A1 Refereed original research article in a scientific journal
Deep sequencing of Escherichia coli exposes colonisation diversity and impact of antibiotics in Punjab, Pakistan
Authors: Khawaja T, Mäklin T, Kallonen T, Gladstone RA, Pöntinen AK, Mero S, Thorpe HA, Samuelsen Ø, Parkhill J, Izhar M, Akhtar MW, Corander J, Kantele A
Publication year: 2024
Journal: Nature Communications
Journal name in source: Nature communications
Journal acronym: Nat Commun
Volume: 15
Issue: 1
ISSN: 2041-1723
eISSN: 2041-1723
DOI: https://doi.org/10.1038/s41467-024-49591-5
Web address : https://www.nature.com/articles/s41467-024-49591-5
Self-archived copy’s web address: https://research.utu.fi/converis/portal/detail/Publication/456913508
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.
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Funding information in the publication:
This study was funded by VTR grants of Helsinki University Hospital [TYH 2012141, TYH 2013218 and TYH 2014216, AK], the Sigrid Jusélius Foundation [1726, AK], Trond Mohn Foundation (BATTALION grant, JC, RAG, AKP, ØS), Wellcome Trust Grant 206194, and Academy of Finland (EuroHPC grant, JC, TM, AMRIWA grant, AK).
