Exploration of antibiotic resistance risks in a veterinary teaching hospital with Oxford Nanopore long read sequencing

Variation in the microbiome of the urogenital tract of Chlamydia-free female koalas (Phascolarctos cinereus) with and without ‘wet bottom’

(2018) Alistair R. Legione et al.   PLoS One

Genomic Analysis of Hospital Plumbing Reveals Diverse Reservoir of Bacterial Plasmids Conferring Carbapenem Resistance

(2018) Rebecca A. Weingarten et al.   mBio

A world of opportunities with nanopore sequencing

(2017) Richard M Leggett et al.   JOURNAL OF EXPERIMENTAL BOTANY

Comparative Evaluation of Four Bacteria-Specific Primer Pairs for 16S rRNA Gene Surveys

(2017) Sofie Thijs et al.   Frontiers in Microbiology

Metagenomic Evidence of the Prevalence and Distribution Patterns of Antimicrobial Resistance Genes in Dairy Agroecosystems

(2016) Dipti W. Pitta et al.   Foodborne Pathogens and Disease

Molecular Methods for Assessment of Antibiotic Resistance in Agricultural Ecosystems: Prospects and Challenges

(2016) Elizabeth Luby et al.   JOURNAL OF ENVIRONMENTAL QUALITY

Analysis of the mouse gut microbiome using full-length 16S rRNA amplicon sequencing

(2016) Jongoh Shin et al.   Scientific Reports

INC-Seq: accurate single molecule reads using nanopore sequencing

(2016) Chenhao Li et al.   GigaScience

Species-level resolution of 16S rRNA gene amplicons sequenced through the MinION™ portable nanopore sequencer

(2016) Alfonso Benítez-Páez et al.   GigaScience

A reference gene catalogue of the pig gut microbiome

(2016) Liang Xiao et al.   Nature Microbiology

Characterization of the resistome in manure, soil and wastewater from dairy and beef production systems

(2016) Noelle R. Noyes et al.   Scientific Reports

Error filtering, pair assembly and error correction for next-generation sequencing reads

(2015) Robert C. Edgar 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

Nanopores: a sequencer in your backpack

(2015) Vivien Marx   NATURE METHODS

The human gut resistome

(2015) W. van Schaik   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Resistance integrons: class 1, 2 and 3 integrons

(2015) Yang Deng et al.   Annals of Clinical Microbiology and Antimicrobials

Estimating Bacterial Diversity for Ecological Studies: Methods, Metrics, and Assumptions

(2015) Julia Birtel et al.   PLoS One

Metagenomic Analysis of Antibiotic Resistance Genes in Dairy Cow Feces following Therapeutic Administration of Third Generation Cephalosporin

(2015) Lindsey Chambers et al.   PLoS One

Poretools: a toolkit for analyzing nanopore sequence data

(2014) N. J. Loman et al.   BIOINFORMATICS

OXA  -Lactamases

(2014) B. A. Evans et al.   CLINICAL MICROBIOLOGY REVIEWS

High Throughput Profiling of Antibiotic Resistance Genes in Urban Park Soils with Reclaimed Water Irrigation

(2014) Feng-Hua Wang et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

What is a resistance gene? Ranking risk in resistomes

(2014) José L. Martínez et al.   NATURE REVIEWS MICROBIOLOGY

Bloom of resident antibiotic-resistant bacteria in soil following manure fertilization

(2014) Nikolina Udikovic-Kolic et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Diverse Antibiotic Resistance Genes in Dairy Cow Manure

(2014) F. Wichmann et al.   mBio

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Diverse and abundant antibiotic resistance genes in Chinese swine farms

(2013) Yong-Guan Zhu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolutionary consequences of antibiotic use for the resistome, mobilome and microbial pangenome

(2013) Michael R. Gillings   Frontiers in Microbiology

Contribution of OqxAB efflux pumps to quinolone resistance in extended-spectrum- -lactamase-producing Klebsiella pneumoniae

(2012) J. M. Rodriguez-Martinez et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Prevalence of the oqxAB gene complex in Klebsiella pneumoniae and Escherichia coli clinical isolates

(2012) Jinyi Yuan et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Identification of acquired antimicrobial resistance genes

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

Intrinsic and acquired resistance mechanisms in enterococcus

(2012) Brian L. Hollenbeck et al.   Virulence

PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers

(2011) William A. Walters et al.   BIOINFORMATICS

Novel gene cassettes and integrons in antibiotic-resistant bacteria isolated from urban wastewaters

(2011) Alexandra Moura et al.   RESEARCH IN MICROBIOLOGY

CD-HIT Suite: a web server for clustering and comparing biological sequences

(2010) Ying Huang et al.   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Genetic diversity of genes encoding OKP and LEN β-lactamases produced by clinical Klebsiella pneumoniae strains in Portugal

(2009) Nuno Mendonça et al.   DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE

Microbial community profiling for human microbiome projects: Tools, techniques, and challenges

(2009) M. Hamady et al.   GENOME RESEARCH

Characteristics of biosecurity and infection control programs at veterinary teaching hospitals

(2008) Katharine M. Benedict et al.   JAVMA-JOURNAL OF THE AMERICAN VETERINARY MEDICAL ASSOCIATION

Analyzing real-time PCR data by the comparative CT method

(2008) Thomas D Schmittgen et al.   Nature Protocols