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2020-08-11Zeitschriftenartikel
ResFinder 4.0 for predictions of phenotypes from genotypes
dc.contributor.authorBortolaia, Valeria
dc.contributor.authorKaas, Rolf
dc.contributor.authorRuppe, Etienne
dc.contributor.authorRoberts, Marilyn C.
dc.contributor.authorSchwarz, Stefan
dc.contributor.authorCattoir, Vincent
dc.contributor.authorPhilippon, Alain
dc.contributor.authorAllesoe, Rosa L.
dc.contributor.authorRebelo, Ana Rita
dc.contributor.authorFlorensa, Alfred Ferrer
dc.contributor.authorFagelhauer, Linda
dc.contributor.authorChakraborty, Trinad
dc.contributor.authorNeumann, Bernd
dc.contributor.authorWerner, Guido
dc.contributor.authorK. Bender, Jennifer
dc.contributor.authorStingl, Kerstin
dc.contributor.authorNguyen, Minh
dc.contributor.authorCoppens, Jasmine
dc.contributor.authorXavier, Basil Britto
dc.contributor.authorMalhotra-Kumar, Surbhi
dc.contributor.authorWesth, Henrik
dc.contributor.authorPinholt, Mette
dc.contributor.authorAnjum, Muna F.
dc.contributor.authorDuggett, Nicholas A.
dc.contributor.authorKempf, Isabelle
dc.contributor.authorNykäsenoja, Suvi
dc.contributor.authorOlkkola, Satu
dc.contributor.authorWieczorek, Kinga
dc.contributor.authorAmaro, Ana
dc.contributor.authorClemente, Lurdes
dc.contributor.authorMossong, Joël
dc.contributor.authorLosch, Serge
dc.contributor.authorRagimbeau, Catherine
dc.contributor.authorLund, Ole
dc.contributor.authorAarestrup, Frank M.
dc.date.accessioned2024-02-23T15:10:26Z
dc.date.available2024-02-23T15:10:26Z
dc.date.issued2020-08-11none
dc.identifier.other10.1093/jac/dkaa345
dc.identifier.urihttp://edoc.rki.de/176904/11516
dc.description.abstractObjectives 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.eng
dc.language.isoengnone
dc.publisherRobert Koch-Institut
dc.rights(CC BY-NC 3.0 DE) Namensnennung - Nicht kommerziell 3.0 Deutschlandger
dc.rights.urihttp://creativecommons.org/licenses/by-nc/3.0/de/
dc.subjectphenotypeeng
dc.subjectgenotypeeng
dc.subjectsalmonellaeng
dc.subjectantimicrobialseng
dc.subjectdatasetseng
dc.subjectwhole-genome sequencingeng
dc.subject.ddc610 Medizin und Gesundheitnone
dc.titleResFinder 4.0 for predictions of phenotypes from genotypesnone
dc.typearticle
dc.identifier.urnurn:nbn:de:0257-176904/11516-5
dc.type.versionpublishedVersionnone
local.edoc.container-titleJournal of Antimicrobial Chemotherapynone
local.edoc.container-issn1460-2091none
local.edoc.pages10none
local.edoc.type-nameZeitschriftenartikel
local.edoc.container-typeperiodical
local.edoc.container-type-nameZeitschrift
local.edoc.container-urlhttps://academic.oup.com/jacnone
local.edoc.container-publisher-nameOxford University Pressnone
local.edoc.container-volume75none
local.edoc.container-issue12none
local.edoc.container-reportyear2020none
local.edoc.container-firstpage3491none
local.edoc.container-lastpage3500none

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