Faecal carriage of extended-spectrum β-lactamase-producing Escherichia coli in a remote region of Niger.

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 bla gene was the major ESBL determinant (98.1%), chromosome-integrated in approximately 50% of cases, in multiple integration sites. When plasmid-borne, bla was found in IncF (57.4%) and IncY plasmids (26.2%). Closely related plasmids were found in different genetic backgrounds. Genomic environment analysis of bla 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 bla. Plasmid spread was also observed. These data suggest a risk of sustainable implementation of ESBL in community faecal carriage.