Faecal carriage of ESBL-producingEscherichia coliin a remote region of Niger

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 and findings: 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. Most 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, bla CTX-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. Conclusions: 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.

Strain intrinsic properties and environmental constraints together shape Escherichia coli dynamics and diversity over a twenty-year human gut time series

“…Pairwise single nucleotide polymorphism (SNP) distance matrices from multiple sequence alignments were performed using pairsnp (https://github.com/gtonkinhill/pairsnp). Clones were defined according to the following strategy (41). First, isolates were grouped by their haplogroup, defined as a combination of their sequence types (ST) according to the Warwick University and Institute Pasteur schemes, their serotype (O:H), and their fimH allele.…”

“…We then focused on specific genetic elements known to be important in the survival of E. coli in its commensal lifestyle in the gut: the virulence associated genes, as it has been proposed that virulence is a by-product of commensalism [53], the antibiotic resistance genes, as antibiotics are major selective agents and the defense islands against phage predation [54]. These factors may be primarily colonization factors [52]. We also compared the ED clones to a control collection of 359 E. coli isolates from the stools of 359 healthy individuals living in France during the same period, to potentially identify ED specific features.…”

“…The most frequent STs were the STs 131 (20%, B2 phylogroup) and 59 (19.5%, F phylogroup) followed by the ST10 (11%, A phylogroup) (Table S2). The clones were first defined as distinct haplogroups (combination of the phylogroup, the ST with both Warwick University and Institut Pasteur schemes, the serotype O:H, the fimH allele) and then confronted to the number of SNPs between isolates within the core genome [52]. Thirty four haplogroups were identified with a number of inter-haplogroup isolate SNPs ≥ 130 (Table S3).…”

“…For the delineation of clones, thirty four distinct haplogroups based on a combination of known typing markers (see methods for precise definition) were first identified (41). Then, the pairwise core genome SNP distance distribution was analyzed and confronted to the haplogroup of the isolates.…”