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Arnaud Dechesne

dblp:425/3286 · DBLP profile ↗
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1ranked-venue papers
0as first author
1since 2021 · last 2023
0000-0002-6638-2158ORCID · reported

Domains — the database's venue-derived domains; a paper can count in several

Applied, interdisciplinary, general and emerging computing · 1 · 1 since 2021

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Interdisciplinary, comprehensive, and emerging computing
1 paper
Bioinformatics and computational biology · 100%

Topics — the 2 heaviest of 2, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Bioinformatics and computational biology › microbiology
antimicrobial resistance
0.712023
Plasmid permissiveness of wastewater microbiomes can be predicted from 16S rRNA sequences by machine learning · Bioinform. 2023
Bioinformatics and computational biology
metagenomics
0.712023
Plasmid permissiveness of wastewater microbiomes can be predicted from 16S rRNA sequences by machine learning · Bioinform. 2023

Methods — techniques the papers use, named apart from their topics

random forest · 0.7machine learning · 0.7
YearPublicationVenuePosition
2023 Plasmid permissiveness of wastewater microbiomes can be predicted from 16S rRNA sequences by machine learning
abstract
MOTIVATION: Wastewater treatment plants (WWTPs) harbor a dense and diverse microbial community. They constantly receive antimicrobial residues and resistant strains, and therefore provide conditions for horizontal gene transfer (HGT) of antimicrobial resistance (AMR) determinants. This facilitates the transmission of clinically important genes between, e.g. enteric and environmental bacteria, and vice versa. Despite the clinical importance, tools for predicting HGT remain underdeveloped. RESULTS: In this study, we examined to which extent water cycle microbial community composition, as inferred by partial 16S rRNA gene sequences, can predict plasmid permissiveness, i.e. the ability of cells to receive a plasmid through conjugation, based on data from standardized filter mating assays using fluorescent bio-reporter plasmids. We leveraged a range of machine learning models for predicting the permissiveness for each taxon in the community, representing the range of hosts a plasmid is able to transfer to, for three broad host-range resistance IncP plasmids (pKJK5, pB10, and RP4). Our results indicate that the predicted permissiveness from the best performing model (random forest) showed a moderate-to-strong average correlation of 0.49 for pB10 [95% confidence interval (CI): 0.44-0.55], 0.43 for pKJK5 (0.95% CI: 0.41-0.49), and 0.53 for RP4 (0.95% CI: 0.48-0.57) with the experimental permissiveness in the unseen test dataset. Predictive phylogenetic signals occurred despite the broad host-range nature of these plasmids. Our results provide a framework that contributes to the assessment of the risk of AMR pollution in wastewater systems. AVAILABILITY AND IMPLEMENTATION: The predictive tool is available as an application at https://github.com/DaneshMoradigaravand/PlasmidPerm.
Danesh Moradigaravand, Liguan Li, Arnaud Dechesne, Joseph Nesme, Roberto de la Cruz, Huda Ahmad, Manuel Banzhaf, Søren J. Sørensen, Barth F. Smets, Jan-Ulrich Kreft
Bioinform.3