Antibiotic perturbations to the gut microbiome

SRS Fishbein, B Mahmud, G Dantas - Nature Reviews Microbiology, 2023 - nature.com
Antibiotic-mediated perturbation of the gut microbiome is associated with numerous
infectious and autoimmune diseases of the gastrointestinal tract. Yet, as the gut microbiome …

Antimicrobial resistance monitoring of water environments: a framework for standardized methods and quality control

K Liguori, I Keenum, BC Davis, J Calarco… - … science & technology, 2022 - ACS Publications
Antimicrobial resistance (AMR) is a grand societal challenge with important dimensions in
the water environment that contribute to its evolution and spread. Environmental monitoring …

AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence

M Feldgarden, V Brover, N Gonzalez-Escalona… - Scientific reports, 2021 - nature.com
Antimicrobial resistance (AMR) is a significant public health threat. With the rise of affordable
whole genome sequencing, in silico approaches to assessing AMR gene content can be …

Metagenomics-enabled microbial surveillance

KKK Ko, KR Chng, N Nagarajan - Nature Microbiology, 2022 - nature.com
Lessons learnt from the COVID-19 pandemic include increased awareness of the potential
for zoonoses and emerging infectious diseases that can adversely affect human health …

[HTML][HTML] Distribution of antibiotic resistance genes in the environment

M Zhuang, Y Achmon, Y Cao, X Liang, L Chen… - Environmental …, 2021 - Elsevier
The prevalence of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs)
in the microbiome is a major public health concern globally. Many habitats in the …

Accelerating antibiotic discovery through artificial intelligence

MCR Melo, JRMA Maasch… - Communications …, 2021 - nature.com
By targeting invasive organisms, antibiotics insert themselves into the ancient struggle of the
host-pathogen evolutionary arms race. As pathogens evolve tactics for evading antibiotics …

A catalogue of 1,167 genomes from the human gut archaeome

CM Chibani, A Mahnert, G Borrel, A Almeida… - Nature …, 2022 - nature.com
The human gut microbiome plays an important role in health, but its archaeal diversity
remains largely unexplored. In the present study, we report the analysis of 1,167 …

Genomics and pathotypes of the many faces of Escherichia coli

J Geurtsen, M de Been, E Weerdenburg… - FEMS microbiology …, 2022 - academic.oup.com
Escherichia coli is the most researched microbial organism in the world. Its varied impact on
human health, consisting of commensalism, gastrointestinal disease, or extraintestinal …

MEGARes and AMR++, v3. 0: an updated comprehensive database of antimicrobial resistance determinants and an improved software pipeline for classification using …

N Bonin, E Doster, H Worley, LJ Pinnell… - Nucleic acids …, 2023 - academic.oup.com
Antimicrobial resistance (AMR) is considered a critical threat to public health, and
genomic/metagenomic investigations featuring high-throughput analysis of sequence data …

Mobile oxazolidinone resistance genes in Gram-positive and Gram-negative bacteria

S Schwarz, W Zhang, XD Du, H Krüger… - Clinical microbiology …, 2021 - Am Soc Microbiol
Seven mobile oxazolidinone resistance genes, including cfr, cfr (B), cfr (C), cfr (D), cfr (E),
optrA, and poxtA, have been identified to date. The cfr genes code for 23S rRNA methylases …