Brendan J Kelly, MD, MS

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Assistant Professor of Medicine (Infectious Diseases) at the Hospital of the University of Pennsylvania
Attending Physician, Penn Presbyterian Medical Center
Attending Physician, Hospital of the University of Pennsylvania
Director Fecal Microbiota Transplantation Program, Hospital of the University of Pennsylvania
Attending Physician, Good Shepherd Penn Partners
Senior Scholar, Center for Clinical Epidemiology and Biostatistics
Director, Antimicrobial Resistance and Healthcare Epidemiology Study collaborative (ARES) Scientific Laboratory, University of Pennsylvania
Department: Medicine

Contact information
731 Blockley Hall
Philadelphia, PA 19104
AB (History and Science)
Harvard College, Harvard University, 2002.
College of Physicians and Surgeons, Columbia University, 2007.
MSCE (Genetic Epidemiology)
Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania, 2013.
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Description of Clinical Expertise

respiratory tract infection; Clostridium difficile infection; HIV

Description of Research Expertise

microbial ecology; next-generation sequencing; respiratory tract microbiome; ventilator-associated infection; antimicrobial resistance; Clostridium difficile infection

Selected Publications

Yarbrough ML, Dumm RE, Bry L, Kelly BJ, Schwartz D, Uberoi A.: Microbiome-Based Diagnostics for Disease: Where Are We Now and Where Are We Headed? Clin Chem 70: 792-797, Jun 2024.

Emilia C. Wilkins, Laura L. Cowden, Anne Jaskowiak-Barr, Lauren Dutcher, Brendan J. Kelly: Stability of gut microbial community composition among donors to a clinical fecal microbiota transplant program. American Society for Microbiology (ASM) Microbe 2024 (Atlanta, GA, United States). June 2024.

Sebastian Pintea, Brendan J. Kelly: Impact of different antibiotic classes on the diversity of the respiratory and gut bacterial communities. American Society for Microbiology (ASM) Microbe 2024 (Atlanta, GA, United States). June 2024.

Matthew J. Ziegler, Leigh Cressman, Anne Jaskowiak-Barr, Pam Tolomeo, Brendan J. Kelly: Post-antibiotic risk for recurrent lower respiratory tract infection during prolonged hospitalisation. European Congress of Clinical Microbiology and Infectious Diseases (ECCMID) 2024 (Barcelona, Spain). April 2024.

Tanneti NS, Patel AK, Tan LH, Marques AD, Perera RAPM, Sherrill-Mix S, Kelly BJ, Renner DM, Collman RG, Rodino K, Lee C, Bushman FD, Cohen NA, Weiss SR.: Comparison of SARS-CoV-2 variants of concern in primary human nasal cultures demonstrates Delta as most cytopathic and Omicron as fastest replicating. mBio 15: e0312923, Apr 2024.

Marques AD, Graham-Wooten J, Fitzgerald AS, Sobel Leonard A, Cook EJ, Everett JK, Rodino KG, Moncla LH, Kelly BJ, Collman RG, Bushman FD.: SARS-CoV-2 evolution during prolonged infection in immunocompromised patients. mBio 15: e0011024, Mar 2024.

Kelly BJ, Kwon JH, Woodworth MH.: Escape Velocity - The Launch of Microbiome Therapies. J Infect Dis Mar 2024.

Montassier E, Kitsios GD, Radder JE, Le Bastard Q, Kelly BJ, Panzer A, Lynch SV, Calfee CS, Dickson RP, Roquilly A.: Robust airway microbiome signatures in acute respiratory failure and hospital-acquired pneumonia. Nat Med Nov 2023.

Ziegler MJ, Huang E, Cowden L, Lautenbach E, Kelly BJ: Spatial distribution of surface microbiota and resistance genes within and between rooms in an intensive care unit. Infectious Diseases Society of America (IDSA) IDWeek 2023 Conference. Boston, MA. October 2023.

Doernberg SB, Arias CA, Altman DR, Babiker A, Boucher HW, Creech CB, Cosgrove SE, Evans SR, Fowler VG, Fritz SA, Hamasaki T, Kelly BJ, Leal SM, Liu C, Lodise TP, Miller LG, Munita JM, Murray BE, Pettigrew MM, Ruffin F, Scheetz MH, Shopsin B, Tran TT, Turner NA, Williams DJ, Zaharoff S, Holland TL; Antibacterial Resistance Leadership Group.: Priorities and Progress in Gram-positive Bacterial Infection Research by the Antibacterial Resistance Leadership Group: A Narrative Review. Clin Infect Dis 77: S295-S304, Oct 2023.

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Last updated: 06/20/2024
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