Suhi Hanif
Masters Student in Epidemiology and Clinical Research, admitted Autumn 2024
All Publications
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Investigating cement-based surfaces as a sustainable flooring solution to improve Ascaris Suum egg removal and inactivation in low-resource settings.
PLoS neglected tropical diseases
2025; 19 (10): e0012919
Abstract
Soil-transmitted helminths, like Ascaris lumbricoides, are significant contributors to disease burden in low- and middle-income countries (LMICs). Infections are associated with morbidity and mortality in children and are often transmitted through eggs in fecally contaminated soil. Interventions, like replacing household soil floors with cement-based alternatives, may reduce exposure to A. lumbricoides eggs, but there are currently no estimates on the removal or survival of Ascaris species eggs on cement-based surfaces. This study addresses that knowledge gap by evaluating the removal of Ascaris suum eggs from mopping and the survival of A. suum eggs on two cement-based mixes: an traditional mortar and a mortar with fly ash, which provides a more sustainable alternative to the traditional mortar mix. We assessed egg survival at two temperatures representing the dry (15°C) and wet (34°C) seasons in Bangladesh using two different egg enumeration methods. After mopping, a mean of 95.6% (SD = 4.0%) of viable eggs were removed from surfaces, with no significant differences between cement-based mixes (p = 0.51). The mean first-order decay rate constants (k) of A. suum eggs across all conditions was 0.029 day-1 (SD = 0.074 day-1). Values of k were similar between mix designs (p = 0.62) but varied significantly between temperatures (p = 4.2x10-25) and egg enumeration methods (p = 2.4x10-8). The k values were greater at 34°C compared to at 15°C, where they showed no significant inactivation. Our k values were comparable to those reported previously for different matrices, indicating comparable inactivation of Ascaris species eggs on cement-based surfaces compared to liquid and semi-solid matrices. These results provide some of the first estimates of removal efficiencies and decay rate constants in realistic environmental conditions for Ascaris species on surfaces while supporting the use of mortar mix designs with fly ash in interventions to reduce Ascaris species transmission in rural LMIC households.
View details for DOI 10.1371/journal.pntd.0012919
View details for PubMedID 41129545
View details for PubMedCentralID PMC12548874
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Flooding and elevated prenatal depression in rural Bangladesh: A mixed methods study.
PLOS global public health
2025; 5 (7): e0004792
Abstract
Prenatal depression can have lasting adverse impacts on child health. Little is known about the impact of floods on prenatal depression in low- and middle-income countries. We conducted a cross-sectional survey of 881 pregnant women from September 24, 2023 to July 19, 2024 in riverine communities in rural Bangladesh. We recorded participant-reported flooding in the past 6 months, administered the Edinburgh Postnatal Depression Scale (EPDS), and obtained water level data and remote sensing data on distance to surface water. We fit generalized linear and log-linear models adjusting for month, wealth, education, age, and gestational age. We conducted 2 focus group discussions with 20 adult women. 3.6% of compounds were flooded in the past 6 months. Flooding of compounds was associated with elevated depression (adjusted prevalence ratio (aPR) = 2.08, 95% CI 1.24, 3.51) and thoughts of self-harm (aPR = 8.40, 95% CI 4.19, 16.10). Latrine flooding was associated with higher depression (aPR = 3.58, 95% CI 2.22, 5.75)). Higher water levels and shorter distance to permanent surface water were significantly associated with mean EPDS scores. Focus groups revealed that domestic violence, inadequate sanitation, gendered vulnerabilities in accessing latrines, childcare difficulties, and food insecurity were key drivers of depression due to floods. Flood preparedness strategies included relocation, storing food, and home modifications. In summary, in rural Bangladesh, flooding, higher water levels, and proximity to water bodies were associated with prenatal depression, and depression following floods was strongly influenced by inadequate sanitation and hygiene infrastructure.
View details for DOI 10.1371/journal.pgph.0004792
View details for PubMedID 40690464
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Potential pathogens and antimicrobial resistance genes in household environments: a study of soil floors and cow dung in rural Bangladesh.
Applied and environmental microbiology
2025: e0066925
Abstract
In low- and middle-income countries, living in homes with soil floors and animal cohabitation may expose children to fecal organisms, increasing the 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 7 potential pathogens in soil only, 38 pathogens in cow dung only, and 182 pathogens in both soil and cow dung. Cow dung exhibited modestly higher potential pathogen genus richness compared to soil floors (Wilcoxon signed-rank test, P = 0.002). Using Bray-Curtis dissimilarity, potential pathogen species community composition differed between floors and cow dung (permutational multivariate analysis of variance, P < 0.001). All soil floor and cow dung samples contained ARGs; detected ARGs confer resistance to antibiotic classes including sulfonamides, rifamycin, aminoglycosides, lincosamides, and tetracycline. Paired floor and cow dung samples shared ARGs against rifamycin and glycopeptides, but otherwise, there was little overlap in resistomes between sample types. Our findings contribute to the growing literature on household soil and domestic animals as potentially important contributors to disease transmission and as reservoirs of antimicrobial resistance in low-income country 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 potential pathogens and antibiotic resistance genes. We detected 182 potential pathogens in both soil and cow dung; organisms present in both sample types at the highest relative abundances were Escherichia coli, Klebsiella pneumoniae, Salmonella enterica, 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, tetracycline, and multiple antibiotics. In soil floors, the most common genes conferred resistance to rifamycin, sulfonamides, and multiple antibiotics. Household soil and cow dung may be important reservoirs of pathogens and antimicrobial resistance in low-income country settings with high levels of animal cohabitation compared to settings with finished household floors and minimal animal cohabitation.
View details for DOI 10.1128/aem.00669-25
View details for PubMedID 40422288
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Evaluating the survival and removal ofEscherichia colifrom surfaces made with traditional and sustainable cement-based materials in field-relevant conditions.
Applied and environmental microbiology
2025: e0213124
Abstract
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, 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: (i) ordinary Portland cement (OPC) concrete (used in the United States), (ii) OPC mortar (used in Bangladesh), and (iii) 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 their potential use as a more sustainable intervention to reduce fecal contamination in rural LMIC household settings.IMPORTANCE: Cement-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 Escherichia 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 efficiencies 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.
View details for DOI 10.1128/aem.02131-24
View details for PubMedID 40062896
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Effects of household concrete floors on maternal and child health: the CRADLE trial - a randomised controlled trial protocol.
BMJ open
2025; 15 (3): e090703
Abstract
Early life soil-transmitted helminth (STH) infection and diarrhoea are associated with growth faltering, anaemia, impaired child development and mortality. Exposure to faecally contaminated soil inside the home may be a key contributor to enteric infections, and a large fraction of rural homes in low-income countries have soil floors. The objective of this study is to measure the effect of installing concrete floors in homes with soil floors on child STH infection and other maternal and child health outcomes in rural Bangladesh.The Cement-based flooRs AnD chiLd hEalth trial is an individually randomised trial in Sirajganj and Tangail districts, Bangladesh. Households with a pregnant woman, a soil floor, walls that are not made of mud and no plan to relocate for 3 years will be eligible. We will randomise 800 households to intervention or control (1:1) within geographical blocks of 10 households to account for strong geographical clustering of enteric infection. Laboratory staff and data analysts will be blinded; participants will be unblinded. We will instal concrete floors when the birth cohort is in utero and measure outcomes at child ages 3, 6, 12, 18 and 24 months. The primary outcome is prevalence of any STH infection (Ascaris lumbricoides, Necator americanus or Trichuris trichiura) detected by quantitative PCR at 6, 12, 18 or 24 months follow-up in the birth cohort. Secondary outcomes include household floor and child hand contamination with Escherichia coli, extended-spectrum beta-lactamase producing E. coli and STH DNA; child diarrhoea, growth and cognitive development; and maternal stress and depression.Study protocols have been approved by institutional review boards at Stanford University and the International Centre for Diarrheal Disease Research, Bangladesh. We will report findings on ClinicalTrials.gov, in peer-reviewed publications and in stakeholder workshops in Bangladesh.NCT05372068.
View details for DOI 10.1136/bmjopen-2024-090703
View details for PubMedID 40032381
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Dirt floors and domestic animals are associated with soilborne exposure to antimicrobial resistantE. coliin rural Bangladeshi households.
bioRxiv : the preprint server for biology
2025
Abstract
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 children's 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.
View details for DOI 10.1101/2025.02.21.639507
View details for PubMedID 40027696
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Pathogens and Antimicrobial Resistance Genes in Household Environments: A Study of Soil Floors and Cow Dung in Rural Bangladesh.
bioRxiv : the preprint server for biology
2024
Abstract
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.
View details for DOI 10.1101/2024.12.06.627269
View details for PubMedID 39677809
View details for PubMedCentralID PMC11642972
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Flooding and elevated prenatal depression in a climate-sensitive community in rural Bangladesh: a mixed methods study.
medRxiv : the preprint server for health sciences
2024
Abstract
Prenatal depression can have lasting adverse impacts on child health. Little is known about the impact of floods on prenatal depression in low- and middle-income countries.We conducted a cross-sectional survey of 881 pregnant women from September 24, 2023 to July 19, 2024 in riverine communities in rural Bangladesh. We recorded participant-reported flooding in the past 6 months, administered the Edinburgh Postnatal Depression Scale (EPDS), and obtained water level data and remote sensing data on distance to surface water. We fit generalized linear and log-linear models adjusting for month, wealth, education, age, and gestational age. We conducted 2 focus group discussions with 20 adult women.3.6% of compounds were flooded in the past 6 months. Compound flooding was associated with elevated depression (adjusted prevalence ratio (aPR) = 2.08, 95% CI 1.14, 3.51) and thoughts of self-harm (aPR=8.40, 95% CI 4.19, 16.10). Latrine flooding was associated with higher depression (aPR=3.58, 95% CI 1.49, 7.29)). Higher water levels and shorter distance to permanent surface water were significantly associated with mean EPDS scores. Focus groups revealed that domestic violence, inadequate sanitation, gendered vulnerabilities in accessing latrines, childcare difficulties, and food insecurity were key drivers of depression due to floods. Flood preparedness strategies included relocation, storing food, and home modifications.Flooding, higher water levels, and proximity to water bodies were associated with prenatal depression in a rural, low-income setting. Inadequate sanitation and hygiene infrastructure were particularly strong drivers of depression.Eunice Kennedy Shriver National Institute of Child Health and Human Development.
View details for DOI 10.1101/2024.11.25.24317922
View details for PubMedID 39649600
View details for PubMedCentralID PMC11623739
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Intermittent preventive treatment for malaria in pregnancy and infant growth: a mediation analysis of a randomised trial.
EBioMedicine
2024; 109: 105397
Abstract
Intermittent preventive treatment for malaria in pregnancy (IPTp) can improve birth outcomes, but whether it confers benefits to postnatal growth is unclear. We investigated the effect of IPTp on infant growth in Uganda and its pathways of effects using causal mediation analyses.We analysed data from 633 infants born to mothers enrolled in a randomised trial of monthly IPTp with dihydroartemisinin-piperaquine (DP) vs. sulfadoxine-pyrimethamine (SP) (NCT02793622). Weight and length were measured from 0 to 12 months of age. Using generalised linear models, we estimated effects of DP vs. SP on gravidity-stratified mean length-for-age (LAZ) and weight-for-length Z-scores (WLZ). We investigated mediation by placental malaria, gestational weight change, maternal anaemia, maternal inflammation-related proteins, preterm birth, birth length, and birth weight. Mediation models adjusted for infant sex, gravidity, gestational age at enrolment, maternal age, maternal parasitaemia at enrolment, education, and wealth.SP increased mean LAZ by 0.18-0.28 Z from birth through age 4 months compared to DP, while DP increased mean WLZ by 0.11-0.28 Z from 2 to 8 months compared to SP among infants of multigravidae; at these ages, confidence intervals for mean differences excluded 0. We did not observe differences among primigravida. Mediators of SP included birth weight, birth length, maternal stem cell factor, and DNER. Mediators of DP included placental malaria and birth length, maternal IL-18, CDCP1, and CD6 at delivery.In high malaria transmission settings, this exploratory study suggests different IPTp regimens may influence infant growth among multigravidae, potentially through distinct pathways, in the exclusive breastfeeding period, when few other interventions are available.Stanford Center for Innovation in Global Health, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bill & Melinda Gates Foundation.
View details for DOI 10.1016/j.ebiom.2024.105397
View details for PubMedID 39418986
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Effects of household concrete floors on maternal and child health - the CRADLE trial: a randomised controlled trial protocol.
medRxiv : the preprint server for health sciences
2024
Abstract
Early life soil-transmitted helminth infection and diarrhea are associated with growth faltering, anemia, impaired child development, and mortality. Exposure to fecally contaminated soil inside the home may be a key contributor to enteric infections, and a large fraction of rural homes in low-income countries have soil floors. The objective of this study is to measure the effect of installing concrete floors in homes with soil floors on child soil-transmitted helminth infection and other maternal and child health outcomes in rural Bangladesh.The Cement-based flooRs AnD chiLd hEalth (CRADLE) trial is an individually randomised trial in Sirajganj and Tangail districts, Bangladesh. Households with a pregnant woman, a soil floor, walls that are not made of mud will be eligible, and no plan to relocate for 3 years. We will randomise 800 households to intervention or control (1:1) within geographic blocks of 10 households to account for strong geographic clustering of enteric infection. Laboratory staff and data analysts will be blinded; participants will be unblinded. We will install concrete floors when the birth cohort is in utero and measure outcomes at child ages 3, 6, 12, 18, and 24 months. The primary outcome is prevalence of any soil-transmitted helminth infection (Ascaris lumbricoides, Necator americanus, or Trichuris trichiura) detected by qPCR at 6, 12, 18, or 24 months follow-up in the birth cohort. Secondary outcomes include household floor and child hand contamination with E. coli, extended-spectrum beta-lactamase producing E. coli, and soil-transmitted helminth DNA; child diarrhea, growth, and cognitive development; and maternal stress and depression.Study protocols have been approved by institutional review boards at Stanford University and the International Centre for Diarrheal Disease Research, Bangladesh (icddr,b). We will report findings on ClinicalTrials.gov, in peer-reviewed publications, and in stakeholder workshops in Bangladesh.NCT05372068, pre-results.
View details for DOI 10.1101/2024.07.26.24311076
View details for PubMedID 39108529
View details for PubMedCentralID PMC11302711
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Pathways through which intermittent preventive treatment for malaria in pregnancy influences child growth faltering: a mediation analysis.
medRxiv : the preprint server for health sciences
2024
Abstract
Intermittent preventive treatment for malaria in pregnancy (IPTp) can improve birth outcomes, but whether it confers benefits to postnatal growth is unclear. We investigated the effect of IPTp on infant growth in Uganda and its pathways of effects using causal mediation analyses.We analyzed data from 633 infants born to mothers enrolled in a randomized trial of monthly IPTp with dihydroartemisinin-piperaquine (DP) vs sulfadoxine-pyrimethamine (SP) (NCT02793622). Weight and length were measured from 0-12 months of age. Using generalized linear models, we estimated effects of DP vs. SP on gravidity-stratified mean length-for-age (LAZ) and weight-for-length Z-scores (WLZ). We investigated mediation by placental malaria, gestational weight change, maternal anemia, maternal inflammation-related proteins, preterm birth, birth length, and birth weight. Mediation models adjusted for infant sex, gravidity, gestational age at enrollment, maternal age, maternal parasitemia at enrollment, education, and wealth.SP increased LAZ by 0.18-0.28 Z from birth through age 4 months compared to DP, while DP increased WLZ by 0.11-0.28 Z from 2-8 months compared to SP among infants of multigravidae. We did not observe these differences among primigravida. Mediators of SP included increased birth weight and length and maternal stem cell factor at delivery. Mediators of DP included placental malaria and birth length, maternal IL-18, CDCP1, and CD6 at delivery.In high malaria transmission settings, different IPTp regimens influenced infant growth among multigravidae through distinct pathways in the period of exclusive breastfeeding, when few other interventions are available.Stanford Center for Innovation and Global Health, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bill & Melinda Gates Foundation.
View details for DOI 10.1101/2024.06.09.24308656
View details for PubMedID 38947035
View details for PubMedCentralID PMC11213035