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Tytuł pozycji:

Prediction of the intestinal resistome by a three-dimensional structure-based method

Tytuł :
Prediction of the intestinal resistome by a three-dimensional structure-based method
Autorzy :
Ruppé, Etienne
Ghozlane, Amine
Tap, Julien
Pons, Nicolas
Alvarez, Anne-Sophie
Maziers, Nicolas
Cuesta, Trinidad
Hernando-Amado, Sara
Clares, Irene
Martínez, Jose Luís
Coque, Teresa
Baquero, Fernando
Lanza, Val
Máiz, Luis
Goulenok, Tiphaine
de Lastours, Victoire
Amor, Nawal
Fantin, Bruno
Wieder, Ingrid
Andremont, Antoine
Van Schaik, Willem
Rogers, Malbert
Zhang, Xinglin
Willems, Rob
De Brevern, Alexandre
Batto, Jean-Michel
Blottiere, Herve
Léonard, Pierre
Léjard, Véronique
Letur, Aline
Levenez, Florence
Weiszer, Kevin
Haimet, Florence
Dore, Joel
Kennedy, Sean
Ehrlich, S. Dusko
Pokaż więcej
Temat :
MESH: Anti-Bacterial Agents/pharmacology
MESH: Bacteria/classification
MESH: Intestines/microbiology
MESH: Protein Conformation
MESH: beta-Lactamases/chemistry
MESH: beta-Lactamases/genetics
MESH: Bacteria/drug effects
MESH: Bacteria/genetics
MESH: Bacterial Proteins/chemistry
MESH: Bacterial Proteins/genetics
MESH: Drug Resistance, Bacterial/genetics
MESH: Gastrointestinal Microbiome/genetics
[SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology
[INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]
Źródło :
Nature Microbiology, Nature Publishing Group, 2019, 4 (1), pp.112-123. ⟨10.1038/s41564-018-0292-6⟩
Wydawca :
Nature Publishing Group, 2019.
Rok publikacji :
2019
Kolekcja :
HAL-Pasteur
Język :
English
ISSN :
2058-5276
DOI :
10.1038/s41564-018-0292-6
Numer akcesji :
edsair.od......2100..a1bb175bae60301b1bccd2e450939618
The intestinal microbiota is considered to be a major reservoir of antibiotic resistance determinants (ARDs) that could potentially be transferred to bacterial pathogens via mobile genetic elements. Yet, this assumption is poorly supported by empirical evidence due to the distant homologies between known ARDs (mostly from culturable bacteria) and ARDs from the intestinal microbiota. Consequently, an accurate census of intestinal ARDs (that is, the intestinal resistome) has not yet been fully determined. For this purpose, we developed and validated an annotation method (called pairwise comparative modelling) on the basis of a three-dimensional structure (homology comparative modelling), leading to the prediction of 6,095 ARDs in a catalogue of 3.9 million proteins from the human intestinal microbiota. We found that the majority of predicted ARDs (pdARDs) were distantly related to known ARDs (mean amino acid identity 29.8%) and found little evidence supporting their transfer between species. According to the composition of their resistome, we were able to cluster subjects from the MetaHIT cohort (n = 663) into six resistotypes that were connected to the previously described enterotypes. Finally, we found that the relative abundance of pdARDs was positively associated with gene richness, but not when subjects were exposed to antibiotics. Altogether, our results indicate that the majority of intestinal microbiota ARDs can be considered intrinsic to the dominant commensal microbiota and that these genes are rarely shared with bacterial pathogens.

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