Acquisition of Escherichia coli carrying extended-spectrum ß-lactamase and carbapenemase genes by hospitalised children with severe acute malnutrition in Niger

Kirsty Sands (), Aditya Kumar Lankapalli, Giulia Lai, Brekhna Hassan, Edward AR Portal, Jordan AT Mathias, Ian Boostrom, Mei Li, Kate Cook, Shonnette Premchand-Branker, Lim S. Jones, Nathan Sayinzonga-Makombe, Sheila Isanaka, Rupa Kanapathipillai, Christopher Mambula, Isabelle Mouniaman, Céline Langendorf, Timothy R. Walsh and Owen B. Spiller
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Kirsty Sands: University of Oxford
Aditya Kumar Lankapalli: University of Oxford
Giulia Lai: Cardiff University
Brekhna Hassan: Cardiff University
Edward AR Portal: University of Oxford
Jordan AT Mathias: Cardiff University
Ian Boostrom: Cardiff University
Mei Li: University of Oxford
Kate Cook: University of Oxford
Shonnette Premchand-Branker: University of Oxford
Lim S. Jones: University Hospital of Wales
Nathan Sayinzonga-Makombe: Epicentre
Sheila Isanaka: Epicentre
Rupa Kanapathipillai: Médecins Sans Frontières
Christopher Mambula: Médecins Sans Frontières
Isabelle Mouniaman: Médecins Sans Frontières
Céline Langendorf: Epicentre
Timothy R. Walsh: University of Oxford
Owen B. Spiller: Cardiff University

Nature Communications, 2025, vol. 16, issue 1, 1-10

Abstract: Abstract Hospitalisation and routine antibiotic treatment are recommended for children with complicated severe acute malnutrition (SAM) but this may exacerbate antimicrobial resistance. Here, we investigate carriage of Gram-negative bacteria in children under five years of age receiving treatment for SAM in Niger, comparing the frequency of colonisation with bacteria carrying resistance genes at admission, during hospital stay and at discharge. E. coli isolates carrying a blaNDM-5 gene were selected for whole-genome sequencing. Rectal colonisation with bacteria carrying ß-lactamase genes is high, with 76% (n = 1042/1371) of children harbouring bacteria carrying a blaCTXM-1-group gene and 25% (n = 338/1371) carrying a blaNDM-5 gene. Over two-thirds of children who did not carry bacteria with a carbapenemase gene at admission are colonised with bacteria carrying a carbapenemase gene at discharge (n = 503/729, 69%). E. coli ST167 carrying blaNDM-5 gene is recovered from 11% (n = 144/1371) of children. Here we highlight infection control and bacterial AMR transmission concerns amongst a vulnerable population in need of medical treatment.

Date: 2025
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DOI: 10.1038/s41467-025-61718-w

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