ResFinder 4.0 for predictions of phenotypes from genotypes - Université de Rennes Accéder directement au contenu
Article Dans Une Revue Journal of Antimicrobial Chemotherapy Année : 2020

ResFinder 4.0 for predictions of phenotypes from genotypes

Guido Werner
  • Fonction : Auteur
  • PersonId : 889339
Mette Pinholt
  • Fonction : Auteur
Joel Mossong
  • Fonction : Auteur
  • PersonId : 888212
Serge Losch
  • Fonction : Auteur

Résumé

Objectives - WGS-based antimicrobial susceptibility testing (AST) is as reliable as phenotypic AST for several antimicrobial/bacterial species combinations. However, routine use of WGS-based AST is hindered by the need for bioinformatics skills and knowledge of antimicrobial resistance (AMR) determinants to operate the vast majority of tools developed to date. By leveraging on ResFinder and PointFinder, two freely accessible tools that can also assist users without bioinformatics skills, we aimed at increasing their speed and providing an easily interpretable antibiogram as output. Methods - The ResFinder code was re-written to process raw reads and use Kmer-based alignment. The existing ResFinder and PointFinder databases were revised and expanded. Additional databases were developed including a genotype-to-phenotype key associating each AMR determinant with a phenotype at the antimicrobial compound level, and species-specific panels for in silico antibiograms. ResFinder 4.0 was validated using Escherichia coli (n = 584), Salmonella spp. (n = 1081), Campylobacter jejuni (n = 239), Enterococcus faecium (n = 106), Enterococcus faecalis (n = 50) and Staphylococcus aureus (n = 163) exhibiting different AST profiles, and from different human and animal sources and geographical origins. Results - Genotype-phenotype concordance was ≥95% for 46/51 and 25/32 of the antimicrobial/species combinations evaluated for Gram-negative and Gram-positive bacteria, respectively. When genotype-phenotype concordance was <95%, discrepancies were mainly linked to criteria for interpretation of phenotypic tests and suboptimal sequence quality, and not to ResFinder 4.0 performance. Conclusions - WGS-based AST using ResFinder 4.0 provides in silico antibiograms as reliable as those obtained by phenotypic AST at least for the bacterial species/antimicrobial agents of major public health relevance considered.
Fichier principal
Vignette du fichier
dkaa345.pdf (611.9 Ko) Télécharger le fichier
Origine : Fichiers éditeurs autorisés sur une archive ouverte
Loading...

Dates et versions

hal-02930733 , version 1 (04-09-2020)

Licence

Paternité - Pas d'utilisation commerciale

Identifiants

Citer

Valeria Bortolaia, Rolf S Kaas, Etienne Ruppe, Marilyn C Roberts, Stefan Schwarz, et al.. ResFinder 4.0 for predictions of phenotypes from genotypes. Journal of Antimicrobial Chemotherapy, 2020, 75 (12), pp.3491-3500. ⟨10.1093/jac/dkaa345⟩. ⟨hal-02930733⟩
303 Consultations
219 Téléchargements

Altmetric

Partager

Gmail Facebook X LinkedIn More