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Brendan Kelly

Assistant Professor of Infectious Diseases & Epidemiology

Education

Affiliations

Bio

Brendan J. Kelly, M.D., M.S., is an infectious diseases physician and molecular epidemiologist at the University of Pennsylvania. He studies how microbes interact in the human respiratory and gastrointestinal tracts, how their interaction relates to infection risk, and how microbial interactions can be engineered to prevent and treat antibiotic-resistant infections. Specifically, Dr. Kelly seeks to understand properties of microbial ecosystems that protect against bacterial pathogen colonization and infection, how microbial ecosystems are altered by antibiotics, and how they recover from infection and antibiotic treatment. He has performed large, clinical-translational studies to better understand two infections that occur commonly during critical illness: bacterial pneumonia and C. difficile colitis. He has also investigated the use of fecal microbiota transplant (FMT) to aid recovery of the intestinal microbiota after C. difficile treatment. During the COVID-19 pandemic, he is leading a study of SARS-CoV-2 variant succession across the Philadelphia metropolitan region.

Preferred Pronouns

He/him/his

Personal Academic Website

Research/Topics of Interest

Antibiotic resistance
Apply models to public health
Compartmental models
Geospatial models
Intra-host modeling
Machine learning models
Network models
Phylogenetic models
Spatial transmission patterns
Statistical models
Time-series models

Pathogens/Diseases of Main Interest/Expertise

COVID-19
Diarrheal diseases
Respiratory diseases

Countries of Work/Collaboration

United States

Projects

Papers

Zhang HL, Kelly BJ, David MZ, Lautenbach E, Huang E, Bekele S, Tolomeo P, Reesey E, Loughrey S, Pegues D, Ziegler MJ, . (2022). SARS-CoV-2 RNA persists on surfaces following terminal disinfection of COVID-19 hospital isolation rooms. American journal of infection control

Marques AD, Sherrill-Mix S, Everett JK, Adhikari H, Reddy S, Ellis JC, Zeliff H, Greening SS, Cannuscio CC, Strelau KM, Collman RG, Kelly BJ, Rodino KG, Bushman FD, Gagne RB, Anis E. (2022). Multiple Introductions of SARS-CoV-2 Alpha and Delta Variants into White-Tailed Deer in Pennsylvania. mBio

Rodino KG, Peaper DR, Kelly BJ, Bushman F, Marques A, Adhikari H, Tu ZJ, Marrero Rolon R, Westblade LF, Green DA, Berry GJ, Wu F, Annavajhala MK, Uhlemann AC, Parikh BA, McMillen T, Jani K, Babady NE, Hahn AM, Koch RT, Grubaugh ND, , Rhoads DD. (2022). Partial ORF1ab Gene Target Failure with Omicron BA.2.12.1. Journal of clinical microbiology

Lenz OC, Marques AD, Kelly BJ, Rodino KG, Cole SD, Perera RAPM, Weiss SR, Bushman FD, Lennon EM. (2022). SARS-CoV-2 Delta Variant (AY.3) in the Feces of a Domestic Cat. Viruses, 14(2)

Marques AD, Sherrill-Mix S, Everett JK, Reddy S, Hokama P, Roche AM, Hwang Y, Glascock A, Whiteside SA, Graham-Wooten J, Khatib LA, Fitzgerald AS, Moustafa AM, Bianco C, Rajagopal S, Helton J, Deming R, Denu L, Ahmed A, Kitt E, Coffin SE, Newbern C, Mell JC, Planet PJ, Badjatia N, Richards B, Wang ZX, Cannuscio CC, Strelau KM, Jaskowiak-Barr A, Cressman L, Loughrey S, Ganguly A, Feldman MD, Collman RG, Rodino KG, Kelly BJ, Bushman FD. (2022). SARS-CoV-2 Variants Associated with Vaccine Breakthrough in the Delaware Valley through Summer 2021. mBio

Ziegler MJ, Babcock HH, Welbel SF, Warren DK, Trick WE, Tolomeo P, Omorogbe J, Garcia D, Habrock-Bach T, Donceras O, Gaynes S, Cressman L, Burnham JP, Bilker W, Reddy SC, Pegues D, Lautenbach E, Kelly BJ, Fuchs B, Martin ND, Han JH, . (2022). Stopping Hospital Infections with Environmental Services (SHINE): A Cluster-Randomized Trial of Intensive Monitoring Methods for Terminal Room Cleaning on Rates of Multidrug-Resistant Organisms in the Intensive Care Unit. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

Marques AD, Sherrill-Mix S, Everett J, Reddy S, Hokama P, Roche AM, Hwang Y, Glascock A, Whiteside SA, Graham-Wooten J, Khatib LA, Fitzgerald AS, Moustafa AM, Bianco C, Rajagopal S, Helton J, Deming R, Denu L, Ahmed A, Kitt E, Coffin SE, Newbern C, Mell JC, Planet PJ, Badjatia N, Richards B, Wang ZX, Cannuscio CC, Strelau KM, Jaskowiak-Barr A, Cressman L, Loughrey S, Ganguly A, Feldman MD, Collman RG, Rodino KG, Kelly BJ, Bushman FD. (2021). SARS-CoV-2 variants associated with vaccine breakthrough in the Delaware Valley through summer 2021. medRxiv : the preprint server for health sciences

Ziegler MJ, Huang E, Bekele S, Reesey E, Tolomeo P, Loughrey S, David MZ, Lautenbach E, Kelly BJ, . (2021). Spatial and temporal effects on SARS-CoV-2 contamination of the healthcare environment. Infection control and hospital epidemiology

Kelly BJ, Bekele S, Loughrey S, Huang E, Tolomeo P, David MZ, Lautenbach E, Han JH, Ziegler MJ, . (2021). Healthcare microenvironments define multidrug-resistant organism persistence. Infection control and hospital epidemiology

Zhang HL, Kelly BJ, David MZ, Lautenbach E, Huang E, Bekele S, Tolomeo P, Reesey E, Loughrey S, Pegues D, Ziegler MJ, . (2021). Severe acute respiratory coronavirus virus 2 (SARS-CoV-2) surface contamination in staff common areas and impact on healthcare worker infection: Prospective surveillance during the coronavirus disease 2019 (COVID-19) pandemic. Infection control and hospital epidemiology

Abdallah HO, Weingart MF, Fuller R, Pegues D, Fitzpatrick R, Kelly BJ. (2021). Subglottic suction frequency and adverse ventilator-associated events during critical illness. Infection control and hospital epidemiology, 42(7)

Rhee RL, Lu J, Bittinger K, Lee JJ, Mattei LM, Sreih AG, Chou S, Miner JJ, Cohen NA, Kelly BJ, Lee H, Grayson PC, Collman RG, Merkel PA. (2021). Dynamic Changes in the Nasal Microbiome Associated With Disease Activity in Patients With Granulomatosis With Polyangiitis. Arthritis & rheumatology (Hoboken, N.J.), 73(9)

Harrigan JJ, Abdallah H, Clarke EL, Oganisian A, Roy JA, Lautenbach E, Reesey E, Wernovsky M, Tolomeo P, Morawski Z, Jacob J, Grippi MA, Kelly BJ. (2021). Respiratory microbiome disruption and risk for ventilator-associated lower respiratory tract infection. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

Richard-Greenblatt M, Ziegler MJ, Bromberg V, Huang E, Abdallah H, Tolomeo P, Lautenbach E, Glaser L, Kelly BJ. (2021). Quantifying the Impact of Nasopharyngeal Specimen Quality on Severe Acute Respiratory Syndrome Coronavirus 2 Test Performance. Open forum infectious diseases, 8(6)

Redding LE, Kelly BJ, Stefanovski D, Lautenbach JK, Tolomeo P, Cressman L, Gruber E, Meily P, Lautenbach E. (2020). Infection. Open forum infectious diseases, 7(1)

Berry ASF, Kelly BJ, Barnhart D, Kelly DJ, Beiting DP, Baldassano RN, Redding LE. (2019). Gut microbiota features associated with Clostridioides difficile colonization in puppies. PloS one, 14(8)

Kelly BJ, Lautenbach E, Han JH, . (2019). The authors reply. Critical care medicine, 47(3)

Ziegler M, Han JH, Landsburg D, Pegues D, Reesey E, Gilmar C, Gorman T, Bink K, Moore A, Kelly BJ, . (2019). Impact of Levofloxacin for the Prophylaxis of Bloodstream Infection on the Gut Microbiome in Patients With Hematologic Malignancy. Open forum infectious diseases, 6(7)

Knecht VR, McGinniss JE, Shankar HM, Clarke EL, Kelly BJ, Imai I, Fitzgerald AS, Bittinger K, Bushman FD, Collman RG. (2019). Molecular analysis of bacterial contamination on stethoscopes in an intensive care unit. Infection control and hospital epidemiology, 40(2)

Kelly BJ, Lautenbach E, Nachamkin I, Coffin SE, Gerber JS, Fuchs BD, Garrigan C, Han X, Bilker WB, Wise J, Tolomeo P, Han JH, . (2018). Combined Biomarkers Predict Acute Mortality Among Critically Ill Patients With Suspected Sepsis. Critical care medicine, 46(7)

Kelly BJ, Tebas P. (2018). Clinical Practice and Infrastructure Review of Fecal Microbiota Transplantation for Clostridium difficile Infection. Chest, 153(1)

Kelly BJ, Lautenbach E, Nachamkin I, Coffin SE, Gerber JS, Fuchs BD, Garrigan C, Han X, Bilker WB, Wise J, Tolomeo P, Han JH, . (2016). Combined biomarkers discriminate a low likelihood of bacterial infection among surgical intensive care unit patients with suspected sepsis. Diagnostic microbiology and infectious disease, 85(1)

Kelly BJ, Imai I, Bittinger K, Laughlin A, Fuchs BD, Bushman FD, Collman RG. (2016). Composition and dynamics of the respiratory tract microbiome in intubated patients. Microbiome, (4)

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