A metagenomic-based method to study hospital air dust resistome

Metagenomic insights into the profile of antibiotic resistomes in a large drinking water reservoir

(2020) Chenyuan Dang et al.   ENVIRONMENT INTERNATIONAL

High contiguity genome sequence of a multidrug-resistant hospital isolate of Enterobacter hormaechei

(2019) Leigh G. Monahan et al.   Gut Pathogens

Nanopore metagenomics enables rapid clinical diagnosis of bacterial lower respiratory infection

(2019) Themoula Charalampous et al.   NATURE BIOTECHNOLOGY

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

Airborne microbial communities in the atmospheric environment of urban hospitals in China

(2018) Xin-Lei Gao et al.   JOURNAL OF HAZARDOUS MATERIALS

PlasFlow: predicting plasmid sequences in metagenomic data using genome signatures

(2018) Pawel S Krawczyk et al.   NUCLEIC ACIDS RESEARCH

Airborne transmission of invasive fusariosis in patients with hematologic malignancies

(2018) Maria Luiza Moretti et al.   PLoS One

Seasonal Disparities in Airborne Bacteria and Associated Antibiotic Resistance Genes in PM2.5 between Urban and Rural Sites

(2018) Jiawen Xie et al.   Environmental Science & Technology Letters

Real-time DNA barcoding in a rainforest using nanopore sequencing: opportunities for rapid biodiversity assessments and local capacity building

(2018) Aaron Pomerantz et al.   GigaScience

Antibiotic-mediated changes in the fecal microbiome of broiler chickens define the incidence of antibiotic resistance genes

(2018) Wenguang Xiong et al.   Microbiome

Global Survey of Antibiotic Resistance Genes in Air

(2018) Jing Li et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Species-level functional profiling of metagenomes and metatranscriptomes

(2018) Eric A. Franzosa et al.   NATURE METHODS

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

Antibiotic resistant airborne bacteria and their multidrug resistance pattern at University teaching referral Hospital in South Ethiopia

(2017) Fithamlak Bisetegen Solomon et al.   Annals of Clinical Microbiology and Antimicrobials

Hospital air: A potential route for transmission of infections caused by β-lactam–resistant bacteria

(2016) Seyed Hamed Mirhoseini et al.   AMERICAN JOURNAL OF INFECTION CONTROL

BLAST-based structural annotation of protein residues using Protein Data Bank

(2016) Harinder Singh et al.   Biology Direct

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Bandage: interactive visualization ofde novogenome assemblies: Fig. 1.

(2015) Ryan R. Wick et al.   BIOINFORMATICS

Metagenomic Assembly Reveals Hosts of Antibiotic Resistance Genes and the Shared Resistome in Pig, Chicken, and Human Feces

(2015) Liping Ma et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Antibiotic Resistome and Its Association with Bacterial Communities during Sewage Sludge Composting

(2015) Jian-Qiang Su et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Metagenomic and network analysis reveal wide distribution and co-occurrence of environmental antibiotic resistance genes

(2015) Bing Li et al.   ISME Journal

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

Aerosolized Antibiotics

(2015) M. I. Restrepo et al.   Respiratory Care

Hospital-associated microbiota and implications for nosocomial infections

(2015) Simon Lax et al.   TRENDS IN MOLECULAR MEDICINE

Occurrence of antibiotics and antibiotic resistance genes in hospital and urban wastewaters and their impact on the receiving river

(2015) Sara Rodriguez-Mozaz et al.   WATER RESEARCH

Bacterial phylogeny structures soil resistomes across habitats

(2014) Kevin J. Forsberg et al.   NATURE

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Longitudinal analysis of microbial interaction between humans and the indoor environment

(2014) S. Lax et al.   SCIENCE

Airborne and Surface-Bound Microbial Contamination in Two Intensive Care Units of a Medical Center in Central Taiwan

(2013) Ping-Yun Huang et al.   Aerosol and Air Quality Research

A novel metatranscriptomic approach to identify gene expression dynamics during extracellular electron transfer

(2013) Shun’ichi Ishii et al.   Nature Communications

New antibiotic agents in the pipeline and how they can help overcome microbial resistance

(2013) Ian M. Gould et al.   Virulence

SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data

(2012) Evguenia Kopylova et al.   BIOINFORMATICS

Identification of acquired antimicrobial resistance genes

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

Nursing and physician attire as possible source of nosocomial infections

(2011) Yonit Wiener-Well et al.   AMERICAN JOURNAL OF INFECTION CONTROL

Bayesian community-wide culture-independent microbial source tracking

(2011) Dan Knights et al.   NATURE METHODS

Quantitative multiplex real-time PCR for detecting class 1, 2 and 3 integrons

(2010) O. Barraud et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Ab initio gene identification in metagenomic sequences

(2010) Wenhan Zhu et al.   NUCLEIC ACIDS RESEARCH

Bacterial counts from hospital doctors' ties are higher than those from shirts

(2009) Pedro-Jose Lopez et al.   AMERICAN JOURNAL OF INFECTION CONTROL

Review of mobile communication devices as potential reservoirs of nosocomial pathogens

(2009) R.R.W. Brady et al.   JOURNAL OF HOSPITAL INFECTION

The potential role of mobile phones in the spread of bacterial infections

(2009) Kabir O. Akinyemi et al.   Journal of Infection in Developing Countries

Are we aware how contaminated our mobile phones with nosocomial pathogens?

(2009) Fatma Ulger et al.   Annals of Clinical Microbiology and Antimicrobials

Air filtration systems and restrictive access conditions improve indoor air quality in clinical units: Penicillium as a general indicator of hospital indoor fungal levels

(2008) Ricardo Araujo et al.   AMERICAN JOURNAL OF INFECTION CONTROL

Bacterial contamination of health care workers' white coats

(2008) Amy M. Treakle et al.   AMERICAN JOURNAL OF INFECTION CONTROL

Cross-Kingdom Amplification Using Bacteria-Specific Primers: Complications for Studies of Coral Microbial Ecology

(2008) J. P. Galkiewicz et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY