ResFinder – an open online resource for identification of antimicrobial resistance genes in next-generation sequencing data and prediction of phenotypes from genotypes

Predicting Antimicrobial Resistance Using Partial Genome Alignments

(2021) D. Aytan-Aktug et al.   mSystems

Prediction of Acquired Antimicrobial Resistance for Multiple Bacterial Species Using Neural Networks

(2020) D. Aytan-Aktug et al.   mSystems

ResFinder 4.0 for predictions of phenotypes from genotypes

(2020) Valeria Bortolaia et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

CRHP Finder, a webtool for the detection of clarithromycin resistance in Helicobacter pylori from whole‐genome sequencing data

(2020) Melodi Yusibova et al.   HELICOBACTER

Understanding and predicting ciprofloxacin minimum inhibitory concentration in Escherichia coli with machine learning

(2020) Bálint Ármin Pataki et al.   Scientific Reports

Using WGS to identify antibiotic resistance genes and predict antimicrobial resistance phenotypes in MDR Acinetobacter baumannii in Tanzania

(2019) Happiness H Kumburu et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

LRE-Finder, a Web tool for detection of the 23S rRNA mutations and the optrA, cfr, cfr(B) and poxtA genes encoding linezolid resistance in enterococci from whole-genome sequences

(2019) Henrik Hasman et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Using Genomics to Track Global Antimicrobial Resistance

(2019) Rene S. Hendriksen et al.   Frontiers in Public Health

Improved Resistance Prediction in Mycobacterium tuberculosis by Better Handling of Insertions and Deletions, Premature Stop Codons, and Filtering of Non-informative Sites

(2019) Camilla Hundahl Johnsen et al.   Frontiers in Microbiology

Developing an in silico minimum inhibitory concentration panel test for Klebsiella pneumoniae

(2018) Marcus Nguyen et al.   Scientific Reports

SCCmecFinder, a Web-Based Tool for Typing of Staphylococcal Cassette Chromosome mec in Staphylococcus aureus Using Whole-Genome Sequence Data

(2018) Hülya Kaya et al.   mSphere

Rapid and precise alignment of raw reads against redundant databases with KMA

(2018) Philip T. L. C. Clausen et al.   BMC BIOINFORMATICS

Proficiency of WHO Global Foodborne Infections Network External Quality Assurance System participants in the identification and susceptibility testing of thermo-tolerant Campylobacter spp. from 2003-2012.

(2018) Susanne Karlsmose Pedersen et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Using machine learning to predict antimicrobial minimum inhibitory concentrations and associated genomic features for nontyphoidal Salmonella

(2018) Marcus Nguyen et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Machine learning and structural analysis of Mycobacterium tuberculosis pan-genome identifies genetic signatures of antibiotic resistance

(2018) Erol S. Kavvas et al.   Nature Communications

PointFinder: a novel web tool for WGS-based detection of antimicrobial resistance associated with chromosomal point mutations in bacterial pathogens

(2017) Ea Zankari et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Whole-Genome Sequencing for Detecting Antimicrobial Resistance in Nontyphoidal Salmonella

(2016) Patrick F. McDermott et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Benchmarking of methods for identification of antimicrobial resistance genes in bacterial whole genome data

(2016) Philip T. L. C. Clausen et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Sharing Data for Global Infectious Disease Surveillance and Outbreak Detection

(2016) Frank M. Aarestrup et al.   TRENDS IN MICROBIOLOGY

Whole-Genome Sequencing Analysis Accurately Predicts Antimicrobial Resistance Phenotypes in Campylobacter spp.

(2015) S. Zhao et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

WGS accurately predicts antimicrobial resistance inEscherichia coli

(2015) Gregory H. Tyson et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

In SilicoDetection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing

(2014) Alessandra Carattoli et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Benchmarking of Methods for Genomic Taxonomy

(2014) M. V. Larsen et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Solving the Problem of Comparing Whole Bacterial Genomes across Different Sequencing Platforms

(2014) Rolf S. Kaas et al.   PLoS One

SRST2: Rapid genomic surveillance for public health and hospital microbiology labs

(2014) Michael Inouye et al.   Genome Medicine

The Comprehensive Antibiotic Resistance Database

(2013) Andrew G. McArthur et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Predicting antimicrobial susceptibilities for Escherichia coli and Klebsiella pneumoniae isolates using whole genomic sequence data

(2013) N. Stoesser et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing

(2012) E. Zankari et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Identification of acquired antimicrobial resistance genes

(2012) E. Zankari et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria

(2012) M. V. Larsen et al.   JOURNAL OF CLINICAL MICROBIOLOGY

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Global Monitoring of Salmonella Serovar Distribution from the World Health Organization Global Foodborne Infections Network Country Data Bank: Results of Quality Assured Laboratories from 2001 to 2007

(2011) Rene S. Hendriksen et al.   Foodborne Pathogens and Disease

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Results of Use of WHO Global Salm-Surv External Quality Assurance System for Antimicrobial Susceptibility Testing of Salmonella Isolates from 2000 to 2007

(2008) R. S. Hendriksen et al.   JOURNAL OF CLINICAL MICROBIOLOGY