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

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 Corander () and Anu Kantele ()
Additional contact information
Tamim Khawaja: Helsinki University Hospital and 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
Sointu Mero: University of Helsinki
Harry A. Thorpe: University of Oslo
Ørjan Samuelsen: University Hospital of North 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
Anu Kantele: Helsinki University Hospital and University of Helsinki

Nature Communications, 2024, vol. 15, issue 1, 1-11

Abstract: 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.

Date: 2024
References: View references in EconPapers View complete reference list from CitEc
Citations:

Downloads: (external link)
https://www.nature.com/articles/s41467-024-49591-5 Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-49591-5

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/s41467-024-49591-5

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().