Gut microbiome dysbiosis in antibiotic-treated COVID-19 patients is associated with microbial translocation and bacteremia

Description: To investigate the relationship between gut microbiome dysbiosis and translocation of bacteria into the blood during SARS-CoV-2 infection in humans, researchers analyzed the blood culture and stool samples from positive COVID-19 patients who were seen at NYU Langone Health and Yale New Haven Hospital in 2020. 67 stool samples were obtained from 60 patients at NYU Langone Health and 63 samples were obtained from 36 patients at Yale New Haven Hospital for a total of 130 stool samples from 96 patients. Clinical characteristics of these patients are described in the supplementary materials for the associated publication. 26 patients had positive blood cultures indicating the presence of bloodstream infection. Supplementary Table 3 includes shotgun metagenomic reads from stool samples mapped to species identified in clinical blood cultures.
Timeframe: 2020
Geographic Coverage: Connecticut - New Haven

New York (State) - New York City

Subject of Study

Subject Domain

Genomics

Infectious Disease

Risk Factors

Population Age

Adult (19 years - 64 years)

Senior (65 years - 79 years)

Aged (80 years and over)

Keywords

Access

Restrictions: Free to All
Instructions: Bacterial 16S rRNA sequencing data extracted from human stool samples are freely available from the Sequence Read Archive (SRA) through BioProject.; Access via BioProject
Raw sequence reads
Accession #: PRJNA746322

Associated Publications

Bernard-Raichon L, Venzon M, Klein J, Axelrad JE, Zhang C, Sullivan AP, Hussey GA, Casanovas-Massana A, Noval MG, Valero-Jimenez AM, Gago J, Putzel G, Pironti A, Wilder E; Yale IMPACT Research Team, Thorpe LE, Littman DR, Dittmann M, Stapleford KA, Shopsin B, Torres VJ, Ko AI, Iwasaki A, Cadwell K, Schluter J. Gut microbiome dysbiosis in antibiotic-treated COVID-19 patients is associated with microbial translocation and bacteremia. Nat Commun. 2022 Nov 1;13(1):5926.

Data Type

Genomic

Equipment Used

Agilent TapeStation System

Illumina MiSeq System

Illumina NovaSeq 6000

LightCycler 480 Instrument II

MP Biomedicals FastPrep-24TM

QIAGEN QIAcube HT

Software Used

Bowtie2 v2.4.5

DADA2 v1.16

Kraken 2

lmerTest v3.1-3

MetaPhlAn2 v3

PyMC3 v3.11

QIIME v1.9.1

scikit-learn v1.0.2

Study Type

Observational

Grant Support: P30 CA016087/NCI NIH

R01 AI121244/NIAID NIH

R01 HL123340/NHLBI NIH

R01 DK093668/NIDDK NIH

R01 AI130945/NIAID NIH

R01 AI140754/NIAID NIH

Jan Vilcek/David Goldfarb Fellowship/NYU Langone Health

Mathers Foundation/Mathers Foundation

T32 AI100853/NIAID NIH

HHMI Faculty Scholars/Howard Hughes Medical Institute

R01 DK124336/NIDDK NIH

R01 AI143639/NIAID NIH

R21 AI139374/NIAID NIH

Crohn’s & Colitis Foundation/Crohn’s & Colitis Foundation

Kenneth Rainin Foundation/Kenneth Rainin Foundation

Judith & Stewart Colton Center for Autoimmunity/NYU Langone Health

Antimicrobial-Resistant Pathogens Program/NYU Langone Health

S10 OD021747/OD NIH

DP2 AI164318/NIAID NIH

R01 CA269617/NCI NIH

OT2 HL161847/NHLBI NIH

19-A0-00-1003686/American Heart Association

Beatrice Kleinberg Neuwirth Fund/Beatrice Kleinberg Neuwirth Fund

Yale COVID-19 Research Resource Fund/Yale University

Bristol Meyers Squibb Foundation/Bristol Meyers Squibb Foundation
Other Resources: SILVA 138
Ribosomal RNA database

MiniKraken 2
Taxonomic classification system

NCBI RefSeq
Genome assemblies
Related Datasets: SARS-CoV-2 infection and gut microbiome dysbiosis in mice