REAGENT or RESOURCE	SOURCE	IDENTIFIER
Biological samples
Stool samples of 100 COVID-19 patients	Clinical Medical Center “Kuskovo” of the Moscow State University of Medicine and Dentistry (MSUMD)	NA
Deposited data
Resistome raw sequence data	Current study	NCBI BioProject: PRJNA1005621
16S rRNA gene amplicon sequencing data	Current study	NCBI BioProject: PRJNA989180
MEGARes database	https://www.meglab.org/	version 2.0
SILVA database	https://www.arb-silva.de/	version 138
Software and algorithms
Trimmomatic	https://github.com/usadellab/Trimmomatic	version 0.39–2
bowtie2	https://github.com/BenLangmead/bowtie2	version 2.4.2
R	https://www.rproject.org/	version 4.2.2
Snakemake workflow for creating resistome profiles used in this study	Current study	https://github.com/bobeobibo/AR-panel-snake
samtools	http://www.htslib.org	version 1.6
DirichletMultinomial R package	https://github.com/mtmorgan/DirichletMultinomial	version 1.40.0
Custom R code and used in this study	Current study	https://figshare.com/articles/software/Targeted_AR_gene_panel_sequencing_data_analysis_R_markdown_/25250899
vegan R package	https://github.com/vegandevs/vegan	version 2.6–4
DESeq2 R package	https://bioconductor.org/packages/release/bioc/html/DESeq2.html	version 1.38.3