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Journal article
Empiric azithromycin alters the upper respiratory microbiome and resistome without anti-inflammatory benefit in COVID-19
Nature microbiology
16 Mar 2026
PMID: 41840216
Featured in Collection : Drexel's Newest Publications
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.
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Details
- Title
- Empiric azithromycin alters the upper respiratory microbiome and resistome without anti-inflammatory benefit in COVID-19
- Creators
- Abigail Glascock - Chan Zuckerberg Initiative (United States)Cole Maguire - The University of Texas at AustinHoang Van Phan - University of California, San FranciscoEmily C. Lydon - Duke UniversityJoanna Schaenman - University of California, Los AngelesCarolyn S. Calfee - University of California, San FranciscoEsther Melamed - The University of Texas at AustinJohn Greenland - Univ Calif San Francisco, San Francisco, CA 94143 USADavid B. Corry - Baylor College of MedicineFarrah Kheradmand - Michael E. DeBakey VA Medical CenterLindsey R. Baden - Brigham and Women's HospitalRafick Sekaly - University Hospitals of ClevelandGrace A. McComsey - University Hospitals of ClevelandElias K. Haddad - Drexel University, Infectious Diseases (and HIV Medicine)Charles B. Cairns - Drexel University, College of MedicineLinda N. Geng - Stanford UniversityBali Pulendran - Emory UniversityAna Fernandez-Sesma - College Station Medical CenterViviana Simon - Icahn School of Medicine at Mount SinaiJordan P. Metcalf - University of Oklahoma Health Sciences CenterNelson I. Agudelo Higuita - Oklahoma Univ, Hlth Sci Ctr, Oklahoma City, OK USAWilliam B. Messer - Oregon Health & Science UniversityMark M. Davis - Stanford UniversityKari C. Nadeau - Stanford UniversityMonica Kraft - University of ArizonaChristian Bime - University of ArizonaDavid J. Erle - University of California, San FranciscoMark A. Atkinson - University of FloridaScott C. Brakenridge - University of South FloridaLauren I. R. Ehrlich - The University of Texas at AustinRuth R. Montgomery - Yale UniversityAlbert C. Shaw - Yale UniversityCatherine L. Hough - Oregon Health & Science UniversityDavid A. Hafler - Yale UniversityAlison D. Augustine - National Institute of Allergy and Infectious DiseasesPatrice M. Becker - National Institutes of HealthBjoern Peters - La Jolla Institute for ImmunologyAl Ozonoff - Boston Children's HospitalAnnmarie Hoch - Boston Children's HospitalSeunghee Kim-Schulze - Icahn School of Medicine at Mount SinaiFlorian Krammer - Icahn School of Medicine at Mount SinaiSteven Bosinger - Emory UniversityWalter Eckalbar - University of California, San FranciscoMatthew C. Altman - Seattle UniversityMichael Wilson - University of California, San FranciscoLeying Guan - Yale UniversityHolden Maecker - Stanford UniversityHanno Steen - Boston Children's HospitalJoann Diray-Arce - Yale UniversityNadine Rouphael - Emory UniversitySteven H. Kleinstein - Yale UniversityNaresh Doni Jayavelu - Behavioral Tech Research, Inc.Elaine F. Reed - University of California, Los AngelesOfer Levy - Harvard Medical SchoolVictoria T. Chu - University of California, San FranciscoCharles R. Langelier - University of California, San FranciscoIMPACC Network
- Publication Details
- Nature microbiology
- Publisher
- Springer
- Number of pages
- 26
- Grant note
- U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID) U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI) Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- College of Medicine; Infectious Diseases (and HIV Medicine); Emergency Medicine
- Web of Science ID
- WOS:001715339500001
- Other Identifier
- 991022170455604721