Sequencing-based methods and resources to study antimicrobial resistance

Bacterial Adaptation to Antibiotics through Regulatory RNAs

(2018) Brice Felden et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Indexed variation graphs for efficient and accurate resistome profiling

(2018) Will P M Rowe et al.   BIOINFORMATICS

ARGs-OAP v2.0 with an expanded SARG database and Hidden Markov Models for enhancement characterization and quantification of antibiotic resistance genes in environmental metagenomes

(2018) Xiaole Yin et al.   BIOINFORMATICS

Antibiotic Resistance

(2018) Idan Yelin et al.   CELL

Diagnosis of bloodstream infections from positive blood cultures and directly from blood samples: recent developments in molecular approaches

(2018) N. Peker et al.   CLINICAL MICROBIOLOGY AND INFECTION

Recent advances in tuberculosis diagnostics in resource-limited settings

(2018) Mitsuko Seki et al.   EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES

Evaluation of the Accelerate Pheno System: Results from Two Academic Medical Centers

(2018) Joseph D. Lutgring et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Surveillance for control of antimicrobial resistance

(2018) Evelina Tacconelli et al.   LANCET INFECTIOUS DISEASES

High-resolution 3D models of Caulobacter crescentus chromosome reveal genome structural variability and organization

(2018) Asli Yildirim et al.   NUCLEIC ACIDS RESEARCH

Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen

(2018) Robert D. Stewart et al.   Nature Communications

PlasmidSeeker: identification of known plasmids from bacterial whole genome sequencing reads

(2018) Märt Roosaare et al.   PeerJ

DeepARG: a deep learning approach for predicting antibiotic resistance genes from metagenomic data

(2018) Gustavo Arango-Argoty et al.   Microbiome

Abundance and diversity of the faecal resistome in slaughter pigs and broilers in nine European countries

(2018) Patrick Munk et al.   Nature Microbiology

Critical Assessment of Metagenome Interpretation Enters the Second Round

(2018) Andreas Bremges et al.   mSystems

Characterization of Wild and Captive Baboon Gut Microbiota and Their Antibiotic Resistomes

(2018) Pablo Tsukayama et al.   mSystems

Urinary symptoms are associated with certain urinary microbes in urogynecologic surgical patients

(2018) Cynthia S. Fok et al.   INTERNATIONAL UROGYNECOLOGY JOURNAL

Commentary on: Urinary symptoms are associated with certain urinary microbes in urogynecologic surgical patients

(2018) Alexandra Mowat   INTERNATIONAL UROGYNECOLOGY JOURNAL

Prediction of Susceptibility to First-Line Tuberculosis Drugs by DNA Sequencing

(2018)   NEW ENGLAND JOURNAL OF MEDICINE

Escherichia coli OxyS RNA triggers cephalothin resistance by modulating the expression of CRP-associated genes

(2018) Hyejin Cho et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Attributable deaths and disability-adjusted life-years caused by infections with antibiotic-resistant bacteria in the EU and the European Economic Area in 2015: a population-level modelling analysis

(2018) Alessandro Cassini et al.   LANCET INFECTIOUS DISEASES

Elucidating the survival and response of carbapenem resistant Klebsiella pneumoniae after exposure to imipenem at sub-lethal concentrations

(2018) Ye Mun Low et al.   Pathogens and Global Health

Prediction of the intestinal resistome by a three-dimensional structure-based method

(2018) Etienne Ruppé et al.   Nature Microbiology

Burden of antimicrobial resistance in an era of decreasing susceptibility

(2017) Glenn S. Tillotson et al.   Expert Review of Anti-Infective Therapy

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

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

Evaluation of the Accelerate Pheno System for Fast Identification and Antimicrobial Susceptibility Testing from Positive Blood Cultures in Bloodstream Infections Caused by Gram-Negative Pathogens

(2017) Matthias Marschal et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Beta-lactamase database (BLDB) – structure and function

(2017) Thierry Naas et al.   JOURNAL OF ENZYME INHIBITION AND MEDICINAL CHEMISTRY

Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation

(2017) John Beaulaurier et al.   NATURE BIOTECHNOLOGY

Shotgun metagenomics, from sampling to analysis

(2017) Christopher Quince et al.   NATURE BIOTECHNOLOGY

Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software

(2017) Alexander Sczyrba et al.   NATURE METHODS

Next-generation approaches to understand and combat the antibiotic resistome

(2017) Terence S. Crofts et al.   NATURE REVIEWS MICROBIOLOGY

Antibiotic susceptibility testing in less than 30 min using direct single-cell imaging

(2017) Özden Baltekin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Defined chromosome structure in the genome-reduced bacterium Mycoplasma pneumoniae

(2017) Marie Trussart et al.   Nature Communications

FARME DB: a functional antibiotic resistance element database

(2017) James C. Wallace et al.   Database-The Journal of Biological Databases and Curation

Towards long-read metagenomics: complete assembly of three novel genomes from bacteria dependent on a diazotrophic cyanobacterium in a freshwater lake co-culture

(2017) Connor B. Driscoll et al.   Standards in Genomic Sciences

Roles of Regulatory RNAs for Antibiotic Resistance in Bacteria and Their Potential Value as Novel Drug Targets

(2017) Petra Dersch et al.   Frontiers in Microbiology

Scaffolding bacterial genomes and probing host-virus interactions in gut microbiome by proximity ligation (chromosome capture) assay

(2017) Martial Marbouty et al.   Science Advances

Antimicrobial resistance surveillance in the genomic age

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

mcr-1in Multidrug-ResistantblaKPC-2-Producing Clinical Enterobacteriaceae Isolates in Singapore

(2016) Jocelyn Qi-Min Teo et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Plasmid with Colistin Resistance Genemcr-1in Extended-Spectrum-β-Lactamase-Producing Escherichia coli Strains Isolated from Pig Slurry in Estonia

(2016) Age Brauer et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Coexistence ofmcr-1andblaNDM-1in Escherichia coli from Venezuela

(2016) Jose F. Delgado-Blas et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Transcriptome Profiling of Antimicrobial Resistance in Pseudomonas aeruginosa

(2016) Ariane Khaledi et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

First Report of the Globally Disseminated IncX4 Plasmid Carrying themcr-1Gene in a Colistin-Resistant Escherichia coli Sequence Type 101 Isolate from a Human Infection in Brazil

(2016) Miriam R. Fernandes et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Rapid drug susceptibility test of Mycobacterium tuberculosis using microscopic time-lapse imaging in an agarose matrix

(2016) Jungil Choi et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Comparing culture and molecular methods for the identification of microorganisms involved in necrotizing soft tissue infections

(2016) Vibeke Børsholt Rudkjøbing et al.   BMC INFECTIOUS DISEASES

The rapid spread of carbapenem-resistant Enterobacteriaceae

(2016) Robert F. Potter et al.   DRUG RESISTANCE UPDATES

Colistin-resistant Escherichia coli clinical isolate harbouring the mcr-1 gene in Ecuador

(2016) D. ORTEGA-PAREDES et al.   EPIDEMIOLOGY AND INFECTION

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

Detection of the plasmid-mediated colistin-resistance genemcr-1in faecal metagenomes of Dutch travellers

(2016) Christian J. H. von Wintersdorff et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

A sampling and metagenomic sequencing-based methodology for monitoring antimicrobial resistance in swine herds

(2016) Patrick Munk et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Consolidating and Exploring Antibiotic Resistance Gene Data Resources

(2016) Basil Britto Xavier et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: a microbiological and molecular biological study

(2016) Yi-Yun Liu et al.   LANCET INFECTIOUS DISEASES

MBT-ASTRA: A suitable tool for fast antibiotic susceptibility testing?

(2016) Katrin Sparbier et al.   METHODS

Interconnected microbiomes and resistomes in low-income human habitats

(2016) Erica C. Pehrsson et al.   NATURE

MEGARes: an antimicrobial resistance database for high throughput sequencing

(2016) Steven M. Lakin et al.   NUCLEIC ACIDS RESEARCH

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

(2016) Baofeng Jia et al.   NUCLEIC ACIDS RESEARCH

Investigation of First Identifiedmcr-1Gene in an Isolate from a U.S. Patient — Pennsylvania, 2016

(2016) Kelly E. Kline et al.   MMWR-MORBIDITY AND MORTALITY WEEKLY REPORT

Developmental dynamics of the preterm infant gut microbiota and antibiotic resistome

(2016) Molly K. Gibson et al.   Nature Microbiology

SSTAR, a Stand-Alone Easy-To-Use Antimicrobial Resistance Gene Predictor

(2016) Tom J. B. de Man et al.   mSphere

Evaluation of an Automated System for Reading and Interpreting Disk Diffusion Antimicrobial Susceptibility Testing of Fastidious Bacteria

(2016) Evgeny A. Idelevich et al.   PLoS One

hybridSPAdes: an algorithm for hybrid assembly of short and long reads

(2015) Dmitry Antipov et al.   BIOINFORMATICS

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

The Tetracycline Destructases: A Novel Family of Tetracycline-Inactivating Enzymes

(2015) Kevin J. Forsberg et al.   CHEMISTRY & BIOLOGY

Rapid antimicrobial susceptibility testing of clinical isolates by digital time-lapse microscopy

(2015) M. Fredborg et al.   EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES

Association of overexpression of efflux pump genes with antibiotic resistance in Pseudomonas aeruginosa strains clinically isolated from urinary tract infection patients

(2015) Katsumi Shigemura et al.   JOURNAL OF ANTIBIOTICS

Resistance gene naming and numbering: is it a new gene or not?

(2015) Ruth M. Hall et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

u-CARE: user-friendly Comprehensive Antibiotic resistance Repository ofEscherichia coli

(2015) Saurav B Saha et al.   JOURNAL OF CLINICAL PATHOLOGY

Direct detection and drug-resistance profiling of bacteremias using inertial microfluidics

(2015) Han Wei Hou et al.   LAB ON A CHIP

Deep learning

(2015) Yann LeCun et al.   NATURE

Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis

(2015) Phelim Bradley et al.   Nature Communications

High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED

(2015) James Kaminski et al.   PLoS Computational Biology

Search Engine for Antimicrobial Resistance: A Cloud Compatible Pipeline and Web Interface for Rapidly Detecting Antimicrobial Resistance Genes Directly from Sequence Data

(2015) Will Rowe et al.   PLoS One

MUBII-TB-DB: a database of mutations associated with antibiotic resistance in Mycobacterium tuberculosis

(2014) Jean-Pierre Flandrois et al.   BMC BIOINFORMATICS

Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology

(2014) Molly K Gibson et al.   ISME Journal

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

A rapid antimicrobial susceptibility test based on single-cell morphological analysis

(2014) J. Choi et al.   Science Translational Medicine

CBMAR: a comprehensive β-lactamase molecular annotation resource

(2014) Abhishikha Srivastava et al.   Database-The Journal of Biological Databases and Curation

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

(2014) Michael Inouye et al.   Genome Medicine

Plasmid Flux in Escherichia coli ST131 Sublineages, Analyzed by Plasmid Constellation Network (PLACNET), a New Method for Plasmid Reconstruction from Whole Genome Sequences

(2014) Val F. Lanza et al.   PLoS Genetics

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

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

A multiplexed microfluidic platform for rapid antibiotic susceptibility testing

(2013) Ritika Mohan et al.   BIOSENSORS & BIOELECTRONICS

Intrinsic antibiotic resistance: Mechanisms, origins, challenges and solutions

(2013) Georgina Cox et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

Genome Sequence-Based Discriminator for Vancomycin-Intermediate Staphylococcus aureus

(2013) L. Rishishwar et al.   JOURNAL OF BACTERIOLOGY

Global spread of antibiotic resistance: the example of New Delhi metallo-β-lactamase (NDM)-mediated carbapenem resistance

(2013) Alan P. Johnson et al.   JOURNAL OF MEDICAL MICROBIOLOGY

MALDI-TOF MS: an upcoming tool for rapid detection of antibiotic resistance in microorganisms

(2013) Markus Kostrzewa et al.   Proteomics Clinical Applications

The true cost of antimicrobial resistance

(2013) R. Smith et al.   BMJ-British Medical Journal

Novel resistance functions uncovered using functional metagenomic investigations of resistance reservoirs

(2013) Erica C. Pehrsson et al.   Frontiers in Microbiology

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

SnapShot: Chromosome Conformation Capture

(2012) Ofir Hakim et al.   CELL

Rapid evolution and spread of carbapenemases among Enterobacteriaceae in Europe

(2012) R. Cantón et al.   CLINICAL MICROBIOLOGY AND INFECTION

Context matters — the complex interplay between resistome genotypes and resistance phenotypes

(2012) Gautam Dantas et al.   CURRENT OPINION IN MICROBIOLOGY

Underlying mechanisms of carbapenem resistance in extended-spectrum β-lactamase-producing Klebsiella pneumoniae and Escherichia coli isolates at a tertiary care centre in Lebanon: role of OXA-48 and NDM-1 carbapenemases

(2012) M. Baroud et al.   INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS

Identification of acquired antimicrobial resistance genes

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

Evidence of Uncultivated Bacteria in the Adult Female Bladder

(2012) A. J. Wolfe 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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Transforming clinical microbiology with bacterial genome sequencing

(2012) Xavier Didelot et al.   NATURE REVIEWS GENETICS

MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads

(2012) Toshiaki Namiki et al.   NUCLEIC ACIDS RESEARCH

Next-generation sequencing and large genome assemblies

(2012) Joseph Henson et al.   PHARMACOGENOMICS

The Shared Antibiotic Resistome of Soil Bacteria and Human Pathogens

(2012) K. J. Forsberg et al.   SCIENCE

Carbapenem-Resistant Enterobacteriaceae: Epidemiology and Prevention

(2011) N. Gupta et al.   CLINICAL INFECTIOUS DISEASES

Characterization of novel antibiotic resistance genes identified by functional metagenomics on soil samples

(2011) Gloria Torres-Cortés et al.   ENVIRONMENTAL MICROBIOLOGY

Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys

(2011) Jeffrey J Werner et al.   ISME Journal

How to apply de Bruijn graphs to genome assembly

(2011) Phillip E C Compeau et al.   NATURE BIOTECHNOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Studying bacterial transcriptomes using RNA-seq

(2010) Nicholas J Croucher et al.   CURRENT OPINION IN MICROBIOLOGY

Assembly algorithms for next-generation sequencing data

(2010) Jason R. Miller et al.   GENOMICS

Updated Functional Classification of  -Lactamases

(2009) K. Bush et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Ongoing Revolution in Bacteriology: Routine Identification of Bacteria by Matrix‐Assisted Laser Desorption Ionization Time‐of‐Flight Mass Spectrometry

(2009) Piseth Seng et al.   CLINICAL INFECTIOUS DISEASES

Antimicrobial Susceptibility Testing: A Review of General Principles and Contemporary Practices

(2009) James H. Jorgensen et al.   CLINICAL INFECTIOUS DISEASES

Species identification of clinical isolates of Bacteroides by matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry

(2009) E. Nagy et al.   CLINICAL MICROBIOLOGY AND INFECTION

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

Continuous base identification for single-molecule nanopore DNA sequencing

(2009) James Clarke et al.   Nature Nanotechnology

Tuberculosis Drug Resistance Mutation Database

(2009) Andreas Sandgren et al.   PLOS MEDICINE

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

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

The growing burden of antimicrobial resistance

(2008) P. M. Hawkey   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Detection of Resistance to Macrolides in Thermotolerant Campylobacter Species by Fluorescence In Situ Hybridization

(2008) M. Haas et al.   JOURNAL OF CLINICAL MICROBIOLOGY

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

ARDB--Antibiotic Resistance Genes Database

(2008) B. Liu et al.   NUCLEIC ACIDS RESEARCH

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE