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

Jacquier, Hervé; Assao, Bachir; Chau, Françoise; Guindo, Ousmane; Condamine, Bénédicte; Magnan, Mélanie; Bridier‐Nahmias, Antoine; Sayingoza-Makombe, Nathan; Moumouni, Aissatou; Page, Anne‐Laure; Langendorf, Céline; Coldiron, Matthew E.; Denamur, Erick; Lastours, Victoire de

doi:10.1016/j.jinf.2023.06.015

Cited by 1 publication

(1 citation statement)

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“…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.…”

Section: Genomementioning

confidence: 99%

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

Condamine,

Morel-Journel,

Tesson

et al. 2024

Preprint

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Escherichia coliis an increasingly antibiotic-resistant opportunistic pathogen. Few data are available on its ecological and evolutionary dynamics in its primary niche, the vertebrate gut. Using Illumina and/or Nanopore technologies, we sequenced whole genomes of 210E. colinatural isolates from 22 stools sampled during a 20-year period in a healthy man (ED) living in France, who did not take any antibiotics. All the phylogroups, except the C, were represented with a predominance of B2 (34.3%), followed by A and F (19% each) phylogroups. Thirty five clones were identified and classified in three phenotypes according to their abundance and persistence time: 25 sub-dominant/transient (52 isolates), five dominant/transient (48 isolates) and five dominant/resident (110 isolates). Four out of the five dominant/resident clones belonged to B2 phylogroup [sequence types (STs)131 and 452] and F-ST59, whereas sub-dominant/transient clones belonged mainly to numerous distinct B1, A and D phylogroup STs. The long residence time of B2 phylogroup clones was counterbalanced by lower colonization ability. Residence time and within-host frequency were positively correlated. By comparing ED strain genomes to a collection of commensalE. coligenomes from 359 French individuals, enriched/specific ED strain genome traits were identified including a metabolic pathway (mhpcluster) and a very rarely reported antiviral defense island encompassing dGTPase and/or Detocs systems. SNP analysis of clonal diversity showed neutral evolution. The normalE. coligut microbiota is shaped by both the intrinsic properties of the strain lineages and the environmental constraints.

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Section: Genomementioning

confidence: 99%