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Community use of oral antibiotics transiently reprofiles the intestinal microbiome in young Bangladeshi children

Author

Listed:
  • Andrew Baldi

    (Walter and Eliza Hall Institute of Medical Research
    The University of Melbourne)

  • Sabine Braat

    (Walter and Eliza Hall Institute of Medical Research
    University of Melbourne School of Population and Global Health
    The University of Melbourne)

  • Mohammed Imrul Hasan

    (Walter and Eliza Hall Institute of Medical Research
    The University of Melbourne
    Bangladesh (icddr, b))

  • Cavan Bennett

    (Walter and Eliza Hall Institute of Medical Research
    The University of Melbourne)

  • Marilou Barrios

    (Walter and Eliza Hall Institute of Medical Research)

  • Naomi Jones

    (Walter and Eliza Hall Institute of Medical Research)

  • Gemma Moir-Meyer

    (Walter and Eliza Hall Institute of Medical Research
    The University of Melbourne)

  • Imadh Abdul Azeez

    (Walter and Eliza Hall Institute of Medical Research
    The University of Melbourne)

  • Stephen Wilcox

    (Walter and Eliza Hall Institute of Medical Research)

  • Mohammad Saiful Alam Bhuiyan

    (Bangladesh (icddr, b))

  • Ricardo Ataide

    (Walter and Eliza Hall Institute of Medical Research
    The University of Melbourne)

  • Danielle Clucas

    (Walter and Eliza Hall Institute of Medical Research
    The University of Melbourne
    The Royal Melbourne Hospital)

  • Leonard C. Harrison

    (Walter and Eliza Hall Institute of Medical Research
    The University of Melbourne)

  • Shams El Arifeen

    (Bangladesh (icddr, b))

  • Rory Bowden

    (The University of Melbourne
    Walter and Eliza Hall Institute of Medical Research)

  • Beverley-Ann Biggs

    (The University of Melbourne
    Royal Melbourne Hospital)

  • Aaron Jex

    (Walter and Eliza Hall Institute of Medical Research
    The University of Melbourne
    University of Melbourne)

  • Sant-Rayn Pasricha

    (Walter and Eliza Hall Institute of Medical Research
    The University of Melbourne
    The Royal Melbourne Hospital
    Clinical Haematology at The Royal Melbourne Hospital and the Peter MacCallum Cancer Centre)

Abstract

Antibiotics may alter the gut microbiome, and this is one of the mechanisms by which antimicrobial resistance may be promoted. Suboptimal antimicrobial stewardship in Asia has been linked to antimicrobial resistance. We aim to examine the relationship between oral antibiotic use and composition and antimicrobial resistance in the gut microbiome in 1093 Bangladeshi infants. We leverage a trial of 8-month-old infants in rural Bangladesh: 61% of children were cumulatively exposed to antibiotics (most commonly cephalosporins and macrolides) over the 12-month study period, including 47% in the first 3 months of the study, usually for fever or respiratory infection. 16S rRNA amplicon sequencing in 11-month-old infants reveals that alpha diversity of the intestinal microbiome is reduced in children who received antibiotics within the previous 7 days; these samples also exhibit enrichment for Enterococcus and Escherichia/Shigella genera. No effect is seen in children who received antibiotics earlier. Using shotgun metagenomics, overall abundance of antimicrobial resistance genes declines over time. Enrichment for an Enterococcus-related antimicrobial resistance gene is observed in children receiving antibiotics within the previous 7 days, but not earlier. Presence of antimicrobial resistance genes is correlated to microbiome composition. In Bangladeshi children, community use of antibiotics transiently reprofiles the gut microbiome.

Suggested Citation

  • Andrew Baldi & Sabine Braat & Mohammed Imrul Hasan & Cavan Bennett & Marilou Barrios & Naomi Jones & Gemma Moir-Meyer & Imadh Abdul Azeez & Stephen Wilcox & Mohammad Saiful Alam Bhuiyan & Ricardo Atai, 2024. "Community use of oral antibiotics transiently reprofiles the intestinal microbiome in young Bangladeshi children," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-51326-5
    DOI: 10.1038/s41467-024-51326-5
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    References listed on IDEAS

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    1. Himel Mallick & Ali Rahnavard & Lauren J McIver & Siyuan Ma & Yancong Zhang & Long H Nguyen & Timothy L Tickle & George Weingart & Boyu Ren & Emma H Schwager & Suvo Chatterjee & Kelsey N Thompson & Je, 2021. "Multivariable association discovery in population-scale meta-omics studies," PLOS Computational Biology, Public Library of Science, vol. 17(11), pages 1-27, November.
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    3. Giorgia Sulis & Pierrick Adam & Vaidehi Nafade & Genevieve Gore & Benjamin Daniels & Amrita Daftary & Jishnu Das & Sumanth Gandra & Madhukar Pai, 2020. "Antibiotic prescription practices in primary care in low- and middle-income countries: A systematic review and meta-analysis," PLOS Medicine, Public Library of Science, vol. 17(6), pages 1-20, June.
    4. Zhenyan Zhang & Qi Zhang & Tingzhang Wang & Nuohan Xu & Tao Lu & Wenjie Hong & Josep Penuelas & Michael Gillings & Meixia Wang & Wenwen Gao & Haifeng Qian, 2022. "Assessment of global health risk of antibiotic resistance genes," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
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