Outcome of Different Sequencing and Assembly Approaches on the Detection of Plasmids and Localization of Antimicrobial Resistance Genes in Commensal Escherichia coli

Evaluation of Machine Learning Models for Predicting Antimicrobial Resistance of Actinobacillus pleuropneumoniae From Whole Genome Sequences

(2020) Zhichang Liu et al.   Frontiers in Microbiology

Monitoring Antimicrobial Resistance and Drug Usage in the Human and Livestock Sector and Foodborne Antimicrobial Resistance in Six European Countries

(2020) Octavio Mesa Varona et al.   Infection and Drug Resistance

Platon: identification and characterization of bacterial plasmid contigs in short-read draft assemblies exploiting protein sequence-based replicon distribution scores

(2020) Oliver Schwengers et al.   Microbial Genomics

Impact of DNA extraction on whole genome sequencing analysis for characterization and relatedness of Shiga toxin-producing Escherichia coli isolates

(2020) Stéphanie Nouws et al.   Scientific Reports

Assembly of long, error-prone reads using repeat graphs

(2019) Mikhail Kolmogorov et al.   NATURE BIOTECHNOLOGY

Next-Generation Sequencing and Emerging Technologies

(2019) Kishore Kumar et al.   SEMINARS IN THROMBOSIS AND HEMOSTASIS

Integrating Whole-Genome Sequencing Data Into Quantitative Risk Assessment of Foodborne Antimicrobial Resistance: A Review of Opportunities and Challenges

(2019) Lucie Collineau et al.   Frontiers in Microbiology

Nanopore sequencing for fast determination of plasmids, phages, virulence markers, and antimicrobial resistance genes in Shiga toxin-producing Escherichia coli

(2019) Narjol González-Escalona et al.   PLoS One

Validating the NCBI AMRFinder Tool and Resistance Gene Database Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of NARMS Isolates

(2019) Michael Feldgarden et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes

(2019) Nicola De Maio et al.   Microbial Genomics

Prevalence of Beta-Lactam and Quinolone/Fluoroquinolone Resistance in Enterobacteriaceae From Dogs in France and Spain—Characterization of ESBL/pAmpC Isolates, Genes, and Conjugative Plasmids

(2019) Véronique Dupouy et al.   Frontiers in Veterinary Science

Rapid, multiplexed, whole genome and plasmid sequencing of foodborne pathogens using long-read nanopore technology

(2019) Tonya L. Taylor et al.   Scientific Reports

Extended-spectrum β-lactamase-producing Proteus mirabilis with multidrug resistance isolated from raw chicken in Singapore: Genotypic and phenotypic analysis

(2019) Siyao Guo et al.   Journal of Global Antimicrobial Resistance

Next-generation sequencing technologies and their application to the study and control of bacterial infections

(2018) J. Besser et al.   CLINICAL MICROBIOLOGY AND INFECTION

Review of antimicrobial resistance surveillance programmes in livestock and meat in EU with focus on humans

(2018) R. Schrijver et al.   CLINICAL MICROBIOLOGY AND INFECTION

Genetic Mechanisms of Antibiotic Resistance and the Role of Antibiotic Adjuvants

(2018) Daniela Santos Pontes et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Evaluating the use of whole-genome sequencing for outbreak investigations in the lack of closely related reference genome

(2018) Mohamed M.H. Abdelbary et al.   INFECTION GENETICS AND EVOLUTION

Plasmids carrying antimicrobial resistance genes in Enterobacteriaceae

(2018) M Rozwandowicz et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Newly identified colistin resistance genes, mcr-4 and mcr-5, from upper and lower alimentary tract of pigs and poultry in China

(2018) Li Chen et al.   PLoS One

The Third Revolution in Sequencing Technology

(2018) Erwin L. van Dijk et al.   TRENDS IN GENETICS

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

(2018) Apostolos Liakopoulos et al.   Scientific Reports

Recent updates of fluoroquinolones as antibacterial agents

(2018) Hend A. A. Ezelarab et al.   ARCHIV DER PHARMAZIE

Horizontal transfer of antibiotic resistance genes in clinical environments

(2018) Nicole A. Lerminiaux et al.   CANADIAN JOURNAL OF MICROBIOLOGY

Rapid detection and discrimination of chromosome- and MCR-plasmid-mediated resistance to polymyxins by MALDI-TOF MS in Escherichia coli: the MALDIxin test

(2018) Laurent Dortet et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Whole Genome Sequencing and Bioinformatic Analysis of Two Foodborne Illness Outbreaks: Campylobacter jejuni and Salmonella enterica

(2018) Kelly F. Oakeson et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Antimicrobial resistance plasmid reservoir in food and food-producing animals

(2018) Jean-Yves Madec et al.   PLASMID

Plasmid-mediated resistance is going wild

(2018) Monika Dolejska et al.   PLASMID

Genome-based prediction of bacterial antibiotic resistance

(2018) Michelle Su 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

Next-Generation Sequencing Technologies

(2018) W. Richard McCombie et al.   Cold Spring Harbor Perspectives in Medicine

IncFII plasmid carrying antimicrobial resistance genes in Shigella flexneri: Vehicle for dissemination

(2018) Dhiviya Prabaa Muthuirulandi Sethuvel et al.   Journal of Global Antimicrobial Resistance

National Antimicrobial Resistance Monitoring System: Two Decades of Advancing Public Health Through Integrated Surveillance of Antimicrobial Resistance

(2017) Beth E. Karp et al.   Foodborne Pathogens and Disease

Identification of a novel transposon-associated phosphoethanolamine transferase gene, mcr-5, conferring colistin resistance in d-tartrate fermenting Salmonella enterica subsp. enterica serovar Paratyphi B

(2017) Maria Borowiak et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Mechanisms of quinolone action and resistance: where do we stand?

(2017) Susana Correia et al.   JOURNAL OF MEDICAL MICROBIOLOGY

Database resources of the National Center for Biotechnology Information

(2017) et al.   NUCLEIC ACIDS RESEARCH

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

(2017) Ryan R. Wick et al.   PLoS Computational Biology

A Review on the Applications of Next Generation Sequencing Technologies as Applied to Food-Related Microbiome Studies

(2017) Yu Cao et al.   Frontiers in Microbiology

Antimicrobial resistance surveillance in the genomic age

(2016) Andrew G. McArthur et al.   Annals of the New York Academy of Sciences

CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database

(2016) Baofeng Jia et al.   NUCLEIC ACIDS RESEARCH

Oxford Nanopore MinION Sequencing and Genome Assembly

(2016) Hengyun Lu et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Mechanisms of drug resistance: quinolone resistance

(2015) David C. Hooper et al.   Annals of the New York Academy of Sciences

Mutations That Enhance the Ciprofloxacin Resistance of Escherichia coli withqnrA1

(2015) Laura Vinué et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly

(2015) Sergey Koren et al.   CURRENT OPINION IN MICROBIOLOGY

VFDB 2016: hierarchical and refined dataset for big data analysis—10 years on

(2015) Lihong Chen et al.   NUCLEIC ACIDS RESEARCH

PacBio Sequencing and Its Applications

(2015) Anthony Rhoads et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes

(2015) Thomas Brettin et al.   Scientific Reports

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

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

Complete sequences of IncHI1 plasmids carrying blaCTX-M-1 and qnrS1 in equine Escherichia coli provide new insights into plasmid evolution

(2014) Monika Dolejska et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

The Complete Genome Sequence of Escherichia coli EC958: A High Quality Reference Sequence for the Globally Disseminated Multidrug Resistant E. coli O25b:H4-ST131 Clone

(2014) Brian M. Forde et al.   PLoS One

Prediction of antibiotic resistance by gene expression profiles

(2014) Shingo Suzuki et al.   Nature Communications

ARG-ANNOT, a New Bioinformatic Tool To Discover Antibiotic Resistance Genes in Bacterial Genomes

(2013) Sushim Kumar Gupta et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Identification of acquired antimicrobial resistance genes

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

BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons

(2011) Nabil-Fareed Alikhan et al.   BMC GENOMICS

Rapid detection of qnr and qepA plasmid-mediated quinolone resistance genes using real-time PCR

(2011) Thomas Guillard et al.   DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE

Safety Profile of the Fluoroquinolones

(2010) Hans H. Liu   DRUG SAFETY

Mutational analysis of quinolone resistance in the plasmid-encoded pentapeptide repeat proteins QnrA, QnrB and QnrS

(2009) J. M. Rodríguez-Martínez et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY