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dc.contributor.authorKhawaja, Tamim
dc.contributor.authorMäklin, Tommi
dc.contributor.authorKallonen, Teemu
dc.contributor.authorGladstone, Rebecca Ashley
dc.contributor.authorPöntinen, Anna Kaarina
dc.contributor.authorMero, Sointu
dc.contributor.authorThorpe, Harry A.
dc.contributor.authorSamuelsen, Ørjan
dc.contributor.authorParkhill, Julian
dc.contributor.authorIzhar, Mateen
dc.contributor.authorAkhtar, M. Waheed
dc.contributor.authorCorander, Jukka
dc.contributor.authorKantele, Anu
dc.date.accessioned2024-09-18T12:35:06Z
dc.date.available2024-09-18T12:35:06Z
dc.date.issued2024-06-18
dc.description.abstractMulti-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. colien_US
dc.identifier.citationKhawaja, Mäklin, Kallonen, Gladstone, Pöntinen, Mero, Thorpe, Samuelsen, Parkhill, Izhar, Akhtar, Corander, Kantele. Deep sequencing of Escherichia coli exposes colonisation diversity and impact of antibiotics in Punjab, Pakistan. Nature Communications. 2024;15(1)en_US
dc.identifier.cristinIDFRIDAID 2283100
dc.identifier.doi10.1038/s41467-024-49591-5
dc.identifier.issn2041-1723
dc.identifier.urihttps://hdl.handle.net/10037/34784
dc.language.isoengen_US
dc.publisherSpringer Natureen_US
dc.relation.journalNature Communications
dc.rights.accessRightsopenAccessen_US
dc.rights.holderCopyright 2024 The Author(s)en_US
dc.rights.urihttps://creativecommons.org/licenses/by/4.0en_US
dc.rightsAttribution 4.0 International (CC BY 4.0)en_US
dc.titleDeep sequencing of Escherichia coli exposes colonisation diversity and impact of antibiotics in Punjab, Pakistanen_US
dc.type.versionpublishedVersionen_US
dc.typeJournal articleen_US
dc.typeTidsskriftartikkelen_US
dc.typePeer revieweden_US


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Attribution 4.0 International (CC BY 4.0)
Except where otherwise noted, this item's license is described as Attribution 4.0 International (CC BY 4.0)