[HTML][HTML] Nanopore sequencing technology, bioinformatics and applications

Y Wang, Y Zhao, A Bollas, Y Wang, KF Au - Nature biotechnology, 2021 - nature.com
Rapid advances in nanopore technologies for sequencing single long DNA and RNA
molecules have led to substantial improvements in accuracy, read length and throughput …

Ecology and evolution of antimicrobial resistance in bacterial communities

MJ Bottery, JW Pitchford, VP Friman - The ISME Journal, 2021 - academic.oup.com
Accumulating evidence suggests that the response of bacteria to antibiotics is significantly
affected by the presence of other interacting microbes. These interactions are not typically …

Rapid pathogen detection by metagenomic next-generation sequencing of infected body fluids

W Gu, X Deng, M Lee, YD Sucu, S Arevalo, D Stryke… - Nature medicine, 2021 - nature.com
We developed a metagenomic next-generation sequencing (mNGS) test using cell-free DNA
from body fluids to identify pathogens. The performance of mNGS testing of 182 body fluids …

Nanopore metagenomics enables rapid clinical diagnosis of bacterial lower respiratory infection

T Charalampous, GL Kay, H Richardson, A Aydin… - Nature …, 2019 - nature.com
The gold standard for clinical diagnosis of bacterial lower respiratory infections (LRIs) is
culture, which has poor sensitivity and is too slow to guide early, targeted antimicrobial …

Towards a genomics-informed, real-time, global pathogen surveillance system

JL Gardy, NJ Loman - Nature Reviews Genetics, 2018 - nature.com
Abstract The recent Ebola and Zika epidemics demonstrate the need for the continuous
surveillance, rapid diagnosis and real-time tracking of emerging infectious diseases. Fast …

Long-read metagenomic sequencing reveals shifts in associations of antibiotic resistance genes with mobile genetic elements from sewage to activated sludge

D Dai, C Brown, H Bürgmann, DGJ Larsson, I Nambi… - Microbiome, 2022 - Springer
Background There is concern that the microbially rich activated sludge environment of
wastewater treatment plants (WWTPs) may contribute to the dissemination of antibiotic …

PLSDB: a resource of complete bacterial plasmids

V Galata, T Fehlmann, C Backes… - Nucleic acids …, 2019 - academic.oup.com
The study of bacterial isolates or communities requires the analysis of the therein included
plasmids in order to provide an extensive characterization of the organisms. Plasmids …

[HTML][HTML] Application of next generation sequencing in laboratory medicine

Y Zhong, F Xu, J Wu, J Schubert… - Annals of laboratory …, 2021 - synapse.koreamed.org
The rapid development of next-generation sequencing (NGS) technology, including
advances in sequencing chemistry, sequencing technologies, bioinformatics, and data …

Toward the early detection of cancer by decoding the epigenetic and environmental fingerprints of cell-free DNA

Y Van Der Pol, F Mouliere - Cancer cell, 2019 - cell.com
Widespread adaptation of liquid biopsy for the early detection of cancer has yet to reach
clinical utility. Circulating tumor DNA is commonly detected though the presence of genetic …

Genome-based prediction of bacterial antibiotic resistance

M Su, SW Satola, TD Read - Journal of clinical microbiology, 2019 - Am Soc Microbiol
Clinical microbiology has long relied on growing bacteria in culture to determine
antimicrobial susceptibility profiles, but the use of whole-genome sequencing for antibiotic …