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Brendan J Kelly, MD, MS
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Assistant Professor of Medicine (Infectious Diseases) at the Hospital of the University of Pennsylvania
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Attending Physician, Hospital of the University of Pennsylvania
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Attending Physician, Penn Presbyterian Medical Center
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Director Fecal Microbiota Transplantation Program, Hospital of the University of Pennsylvania
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Attending Physician, Good Shepherd Penn Partners
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Senior Scholar, Center for Clinical Epidemiology and Biostatistics
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Director, Antimicrobial Resistance and Healthcare Epidemiology Study collaborative (ARES) Scientific Laboratory, University of Pennsylvania
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Department: Medicine
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Graduate Group Affiliations
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Contact information
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731 Blockley Hall
Philadelphia, PA 19104
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Philadelphia, PA 19104
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Publications
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Links
c4 Search PubMed for articles
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c4 Search PubMed for articles
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Education:
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3c Harvard College, Harvard University, 2002.
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50 College of Physicians and Surgeons, Columbia University, 2007.
21 9 MSCE 21 (Genetic Epidemiology) c
67 Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania, 2013.
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Permanent link21 7 AB 20 (History and Science) c
3c Harvard College, Harvard University, 2002.
21 7 MD c
50 College of Physicians and Surgeons, Columbia University, 2007.
21 9 MSCE 21 (Genetic Epidemiology) c
67 Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania, 2013.
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Description of Clinical Expertise
51 respiratory tract infection; Clostridium difficile infection; HIV71
Description of Research Expertise
b7 microbial ecology; next-generation sequencing; respiratory tract microbiome; ventilator-associated infection; antimicrobial resistance; Clostridium difficile infectione 29
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13c Ziegler MJ, Anesi J, Tolomeo P, Glaser L, Cowden L, Cressman L, Huang E, Patel A, Lautenbach E, Pegues DA, Kelly BJ.: Screening and targeted prophylaxis for Clostridioides difficile infection. Clin Microbiol Infect 31(11): 1907-1913, Nov 2025.
17d Ziegler MJ, Loughrey S, Bekele S, Huang E, Tolomeo P, David MZ, Lautenbach E, Glaser LJ, Kelly BJ.: Comparative performance of sponge versus flocked swabs for culture-based and metagenomic detection of microbial contamination in the healthcare environment. Infect Control Hosp Epidemiol 46(8): 1-7, May 2025.
a3 Kelly BJ, Kwon JH, Woodworth MH.: Reply to Olle et al. J Infect Dis 231(2): 545, Feb 2025.
173 Ziegler MJ, Anesi J, Tolomeo P, Glaser L, Cowden C, Cressman L, Huang E, Patel A, Lautenbach E, Kelly BJ: Screening and targeted prophylaxis for Clostridioides difficile infection: STOP-CDI. Infectious Diseases Society of America, IDWeek. Oral Presentation; 2024 Oct; Los Angeles, CA. October 2024.
c3 Kelly BJ, Kwon JH, Woodworth MH.: Escape Velocity-the Launch of Microbiome Therapies. J Infect Dis 230(30): 2-4, Jul 2024.
ff 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(6): 792-797, Jun 2024.
17e 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). 14(1): 155, June 2024.
72 Matthew J. Ziegler, Leigh Cressman, Anne Jaskowiak-Barr, Pam Tolomeo, 108 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.
183 Tanneti NS, Patel AK, Tan LH, Marques AD, Perera RAPM, Sherrill-Mix S, Kelly BJ, Collman RG, Rodino K, Lee C, Bushman FD, Cohen NA, Weiss SR.: Comparison of SARS-CoV-2 variants in primary human nasal cultures indicates Delta as most cytopathic and Omicron as fastest replicating. bioRxiv 15(4): e0312923, Apr 2024.
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Selected Publications
f5 Lucky CW, Medernach RL, Kelly BJ, Kwon JH, Woodworth MH.: Microbiome Therapeutics for Clostridioides difficile Infection. Infect Dis Clin North Am 39(4): 663-683, Dec 2025.13c Ziegler MJ, Anesi J, Tolomeo P, Glaser L, Cowden L, Cressman L, Huang E, Patel A, Lautenbach E, Pegues DA, Kelly BJ.: Screening and targeted prophylaxis for Clostridioides difficile infection. Clin Microbiol Infect 31(11): 1907-1913, Nov 2025.
17d Ziegler MJ, Loughrey S, Bekele S, Huang E, Tolomeo P, David MZ, Lautenbach E, Glaser LJ, Kelly BJ.: Comparative performance of sponge versus flocked swabs for culture-based and metagenomic detection of microbial contamination in the healthcare environment. Infect Control Hosp Epidemiol 46(8): 1-7, May 2025.
a3 Kelly BJ, Kwon JH, Woodworth MH.: Reply to Olle et al. J Infect Dis 231(2): 545, Feb 2025.
173 Ziegler MJ, Anesi J, Tolomeo P, Glaser L, Cowden C, Cressman L, Huang E, Patel A, Lautenbach E, Kelly BJ: Screening and targeted prophylaxis for Clostridioides difficile infection: STOP-CDI. Infectious Diseases Society of America, IDWeek. Oral Presentation; 2024 Oct; Los Angeles, CA. October 2024.
c3 Kelly BJ, Kwon JH, Woodworth MH.: Escape Velocity-the Launch of Microbiome Therapies. J Infect Dis 230(30): 2-4, Jul 2024.
ff 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(6): 792-797, Jun 2024.
17e 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). 14(1): 155, June 2024.
72 Matthew J. Ziegler, Leigh Cressman, Anne Jaskowiak-Barr, Pam Tolomeo, 108 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.
183 Tanneti NS, Patel AK, Tan LH, Marques AD, Perera RAPM, Sherrill-Mix S, Kelly BJ, Collman RG, Rodino K, Lee C, Bushman FD, Cohen NA, Weiss SR.: Comparison of SARS-CoV-2 variants in primary human nasal cultures indicates Delta as most cytopathic and Omicron as fastest replicating. bioRxiv 15(4): e0312923, Apr 2024.
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