Sequencing-based methods and resources to study antimicrobial resistance

M Boolchandani, AW D'Souza, G Dantas - Nature Reviews Genetics, 2019 - nature.com
Antimicrobial resistance extracts high morbidity, mortality and economic costs yearly by
rendering bacteria immune to antibiotics. Identifying and understanding antimicrobial …

Using genomics to track global antimicrobial resistance

RS Hendriksen, V Bortolaia, H Tate, GH Tyson… - Frontiers in public …, 2019 - frontiersin.org
The recent advancements in rapid and affordable DNA sequencing technologies have
revolutionized diagnostic microbiology and microbial surveillance. The availability of …

CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database

BP Alcock, AR Raphenya, TTY Lau… - Nucleic acids …, 2020 - academic.oup.com
Abstract The Comprehensive Antibiotic Resistance Database (CARD; https://card. mcmaster.
ca) is a curated resource providing reference DNA and protein sequences, detection models …

DeepARG: a deep learning approach for predicting antibiotic resistance genes from metagenomic data

G Arango-Argoty, E Garner, A Pruden, LS Heath… - Microbiome, 2018 - Springer
Background Growing concerns about increasing rates of antibiotic resistance call for
expanded and comprehensive global monitoring. Advancing methods for monitoring of …

[HTML][HTML] Antibiotic resistance: Global health crisis and metagenomics

S Yadav, A Kapley - Biotechnology Reports, 2021 - Elsevier
Antibiotic resistance is a global problem which affects human health. The imprudent use of
antibiotics (medicine, agriculture, aquaculture, and food industry) has resulted in the broader …

Integrating whole-genome sequencing data into quantitative risk assessment of foodborne antimicrobial resistance: a review of opportunities and challenges

L Collineau, P Boerlin, CA Carson… - Frontiers in …, 2019 - frontiersin.org
Whole-genome sequencing (WGS) will soon replace traditional phenotypic methods for
routine testing of foodborne antimicrobial resistance (AMR). WGS is expected to improve …

[HTML][HTML] Platforms for elucidating antibiotic resistance in single genomes and complex metagenomes

CL Gupta, RK Tiwari, E Cytryn - Environment international, 2020 - Elsevier
Antibiotic or antimicrobial resistance (AR) facilitated by the vertical and/or horizontal transfer
of antibiotic resistance genes (ARGs), is a serious global health challenge. While …

Microbial dark matter: from discovery to applications

Y Zha, H Chong, P Yang, K Ning - Genomics, Proteomics and …, 2022 - academic.oup.com
With the rapid increase of the microbiome samples and sequencing data, more and more
knowledge about microbial communities has been gained. However, there is still much more …

Rapid inference of antibiotic resistance and susceptibility by genomic neighbour ty**

K Břinda, A Callendrello, KC Ma, DR MacFadden… - Nature …, 2020 - nature.com
Surveillance of drug-resistant bacteria is essential for healthcare providers to deliver
effective empirical antibiotic therapy. However, traditional molecular epidemiology does not …

Application of high-throughput sequencing technologies and analytical tools for pathogen detection in urban water systems: Progress and future perspectives

Y Zhao, F Huang, W Wang, R Gao, L Fan… - Science of the Total …, 2023 - Elsevier
The ubiquitous presence of pathogenic microorganisms, such as viruses, bacteria, fungi,
and protozoa, in urban water systems poses a significant risk to public health. The …