Download This Paper
Preprints with The Lancet is a collaboration between The Lancet Group of journals and SSRN to facilitate the open sharing of preprints for early engagement, community comment, and collaboration. Preprints available here are not Lancet publications or necessarily under review with a Lancet journal. These preprints are early-stage research papers that have not been peer-reviewed. The usual SSRN checks and a Lancet-specific check for appropriateness and transparency have been applied. The findings should not be used for clinical or public health decision-making or presented without highlighting these facts. For more information, please see the FAQs.
Massive Prevalence of Faecal Carriage of ESBL-Producing Escherichia Coli in Community in Niger Due to the Spread of blac CTX-M-15 Gene in Multiple Commensal Clones
22 Pages Posted: 3 May 2022
More...Abstract
Background: Data on extended-spectrum β--lactamase-producing Escherichia coli (ESBL- E. coli) carriage in community settings, especially in developing countries, are scarce. Here, we describe the population structure and molecular characteristics of resistance of ESBL- E. coli faecal isolates in a rural African population.
Methods: Between April and May 2017, stools of 383 healthy participants were collected from 20 villages in rural Southern Niger during a clinical trial on ciprofloxacin prophylaxis carried out during a meningococcal meningitis outbreak. Of 383 individuals, 354 (92.4%) were carriers of ESBL- E. coli before any ciprofloxacin intake. A subset of 90 of these ESBL- E. coli containing stools were selected for further analysis, from which 109 different ESBL- E. coli were recovered and whole genome sequenced by short-(Illumina) and long-(Nanopore) reads.FindingsMost belonged to the commensal-adapted phylogroup A (91, 83.5%), with high clonal diversity (57 distinct clones). One-quarter harboured the high pathogenicity island previously associated with a longer duration of faecal carriage.The bla CTX-M-15 gene was the major ESBL determinant (107, 98.1%). It was chromosome-integrated in approximately half of the cases (48, 44.9%), at multiple integration sites in diverse chromosomal genetic backgrounds. When plasmid-borne, blaCTX-M-15 was found in a large diversity of incompatibility groups. A single genetic background was found for 20 distinct plasmids, whereas very closely related plasmids were found in different genetic backgrounds in six cases, suggesting plasmid spread among strains. No geographical or social links to resistance patterns were observed.
Interpretation: Massive prevalence of community faecal carriage of CTX-M-15-producing E. coli was observed in a rural region of Niger without apparent antibiotic selective pressure. E. coli were highly diverse, well adapted commensal strains, with chromosomal integration of CTX-M-15 encoding gene in almost half of the cases. Evidence of clonal and plasmid spread suggest a risk of sustainable implementation in community faecal carriage.
Trial Registration Details: The trial is registered at ClinicalTrials.gov (NCT02724046).
Funding Information: This work was partially supported by a grant from the “Fondation pour la Recherche Médicale” (Equipe FRM 2016, grant number DEQ20161136698). The parent study was funded by Médecins Sans Frontières.
Declaration of Interests: None.
Ethics Approval Statement: The parent study protocol, which included this sub-study, was reviewed and approved by the National Consultative Ethics Committee of Niger (Ref: 003/2016/CCNE) and the Ethics Review Board of Médecins Sans Frontières (Ref: 1603). Written informed consent was obtained from individual participants.
Keywords: ESBL-E. coli, community, developing country, faecal carriage, chromosomal integration
Suggested Citation: Suggested Citation