RT Journal Article
SR Electronic
T1 Prediction of the intestinal resistome by a novel 3D-based method
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 196014
DO 10.1101/196014
A1 Etienne Ruppé
A1 Amine Ghozlane
A1 Julien Tap
A1 Nicolas Pons
A1 Anne-Sophie Alvarez
A1 Nicolas Maziers
A1 Trinidad Cuesta
A1 Sara Hernando-Amado
A1 Jose Luís Martínez
A1 Teresa M. Coque
A1 Fernando Baquero
A1 Val F. Lanza
A1 Luis Maiz
A1 Tiphaine Goulenok
A1 Victoire de Lastours
A1 Nawal Amor
A1 Bruno Fantin
A1 Ingrid Wieder
A1 Antoine Andremont
A1 Willem van Schaik
A1 Malbert Rogers
A1 Xinglin Zhang
A1 Rob J.L. Willems
A1 Alexandre G. De Brevern
A1 Jean-Michel Batto
A1 Hervé Blottière
A1 Pierre Léonard
A1 Véronique Léjard
A1 Aline Letur
A1 Florence Levenez
A1 Kevin Weiszer
A1 Florence Haimet
A1 Joël Doré
A1 Sean P. Kennedy
A1 S. Dusko Ehrlich
YR 2017
UL http://biorxiv.org/content/early/2017/09/29/196014.abstract
AB The intestinal microbiota is considered to be a major reservoir of antibiotic resistance determinants (ARDs) that could potentially be transferred to bacterial pathogens. Yet, this question remains hypothetical because of the difficulty to identify ARDs from intestinal bacteria. Here, we developed and validated a new annotation method (called pairwise comparative modelling, PCM) based on homology modelling in order to characterize the Human resistome. We were able to predict 6,095 ARDs in a 3.9 million protein catalogue from the Human intestinal microbiota. We found that predicted ARDs (pdARDs) were distantly related to known ARDs (mean amino-acid identity 29.8%). Among 3,651 pdARDs that were identified in metagenomic species, 3,489 (95.6%) were assumed to be located on the bacterial chromosome. Furthermore, genes associated with mobility were found in the neighbourhood of only 7.9% (482/6,095) of pdARDs. According to the composition of their resistome, we were able to cluster subjects from the MetaHIT cohort (n=663) into 6 “resistotypes”. Eventually, 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 support that most ARDs in the intestinal microbiota should be considered as intrinsic genes of commensal microbiota with a low risk of transfer to bacterial pathogens.