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. 2025 Nov 12;59(47):25173–25185. doi: 10.1021/acs.est.5c10329

Dirt Floors and Domestic Animals Are Associated with Soilborne Exposure to Antimicrobial-Resistant E. coli in Rural Bangladeshi Households

Ayse Ercumen †,*, Md Sakib Hossain ‡, Tahani Tabassum ‡, Ashrin Haque ‡, Amanta Rahman ‡, Md Hajbiur Rahman ‡, Claire Anderson §, Sumaiya Tazin †, Suhi Hanif ∥, Gabriella Barratt Heitmann ∥, Md Rana Miah ⊥, Afsana Yeamin ⊥, Farjana Jahan ⊥, Abul Kasham Shoab ⊥, Zahid Hayat Mahmud ‡, Mahbubur Rahman ⊥, Jade Benjamin-Chung ∥,#
PMCID: PMC12676737  PMID: 41221823

Abstract

Soil can harbor enteropathogens and antimicrobial-resistant organisms from domestic animals. We enrolled 49 households with young children (28 soil floors and 21 concrete floors) in Bangladesh and recorded animal ownership/management. Staff swabbed the floor of children’s sleeping area and collected floor dust and child hand rinses. We used IDEXX QuantiTray/2000 with and without cefotaxime supplementation to enumerate cefotaxime-resistant and generic E. coli. Soil floors had 40 times more dust than concrete (8.0 vs 0.2 g/m2, 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 increased with animal cohabitation: 36% in compounds without animals, 79% in compounds with animals, and 100% if animals stayed indoors overnight or if floors had animal feces; associations were strongest for chickens. Compounds with soil floors and animals had the highest contamination; those with concrete floors and no animals had the lowest. In multivariable models, generic and cefotaxime-resistant E. coli counts were 1.5–2 log higher on soil floors; counts on floors and child hands were 0.17–0.24 log higher for every 10 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.

Keywords: Floor, soil, domestic animals, antimicrobial resistance

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Introduction

Domestic soils are increasingly recognized as a risk factor for infectious diseases in low-income countries. Children can ingest soil via geophagia, in the form of dust, and indirectly via soil-contaminated food, water, hands, and objects. − Soil exposure has been linked to diarrhea, , soil-transmitted helminth infections, environmental enteropathy, , and stunting. , Pathogens can be deposited on soil surfaces via unsafe management of human/animal feces and can have prolonged survival in soil. In low- and middle-income countries, 42% of household floors are constructed with unimproved materials (e.g., soil, sand, dung, wood), and in Bangladesh, 63% of rural households have soil floors. Indoor floors made of soil could present a pathway of soilborne exposure to fecal organisms in these settings.

Studies have enumerated fecal indicators in outdoor and indoor domestic soils in low-income countries. In Mozambique, outdoor soil samples from house and latrine entrances contained pathogens and human and animal fecal markers, and quantitative microbial risk assessment models showed substantial risk of child enteric infections from ingesting fecally contaminated domestic soil. In our previous study in rural Bangladesh, one gram of outdoor courtyard soil harbored >120,000 most probable number (MPN) of E. coli, and higher E. coli counts in courtyard soil were associated with higher E. coli counts in other domestic domains, such as child hands, stored drinking water, and stored food. Fecal indicator bacteria and animal-specific fecal markers have also been commonly detected on indoor household floors in Bangladesh, Peru, Tanzania, and Ethiopia. −

Soil is also a critical reservoir for antimicrobial-resistant organisms because pathogens from human or animal fecal waste deposited on soil surfaces can exchange resistance genes with the high density of native soil microorganisms. Antimicrobial-resistant organisms adapted to soil can then permeate other compartments in the domestic environment. In a study in rural Bangladesh, 42% of E. coli isolates from outdoor courtyard soil were resistant to ≥1 antibiotic, and 13% were resistant to ≥3 antibiotics. In Tanzania, 10% of soil samples from household yards harbored multidrug-resistant E. coli. Studies in both high- and low-income countries have detected antimicrobial-resistant organisms and antimicrobial resistance genes on indoor floors and in floor dust in public buildings (e.g., universities, offices), settings with high antimicrobial use (e.g., hospitals, athletic facilities), − and barns at poultry and pig farms. − Studies in the US and Europe have also detected antimicrobial-resistant organisms on residential (e.g., bathroom, laundry) floors and in indoor dust. − We are not aware of any studies of antimicrobial-resistant organisms on indoor household floors in low-income countries.

Domestic animals often share living spaces with household members in low-income countries, enabling the zoonotic transmission of pathogens and antimicrobial-resistant organisms. Exposure to animals and their feces in the domestic environment is associated with increased risk of child diarrhea , and growth deficits. , A recent review found that backyard animal husbandry (i.e., small-scale informal animal production within the premises) in low-income countries is associated with exchange of antimicrobial resistance between domestic animals and household members. A sequencing study in Bangladesh demonstrated overlap between human and animal microbiomes and resistomes. There is growing evidence that domestic soil mediates transmission of pathogens and antimicrobial-resistant organisms between animals and humans in settings where they commonly cohabitate. Presence of domestic animals and their fecal waste has been associated with increased abundance of E. coli and animal-specific fecal markers in outdoor domestic soil (e.g., courtyard, home entrance) in Bangladesh and Zimbabwe. ,, In Ethiopia, fecal indicator levels on indoor floors were higher in households that raised domestic animals and kept them inside during the day. Also in Ethiopia, Campylobacter loads on indoor floors were associated with Campylobacter loads in child and chicken feces, indicating potential animal-to-human transmission via floors. , Evidence on the links between residential floors, domestic animals, and antimicrobial resistance is more limited. In one study of 90 homes in North Carolina, the abundance of the tetracycline resistance gene tet(W) in settled indoor dust on the doorsill correlated with the county’s livestock density. One study in a residential setting in Portugal found overlapping antimicrobial resistance patterns between the inhabitants of a home, their dog, and the laundry floor.

Improved flooring materials such as concrete can potentially interrupt soilborne transmission of fecal and/or antimicrobial-resistant microorganisms in low-income countries by providing a floor surface that is easy to clean, does not support microbial survival and growth, and reduces soil and dust exposure. Growing literature suggests that improved flooring materials are associated with reduced child diarrhea and enteric infections. − Few studies have investigated associations between flooring materials and fecal contamination of floors or other fecal-oral transmission pathways to explore the mechanisms behind these health benefits. In one study in Peru, dirt floors in the house entrance and kitchen areas had significantly higher E. coli counts than cement floors in the same areas. In the same setting, unfinished floors appeared to have higher detection of animal but not human molecular fecal markers than finished floors. In our previous study in rural Bangladesh, children in homes with soil floors had higher levels of E. coli on their hands than those in homes with concrete floors. We are not aware of any studies that have investigated associations between floor material and antimicrobial resistance or explored how floor material and the presence of domestic animals jointly affect exposure to fecal and/or antimicrobial-resistant organisms via household floors.

Efforts to implement improved floor materials as a public health intervention are considered in low-income countries but lack of conclusive causal evidence on health benefits hinders scale-up. Similarly, intervention designs are underway for safe management of domestic animals but there is no consensus on which specific practices should be targeted to effectively reduce zoonotic disease transmission. , Filling these data gaps will allow for the design and implementation of strategies to mitigate fecal contamination in the domestic environment. Here, we aimed to investigate associations between flooring material, animal ownership and management practices, and detection of E. coli and antimicrobial resistant E. coli on floors and young children’s hands among households in rural Bangladesh.

Materials and Methods

Enrollment

We enrolled 49 households in rural villages of Sirajganj district in northwestern Bangladesh between August 2 and October 4, 2023. The study communities were located in riverine areas that frequently experience flooding. Bangladesh has a subtropical climate with a pronounced monsoon season in June–October; our data collection occurred in the late monsoon period with warm and rainy conditions. The study area (Sthal union in Chauhali subdistrict) was chosen to be adjacent to but not overlapping with an ongoing randomized trial of improved floor materials by our team. Our study design was cross-sectional to allow exploration of multiple associations for hypothesis generation.

Field staff from the International Centre for Diarrheoal Disease Research, Bangladesh (icddr,b) screened each village in the union to list eligible households. Households were eligible if they had a child <2 years and indoor floors exclusively made of soil or exclusively made of concrete. Households were excluded if they had a mix of indoor floor materials. Animal husbandry, specifically cattle rearing, is common in Sirajganj. Anthrax is endemic among ruminants in the area, and outbreaks have been documented among cattle and residents. To ensure biosafety for field staff when collecting soil samples, households were excluded from enrollment if they reported a case of anthrax among their domestic animals or compound members at any time; this led to the exclusion of <5% of screened households. Field staff enrolled eligible households in the order they were listed in the screening until the targeted sample size of 50 households was reached; one household was later removed from the sample because they were mistakenly enrolled despite reporting anthrax symptoms.

The study was approved by the Institutional Review Board of Stanford University (63990) and the Ethical Review Committee of the icddr,b (PR-22069). The female caregiver of the child <2 years provided written informed consent in Bengali.

Data Collection

Trained field staff administered a structured questionnaire to record animal ownership and management practices, including the number of chickens/ducks, cattle/buffalo, and goats/sheep owned; how frequently these animals were allowed to roam free inside the home or compound; and where the animals were kept at night. Households in rural Bangladesh are typically clustered in extended family compounds with a shared courtyard; we recorded animal ownership and roaming separately for the enrolled household to capture the most direct exposure and for the surrounding compound to capture indirect exposure via adjacent households whose animals access the shared compound space. Roaming “inside the home” referred to the indoor area of the home where the child <2 years lived, while roaming “in the compound” referred to both indoor and outdoor areas within the boundaries of the extended-family compound, including the shared courtyard. Roaming frequency was recorded as never, sometimes, or always. The nighttime locations for animals were recorded as categorical variables with answer options based on prepiloting observations in the study area. For cattle/buffalo, options included outdoors within the compound, in barn/shed, in a different house within the compound, and inside the home where the child <2 years lived. For chickens/ducks and goats/sheep, options included outdoors within the compound and inside the home where the child <2 years lived. Field staff also observed whether any animal feces were present on the floor of the room where the child <2 years slept, whether the mother washed the child’s hands during the household visit and whether visible dirt was present under the fingernails and on the palms and finger pads of the mother and the child.

Sample Collection

Field staff collected floor swabs and dust from floors in all enrolled households. In a systematic subset of 36 households (first 2 households visited on each day of data collection), they also collected a hand rinse sample from the child <2 years.

Floor Swabs

Field staff identified the room where the child slept and used a bleach- and ethanol-sterilized metal stencil to mark a 50 cm × 50 cm square closest to where the child’s head rests when sleeping. This area was selected to represent where the child consistently spends time and because animal presence in young children’s sleeping area has been associated with child growth faltering in rural Bangladesh. Field staff swabbed the area inside the stencil once horizontally and once vertically using a sterile Whirlpak Hydrated PolySponge (Nasco, Modesto, CA) and placed the sponge in a sterile Whirlpak (Nasco, Modesto, CA).

Floor Dust

Field staff then marked up to 10 additional 50 × 50 cm squares starting from closest to the swabbed area. For each square, they swept the area inside the stencil once horizontally and once vertically using a clean (nonsterile) brush and scooped the dust into a preweighed sterile Whirlpak using a commercially single-packed sterile scoop. A new brush was used for each household. The goal of sweeping multiple squares was to obtain sufficient dust for additional analyses outside the scope of this current work (e.g., detection of helminth eggs), and 10 squares were selected based on prepilot observations as the maximum number of 50 × 50 cm areas within a typical room in the study area. Field staff continued to sweep until they reached the maximum number of possible squares within the room, up to 10 squares. They recorded how many squares they were able to sweep.

Hand Rinses

Field staff instructed the caregiver to place the child’s left-hand into a sterile Whirlpak prefilled with 250 mL of sterile deionized water. Once the hand was submerged, they massaged it from outside the bag for 15 s and then shook the bag with the hand inside for 15 s. They repeated the process for the child’s right hand using the same Whirlpak.

Ethanol-sterilized gloves were worn for the sample collection. Field staff collected 10% field blanks and duplicates. Floor swab blanks were collected by removing the prehydrated sponge from the Whirlpak and placing it back in. Hand rinse blanks were collected by opening the prefilled Whirlpak and performing the massaging and shaking steps without a hand in the bag. Samples were transported on ice to the Laboratory of Environmental Health at icddr,b, preserved at 4 °C overnight, and processed within 24 h of collection.

Sample Processing

Lab staff recorded the weight of the Whirlpak containing floor dust and subtracted the prerecorded weight of the bag. Floor swab samples were eluted from the sponge by adding 100 mL of sterile deionized water to the Whirlpak containing the sponge, massaging the sponge from outside the bag for 15 s, and then swirling the bag for 15 s. The liquid was decanted into a new sterile Whirlpak. The process was repeated a total of three times to generate 300 mL of eluate in the Whirlpak. Lab staff generated two 100 mL aliquots with 1:10 dilution (10 mL of eluate + 90 mL of sterile deionized water) and two 100 mL aliquots with 1:100 dilution (10 mL of 1:10 diluted eluate + 90 mL of sterile deionized water) for swab samples and one 100 mL aliquot for hand rinse samples (50 mL sample + 50 mL of sterile deionized water).

Enumeration of E. coli

We enumerated generic and cefotaxime-resistant E. coli in floor swab samples using both dilutions (1:10 and 1:100). We only enumerated generic E. coli in hand rinse samples due to budget limitations. Lab staff used IDEXX QuantiTray/2000 with Colilert-18 (IDEXX Laboratories, Westbrook, MA) to enumerate E. coli. For swab samples, they added 80 μL of filter-sterilized 5 mg/mL cefotaxime solution to the second set of both dilutions to enumerate cefotaxime-resistant E. coli. The final cefotaxime concentration was 4 μg/mL in a 100 mL sample aliquot. The antibiotic solution was added once Colilert-18 was fully dissolved. We used floor swab samples to quantify E. coli per unit floor area (rather than using floor dust samples to quantify E. coli per unit mass of dust) because we expect the former to more directly represent the risk of exposure from child contact with floors. Lab staff performed 10% lab blanks by processing 100 mL of sterile deionized water. Trays were incubated at 35 °C for 18 h. Lab staff counted the number of small and large wells that were positive for E. coli (yellow and fluorescent under UV) and determined the MPN using the IDEXX conversion table.

Counts for trays below the lower detection limit (1 MPN/100 mL) were imputed as half the lower detection limit (0.5 MPN), and counts for trays above the upper detection limit (2419.6 MPN/100 mL) were imputed as 2420 MPN. For swab samples, if both dilutions were within the detection limits, we calculated an average count weighted by the volume processed (1 or 10 mL of eluate). If the 1:100 dilution was below the lower detection limit, we assigned the count from the 1:10 dilution to the sample. If the 1:10 dilution was above the upper detection limit, we assigned the count from the 1:100 dilution to the sample. If either dilution had E. coli detected, we considered the sample positive. MPN counts were normalized to the unit floor sampling area (0.25 m2) for floor swabs and to two hands for child hand rinses. We calculated the percent relative abundance of cefotaxime-resistant E. coli for each sample by dividing the MPN from the tray processed with cefotaxime supplementation by the MPN from the tray processed without cefotaxime supplementation.

Statistical Analysis

We generated binary variables for whether the household had a soil floor; whether the household or the compound owned any chickens/ducks, cattle/buffalo, goats/sheep, or any animal; whether these animals ever roamed free inside the home or in the compound; whether they were kept inside the home at night; and whether any cattle/buffalo, chicken/duck, goat/sheep, or any animal feces were observed on the floor of the child’s sleeping area. We used Mann–Whitney U-tests to compare dust weight per m2 between households with soil vs concrete floors. We used chi-square tests to compare the prevalence and Mann–Whitney U-tests to compare the log10-transformed MPN of generic and cefotaxime-resistant E. coli and the relative abundance of cefotaxime-resistant E. coli between these categories. Assuming a standard deviation of 1.1 log10 MPN per unit floor area and a one-sided α of 0.05, our sample size of 50 households had 80% power to detect a 0.78-log10 MPN minimum difference in E. coli counts in floor swabs between households with concrete vs soil floors.

To explore dose–response relationships, we categorized households by counts of generic and cefotaxime-resistant E. coli and by the percent abundance of cefotaxime-resistant E. coli (none detected and bottom, middle, and top tertiles). We compared the number of animals owned across these categories. We also compared E. coli prevalence and counts across categories of animal cohabitation intensity (no animal owned by any household in compound, no animal owned by household, animals owned by household but kept outside at night, animals owned by household and kept inside at night) and frequency of animal roaming inside the home or compound (never, sometimes, always). We used the Cuzick nonparametric test for trends across ordered groups for these comparisons.

To assess combined effects of floor type and animal ownership, we used chi-square tests to compare E. coli prevalence and Kruskal–Wallis tests to compare log10-tranformed E. coli counts between cross-categories of soil vs concrete floors and households owning at least one vs no animal. We used multivariable regression with generalized linear models and Gaussian error distribution to estimate associations between floor type and log10-tranformed E. coli counts adjusting for the number of animals owned. We conducted analyses separately for each animal type and for all three animal types combined (i.e., “any animal”).

Results and Discussion

Household Characteristics

We enrolled households between Aug 2 and Oct 4, 2023. Of the 49 enrolled households, 57% (28) had soil floors and 43% (21) had concrete floors (Table S1). The main roof and wall material was tin. Compounds contained an average of 1.7 households and 6.0 residents (1.1 children <2 years, 1.5 children 2–18 years, 3.4 adults >18 years); these demographic indicators were similar between households with soil vs concrete floors (Table S1). We did not collect data on socioeconomic indicators, but in our concurrent randomized trial in the same area, mothers of young children had an average 6.2 years of education; the most common occupation for fathers was laborer; and 59% of households had a monthly household income <100 USD.

During the data collection visit, respondents were observed to wash the young child’s hand in 21% (6) of households with soil floors and 5% (1) of households with concrete floors (Table S1). However, children were observed to have clean hands in 32% (9) of households with soil floors and 52% (11) of households with concrete floors, while mothers had clean hands in 11% (3) of households with soil floors and 38% (8) of households with concrete floors (Table S1).

Floor Type and Animal Management Practices

Of 49 households, 71% (35) owned ≥ 1 animal (59% chickens/ducks, 49% cattle/buffalo, 43% goats/sheep) and 78% (38) of compounds owned ≥ 1 animal (Table S2, Figure S1). Households owned a mean of 16 animals (13 chickens/ducks, 2 cattle/buffalo, and 2 goats/cows) (Table S2). A higher percentage of households with soil floors owned ≥ 1 animal. Households with soil floors owned a larger number of cows but a similar number of chickens, goats, and overall animals as households with concrete floors (Table S2). Among households that owned animals, at least one type of animal was reported to stay inside the home at night in 41% of households with soil floors and none of households with concrete floors (Table S2, Figure S1). Animal feces were observed in a child’s sleeping area on 14% of soil floors and none of concrete floors (Table S2).

Among the 35 households that owned ≥ 1 animal, free roaming animals inside the home were reported in 91% of households with soil floors vs 69% with concrete floors (Table S2, Figure S1). Among the 38 compounds that owned ≥ 1 animal, free roaming animals in the compound were reported in 100% of households with soil floors and 80% with concrete floors (Table S2 and Figure S1). Almost all households that owned ≥ 1 chicken/duck reported that these roam free in the home or compound. Approximately half of households that owned cattle/buffalo reported that these roam inside the home or in the compound, while among households that owned goats/sheep, approximately 75% reported that these roam inside the home and almost all reported that they roam in the compound (Table S3). Among households that did not own any animals, 14–21% reported free roaming animals in the home or compound (Table S3).

E. coli Counts

We detected generic E. coli on 94% (46/49) of floors at a mean log10-transformed MPN of 3.8 (standard deviation [SD] = 1.5) per 0.25 m2 and on 53% (19/36) of child hands at a mean log-10 transformed MPN of 1.3 (SD = 1.0) per two hands (Table ). We detected cefotaxime-resistant E. coli on 69% (34/49) of floors at a mean log10-transformed MPN of 2.5 (SD = 1.3) per 0.25 m2. The mean relative abundance of cefotaxime-resistant E. coli on floors was 10.5% (SD = 22.9).

1. Dust Weight on Floors and Prevalence and Abundance of Generic and Cefotaxime-Resistant E. coli on Floor Swabs and Child Hands by Household Floor Type and Animal Ownership in the Compound .

  All Soil floor Concrete floor p-value Animals No animals p-value
Floor sweeps N = 49 N = 28 N = 21   N = 38 N = 11  
Dust weight (g/m2) 4.7 (10.6) 8.0 (13.1) 0.2 (0.3) 0.005 5.6 (11.8) 1.3 (2.0) 0.06
Floor swabs N = 49 N = 28 N = 21   N = 38 N = 11  
Generic E. coli (per 0.25 m2)              
Prevalence, % (n) 93.9 (46) 100.0 (28) 85.7 (18) 0.04 97.4 (37) 81.8 (9) 0.06
Log10 MPN, mean (SD) 3.8 (1.5) 4.7 (1.0) 2.7 (1.2) <0.0005 4.1 (1.4) 3.1 (1.6) 0.03
Cefotaxime-resistant E. coli (per 0.25 m2)              
Prevalence, % (n) 69.4 (34) 89.3 (25) 42.9 (9) <0.0005 79.0 (30) 36.4 (4) 0.007
Log10 MPN, mean (SD) 2.5 (1.3) 3.1 (1.1) 1.6 (0.9) <0.0005 2.7 (1.3) 1.8 (0.9) 0.03
Percent abundance, mean (SD) 10.5 (22.9) 11.7 (26.0) 8.7 (17.5) 0.13 12.9 (25.0) 0.8 (1.6) 0.02
Child hands N = 36 N = 19 N = 17   N = 27 N = 9  
Generic E. coli (per 2 hands)              
Prevalence, % (n) 52.8 (19) 57.9 (11) 47.1 (8) 0.52 55.6 (15) 44.4 (4) 0.56
Log10 MPN, mean (SD) 1.3 (1.0) 1.6 (1.1) 1.0 (0.9) 0.14 1.3 (0.9) 1.3 (1.3) 0.82
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a

MPN: Most probable number, SD: Standard deviation.

b

p-value obtained from chi2 test for prevalence outcomes and Mann–Whitney U-test for dust weight, log10 MPN, and percent abundance outcomes.

c

Percent abundance calculated as ratio of MPN from IDEXX trays with vs without cefotaxime supplementation for a given sample.

Associations with Floor Type

There was approximately 40 times more dust on soil floors than concrete floors (mean = 8.0 g vs 0.2 g per m2, p-value = 0.005, Table ). E. coli was detected on 100% of soil floors vs 86% of concrete floors (p-value = 0.04), and counts per unit area were 2-log higher on soil vs concrete floors (log10-mean = 4.7 vs 2.7, p-value <0.0005, Table ). Cefotaxime-resistant E. coli was detected on 89% of soil floors and 43% of concrete floors (p-value <0.0005), and counts per unit area were 1.5-log higher on soil vs concrete floors (log10-mean = 3.1 vs 1.6, p-value <0.0005, Table ). The relative abundance of cefotaxime-resistant E. coli was roughly 10% on both soil and concrete floors. E. coli was detected on 58% of child hands in homes with soil floors and 47% in homes with concrete floors, and counts per two hands appeared higher in homes with soil vs concrete floors (log10-mean = 1.6 vs 1.0); however, the associations with floor type could not be distinguished from chance (Table ).

Associations with Animal Ownership

E. coli was detected on floors in 100% of households with animals vs 79% of households without animals (p-value = 0.005, Table S4) and in 97% of compounds with animals vs 82% of compounds without animals (p-value = 0.06, Table ). E. coli counts per unit area were approximately 1-log higher in households/compounds with vs without animals (Table , Table S5). Households in the highest tertile of E. coli counts on floors (range: 4.9–5.9 log10-MPN) owned on average 26.9 animals (21.8 chickens/ducks, 2.8 cattle/buffalo, 2.3 goat/sheep) while those in the lowest tertile (range: 1.5–3.3 log10-MPN) owned 12.7 animals (9.1 chickens/ducks, 1.5 cattle/buffalo, 2.1 goat/sheep) and those with no E. coli on floors owned no animals (trend test p-value = 0.004, Table S6, Figure ). Results were similar for animal ownership by the compound, and associations were driven by chicken and duck ownership (Tables S4–S6, Figure ).

1.

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Mean number of animals owned by household by categories of (a) E. coli counts on floor swabs, (b) cefotaxime-resistant E. coli counts on floor swabs, (c) relative abundance of cefotaxime-resistant E. coli on floor swabs, and (d) E. coli counts on child hands. E. coli counts are categorized as none and bottom, middle, and top tertiles. Circles denote means, and the error bars denote standard errors (SE). Asterisks denote statistically significant trends (p < 0.05) determined by the Cuzick nonparametric test for trends across ordered groups.

Cefotaxime-resistant E. coli was detected on floors in 77% of households with animals vs 50% of households without animals (p-value = 0.06, Table S4), and in 79% of compounds with animals vs 36% of compounds without animals (p-value = 0.007, Table ). Counts of cefotaxime-resistant E. coli per unit floor area were approximately 1-log higher in households/compounds with vs without animals (p-values <0.05, Table S5). The relative abundance of cefotaxime-resistant E. coli on floors was over 10 times higher in compounds with vs without animals (13% vs <1%, p-value = 0.02, Table ). Households in the highest tertile of cefotaxime-resistant E. coli counts on floors (range: 3.5–5.3 log10-MPN) owned on average 29.6 animals (24.7 chickens/ducks, 2.4 cattle/buffalo, 2.5 goat/sheep) while those in the lowest tertile (range: 1.5–2.7 log10-MPN) owned 12.3 animals (9.5 chickens/ducks, 0.6 cattle/buffalo, 2.2 goat/sheep) and those with no cefotaxime-resistant E. coli on floors owned 7.9 animals (5.5 chickens/ducks, 1.2 cattle/buffalo, 1.1 goats/sheep (trend test p-value = 0.01, Table S6, Figure ). Associations were driven by chicken and duck ownership (Tables S4–S6, Figure ).

E. coli was detected on 56–58% of child hands if the household or compound owned animals vs 42–44% of child hands if the household or compound did not own animals, but the differences could not be distinguished from chance (Table , Table S7). E. coli counts per two hands were on the order of 1-log and appeared similar in households/compounds with vs without animals (Table , Table S7). However, children in the highest tertile of E. coli counts on their hands (range: 2.4–3.8 log10-MPN) lived in households that owned on average 45.5 animals (40.0 chickens/ducks, 3.8 cattle/buffalo, 2.0 goats/sheep) while those in the lowest tertile (range: 1.0–1.6 log10-MPN) lived in households with 22.4 animals (18.0 chickens/ducks, 1.1 cattle/buffalo, 3.3 goats/sheep), and those with no E. coli on their hands lived in households with 7.4 animals (5.8 chickens/ducks, 0.8 cattle/buffalo, 0.8 goats/sheep) (trend test p-value = 0.06, Table S8, Figure ).

Associations with Animal Management Practices

Floors had significantly higher prevalence and counts of generic and cefotaxime-resistant E. coli if any animals, specifically chickens, ever roamed free inside the home or in the compound (p-values <0.05, Tables S4–S5). Prevalence and counts on floors increased progressively with the roaming frequency (Table S9, Figure ). Cefotaxime-resistant E. coli was detected on 46% of floors (log10-mean = 1.9) if animals never roamed in the compound, 75% of floors (log10-mean = 2.6) if they roamed sometimes, and 100% of floors (log10-mean = 3.4) if they always roamed in the compound (trend test p-value = 0.02, Table S9, Figure ). Trends were similar for roaming inside the home (Figure ).

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Log-10 transformed most probable number (MPN) and prevalence of generic and cefotaxime-resistant E. coli by animal management practices: (a) free roaming frequency of animals inside the home, (b) free roaming frequency of animals in the compound, (c) animal cohabitation intensity categorized as animals owned by household and kept inside the home at night, animals owned by household but kept outdoors at night, no animal owned by household, no animal owned by any household in the compound, and (d) cross-categories of household floor type and animal ownership. The compound is a cluster of extended-family households sharing a courtyard. Circles denote means, and the error bars denote standard errors (SE). Asterisks denote statistically significant trends (p < 0.05) determined by the Cuzick nonparametric test for trends across ordered groups for panels a-c and by the Kruskal–Wallis test for panel d.

The prevalence and counts of generic and cefotaxime-resistant E. coli on floors increased progressively as the intensity of animal cohabitation increased (Table S10, Figure ). Cefotaxime-resistant E. coli was detected on 36% of floors (log10-mean = 1.8) if the compound did not own animals, 50% of floors (log10-mean = 1.8) if the household did not own animals, 69% of floors (log10-mean = 2.6) if the household owned animals but kept them outside at night, and 100% of floors (log10-mean = 3.3) if the household owned animals and kept them indoors at night (trend test p-value = 0.01, Table S10, Figure ).

Notably, 100% of floors where animal feces were observed harbored generic and cefotaxime-resistant E. coli (Table S4). Counts were almost 2-log higher on floors with vs without animal feces (log10-mean = 5.4 vs 3.7 for generic E. coli, 4.0 vs 2.4 for cefotaxime-resistant E. coli, p-values <0.05, Table S5). Roaming frequency or cohabitation intensity were not associated with E. coli prevalence or counts on child hands (Tables S11 and S12).

Associations with Floor Type and Animal Ownership Combined

The prevalence and counts of generic and cefotaxime-resistant E. coli progressively increased across cross-categories of floor material and animal ownership (concrete floor and no animals < concrete floor and animals < soil floor and no animals < soil floor and animals; p-value = 0.001, Table S13, Figure ). In multivariable regression models controlling for floor type and animal ownership, 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 0.13–0.16 log higher for every 10 additional animals owned (p-values <0.05, Table ). When broken down by animal type, generic E. coli counts on floors and child hands and cefotaxime-resistant E. coli counts on floors were 0.17–0.24 higher for every 10 additional chickens owned (p-values <0.05); there were no associations with the number of cows and goats owned (Table ).

2. Adjusted Associations between Household Floor Type/Animal Ownership and Log10-Transformed Most Probable Number (MPN) of E. coli and Cefotaxime-Resistant E. coli on Floor Swabs and E. coli on Child Hands .

  Generic E. coli on floors
 Cefotaxime-resistant E. coli on floors
 Generic E. coli on child hands
  Δlog10 (95% CI) p-value Δlog10 (95% CI) p-value Δlog10 (95% CI) p-value
Any animal            
Soil vs concrete floor 2.06 (1.46, 2.67) <0.0005 1.52 (0.97, 2.07) <0.0005 0.57 (−0.94, 1.18) 0.07
Number of animals 0.13 (0.01, 0.24) 0.03 0.16 (0.05, 0.26) 0.003 0.14 (0.05, 0.24) 0.01
By animal type            
Soil vs concrete floor 2.16 (1.53, 2.79) <0.0005 1.62 (1.04, 2.20) <0.0005 0.49 (−0.13, 1.12) 0.12
Number of chickens 0.21 (0.96, 0.36) 0.01 0.24 (0.10, 0.38) 0.001 0.17 (0.02, 0.31) 0.02
Number of cows –0.02 (−0.16, 0.12) 0.79 –0.01 (−0.15, 0.12) 0.87 0.08 (−0.07, 0.24) 0.30
Number of goats –0.08 (−0.19, 0.04) 0.20 –0.08 (−0.18, 0.03) 0.16 –0.5 (−0.17, 0.06) 0.34
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a

Δlog10: Difference in mean log10-transformed MPN counts; CI: Confidence interval.

b

Δlog10 reported for every additional 10 animals and every additional 10 chickens.

Discussion

Among 49 households in rural Bangladesh, all soil floors harbored E. coli and most (89%) harbored cefotaxime-resistant E. coli, while most concrete floors (86%) harbored E. coli and 43% harbored cefotaxime-resistant E. coli. Soil floors had 40 times more loose dust per m2 than concrete floors, as captured by floor sweeps. Therefore, the increased detection of E. coli and cefotaxime-resistant E. coli in swab samples from soil floors may reflect more dust per unit floor area swabbed rather than a higher microbial abundance per unit mass of dust. We purposefully opted to quantify E. coli per unit floor area because this integrates the environmental concentration (E. coli per gram of dust) with the potential for exposure (grams of dust per unit floor area available for child contact or ingestion). We expect reduced fecal contamination per unit floor area to translate to reduced child exposure to infectious agents, which may occur through direct ingestion of dust, contamination of child and caregiver hands by contact with floors, and contamination of stored water and food by aerosolized dust or by contact with contaminated hands. While both child and caregiver hands were observed to be visually cleaner in households with soil floors in our study, our findings show limited evidence of reduced E. coli contamination of child hands by concrete vs soil floors but support the dustborne pathway. Less dust per unit floor area may also plausibly reduce dustborne exposure to chemical contaminants such as lead. These findings lend support to growing evidence on child health benefits associated with improved floors.

Our study adds to prior evidence that soil floors can be a source of exposure to antimicrobial-resistant organisms. Further antibiotic susceptibility testing of cefotaxime-resistant E. coli isolates from positive IDEXX trays in our study found that all isolates were multidrug-resistant (resistant to ≥3 antimicrobials), and one isolate was extensively drug-resistant (resistant to ≥12 antimicrobials). 85% of isolates contained the bla CTX‑M gene, while 9% of isolates were classified as diarrheagenic and 6% as extraintestinal pathogenic E. coli. Additionally, metagenomic sequencing of soil floor samples in a subset of 10 households from this study detected 45 antimicrobial resistance genes that confer resistance to rifamycin, sulfonamides, tetracyclines, and aminoglycosides, among other drug classes. In a previous study in rural Bangladesh, 42% of E. coli isolates from outdoor courtyard soil were antimicrobial-resistant and 13% were multidrug-resistant. The higher prevalence of antimicrobial-resistant E. coli we observed on soil floors (89%) may indicate enhanced bacterial survival in the indoor environment. Exposure to sunlight in the outdoor environment can inactivate bacteria; in our previous work in Bangladesh, outdoor soil samples from sunlit areas had lower E. coli counts than samples from shaded areas. The WHO recommends monitoring ESBL-producing E. coli across environmental reservoirs, such as surface waters. Our findings also support monitoring ESBL-producing E. coli on floors, particularly unimproved soil floors.

The relative abundance of cefotaxime-resistant E. coli on floors was 10 times higher in households that owned animals. The prevalence and counts of both generic and cefotaxime-resistant E. coli increased with increasing animal cohabitation intensity (no animals owned by any household in compound < no animals owned by household < animals owned by household but kept outdoors at night < animals owned by household and kept indoors at night) and the frequency of animals roaming free in the household or compound. Notably, households with concrete floors were less likely to let animals roam free inside the home, and no households with concrete floors kept their animals indoors at night or had animal feces observed on floors. A desire to keep concrete floors clean as an aspirational household asset may trigger hygienic animal management practices as an additional benefit. Our findings are consistent with previous evidence of increased E. coli contamination of soil when households owned domestic animals and/or kept them indoors. Domestic animals are also recognized as reservoirs of antimicrobial resistance due to frequent use of antimicrobials in animal husbandry. Frequent antibiotic treatment of sick animals and use of antibiotics for healthy animals to promote growth or for prophylaxis is reported among Bangladeshi households. − A recent review identified soil as an important pathway for transmission of antimicrobial resistance between animals and humans in low-income countries. A study in Bangladesh found overlapping alleles of antimicrobial resistance genes between humans and domestic animals; chickens had the most overlap with humans. Importantly, in our study, households with soil floors and animals had the highest prevalence and counts of both generic and cefotaxime-resistant E. coli, while those with concrete floors and no animals had the lowest. Improved management of domestic animals may be critical to achieving the full benefits of concrete floors to prevent the transmission of enteric infections and antimicrobial resistance.

A study in Kenya identified animal type as a determinant of the extent of animal contact with, and risk of contamination on, floors. Cattle were more likely to be kept in designated sheds during both the day and at night. In contrast, chickens were mostly kept indoors at night, and they roamed in and out of the living space during the day, even among households who did not own chickens themselves. In our analysis, both small and large animals were reported to roam free inside the home or in the compound, although chickens did so more often than larger animals. In parallel, we observed stronger relationships between contamination on floors and the presence, number, nighttime location, and roaming frequency of chickens/ducks than cattle/buffalo or goats/sheep. In our prior work in rural Bangladesh, chicken feces were observed in the compound more frequently than cow, goat and sheep feces (87% vs 19–30% of compounds), and the presence of chickens/chicken feces was more strongly associated with E. coli contamination of courtyard soil, child hands, stored water, and food than other domestic animals. In a study in Uganda, ownership of chickens, but not cows, goats, or sheep, was associated with higher risk of child diarrhea, and in Ethiopia, indoor nighttime corralling of chickens, but not other domestic animals, was associated with reduced child growth. In Nepal, households that owned chickens were more likely to have third-generation cephalosporin-resistant and extended-spectrum beta-lactamase (ESBL)-producing E. coli in soil. Our findings support efforts to improve hygienic management of chickens in low-income settings.

Study limitations include a small sample size, limiting our statistical precision; however, given the magnitude of the associations we observed, we were able to distinguish estimates from chance, despite our small sample size. Another limitation is that we did not collect data on the socioeconomic status of enrolled households, which is likely associated with both our study exposures (floor type, animal ownership) and outcomes (E. coli on floors and hands). We expect households with concrete floors to be wealthier; therefore, confounding by socioeconomic status may have exaggerated the reduction in contamination that we observed in households with concrete floors. In contrast, wealthier households typically own more animals; therefore, confounding by socioeconomic status may have attenuated the increase in contamination observed in households with animals. Additionally, we collected data only at one time point (during the wet and warm monsoon season). Therefore, our findings do not capture seasonal or temporal trends, and the relationships we observed between floor type, animals, and fecal contamination may not apply to the dry or cold seasons. Further, we only measured contamination on floors and child hands. Fecal-oral transmission can occur through several pathways, and future studies should assess the influence of floor material and animal management on additional pathways such as caregiver hands, stored drinking water, and food.

Finally, we relied on E. coli as a fecal indicator organism, which does not correlate well with nonbacterial pathogens. , Our findings may not be representative of contamination of floors and hands with viruses, protozoa, or helminth eggs. However, E. coli measured in environmental matrices is predictive of child diarrhea and growth outcomes. − Additionally, antimicrobial resistance is primarily associated with bacterial pathogens, and ESBL-producing E. coli is the recommended sentinel organism for global monitoring of antimicrobial-resistant bacteria in the environment because of its high disease burden; ease of transmission between animals, humans, and the environment; and availability of facilities for its enumeration even in low-income settings. Our study focused on cefotaxime-resistant E. coli using a previously validated method; the method targets presumptive ESBL-producing E. coli because resistance to cefotaxime, a third-generation cephalosporin, is conferred by ESBL production.

Our findings indicate that indoor soil floors can present a pathway for soilborne exposure to enteric and antimicrobial-resistant organisms in rural Bangladeshi households, especially when domestic animals share living spaces with humans. Specific animal management practices, such as allowing animals to roam free in the living space, keeping them inside the house at night, and the presence of animal feces on the floor were associated with higher levels of floor contamination. Chickens were more strongly associated with floor contamination than cattle, goats, and sheep. Our findings support emerging intervention strategies to implement corralling and nighttime containment of domestic animals, especially chickens, to reduce the transmission of enteric infections and antimicrobial resistance as well as broader interventions focused on housing improvements, including improved floors. Future studies should investigate whether improved floor materials are associated with lower risk of enteric infections and carriage of antimicrobial-resistant organisms and evaluate health benefits from safe animal husbandry practices in tandem with flooring improvements.

Supplementary Material

es5c10329_si_001.pdf (268.1KB, pdf)

Acknowledgments

This study is funded by grants from the National Institute of Child Health and Human Development to Stanford University (R01HD108196).

The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acs.est.5c10329.

  • Characteristics of enrolled households (Table S1), animal ownership and management practices (Tables S2 and S3; Figure S1), floor contamination by animal ownership and management practices (Tables S4–S6, S9, and S10), child hand contamination by animal ownership and management practices (Tables S7, S8, S11, and S12), and floor and child hand contamination by cross-categories of floor type and animal ownership (Table S13) (PDF)

The authors declare no competing financial interest.

Changes were made to Figure 1 after this paper was published ASAP on November 12, 2025. The corrected version was reposted on November 17, 2025.

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