Faecal carriage of extended-spectrum β-lactamase-producing Escherichia coli in a remote region of Niger - 05/08/23
, Bachir Assao c, Françoise Chau a, Ousmane Guindo c, Bénédicte Condamine a, Mélanie Magnan a, Antoine Bridier-Nahmias a, Nathan Sayingoza-Makombe c, Aissatou Moumouni c, Anne-Laure Page d, Céline Langendorf d, Matthew E. Coldiron d, Erick Denamur a, e, 1, Victoire de Lastours a, f, 1Summary |
Objective |
Whole genome sequencing (WGS) of extended-spectrum β-lactamase-producing Escherichia coli (ESBL-E. coli) in developing countries is lacking. Here we describe the population structure and molecular characteristics of ESBL-E. coli faecal isolates in rural Southern Niger.
Methods |
Stools of 383 healthy participants were collected among which 92.4% were ESBL-Enterobacterales carriers. A subset of 90 ESBL-E. coli containing stools (109 ESBL-E. coli isolates) were further analysed by WGS, using short- and long-reads.
Results |
Most isolates belonged to the commensalism-adapted phylogroup A (83.5%), with high clonal diversity. The blaCTX-M-15 gene was the major ESBL determinant (98.1%), chromosome-integrated in approximately 50% of cases, in multiple integration sites. When plasmid-borne, blaCTX-M-15 was found in IncF (57.4%) and IncY plasmids (26.2%). Closely related plasmids were found in different genetic backgrounds. Genomic environment analysis of blaCTX-M-15 in closely related strains argued for mobilisation between plasmids or from plasmid to chromosome.
Conclusions |
Massive prevalence of community faecal carriage of CTX-M-15-producing E. coli was observed in a rural region of Niger due to the spread of highly diverse A phylogroup commensalism-adapted clones, with frequent chromosomal integration of blaCTX-M-15. Plasmid spread was also observed. These data suggest a risk of sustainable implementation of ESBL in community faecal carriage.
Le texte complet de cet article est disponible en PDF.Graphical Abstract |
Highlights |
● | Phylogroup A belonging of most of the ESBL-producing E. coli. |
● | Chromosomal integration of the blaCTX-M-15 gene in 45% of the isolates. |
● | Both clone and plasmid spread of the blaCTX-M-15 gene. |
● | Highly conserved genetic environment of the blaCTX-M-15 gene suggesting its mobilisation. |
● | WGS epidemiological studies on commensal and clinical E. coli in Africa warranted. |
Keywords : ESBL – E. coli, Community, Developing country, Faecal carriage, Chromosomal integration
Plan
Vol 87 - N° 3
P. 199-209 - septembre 2023 Retour au numéro
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