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Protocols

ResFinder specifications

Information


Unique identifier OMICS_12778
Name ResFinder
Restrictions to use None
Community driven No
Data access Browse
User data submission Allowed
Version 3.0
Maintained Yes

Maintainers


  • person_outline Valeria Bortolaia
  • person_outline Ea Zankari

Additional information


https://cge.cbs.dtu.dk/services/ResFinder/instructions.php

Publication for ResFinder

ResFinder citations

 (241)
call_split

Genomic and functional characterisation of IncX3 plasmids encoding blaSHV 12 in Escherichia coli from human and animal origin

2018
Sci Rep
PMCID: 5955891
PMID: 29769695
DOI: 10.1038/s41598-018-26073-5
call_split See protocol

[…] of the putative ORFs against the NCBI non-redundant proteins (NR) database, Pfam, and Interpro scan were used to assess their putative functions by identification of structural features and motifs,. ResFinder (version 2.1), PlasmidFinder (version 1.3) and ISfinder were used to determine the presence of resistance genes, replicon types and insertion sequences, respectively–. Plasmid sequences were […]

library_books

Acquisition and dissemination of cephalosporin resistant E. coli in migratory birds sampled at an Alaska landfill as inferred through genomic analysis

2018
Sci Rep
PMCID: 5943298
PMID: 29743625
DOI: 10.1038/s41598-018-25474-w

[…] es were detected from trimmed, unique high quality reads using SRST2 and matched to the ARGannot resistance gene database. This manually curated AMR gene database includes sequences found in both the ResFinder database and the Comprehensive Antibiotic Resistance Database (CARD), and includes both acquired resistance genes and point mutations in chromosomal target genes. AMR gene sequences from eac […]

call_split

Genetic diversity and virulence profiles of Listeria monocytogenes recovered from bulk tank milk, milk filters, and milking equipment from dairies in the USA (2002 to 2014)

2018
PLoS One
PMCID: 5942804
PMID: 29742151
DOI: 10.1371/journal.pone.0197053
call_split See protocol

[…] . A Maximum Likelihood phylogenetic tree was inferred with 100 bootstrap replicates using RAxML v. 8.0 with parameters set to default [].Acquired antibiotic resistance genes were identified using the ResFinder (v. 1.0) program hosted by the Center for Genomic Epidemiology webserver [, ]. The functionality of resistance genes identified in silico was evaluated using an automated microdilution proce […]

library_books

Genomic epidemiology of Shigella in the UK shows transmission of pathogen sublineages and determinants of antimicrobial resistance

2018
Sci Rep
PMCID: 5943296
PMID: 29743642
DOI: 10.1038/s41598-018-25764-3

[…] , and S. sonnei respectively. Multiple sequence alignments were used to infer maximum likelihood phylogenetic trees using RAxML with 100 bootstrap replicates. Acquired AMR genes were identified using ResFinder on draft genome assemblies (generated by) and QRDR mutations were detected as previously described. All sequence data are publically available at the European Nucleotide Archive under projec […]

library_books

Genome based analysis of Carbapenemase producing Klebsiella pneumoniae isolates from German hospital patients, 2008 2014

2018
PMCID: 5930415
PMID: 29744043
DOI: 10.1186/s13756-018-0352-y

[…] WGS data of all isolates were analysed using Resfinder [], PlasmidFinder and the MLST tool [] provided by the Centre for Genomic Epidemiology (https://cge.cbs.dtu.dk/services/; last access: 25/04/2018). Determination of capsular type for Klebsie […]

library_books

Genomic Characterization of Nonclonal mcr 1 Positive Multidrug Resistant Klebsiella pneumoniae from Clinical Samples in Thailand

2018
PMCID: 5946733
PMID: 29688801
DOI: 10.1089/mdr.2017.0400

[…] ed to circularized contigs to detect/correct errors.Comparative genomic analyses were performed using Geneious (Biomatters, Auckland, New Zealand). Antimicrobial resistance genes were annotated using ResFinder 2.0. Genomes were annotated using the NCBI Prokaryotic Genome Annotation Pipeline version 4.1. Single-nucleotide polymorphism (SNP)-based dendrograms were generated using Geneious and RAxML. […]

Citations

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ResFinder institution(s)
National Food Institute, Technical University of Denmark, Lyngby, Denmark; Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
ResFinder funding source(s)
Supported by the Center for Genomic Epidemiology grant 09-067103/DSF from the Danish Council for Strategic Research and by the European Union Reference Laboratory for Antimicrobial Resistance.

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