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Dec 07, 2024;

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

Anna T Nguyen, Kalani Ratnasiri, Gabriella Barratt Heitmann, Sumaiya Tazin, Claire Anderson, Suhi Hanif, Afsana Yeamin, Abul Kasham Shoab, Ireen Sultana Shanta, Farjana Jahan, Sakib Hossain, Zahid Hayat Mahmud, Mohammad Jubair, Mustafizur Rahman, Mahbubur Rahman, Ayse Ercumen, Jade Benjamin-Chung
Author Information
  1. Anna T Nguyen: Department of Epidemiology & Population Health, Stanford University. ORCID
  2. Kalani Ratnasiri: Department of Epidemiology & Population Health, Stanford University. ORCID
  3. Gabriella Barratt Heitmann: Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA.
  4. Sumaiya Tazin: Department of Forestry and Environmental Resources, North Carolina State University.
  5. Claire Anderson: Department of Civil & Environmental Engineering, Stanford University. ORCID
  6. Suhi Hanif: Department of Epidemiology & Population Health, Stanford University.
  7. Afsana Yeamin: Environmental Health and WASH, International Centre for Diarrhoeal Disease Research, Bangladesh.
  8. Abul Kasham Shoab: Environmental Health and WASH, International Centre for Diarrhoeal Disease Research, Bangladesh.
  9. Ireen Sultana Shanta: Emerging Infections, Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh.
  10. Farjana Jahan: Environmental Health and WASH, International Centre for Diarrhoeal Disease Research, Bangladesh.
  11. Sakib Hossain: Laboratory of Environmental Health, International Centre for Diarrhoeal Disease Research, Bangladesh.
  12. Zahid Hayat Mahmud: Laboratory of Environmental Health, International Centre for Diarrhoeal Disease Research, Bangladesh.
  13. Mohammad Jubair: Genomics Centre, International Centre for Diarrhoeal Disease Research, Bangladesh.
  14. Mustafizur Rahman: Genomics Centre, International Centre for Diarrhoeal Disease Research, Bangladesh. ORCID
  15. Mahbubur Rahman: Environmental Health and WASH, International Centre for Diarrhoeal Disease Research, Bangladesh.
  16. Ayse Ercumen: Department of Forestry and Environmental Resources, North Carolina State University.
  17. Jade Benjamin-Chung: Department of Epidemiology & Population Health, Stanford University. ORCID
PMID: 39677809 DOI: 10.1101/2024.12.06.627269

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 (N=8 households), (N=6), (N=2), and (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.

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Grants

  1. F31 AI179107/NIAID NIH HHS
  2. R01 HD108196/NICHD NIH HHS
Journal Article Preprint
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