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Deep sequencing of Escherichia coli exposes colonisation diversity and impact of antibiotics in Punjab, Pakistan

Author

Listed:
  • Tamim Khawaja

    (Helsinki University Hospital and University of Helsinki
    University of Helsinki
    University of Helsinki)

  • Tommi Mäklin

    (University of Helsinki)

  • Teemu Kallonen

    (Turku University Hospital)

  • Rebecca A. Gladstone

    (University of Oslo)

  • Anna K. Pöntinen

    (University of Oslo
    University Hospital of North Norway)

  • Sointu Mero

    (University of Helsinki
    University of Helsinki)

  • Harry A. Thorpe

    (University of Oslo)

  • Ørjan Samuelsen

    (University Hospital of North Norway
    UiT The Arctic University of Norway)

  • Julian Parkhill

    (University of Cambridge)

  • Mateen Izhar

    (Shaikh Zayed Post-Graduate Medical Institute)

  • M. Waheed Akhtar

    (University of the Punjab)

  • Jukka Corander

    (University of Helsinki
    University of Oslo
    Wellcome Sanger Institute)

  • Anu Kantele

    (Helsinki University Hospital and University of Helsinki
    University of Helsinki
    University of Helsinki)

Abstract

Multi-drug resistant (MDR) E. coli constitute a major public health burden globally, reaching the highest prevalence in the global south yet frequently flowing with travellers to other regions. However, our comprehension of the entire genetic diversity of E. coli colonising local populations remains limited. We quantified this diversity, its associated antimicrobial resistance (AMR), and assessed the impact of antibiotic use by recruiting 494 outpatients and 423 community dwellers in the Punjab province, Pakistan. Rectal swab and stool samples were cultured on CLED agar and DNA extracted from plate sweeps was sequenced en masse to capture both the genetic and AMR diversity of E. coli. We assembled 5,247 E. coli genomes from 1,411 samples, displaying marked genetic diversity in gut colonisation. Compared with high income countries, the Punjabi population generally showed a markedly different distribution of genetic lineages and AMR determinants, while use of antibiotics elevated the prevalence of well-known globally circulating MDR clinical strains. These findings implicate that longitudinal multi-regional genomics-based surveillance of both colonisation and infections is a prerequisite for developing mechanistic understanding of the interplay between ecology and evolution in the maintenance and dissemination of (MDR) E. coli.

Suggested Citation

  • Tamim Khawaja & Tommi Mäklin & Teemu Kallonen & Rebecca A. Gladstone & Anna K. Pöntinen & Sointu Mero & Harry A. Thorpe & Ørjan Samuelsen & Julian Parkhill & Mateen Izhar & M. Waheed Akhtar & Jukka Co, 2024. "Deep sequencing of Escherichia coli exposes colonisation diversity and impact of antibiotics in Punjab, Pakistan," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
  • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-49591-5
    DOI: 10.1038/s41467-024-49591-5
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    References listed on IDEAS

    as
    1. Sergio Arredondo-Alonso & George Blundell-Hunter & Zuyi Fu & Rebecca A. Gladstone & Alfred Fillol-Salom & Jessica Loraine & Elaine Cloutman-Green & Pål J. Johnsen & Ørjan Samuelsen & Anna K. Pöntinen , 2023. "Evolutionary and functional history of the Escherichia coli K1 capsule," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    2. Guilhem Royer & Olivier Clermont & Julie Marin & Bénédicte Condamine & Sara Dion & François Blanquart & Marco Galardini & Erick Denamur, 2023. "Epistatic interactions between the high pathogenicity island and other iron uptake systems shape Escherichia coli extra-intestinal virulence," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    3. Cameron J. Reid & Max L. Cummins & Stefan Börjesson & Michael S. M. Brouwer & Henrik Hasman & Anette M. Hammerum & Louise Roer & Stefanie Hess & Thomas Berendonk & Kristina Nešporová & Marisa Haenni &, 2022. "A role for ColV plasmids in the evolution of pathogenic Escherichia coli ST58," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
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