, School of Medicine, University of Virginia, Charlottesville, Virginia
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5
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Kabir F, Iqbal J, Jamil Z, Iqbal NT, Mallawaarachchi I, Aziz F, Kalam A, Muneer S, Hotwani A, Ahmed S, Umrani F, Syed S, Sadiq K, Ma JZ, Moore SR, Ali A. Impact of enteropathogens on faltering growth in a resource-limited setting. Front Nutr 2023; 9:1081833. [PMID: 36704796 PMCID: PMC9871909 DOI: 10.3389/fnut.2022.1081833] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 12/08/2022] [Indexed: 01/12/2023] Open
Abstract
Introduction Environmental enteropathy is an important contributor to childhood malnutrition in the developing world. Chronic exposure to fecal pathogens leads to alteration in intestinal structure and function, resulting in impaired gut immune function, malabsorption, and growth faltering leading to environmental enteropathy. Methods A community-based intervention study was carried out on children till 24 months of age in Matiari district, Pakistan. Blood and fecal specimens were collected from the enrolled children aged 3-6 and 9 months. A real-time PCR-based TaqMan array card (TAC) was used to detect enteropathogens. Results Giardia, Campylobacter spp., enteroaggregative Escherichia coli (EAEC), Enteropathogenic Escherichia coli (EPEC), Enterotoxigenic Escherichia coli (ETEC), and Cryptosporidium spp. were the most prevailing enteropathogens in terms of overall positivity at both time points. Detection of protozoa at enrollment and 9 months was negatively correlated with rate of change in height-for-age Z (ΔHAZ) scores during the first and second years of life. A positive association was found between Giardia, fecal lipocalin (LCN), and alpha 1-Acid Glycoprotein (AGP), while Campylobacter spp. showed positive associations with neopterin (NEO) and myeloperoxidase (MPO). Conclusion Protozoal colonization is associated with a decline in linear growth velocity during the first 2 years of life in children living in Environmental enteric dysfunction (EED) endemic settings. Mechanistic studies exploring the role of cumulative microbial colonization, their adaptations to undernutrition, and their influence on gut homeostasis are required to understand symptomatic enteropathogen-induced growth faltering.
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Affiliation(s)
- Furqan Kabir
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan
| | - Junaid Iqbal
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan,Department of Biological and Biomedical Sciences, The Aga Khan University, Karachi, Pakistan
| | - Zehra Jamil
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan,Department of Biological and Biomedical Sciences, The Aga Khan University, Karachi, Pakistan
| | - Najeeha Talat Iqbal
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan,Department of Biological and Biomedical Sciences, The Aga Khan University, Karachi, Pakistan
| | - Indika Mallawaarachchi
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, United States
| | - Fatima Aziz
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan
| | - Adil Kalam
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan
| | - Sahrish Muneer
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan
| | - Aneeta Hotwani
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan
| | - Sheraz Ahmed
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan
| | - Fayaz Umrani
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan
| | - Sana Syed
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan,Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Virginia, Charlottesville, VA, United States
| | - Kamran Sadiq
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan
| | - Jennie Z. Ma
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, United States
| | - Sean R. Moore
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Virginia, Charlottesville, VA, United States,*Correspondence: Sean R. Moore,
| | - Asad Ali
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan,Asad Ali,
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6
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Corden E, Siddiqui SH, Sharma Y, Raghib MF, Adorno W, Zulqarnain F, Ehsan L, Shrivastava A, Ahmed S, Umrani F, Rahman N, Ali R, Iqbal NT, Moore SR, Ali SA, Syed S. Distance from Healthcare Facilities Is Associated with Increased Morbidity of Acute Infection in Pediatric Patients in Matiari, Pakistan. Int J Environ Res Public Health 2021; 18:11691. [PMID: 34770204 PMCID: PMC8583418 DOI: 10.3390/ijerph182111691] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 10/29/2021] [Accepted: 11/04/2021] [Indexed: 12/21/2022]
Abstract
The relationship between environmental factors and child health is not well understood in rural Pakistan. This study characterized the environmental factors related to the morbidity of acute respiratory infections (ARIs), diarrhea, and growth using geographical information systems (GIS) technology. Anthropometric, address and disease prevalence data were collected through the SEEM (Study of Environmental Enteropathy and Malnutrition) study in Matiari, Pakistan. Publicly available map data were used to compile coordinates of healthcare facilities. A Pearson correlation coefficient (r) was used to calculate the correlation between distance from healthcare facilities and participant growth and morbidity. Other continuous variables influencing these outcomes were analyzed using a random forest regression model. In this study of 416 children, we found that participants living closer to secondary hospitals had a lower prevalence of ARI (r = 0.154, p < 0.010) and diarrhea (r = 0.228, p < 0.001) as well as participants living closer to Maternal Health Centers (MHCs): ARI (r = 0.185, p < 0.002) and diarrhea (r = 0.223, p < 0.001) compared to those living near primary facilities. Our random forest model showed that distance has high variable importance in the context of disease prevalence. Our results indicated that participants closer to more basic healthcare facilities reported a higher prevalence of both diarrhea and ARI than those near more urban facilities, highlighting potential public policy gaps in ameliorating rural health.
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Affiliation(s)
- Elise Corden
- Department of Pediatrics, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA; (E.C.); (Y.S.); (M.F.R.); (F.Z.); (L.E.); (A.S.); (S.R.M.)
| | - Saman Hasan Siddiqui
- Department of Paediatrics and Child Health, Aga Khan University, Karachi 74800, Pakistan; (S.H.S.); (S.A.); (F.U.); (N.R.); (R.A.); (N.T.I.)
| | - Yash Sharma
- Department of Pediatrics, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA; (E.C.); (Y.S.); (M.F.R.); (F.Z.); (L.E.); (A.S.); (S.R.M.)
| | - Muhammad Faraz Raghib
- Department of Pediatrics, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA; (E.C.); (Y.S.); (M.F.R.); (F.Z.); (L.E.); (A.S.); (S.R.M.)
| | - William Adorno
- Department of Engineering Systems and Environment, University of Virginia, Charlottesville, VA 22903, USA;
| | - Fatima Zulqarnain
- Department of Pediatrics, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA; (E.C.); (Y.S.); (M.F.R.); (F.Z.); (L.E.); (A.S.); (S.R.M.)
| | - Lubaina Ehsan
- Department of Pediatrics, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA; (E.C.); (Y.S.); (M.F.R.); (F.Z.); (L.E.); (A.S.); (S.R.M.)
| | - Aman Shrivastava
- Department of Pediatrics, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA; (E.C.); (Y.S.); (M.F.R.); (F.Z.); (L.E.); (A.S.); (S.R.M.)
| | - Sheraz Ahmed
- Department of Paediatrics and Child Health, Aga Khan University, Karachi 74800, Pakistan; (S.H.S.); (S.A.); (F.U.); (N.R.); (R.A.); (N.T.I.)
| | - Fayaz Umrani
- Department of Paediatrics and Child Health, Aga Khan University, Karachi 74800, Pakistan; (S.H.S.); (S.A.); (F.U.); (N.R.); (R.A.); (N.T.I.)
| | - Najeeb Rahman
- Department of Paediatrics and Child Health, Aga Khan University, Karachi 74800, Pakistan; (S.H.S.); (S.A.); (F.U.); (N.R.); (R.A.); (N.T.I.)
| | - Rafey Ali
- Department of Paediatrics and Child Health, Aga Khan University, Karachi 74800, Pakistan; (S.H.S.); (S.A.); (F.U.); (N.R.); (R.A.); (N.T.I.)
| | - Najeeha T. Iqbal
- Department of Paediatrics and Child Health, Aga Khan University, Karachi 74800, Pakistan; (S.H.S.); (S.A.); (F.U.); (N.R.); (R.A.); (N.T.I.)
| | - Sean R. Moore
- Department of Pediatrics, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA; (E.C.); (Y.S.); (M.F.R.); (F.Z.); (L.E.); (A.S.); (S.R.M.)
| | - Syed Asad Ali
- Department of Paediatrics and Child Health, Aga Khan University, Karachi 74800, Pakistan; (S.H.S.); (S.A.); (F.U.); (N.R.); (R.A.); (N.T.I.)
| | - Sana Syed
- Department of Pediatrics, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA; (E.C.); (Y.S.); (M.F.R.); (F.Z.); (L.E.); (A.S.); (S.R.M.)
- Department of Paediatrics and Child Health, Aga Khan University, Karachi 74800, Pakistan; (S.H.S.); (S.A.); (F.U.); (N.R.); (R.A.); (N.T.I.)
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22903, USA
- School of Data Science, University of Virginia, Charlottesville, VA 22903, USA
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7
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Jamil Z, Iqbal NT, Idress R, Ahmed Z, Sadiq K, Mallawaarachchi I, Iqbal J, Syed S, Hotwani A, Kabir F, Ahmed K, Ahmed S, Umrani F, Ma JZ, Aziz F, Kalam A, Moore SR, Ali SA. Gut integrity and duodenal enteropathogen burden in undernourished children with environmental enteric dysfunction. PLoS Negl Trop Dis 2021; 15:e0009584. [PMID: 34264936 PMCID: PMC8352064 DOI: 10.1371/journal.pntd.0009584] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 08/09/2021] [Accepted: 06/17/2021] [Indexed: 11/18/2022] Open
Abstract
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. EED is a subclinical condition of compromised gut integrity secondary to frequent and repeated exposure to enteropathogens in global settings with a high prevalence of undernutrition. In this study, we reported association of gut mucosal architecture with a dual sugar intestinal permeability assay (lactulose-rhamnose) in Pakistani children. In the presence of duodenal enteropathogens, features such as chronic inflammation, intra-epithelial lymphocytosis, enterocyte injury and Paneth cell reduction were consistently observed. When comparing undernourished cases and controls living in the same setting, we found urinary excretion of the sugars was similar among groups; however, variability in HAZ among children at 24 months was partially explained by a model that includes excretion values.
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Affiliation(s)
- Zehra Jamil
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Najeeha Talat Iqbal
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Romana Idress
- Department of Pathology & Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Zubair Ahmed
- Department of Pathology & Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Kamran Sadiq
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Indika Mallawaarachchi
- Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia, United States of America
| | - Junaid Iqbal
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Sana Syed
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition; Department of Pediatrics, University of Virginia, Charlottesville, Virginia, United States of America
| | - Aneeta Hotwani
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Furqan Kabir
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Kumail Ahmed
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Sheraz Ahmed
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Fayaz Umrani
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Jennie Z. Ma
- Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia, United States of America
| | - Fatima Aziz
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Adil Kalam
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Sean R. Moore
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition; Department of Pediatrics, University of Virginia, Charlottesville, Virginia, United States of America
- * E-mail: (SRM); (SAA)
| | - Syed Asad Ali
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
- * E-mail: (SRM); (SAA)
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Iqbal NT, Syed S, Sadiq K, Khan MN, Iqbal J, Ma JZ, Umrani F, Ahmed S, Maier EA, Denson LA, Haberman Y, McNeal MM, Setchell KDR, Zhao X, Qureshi S, Shen L, Moskaluk CA, Liu TC, Yilmaz O, Brown DE, Barratt MJ, Kung VL, Gordon JI, Moore SR, Ali SA. Study of Environmental Enteropathy and Malnutrition (SEEM) in Pakistan: protocols for biopsy based biomarker discovery and validation. BMC Pediatr 2019; 19:247. [PMID: 31331393 PMCID: PMC6643315 DOI: 10.1186/s12887-019-1564-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 05/31/2019] [Indexed: 12/26/2022] Open
Abstract
Background Environmental Enteropathy (EE), characterized by alterations in intestinal structure, function, and immune activation, is believed to be an important contributor to childhood undernutrition and its associated morbidities, including stunting. Half of all global deaths in children < 5 years are attributable to under-nutrition, making the study of EE an area of critical priority. Methods Community based intervention study, divided into two sub-studies, 1) Longitudinal analyses and 2) Biopsy studies for identification of EE features via omics analyses. Birth cohorts in Matiari, Pakistan established: moderately or severely malnourished (weight for height Z score (WHZ) < − 2) children, and well-nourished (WHZ > 0) children. Blood, urine, and fecal samples, for evaluation of potential biomarkers, will be collected at various time points from all participants (longitudinal analyses). Participants will receive appropriate educational and nutritional interventions; non-responders will undergo further evaluation to determine eligibility for further workup, including upper gastrointestinal endoscopy. Histopathological changes in duodenal biopsies will be compared with duodenal biopsies obtained from USA controls who have celiac disease, Crohn’s disease, or who were found to have normal histopathology. RNA-Seq will be employed to characterize mucosal gene expression across groups. Duodenal biopsies, luminal aspirates from the duodenum, and fecal samples will be analyzed to define microbial community composition (omic analyses). The relationship between histopathology, mucosal gene expression, and community configuration will be assessed using a variety of bioinformatic tools to gain better understanding of disease pathogenesis and to identify mechanism-based biomarkers. Ethical review committees at all collaborating institutions have approved this study. All results will be made available to the scientific community. Discussion Operational and ethical constraints for safely obtaining intestinal biopsies from children in resource-poor settings have led to a paucity of human tissue-based investigations to understand and reverse EE in vulnerable populations. Furthermore, EE biomarkers have rarely been correlated with gold standard histopathological confirmation. The Study of Environmental Enteropathy and Malnutrition (SEEM) is designed to better understand the pathophysiology, predictors, biomarkers, and potential management strategies of EE to inform strategies to eradicate this debilitating pathology and accelerate progress towards the 2030 Sustainable Development Goals. Trial registration Retrospectively registered; clinicaltrials.gov ID NCT03588013. Electronic supplementary material The online version of this article (10.1186/s12887-019-1564-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Najeeha T Iqbal
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan.,Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
| | - Sana Syed
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan.,Department of Pediatrics, University of Virginia, Charlottesville, VA, USA
| | - Kamran Sadiq
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Marium N Khan
- Department of Pediatrics, University of Virginia, Charlottesville, VA, USA
| | - Junaid Iqbal
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan.,Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
| | - Jennie Z Ma
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Fayaz Umrani
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Sheraz Ahmed
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Elizabeth A Maier
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Lee A Denson
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Yael Haberman
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Monica M McNeal
- Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kenneth D R Setchell
- Clinical Mass Spectrometry, Division of Pathology and Laboratory Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Xueheng Zhao
- Clinical Mass Spectrometry, Division of Pathology and Laboratory Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Shahida Qureshi
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Lanlan Shen
- Department of Pediatrics, Baylor College of Medicine, USDA/ARS Children's Nutrition Research Center, Houston, TX, USA
| | | | - Ta-Chiang Liu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Omer Yilmaz
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Koch Institute for Integrative Cancer Research at MIT and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Donald E Brown
- Data Science Institute, University of Virginia, Charlottesville, VA, USA
| | - Michael J Barratt
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Vanderlene L Kung
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Jeffrey I Gordon
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Sean R Moore
- Department of Pediatrics, University of Virginia, Charlottesville, VA, USA.
| | - S Asad Ali
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan.
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