Biology subjects

Benjamin-Chung, J.

Publications and source records attributed to Benjamin-Chung, J..

9 recordsLinked to original sources

bioRxiv2025

Associations between floor material and E. coli contamination in rural Bangladeshi households

Soil floors are common in low-income countries and can harbor contamination from unsafely managed human and animal fecal waste. Soil/dust ingestion directly from floors or indirectly via hands, drinking water and food can significantly contribute to childrens ingestion of fecal organisms. We assessed if finished (e.g., concrete) floors are associated with lower E. coli contamination in the domestic environment in rural Bangladesh. We collected samples from 1864 households over 3.5 years, including stored drinking water, child and caregiver hand rinses, courtyard soil, food, and flies (n=24,118 samples), and enumerated E. coli using IDEXX Quanti-Tray/2000. Controlling for potential confounders (socio-demographics, water/sanitation status, animal ownership), households with finished floors had slightly lower log10-transformed E. coli counts ({Delta}log10= -0.10 (-0.20, 0.00)) and prevalence (prevalence ratio=0.90 (0.83, 0.98)) on child hands than households with soil floors; floor material was not associated with contamination levels in other sample types. Finished floors were associated with lower E. coli contamination of child hands, food and stored drinking water following periods of higher rainfall and temperature, and lower E. coli contamination of child hands in households with more domestic animals. Measures to control enteric infections in low-income countries should test flooring improvements to reduce exposure to fecal contamination.

microbiology↗

bioRxiv2025

Dirt floors and domestic animals are associated with soilborne exposure to antimicrobial resistant E. coli in rural Bangladeshi households

Soil can harbor enteropathogens and antimicrobial-resistant organisms in settings with domestic animals. We enrolled 49 households with young children (28 soil floors, 21 concrete floors) in Bangladesh and recorded animal ownership/management. Staff swabbed the floor of childrens sleeping area with a sterile sponge and collected floor dust and a child hand rinse. We used IDEXX QuantiTray/2000 with and without cefotaxime supplementation to enumerate cefotaxime-resistant and generic E. coli. There was 8.0 g/m2 of dust on soil floors vs. 0.2 g/m2 on concrete floors (p-value=0.005). We detected E. coli on 100% of soil vs. 86% of concrete floors and cefotaxime-resistant E. coli on 89% of soil vs. 43% of concrete floors (p-values<0.05). Cefotaxime-resistant E. coli prevalence on floors was 36% in compounds without animals, 79% in compounds with animals and 100% if animals stayed indoors overnight or the floor had animal feces; associations were strongest for chickens. In multivariable models, generic and cefotaxime-resistant E. coli counts were 1.5-2 log higher on soil vs. concrete floors, and counts on floors and child hands were 0.17-0.24 log higher for every 10 additional chickens owned (p-values<0.05). Efforts to mitigate infections and antimicrobial resistance in low-income countries should test flooring improvements and hygienic animal management. SynopsisIn rural Bangladeshi households, generic and cefotaxime-resistant E. coli were more common on soil floors than concrete floors and among households with higher cohabitation intensity with domestic animals, especially chickens.

microbiology↗

bioRxiv2025

Investigating Cement-Based Surfaces as a Sustainable Flooring Solution to Improve Ascaris Egg Removal and Inactivation in Low-Resource Settings

Soil-transmitted helminths, like Ascaris, are significant contributors to disease burden in low- and middle-income countries (LMICs). Infections are associated with growth faltering and mortality in children and are often transmitted through contact with eggs in fecally contaminated soil. Interventions, like replacing household soil floors with cement-based alternatives, may reduce exposure to Ascaris eggs, but there are currently no estimates on the removal or survival of Ascaris eggs on cement-based surfaces. This study addresses that knowledge gap by evaluating the removal of Ascaris eggs from mopping and the survival of Ascaris eggs on two cement-based mixes: an Ordinary Portland Cement (OPC) mortar and an OPC mortar with fly ash, which provides a more sustainable alternative to the OPC mortar mix. We assessed egg survival at two temperatures representing the dry (15{degrees}C) and wet (34{degrees}C) seasons in Bangladesh using two different egg enumeration methods. After mopping, over 92% of viable eggs were removed from surfaces, with no significant differences between cement-based mixes (p = 0.51). The first-order decay rate constants (k) of Ascaris eggs were similar between mix designs (p = 0.62) but varied significantly between temperatures (p = 4.2 x 10-25) and egg enumeration methods (p = 2.4 x 10-8). The k values were of greater magnitude at 34{degrees}C compared to at 15{degrees}C. At 15{degrees}C, k values were not significantly different from zero, indicating no inactivation. The k values we obtained were comparable to those reported in previous studies for different matrices, indicating comparable inactivation of Ascaris eggs on cement-based surfaces compared to liquid and semi-solid matrices. These results provide some of the first estimates of removal efficiencies and inactivation times in realistic environmental conditions for Ascaris on surfaces while supporting the use of OPC mortar mix designs with fly ash in interventions to reduce Ascaris transmission in rural LMIC households. Author SummarySoil-transmitted helminths, like Ascaris, are parasites that are major contributors to disease in children and women of childbearing age in low- and middle-income countries. Interventions, like replacing soil floors in households with cement-based flooring, may reduce exposure to Ascaris eggs which cause infections, but there is little information on how or why these interventions may be effective. This study investigates the effectiveness of simple cleaning methods, like mopping, in removing Ascaris eggs from cement-based surfaces and explores how long these eggs can survive on these surfaces under different environmental conditions. We tested two types of cement-based surfaces, a traditional cement-based mortar mix, and a more sustainable cement-based mortar mix, and found that mopping removed over 92% of Ascaris eggs, with no differences between cement mixes. Experiments simulating wet and dry seasonal conditions showed that Ascaris eggs survive longer in cooler environments, again with no differences between cement mixes. These findings provide important insights into the role of cement-based flooring in interrupting disease transmission and suggest sustainable cement-based mortar mixes are a feasible alternative to traditional cement-based mortar mixes.

microbiology↗

bioRxiv2024

Pathogens and Antimicrobial Resistance Genes in Household Environments: A Study of Soil Floors and Cow Dung in Rural Bangladesh

In low- and middle-income countries, living in homes with soil floors and animal cohabitation may expose children to fecal organisms, increasing risk of enteric and antimicrobial-resistant infections. Our objective was to understand whether cow cohabitation in homes with soil floors in rural Bangladesh contributed to the presence and diversity of potential pathogens and antimicrobial resistance genes (ARGs) in the home. In 10 randomly selected households in rural Sirajganj District, we sampled floor soil and cow dung, which is commonly used as sealant in soil floors. We extracted DNA and performed shotgun metagenomic sequencing to explore potential pathogens and ARGs in each sample type. We detected 6 potential pathogens in soil only, 49 pathogens in cow dung only, and 167 pathogens in both soil and cow dung. Pathogen species with relative abundances >5% in both soil floors and cow dung from the same households included E. coli (N=8 households), Salmonella enterica (N=6), Klebsiella pneumoniae (N=2), and Pseudomonas aeruginosa (N=1). Cow dung exhibited modestly higher pathogen genus richness compared to soil floors (Wilcoxon signed-rank test p=0.002). Using Bray-Curtis dissimilarity, pathogen species community composition differed between floors and cow dung (PERMANOVA p<0.001). All soil floors and cow dung samples contained ARGs against antibiotic classes including sulfonamides, rifamycin, aminoglycosides, lincosamides, and tetracycline. Paired floor and cow dung samples shared ARGs against rifamycin. Our findings support the development of interventions to reduce soil and animal feces exposure in rural, low-income settings. ImportanceIn low-income countries, inadequate housing materials and animal cohabitation can lead to fecal contamination of rural homes. Contaminated soil floors are difficult to clean and may harbor organisms causing illness and antibiotic resistance, especially in young children, who frequently ingest soil. We sequenced soil floor and cow dung samples from households in Sirajganj district, Bangladesh and identified pathogens and antibiotic resistance genes. We detected 167 pathogens in both soil and cow dung; pathogens present in both sample types at the highest relative abundances were E. coli, Salmonella enterica, Klebsiella pneumoniae, and Pseudomonas aeruginosa. Antibiotic resistance genes were found in all samples. In cow dung, the most common genes conferred resistance to the antibiotics lincosamide, rifamycin, cephamycin, and tetracycline. In soil floors, the most common genes conferred resistance to rifamycin, sulfonamides, and aminoglycosides. Household soil and cow dung may be important reservoirs of pathogens and antimicrobial resistance in low-income countries.

microbiology↗

bioRxiv2024

Evaluating the Survival and Removal of Escherichia coli from Surfaces Made with Traditional and Sustainable Cement-Based Materials in Field-Relevant Conditions

Soil household floors are common in low- and middle-income countries (LMICs) and can serve as reservoirs of enteric pathogens. Cement-based floors may interrupt pathogen transmission, but little is known about pathogen survival or removal from cement-based surfaces. This study investigated the survival of Escherichia coli (E. coli), an indicator of fecal contamination, on cement-based surfaces and evaluated its reduction through common household activities (mopping, sweeping, and walking). We compared E. coli fate on three mixes: 1) Ordinary Portland Cement (OPC) concrete (used in the United States), 2) OPC mortar (used in Bangladesh), and 3) OPC mortar with fly ash (a sustainable alternative to the Bangladesh mix). Additionally, we compared outcomes on cement-based surfaces with and without soil and at two temperatures representing the dry and wet seasons in Bangladesh. After 4 hours on the cement-based surfaces, E. coli decayed more than 1.1 log10(C/Co) under all conditions tested, which is significantly faster than in bulk soils. The higher temperature increased the decay rate constant (p = 5.56*10-8) while soil presence decreased it (p = 2.80*10-6). Sweeping and mopping resulted in high levels of removal for all mixes, with a mean removal of 71% and 78%, respectively, versus 22% for walking. The concrete and mortar mix designs did not impact E. coli survival or removal (p > 0.20). Cement-based floors made with a fly ash mix performed similarly to traditional cement-based floors, supporting its potential use as a more sustainable intervention to reduce fecal contamination in rural LMIC household settings. ImportanceCement-based surfaces may serve as a health intervention to reduce the fecal-oral transmission of pathogens in household settings, but there is a critical lack of evidence about the fate of indicator organisms on these surfaces, especially in field-relevant conditions. This study provides some of the first insights into E. coli survival on cement-based surfaces and the effectiveness of daily activities for removing E. coli. Additionally, this study explores the fate of E. coli on cement-based surfaces made with fly ash (which contributes fewer CO2 emissions) versus traditional cement mixes. We found that E. coli had similar survival and removal across all mix designs, demonstrating that fly ash mixes are feasible for use in household settings (e.g., in floors). The findings enhance understanding of fecal-oral transmission pathways and support the use of fly ash mixes in cement-based flooring in future epidemiologic studies assessing effects on enteric disease burdens.

microbiology↗

bioRxiv2020

Effect of sanitation improvements on soil-transmitted helminth eggs in courtyard soil from rural Bangladesh: Evidence from a cluster-randomized controlled trial

Improved sanitation has been hypothesized to reduce soil-transmitted helminth (STH) infections by reducing the prevalence and abundance of STH eggs/larvae in soil. We evaluated the effect of a randomized sanitation program (providing households with an improved dual-pit latrine, tools for child/animal feces management, and behavioral messaging) on reducing STH eggs in soil from household courtyards. We collected soil samples from 1405 households enrolled in the sanitation intervention (n=419) and control (n=914) groups of a cluster-randomized controlled trial (WASH Benefits) in rural Bangladesh approximately 2 years after the initiation of the interventions. We analyzed samples for Ascaris lumbricoides, Trichuris trichiura, and hookworm eggs by microscopy. We estimated prevalence ratios (PR) and relative egg count reductions (ECR) to compare the prevalence of any STH eggs and arithmetic and geometric mean egg counts for any STH per gram of soil between the sanitation and control arms. Among intervention households, latrines achieved high and sustained user uptake by adults while child open defecation remained common and most households did not dispose of child feces hygienically. In courtyard soil from control households, the prevalence of any STH eggs was 75.7% and the prevalence of any larvated STH eggs was 67.3%. A. lumbricoides was detected in 63.0% of control samples and T. trichiura in 55.7% of control samples; hookworm was not detected in any sample. The arithmetic mean egg count for any STH was 3.96 eggs/dry gram, while the geometric mean was 1.58 eggs/dry gram. There was no difference between the intervention and control groups in the prevalence of any STH eggs (PR=0.98 (95% CI: 0.91-1.05)) or mean egg counts (ECR=0.08 (95% CI: -0.10, 0.26) for geometric mean and 0.07 (95% CI: -0.22, 0.37) for arithmetic mean). Adjusted models gave similar results. A compound-level sanitation intervention that provided improved latrines and tools for disposal of child and animal feces did not have an impact on environmental reservoirs of STH eggs. In order to effectively reduce the prevalence and abundance of STH eggs in the environment, sustained, widespread use of sanitation strategies to isolate and hygienically dispose of child and animal feces may need to complement traditional strategies for containment of adult human feces. Author summaryImproved sanitation has been hypothesized to reduce soil-transmitted helminth (STH) infections by reducing the prevalence and abundance of STH eggs/larvae in soil. We evaluated the effect of a randomized sanitation program (providing households with an improved dual-pit latrine, tools for child/animal feces management, and behavioral messaging) on reducing STH eggs in soil from household courtyards. We collected soil samples from 1405 households enrolled in the control and sanitation groups of a cluster-randomized controlled trial (WASH Benefits) in rural Bangladesh approximately 2 years after the initiation of the interventions. We analyzed samples for Ascaris lumbricoides, Trichuris trichiura and hookworm eggs by microscopy. We found no effect of the sanitation intervention on STH eggs in soil. In order to effectively reduce the prevalence and abundance of STH eggs in the environment, sustained, widespread use of sanitation strategies to isolate and hygienically dispose of child and animal feces may need to complement traditional strategies for containment of adult human feces.

ecology↗

bioRxiv2019

Comparison of multi-parallel qPCR and Kato-Katz for detection of soil-transmitted helminth infection among children in rural Bangladesh

An active area of research investigates whether soil-transmitted helminths (STH) can be locally eliminated in endemic settings. In such settings, highly sensitive diagnostics are needed to detect STH infection. We compared double-slide Kato-Katz, the most commonly used copromicroscopic detection method, to multi-parallel quantitative polymerase chain reaction (qPCR) in 2,800 stool samples from children 2-12 years in rural Bangladesh. We estimated the sensitivity and specificity of each diagnostic using Bayesian latent class analysis. Compared to Kato-Katz, STH prevalence using qPCR was almost 3-fold higher for hookworm species and nearly 2-fold higher for Trichuris trichiura. Ascaris lumbricoides prevalence was lower using qPCR, and 26% of samples classified as A. lumbricoides positive by Kato-Katz were negative by qPCR. Amplicon sequencing of the 18S rDNA from 10 samples confirmed that A. lumbricoides was absent in samples classified as positive by Kato-Katz and negative by qPCR. The sensitivity of Kato-Katz was 49% for A. lumbricoides, 32% for hookworm, and 52% for T. trichiura; the sensitivity of qPCR was 79% for A. lumbricoides, 93% for hookworm, and 90% for T. trichiura. Specificity was [≥] 97% for both tests for all STH except for Kato-Katz for A. lumbricoides (specificity = 68%). There were moderate negative, monotonic correlations between qPCR cycle quantification values and eggs per gram quantified by Kato-Katz. While it is widely assumed that Kato-Katz has few false positives, our results indicate otherwise. Our findings suggest that qPCR is more appropriate than Kato-Katz in low intensity infection settings because of its higher sensitivity and specificity.\n\nAuthor summarySoil-transmitted helminth infections (STH) (e.g., Ascaris, hookworm, Trichuris) contribute to a large burden of disease among children in low- and middle-income countries. There is increasing interest in implementing large-scale deworming programs to eliminate STH in certain settings. Efforts to monitor whether local elimination has occurred require sensitive diagnostic tests that will not miss positive cases. Kato-Katz, a microscopy-based diagnostic test, has commonly been used to identify STH eggs in stool, but in settings where infection intensity is low, this method frequently misses positive samples because it requires visual identification of small numbers of eggs, and eggs may degrade prior to visualization. Quantitative polymerase chain reaction (qPCR) is a molecular diagnostic method that may miss fewer infections because it identifies STH DNA in stool, which can be detected in very small quantities and is less likely to degrade. This study compared the performance of Kato-Katz and qPCR using 2,800 stool samples from children aged 2-12 years in rural Bangladesh. qPCR detected substantially more hookworm and Trichuris infections than Kato-Katz. 26% of samples were classified as Ascaris positive by Kato-Katz and negative by qPCR. We conclude that qPCR is a more appropriate diagnostic method than Kato-Katz in low infection intensity settings.

epidemiology↗

bioRxiv2019

Effects of water, sanitation, handwashing and nutritional interventions on soil-transmitted helminth infections in young children: a cluster-randomized controlled trial in rural Bangladesh

BackgroundSoil transmitted helminths (STH) infect >1.5 billion people. Mass drug administration (MDA) reduces infection; however, drug resistance is emerging and reinfection occurs rapidly. We conducted a randomized controlled trial in Bangladesh (WASH Benefits, NCT01590095) to assess whether water, sanitation, hygiene and nutrition interventions, alone and combined, reduce STH in a setting with ongoing MDA. Methodology/Principal FindingsWe randomized clusters of pregnant women into water treatment, sanitation, handwashing, combined water+sanitation+handwashing (WSH), nutrition, nutrition+WSH (N+WSH) or control arms. After 2.5 years of intervention, we enumerated STH infections in children aged 2-12 years with Kato-Katz. We estimated intention-to-treat intervention effects on infection prevalence and intensity. Participants and field staff were not blinded; laboratory technicians and data analysts were blinded. In 2012-2013, we randomized 5551 women in 720 clusters. In 2015-2016, we enrolled 7795 children of 4102 available women for STH follow-up and collected stool from 7187. Prevalence among controls was 36.8% for A. lumbricoides, 9.2% for hookworm and 7.5% for T. trichiura. Most infections were low-intensity. Compared to controls, the water intervention reduced hookworm (prevalence ratio [PR]=0.69 (0.50, 0.95), prevalence difference [PD]=-2.83 (-5.16, -0.50)) but did not affect other STH. Sanitation improvements reduced T. trichiura (PR=0.71 (0.52, 0.98), PD=-2.17 (-4.03, -0.38)), had a similar borderline effect on hookworm and no effect on A. lumbricoides. Handwashing and nutrition interventions did not reduce any STH. WSH and N+WSH reduced hookworm prevalence by 29-33% (2-3 percentage points) and marginally reduced A. lumbricoides. Effects on infection intensity were similar. Conclusions/SignificanceIn a low-intensity infection setting with MDA, we found modest but sustained hookworm reduction from water treatment, sanitation and combined WSH interventions. Interventions more effectively reduced STH species with no persistent environmental reservoirs. Our findings highlight waterborne transmission for hookworm and suggest that water treatment and sanitation improvements can augment MDA programs to interrupt STH transmission. Author summarySoil-transmitted helminths (STH) infect >1.5 billion people worldwide. Mass-administration of deworming drugs is the cornerstone of global strategy for STH control but treated individuals often rapidly get reinfected and there is also concern about emerging drug resistance. Interventions to treat drinking water, wash hands at critical times and isolate human feces from the environment through improved sanitation could reduce STH transmission by reducing the spread of ova from the feces of infected individuals into the environment and subsequently to new hosts, while nutrition improvements could reduce host susceptibility to infection. Existing evidence on the effect of these interventions on STH is scarce. In a setting with ongoing mass-drug administration, we assessed the effect of individual and combined water, sanitation, handwashing and nutrition interventions on STH infection in children. Approximately 2.5 years after delivering interventions, we found reductions in STH infection from water treatment and sanitation interventions; there was no reduction from the handwashing and nutrition interventions. While the reductions were modest in magnitude compared to cure rates achieved by deworming drugs, they indicated sustained reduction in environmental transmission. The reductions were more pronounced for STH species that do not have persistent environmental reservoirs. These findings suggest that water treatment and sanitation interventions can augment mass-drug administration programs in striving toward elimination of STH.

clinical trials↗

bioRxiv2017

Spillover effects of a combined water, sanitation, and handwashing intervention in rural Bangladesh: a randomized controlled trial

BackgroundWater, sanitation, and handwashing (WSH) interventions may confer indirect benefits (\"spillovers\") on neighbors of recipients by interrupting pathogen transmission. We measured geographically local spillovers in WASH Benefits, a cluster-randomized trial in rural Bangladesh, by comparing outcomes among neighbors of intervention vs. control participants.\n\nMethodsWASH Benefits had randomly allocated geographically-defined clusters to a compound-level intervention (chlorinated drinking water, upgraded sanitation, and handwashing promotion) or control and followed children for two years. We enrolled neighboring children age-matched to trial participants that would have been eligible for WASH Benefits had they been conceived slightly earlier or later. After 28 months of intervention, we quantified fecal indicator bacteria in toy rinse and drinking water samples, measured soil-transmitted helminth infections, and recorded caregiver-reported diarrhea and respiratory illness. Neither fieldworkers nor participants were masked. Analysis was intention-to-treat.\n\nResultsWe enrolled neighbors of WASH Benefits participants in 90 control (N=900) and 90 intervention clusters (N=899). Neighbors characteristics were balanced across arms. The prevalence of any detectable E. coli in tubewell samples was lower for neighbors of intervention vs. control (prevalence ratio=0.83; 0.73, 0.95). There was no difference in E. coli and coliform prevalence between arms for other environmental samples. Disease prevalence was similar in neighbors of intervention vs. control participants: Ascaris (prevalence difference [PD]=0.00; -0.07, 0.08), hookworm (PD=0.01; -0.01, 0.04), Trichuris (PD=0.02; -0.02, 0.05), diarrhea (PD=0.00; -0.02,0.03), respiratory illness (PD=-0.01; -0.04, 0.03).\n\nConclusionsWe found spillover effects of a compound-level combined WSH intervention for tubewell water contamination but not for child health outcomes.\n\nKey MessagesO_LIWater, sanitation, and handwashing (WSH) interventions may confer indirect benefits (\"spillovers\") on neighbors of recipients by interrupting pathogen transmission, reducing environmental contamination, or spurring the adoption of health behaviors.\nC_LIO_LIWe conducted a randomized trial in rural Bangladesh to measure whether neighbors of a compound-level WSH intervention improved hygiene behaviors and had lower prevalence environmental contamination, soil-transmitted helminth infection, diarrhea, and respiratory illness among children under 5 years after two years of intervention.\nC_LIO_LIWe did not find evidence of intervention adoption or improved hygiene behavior among neighbors of a WSH intervention delivered for 2 years.\nC_LIO_LIThe WSH intervention reduced fecal contamination of neighbors tubewell water but did not lead to spillovers for other proximal measures of contamination in the domestic environment or for child health outcomes. For proximal spillover effects to translate to distal spillover effects, improvements in neighbors health behaviors may have been necessary.\nC_LI

epidemiology↗