Evidence map›Paper›PMID 41840216›Full record

ArticleNature microbiology2026

Empiric azithromycin alters the upper respiratory microbiome and resistome without anti-inflammatory benefit in COVID-19.

Abigail Glascock, Cole Maguire, Hoang Van Phan, Emily C Lydon, Joanna Schaenman, Carolyn S Calfee, Esther Melamed, John Greenland, David B Corry, Farrah Kheradmand and 47 more

Abstract readMulticenter Study
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature microbiology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

57 authors.

Abigail Glascock *Chan Zuckerberg Biohub San Francisco, San Francisco, CA, USA.
Cole Maguire *University of Texas at Austin, Austin, TX, USA.ORCID http://orcid.org/0000-0001-8986-9762
Hoang Van PhanUniversity of California San Francisco, San Francisco, CA, USA.
Emily C LydonUniversity of California San Francisco, San Francisco, CA, USA.
Joanna SchaenmanUniversity of California Los Angeles, Los Angeles, CA, USA.
Carolyn S CalfeeUniversity of California San Francisco, San Francisco, CA, USA.
Esther MelamedUniversity of Texas at Austin, Austin, TX, USA.
John GreenlandUniversity of California San Francisco, San Francisco, CA, USA.ORCID http://orcid.org/0000-0003-1422-8367
David B CorryBaylor College of Medicine and the Center for Translational Research on Inflammatory Diseases, Houston, TX, USA.ORCID http://orcid.org/0000-0001-9729-1016
Farrah KheradmandBaylor College of Medicine and the Center for Translational Research on Inflammatory Diseases, Houston, TX, USA.ORCID http://orcid.org/0000-0001-5343-103X
Lindsey R BadenBrigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0009-0004-1752-1926
Rafick SekalyCase Western Reserve University and University Hospitals of Cleveland, Cleveland, OH, USA.
Grace A McComseyCase Western Reserve University and University Hospitals of Cleveland, Cleveland, OH, USA.ORCID http://orcid.org/0000-0003-2690-8888
Elias K HaddadDrexel University, Tower Health Hospital, Philadelphia, PA, USA.ORCID http://orcid.org/0000-0001-6924-4300
Charles B CairnsDrexel University, Tower Health Hospital, Philadelphia, PA, USA.ORCID http://orcid.org/0000-0003-2291-5415
Linda N GengStanford University School of Medicine, Palo Alto, CA, USA.ORCID http://orcid.org/0000-0002-9891-5705
Bali PulendranStanford University School of Medicine, Palo Alto, CA, USA.ORCID http://orcid.org/0000-0001-6517-4333
Ana Fernandez-SesmaDepartment of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.ORCID http://orcid.org/0000-0002-3405-6702
Viviana SimonDepartment of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.ORCID http://orcid.org/0000-0002-6416-5096
Jordan P MetcalfOklahoma University Health Sciences Center, Oklahoma City, OK, USA.ORCID http://orcid.org/0000-0003-4359-5270
Nelson I Agudelo HiguitaOklahoma University Health Sciences Center, Oklahoma City, OK, USA.ORCID http://orcid.org/0000-0002-9363-6280
William B MesserOregon Health and Science University, Portland, OR, USA.ORCID http://orcid.org/0000-0002-4381-6347
Mark M DavisStanford University School of Medicine, Palo Alto, CA, USA.ORCID http://orcid.org/0000-0001-6868-657X
Kari C NadeauStanford University School of Medicine, Palo Alto, CA, USA.ORCID http://orcid.org/0000-0002-2146-2955
Monica KraftUniversity of Arizona, Tucson, AZ, USA.
Christian BimeUniversity of Arizona, Tucson, AZ, USA.
David J ErleUniversity of California San Francisco, San Francisco, CA, USA.ORCID http://orcid.org/0000-0002-2171-0648
Mark A AtkinsonUniversity of Florida, Gainesville, FL, USA.ORCID http://orcid.org/0000-0001-8489-4782
Scott C BrakenridgeUniversity of Florida, Gainesville, FL, USA.
Lauren I R EhrlichUniversity of Texas at Austin, Austin, TX, USA.ORCID http://orcid.org/0000-0002-1697-1755
Ruth R MontgomeryYale School of Medicine, New Haven, CT, USA.ORCID http://orcid.org/0000-0002-8661-4454
Albert C ShawYale School of Medicine, New Haven, CT, USA.
Catherine L HoughOregon Health and Science University, Portland, OR, USA.
David A HaflerYale School of Medicine, New Haven, CT, USA.ORCID http://orcid.org/0000-0003-4664-535X
Alison D AugustineNational Institute of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD, USA.
Patrice M BeckerNational Institute of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD, USA.ORCID http://orcid.org/0000-0002-1170-8587
Bjoern PetersLa Jolla Institute for Immunology, La Jolla, CA, USA.ORCID http://orcid.org/0000-0002-8457-6693
Al OzonoffBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0003-4233-5899
Annmarie HochClinical and Data Coordinating Center (CDCC) Precision Vaccines Program, Boston Children's Hospital, Boston, MA, USA.ORCID http://orcid.org/0000-0003-0836-2164
Seunghee Kim-SchulzeIcahn School of Medicine at Mount Sinai, New York, NY, USA.ORCID http://orcid.org/0000-0003-0192-4400
Florian KrammerDepartment of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.ORCID http://orcid.org/0000-0003-4121-776X
Steven BosingerEmory School of Medicine, Atlanta, GA, USA.ORCID http://orcid.org/0000-0002-2116-5061
Walter EckalbarUniversity of California San Francisco, San Francisco, CA, USA.
Matthew C AltmanBenaroya Research Institute, University of Washington, Seattle, WA, USA.ORCID http://orcid.org/0000-0002-1784-8505
Michael WilsonUniversity of California San Francisco, San Francisco, CA, USA.ORCID http://orcid.org/0000-0002-8705-5084
Leying GuanYale School of Public Health, New Haven, CT, USA.ORCID http://orcid.org/0000-0003-0609-1073
Holden MaeckerStanford University School of Medicine, Palo Alto, CA, USA.ORCID http://orcid.org/0000-0003-0795-9946
Hanno SteenPrecision Vaccines Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0000-0003-0179-6648
IMPACC Network
Joann Diray-ArceBoston Children's Hospital and Harvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0000-0003-2183-4269
Nadine RouphaelEmory School of Medicine, Atlanta, GA, USA.
Steven H KleinsteinYale School of Public Health, New Haven, CT, USA.ORCID http://orcid.org/0000-0003-4957-1544
Naresh Doni JayaveluBenaroya Research Institute, University of Washington, Seattle, WA, USA.ORCID http://orcid.org/0000-0001-5613-0830
Elaine F ReedUniversity of California Los Angeles, Los Angeles, CA, USA.
Ofer LevyBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0002-5859-1945
Victoria T ChuUniversity of California San Francisco, San Francisco, CA, USA.ORCID http://orcid.org/0000-0002-7480-965X
Charles R LangelierChan Zuckerberg Biohub San Francisco, San Francisco, CA, USA. chaz.langelier@ucsf.edu.ORCID http://orcid.org/0000-0002-6708-4646

Funding

Clinical and Translational Science Collaborative of Northern Ohio, Catalyzing Linkages to Equity in Health (CLE Health)UM1TR004528 · NCATS · CASE WESTERN RESERVE UNIVERSITY · PI GRACE A MCCOMSEY · 2023 to 2026
$32.1M
Project 3 - Lymph NodesU54AI142766 · NIAID · UNIVERSITY OF FLORIDA · PI ATKINSON, MARK A., BODENMILLER, BERND · 2018 to 2021
$6.9M
Metagenomic surveillance of pathogen and antimicrobial resistance gene transmission in hospitalized neonatesK23AI185326 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI CHU, VICTORIA TIEN-YU · 2024 to 2025
$395k
NCATS NIH HHS UM1 TR004528NIAID NIH HHS K23 AI185326NIAID NIH HHS U54 AI142766
6 · The paper itself

Abstract

Azithromycin is a widely used antibiotic and was frequently used to treat hospitalized patients during the COVID-19 pandemic. The impact of empiric azithromycin use on the respiratory microbiome in patients with viral respiratory infections is unclear. Here we used longitudinal metatranscriptomics on nasal swabs from a prospective multicentre cohort of 1,164 patients hospitalized for COVID-19. We compared the upper respiratory microbiome, resistome and systemic immune response in patients treated with azithromycin (n = 366) with those who received no antibiotics (n = 474) or other antibiotics (n = 324). We found that azithromycin altered microbiome composition and increased the expression and relative proportion of macrolide/lincosamide/streptogramin (MLS) resistance genes. These changes occurred after 1 day of exposure and persisted for over a week. MLS resistance gene expression was associated with commensals and potential pathogens, while there were no differences in host inflammatory gene expression in blood and airways. This demonstrates that empiric azithromycin treatment impacts the upper respiratory microbiome and resistome without apparent anti-inflammatory benefit.

Indexed as

Anti-Bacterial AgentsAzithromycinCOVID-19 Drug TreatmentMicrobiotaRespiratory SystemAgedAnti-Inflammatory AgentsBacteriaCOVID-19FemaleHumansMaleMiddle AgedPandemicsProspective StudiesSARS-CoV-2Anti-Bacterial AgentsAnti-Inflammatory AgentsAzithromycin

Identifiers

PMID41840216
PMCPMC13056551

What Socratic holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.