Understanding and overcoming the pitfalls and biases of next-generation sequencing (NGS) methods for use in the routine clinical microbiological diagnostic …

SA Boers, R Jansen, JP Hays - European Journal of Clinical Microbiology …, 2019 - Springer
Recent advancements in next-generation sequencing (NGS) have provided the foundation
for modern studies into the composition of microbial communities. The use of these NGS …

Rapid methods for antimicrobial resistance diagnostics

GD Kaprou, I Bergšpica, EA Alexa, A Alvarez-Ordóñez… - Antibiotics, 2021 - mdpi.com
Antimicrobial resistance (AMR) is one of the most challenging threats in public health; thus,
there is a growing demand for methods and technologies that enable rapid antimicrobial …

Extensive unexplored human microbiome diversity revealed by over 150,000 genomes from metagenomes spanning age, geography, and lifestyle

E Pasolli, F Asnicar, S Manara, M Zolfo, N Karcher… - Cell, 2019 - cell.com
The body-wide human microbiome plays a role in health, but its full diversity remains
uncharacterized, particularly outside of the gut and in international populations. We …

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 …

Rapid MinION profiling of preterm microbiota and antimicrobial-resistant pathogens

RM Leggett, C Alcon-Giner, D Heavens, S Caim… - Nature …, 2020 - nature.com
The MinION sequencing platform offers near real-time analysis of DNA sequence; this
makes the tool attractive for deployment in fieldwork or clinical settings. We used the MinION …

Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples

G Lear, I Dickie, J Banks, S Boyer, HL Buckley… - New Zealand Journal of …, 2018 - JSTOR
Advances in the sequencing of DNA extracted from media such as soil and water offer huge
opportunities for biodiversity monitoring and assessment, particularly where the collection or …

Shotgun metagenome data of a defined mock community using Oxford Nanopore, PacBio and Illumina technologies

V Sevim, J Lee, R Egan, A Clum, H Hundley, J Lee… - Scientific data, 2019 - nature.com
Metagenomic sequence data from defined mock communities is crucial for the assessment
of sequencing platform performance and downstream analyses, including assembly, binning …

Portable nanopore-sequencing technology: Trends in development and applications

P Chen, Z Sun, J Wang, X Liu, Y Bai, J Chen… - Frontiers in …, 2023 - frontiersin.org
Sequencing technology is the most commonly used technology in molecular biology
research and an essential pillar for the development and applications of molecular biology …

Diagnostics and analysis of SARS-CoV-2: current status, recent advances, challenges and perspectives

T Dong, M Wang, J Liu, P Ma, S Pang, W Liu… - Chemical Science, 2023 - pubs.rsc.org
The disastrous spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
has induced severe public healthcare issues and weakened the global economy …

Testing the advantages and disadvantages of short-and long-read eukaryotic metagenomics using simulated reads

WS Pearman, NE Freed, OK Silander - BMC bioinformatics, 2020 - Springer
Background The first step in understanding ecological community diversity and dynamics is
quantifying community membership. An increasingly common method for doing so is …