Urban metagenomics uncover antibiotic resistance reservoirs in coastal beach and sewage waters

The widespread dissemination of integrons throughout bacterial communities in a riverine system

(2018) Gregory C. A. Amos et al.   ISME Journal

Surveying what’s flushed away

(2018) Gregorio Iraola et al.   NATURE REVIEWS MICROBIOLOGY

Detection of qnrVC6 , within a new genetic context, in an NDM-1-producing Citrobacter freundii clinical isolate from Uruguay

(2018) Inés Bado et al.   Journal of Global Antimicrobial Resistance

Novel Insights into Selection for Antibiotic Resistance in Complex Microbial Communities

(2018) Aimee K. Murray et al.   mBio

Aquatic urban ecology at the scale of a capital: community structure and interactions in street gutters

(2017) Vincent Hervé et al.   ISME Journal

Human embryos: Collect reliable data on embryo selection

(2017) Charis Thompson   NATURE

Sewers as potential reservoirs of antibiotic resistance

(2017) Olga Auguet et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Shotgun metagenomic sequencing reveals freshwater beach sands as reservoir of bacterial pathogens

(2017) Mahi M. Mohiuddin et al.   WATER RESEARCH

Antimicrobial Resistance and Cytotoxicity of Citrobacter spp. in Maanshan Anhui Province, China

(2017) Liyun Liu et al.   Frontiers in Microbiology

MetaMLST: multi-locus strain-level bacterial typing from metagenomic samples

(2016) Moreno Zolfo et al.   NUCLEIC ACIDS RESEARCH

Identification and analysis of integrons and cassette arrays in bacterial genomes

(2016) Jean Cury 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

Antibiotic resistance is the quintessential One Health issue

(2016) T. P. Robinson et al.   TRANSACTIONS OF THE ROYAL SOCIETY OF TROPICAL MEDICINE AND HYGIENE

The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report

(2016)   Microbiome

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

(2015) Dinghua Li et al.   BIOINFORMATICS

Sepsis caused by New Delhi metallo-β-lactamase (blaNDM-1) and qnrD-producing Morganella morganii, treated successfully with fosfomycin and meropenem: case report and literature review

(2015) Verónica Seija et al.   INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES

Beach sand and the potential for infectious disease transmission: observations and recommendations

(2015) Helena M. Solo-Gabriele et al.   JOURNAL OF THE MARINE BIOLOGICAL ASSOCIATION OF THE UNITED KINGDOM

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

Impact of in-sewer transformation on 43 pharmaceuticals in a pressurized sewer under anaerobic conditions

(2015) Aleksandra Jelic et al.   WATER RESEARCH

Sewage Reflects the Microbiomes of Human Populations

(2015) Ryan J. Newton et al.   mBio

Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics

(2015) Ebrahim Afshinnekoo et al.   Cell Systems

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Costs of antibiotic resistance - separating trait effects and selective effects

(2014) Alex R. Hall et al.   Evolutionary Applications

Global dissemination of a multidrug resistant Escherichia coli clone

(2014) N. K. Petty et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Functional metagenomic analysis reveals rivers are a reservoir for diverse antibiotic resistance genes

(2014) G.C.A. Amos et al.   VETERINARY MICROBIOLOGY

Polyclonal endemicity of Acinetobacter baumannii in ventilated patients in an intensive care unit in Uruguay

(2013) Julio Cesar Medina-Presentado et al.   INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

PATRIC, the bacterial bioinformatics database and analysis resource

(2013) Alice R. Wattam et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Limin Fu et al.   BIOINFORMATICS

Extended-spectrum  -lactamases and plasmid-mediated quinolone resistance in enterobacterial clinical isolates in the paediatric hospital of Uruguay

(2011) V. Garcia-Fulgueiras et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

VFDB 2012 update: toward the genetic diversity and molecular evolution of bacterial virulence factors

(2011) L. Chen et al.   NUCLEIC ACIDS RESEARCH

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Effect of Subinhibitory Concentrations of Antibiotics on Intrachromosomal Homologous Recombination in Escherichia coli

(2009) E. Lopez et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Multistate Outbreak ofPseudomonas fluorescensBloodstream Infection after Exposure to Contaminated Heparinized Saline Flush Prepared by a Compounding Pharmacy

(2008) Mark D. Gershman et al.   CLINICAL INFECTIOUS DISEASES

Antibiotics and antibiotic resistance in water environments

(2008) Fernando Baquero et al.   CURRENT OPINION IN BIOTECHNOLOGY