Publikationsdatenbank

ResFinder 4.0 for predictions of phenotypes from genotypes (2020)

Art

Zeitschriftenartikel / wissenschaftlicher Beitrag

Autoren

Bortolaia, Valeria

Kaas, Rolf S.

Ruppe, Etienne

Roberts, Marilyn C.

Schwarz, Stefan (WE 7)

Cattoir, Vincent

Philippon, Alain

Allesoe, Rosa L.

Rebelo, Ana Rita

Florensa, Alfred Ferrer

Fagelhauer, Linda

Chakraborty, Trinad

Neumann, Bernd

Werner, Guido

Bender, Jennifer K.

Stingl, Kerstin

Nguyen, Minh

Coppens, Jasmine

Xavier, Basil Britto

Malhotra-Kumar, Surbhi

Westh, Henrik

Pinholt, Mette

Anjum, Muna F.

Duggett, Nicholas A.

Kempf, Isabelle

Nykäsenoja, Suvi

Olkkola, Satu

Wieczorek, Kinga

Amaro, Ana

Clemente, Lurdes

Mossong, Joël

Losch, Serge

Ragimbeau, Catherine

Lund, Ole

Aarestrup, Frank M.

Quelle

The journal of antimicrobial chemotherapy : JAC

Bandzählung: 75

Heftzählung: 12

Seiten: 3491 – 3500

ISSN: 0305-7453

Sprache

Englisch

Verweise

URL (Volltext): https://academic.oup.com/jac/article/75/12/3491/5890997

DOI: 10.1093/jac/dkaa345

Pubmed: 32780112

Kontakt

Institut für Mikrobiologie und Tierseuchen

Robert-von-Ostertag-Str. 7-13
14163 Berlin
+49 30 838 51843 / 66949
mikrobiologie@vetmed.fu-berlin.de

Abstract / Zusammenfassung

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.