| 2024 |
Tanneti, Nikhila S.; Patel, Anant K.; Tan, Li Hui; Marques, Andrew D.; Perera, Ranawaka A. P. M.; Sherrill-Mix, Scott; Kelly, Brendan J.; Renner, David M.; Collman, Ronald G.; Rodino, Kyle; Lee, Carole; Bushman, Frederic D.; Cohen, Noam A.; Weiss, Susan R. |
Comparison of SARS-CoV-2 variants of concern in primary human nasal cultures demonstrates Delta as most cytopathic and Omicron as fastest replicating |
mBio |
10.1128/mbio.03129-23 |
| 2024 |
Kelly, Brendan J; Kwon, Jennie H; Woodworth, Michael H |
Escape Velocity—the Launch of Microbiome Therapies |
The Journal of Infectious Diseases |
10.1093/infdis/jiae099 |
| 2024 |
Yarbrough, Melanie L; Dumm, Rebekah E; Bry, Lynn; Kelly, Brendan J; Schwartz, Drew; Uberoi, Aayushi |
Microbiome-Based Diagnostics for Disease: Where Are We Now and Where Are We Headed? |
Clinical Chemistry |
10.1093/clinchem/hvae069 |
| 2024 |
Marques, Andrew D.; Graham-Wooten, Jevon; Fitzgerald, Ayannah S.; Sobel Leonard, Ashley; Cook, Emma J.; Everett, John K.; Rodino, Kyle G.; Moncla, Louise H.; Kelly, Brendan J.; Collman, Ronald G.; Bushman, Frederic D. |
SARS-CoV-2 evolution during prolonged infection in immunocompromised patients |
mBio |
10.1128/mbio.00110-24 |
| 2023 |
Redding, Laurel E.; Habing, Greg G.; Tu, Vincent; Bittinger, Kyle L.; O’Day, Jack; Pancholi, Preeti; Wang, Shu‐Hua; Alexander, Andrew; Kelly, Brendan J.; Weese, J. Scott; Stull, Jason W. |
Infrequent intrahousehold transmission of Clostridioides difficile between pet owners and their pets |
Zoonoses and Public Health |
10.1111/zph.13032 |
| 2023 |
Doernberg, Sarah B; Arias, Cesar A; Altman, Deena R; Babiker, Ahmed; Boucher, Helen W; Creech, C Buddy; Cosgrove, Sara E; Evans, Scott R; Fowler, Vance G; Fritz, Stephanie A; Hamasaki, Toshimitsu; Kelly, Brendan J; Leal, Sixto M; Liu, Catherine; Lodise, Thomas P; Miller, Loren G; Munita, Jose M; Murray, Barbara E; Pettigrew, Melinda M; Ruffin, Felicia; Scheetz, Marc H; Shopsin, Bo; Tran, Truc T; Turner, Nicholas A; Williams, Derek J; Zaharoff, Smitha; Holland, Thomas L; Patel, Robin; King, Heather; Kinamon, Tori; Dai, Weixiao; Geres, Holly; Deckard, Nancie; Schuler, Carl; Bunn, Ivra; Sharma, Shrabani; Wickward, Cathy; Waller, Jason; Wilson, Holly; Mehigan, Maureen; Ghazaryan, Varduhi; Raterman, Erica; Samuel, Tamika; Lee, Marina |
Priorities and Progress in Gram-positive Bacterial Infection Research by the Antibacterial Resistance Leadership Group: A Narrative Review |
Clinical Infectious Diseases |
10.1093/cid/ciad565 |
| 2023 |
Anderson, Thayer L.; Nande, Anjalika; Merenstein, Carter; Raynor, Brinkley; Oommen, Anisha; Kelly, Brendan J.; Levy, Michael Z.; Hill, Alison L. |
Quantifying individual-level heterogeneity in infectiousness and susceptibility through household studies |
Epidemics |
10.1016/j.epidem.2023.100710 |
| 2023 |
Montassier, Emmanuel; Kitsios, Georgios D.; Radder, Josiah E.; Le Bastard, Quentin; Kelly, Brendan J.; Panzer, Ariane; Lynch, Susan V.; Calfee, Carolyn S.; Dickson, Robert P.; Roquilly, Antoine |
Robust airway microbiome signatures in acute respiratory failure and hospital-acquired pneumonia |
Nature Medicine |
10.1038/s41591-023-02617-9 |
| 2022 |
Smith, Alexander B.; Jenior, Matthew L.; Keenan, Orlaith; Hart, Jessica L.; Specker, Jonathan; Abbas, Arwa; Rangel, Paula C.; Di, Chao; Green, Jamal; Bustin, Katelyn A.; Gaddy, Jennifer A.; Nicholson, Maribeth R.; Laut, Clare; Kelly, Brendan J.; Matthews, Megan L.; Evans, Daniel R.; Van Tyne, Daria; Furth, Emma E.; Papin, Jason A.; Bushman, Frederic D.; Erlichman, Jessi; Baldassano, Robert N.; Silverman, Michael A.; Dunny, Gary M.; Prentice, Boone M.; Skaar, Eric P.; Zackular, Joseph P. |
Enterococci enhance Clostridioides difficile pathogenesis |
Nature |
10.1038/s41586-022-05438-x |
| 2022 |
Marques, Andrew D.; Sherrill-Mix, Scott; Everett, John K.; Adhikari, Hriju; Reddy, Shantan; Ellis, Julie C.; Zeliff, Haley; Greening, Sabrina S.; Cannuscio, Carolyn C.; Strelau, Katherine M.; Collman, Ronald G.; Kelly, Brendan J.; Rodino, Kyle G.; Bushman, Frederic D.; Gagne, Roderick B.; Anis, Eman |
Multiple Introductions of SARS-CoV-2 Alpha and Delta Variants into White-Tailed Deer in Pennsylvania |
mBio |
10.1128/mbio.02101-22 |
| 2022 |
Rodino, Kyle G.; Peaper, David R.; Kelly, Brendan J.; Bushman, Frederic; Marques, Andrew; Adhikari, Hriju; Tu, Zheng Jin; Marrero Rolon, Rebecca; Westblade, Lars F.; Green, Daniel A.; Berry, Gregory J.; Wu, Fann; Annavajhala, Medini K.; Uhlemann, Anne-Catrin; Parikh, Bijal A.; McMillen, Tracy; Jani, Krupa; Babady, N. Esther; Hahn, Anne M.; Koch, Robert T.; Grubaugh, Nathan D.; Rhoads, Daniel D. |
Partial ORF1ab Gene Target Failure with Omicron BA.2.12.1 |
Journal of Clinical Microbiology |
10.1128/jcm.00600-22 |
| 2022 |
Lenz, Olivia C.; Marques, Andrew D.; Kelly, Brendan J.; Rodino, Kyle G.; Cole, Stephen D.; Perera, Ranawaka A. P. M.; Weiss, Susan R.; Bushman, Frederic D.; Lennon, Elizabeth M. |
SARS-CoV-2 Delta Variant (AY.3) in the Feces of a Domestic Cat |
Viruses |
10.3390/v14020421 |
| 2022 |
Zhang, Helen L.; Kelly, Brendan J.; David, Michael Z.; Lautenbach, Ebbing; Huang, Elizabeth; Bekele, Selamawit; Tolomeo, Pam; Reesey, Emily; Loughrey, Sean; Pegues, David; Ziegler, Matthew J. |
SARS-CoV-2 RNA persists on surfaces following terminal disinfection of COVID-19 hospital isolation rooms |
American Journal of Infection Control |
10.1016/j.ajic.2022.01.014 |
| 2022 |
Marques, Andrew D.; Sherrill-Mix, Scott; Everett, John K.; Reddy, Shantan; Hokama, Pascha; Roche, Aoife M.; Hwang, Young; Glascock, Abigail; Whiteside, Samantha A.; Graham-Wooten, Jevon; Khatib, Layla A.; Fitzgerald, Ayannah S.; Moustafa, Ahmed M.; Bianco, Colleen; Rajagopal, Swetha; Helton, Jenna; Deming, Regan; Denu, Lidiya; Ahmed, Azad; Kitt, Eimear; Coffin, Susan E.; Newbern, Claire; Mell, Josh Chang; Planet, Paul J.; Badjatia, Nitika; Richards, Bonnie; Wang, Zi-Xuan; Cannuscio, Carolyn C.; Strelau, Katherine M.; Jaskowiak-Barr, Anne; Cressman, Leigh; Loughrey, Sean; Ganguly, Arupa; Feldman, Michael D.; Collman, Ronald G.; Rodino, Kyle G.; Kelly, Brendan J.; Bushman, Frederic D. |
SARS-CoV-2 Variants Associated with Vaccine Breakthrough in the Delaware Valley through Summer 2021 |
mBio |
10.1128/mbio.03788-21 |
| 2022 |
Ziegler, Matthew J; Babcock, Hilary H; Welbel, Sharon F; Warren, David K; Trick, William E; Tolomeo, Pam; Omorogbe, Jacqueline; Garcia, Diana; Habrock-Bach, Tracy; Donceras, Onofre; Gaynes, Steven; Cressman, Leigh; Burnham, Jason P; Bilker, Warren; Reddy, Sujan C; Pegues, David; Lautenbach, Ebbing; Kelly, Brendan J; Fuchs, Barry; Martin, Niels D; Han, Jennifer H |
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 |
10.1093/cid/ciac070 |
| 2021 |
Rhee, Rennie L.; Lu, Jiarui; Bittinger, Kyle; Lee, Jung‐Jin; Mattei, Lisa M.; Sreih, Antoine G.; Chou, Sherry; Miner, Jonathan J.; Cohen, Noam A.; Kelly, Brendan J.; Lee, Hongzhe; Grayson, Peter C.; Collman, Ronald G.; Merkel, Peter A. |
Dynamic Changes in the Nasal Microbiome Associated With Disease Activity in Patients With Granulomatosis With Polyangiitis |
Arthritis & Rheumatology |
10.1002/art.41723 |
| 2021 |
Kelly, Brendan J.; Bekele, Selamawit; Loughrey, Sean; Huang, Elizabeth; Tolomeo, Pam; David, Michael Z.; Lautenbach, Ebbing; Han, Jennifer H.; Ziegler, Matthew J. |
Healthcare microenvironments define multidrug-resistant organism persistence |
Infection Control & Hospital Epidemiology |
10.1017/ice.2021.323 |
| 2021 |
Richard-Greenblatt, Melissa; Ziegler, Matthew J; Bromberg, Valerie; Huang, Elizabeth; Abdallah, Hatem; Tolomeo, Pam; Lautenbach, Ebbing; Glaser, Laurel; Kelly, Brendan J |
Quantifying the Impact of Nasopharyngeal Specimen Quality on Severe Acute Respiratory Syndrome Coronavirus 2 Test Performance |
Open Forum Infectious Diseases |
10.1093/ofid/ofab235 |
| 2021 |
Harrigan, James J; Abdallah, Hatem O; Clarke, Erik L; Oganisian, Arman; Roy, Jason A; Lautenbach, Ebbing; Reesey, Emily; Wernovsky, Magda; Tolomeo, Pam; Morawski, Zygmunt; Jacob, Jerry; Grippi, Michael A; Kelly, Brendan J |
Respiratory Microbiome Disruption and Risk for Ventilator-Associated Lower Respiratory Tract Infection |
Clinical Infectious Diseases |
10.1093/cid/ciab678 |
| 2021 |
Zhang, Helen L.; Kelly, Brendan J.; David, Michael Z.; Lautenbach, Ebbing; Huang, Elizabeth; Bekele, Selamawit; Tolomeo, Pam; Reesey, Emily; Loughrey, Sean; Pegues, David; Ziegler, Matthew J. |
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 & Hospital Epidemiology |
10.1017/ice.2021.468 |
| 2021 |
Ziegler, Matthew J.; Huang, Elizabeth; Bekele, Selamawit; Reesey, Emily; Tolomeo, Pam; Loughrey, Sean; David, Michael Z.; Lautenbach, Ebbing; Kelly, Brendan J. |
Spatial and temporal effects on severe acute respiratory coronavirus virus 2 (SARS-CoV-2) contamination of the healthcare environment |
Infection Control & Hospital Epidemiology |
10.1017/ice.2021.530 |
| 2021 |
Abdallah, Hatem O.; Weingart, Melanie F.; Fuller, Risa; Pegues, David; Fitzpatrick, Rebecca; Kelly, Brendan J. |
Subglottic suction frequency and adverse ventilator-associated events during critical illness |
Infection Control & Hospital Epidemiology |
10.1017/ice.2020.1298 |
| 2020 |
Redding, Laurel E; Kelly, Brendan J; Stefanovski, Darko; Lautenbach, John K; Tolomeo, Pam; Cressman, Leigh; Gruber, Eli; Meily, Paige; Lautenbach, Ebbing |
Pet Ownership Protects Against Recurrence of Clostridioides difficile Infection |
Open Forum Infectious Diseases |
10.1093/ofid/ofz541 |
| 2019 |
Berry, Alexander S. F.; Kelly, Brendan J.; Barnhart, Denise; Kelly, Donna J.; Beiting, Daniel P.; Baldassano, Robert N.; Redding, Laurel E. |
Gut microbiota features associated with Clostridioides difficile colonization in puppies |
PLOS ONE |
10.1371/journal.pone.0215497 |
| 2019 |
Ziegler, Matthew; Han, Jennifer H; Landsburg, Daniel; Pegues, David; Reesey, Emily; Gilmar, Cheryl; Gorman, Theresa; Bink, Kristen; Moore, Amy; Kelly, Brendan J |
Impact of Levofloxacin for the Prophylaxis of Bloodstream Infection on the Gut Microbiome in Patients With Hematologic Malignancy |
Open Forum Infectious Diseases |
10.1093/ofid/ofz252 |
| 2019 |
Kelly, Brendan J.; Lautenbach, Ebbing; Han, Jennifer H. |
The authors reply |
Critical Care Medicine |
10.1097/CCM.0000000000003587 |
| 2018 |
Ziegler, Matthew; Han, Jennifer H; Landsburg, Daniel; Pegues, David; Reesey, Emily; Gilmar, Cheryl; Gorman, Theresa; Bink, Kristen; Moore, Amy; Kelly, Brendan J |
1595. Impact of Levofloxacin for the Prophylaxis of Bloodstream Infection on the Gut Microbiome in Patients with Hematologic Malignancy |
Open Forum Infectious Diseases |
10.1093/ofid/ofy210.1423 |
| 2018 |
Weingart, Melanie F; Vecker, Risa; Fitzpatrick, Rebecca; Lautenbach, Ebbing; Pegues, David A; Kelly, Brendan J |
2105. Electronic Records of Daily Subglottic Suctioning Predict Infectious and Non-infectious Adverse Ventilator-Associated Events During Critical Care |
Open Forum Infectious Diseases |
10.1093/ofid/ofy210.1761 |
| 2018 |
Clarke, Erik; Reesey, Emily; Lautenbach, Ebbing; Wernovsky, Magda; Kelly, Brendan J |
614. Modeling Changes in Gastrointestinal and Respiratory Tract Bacterial Community Diversity Attributable to Common Antibiotic Exposures During Long-Term Acute Care |
Open Forum Infectious Diseases |
10.1093/ofid/ofy210.621 |
| 2018 |
Kelly, Brendan J.; Tebas, Pablo |
Clinical Practice and Infrastructure Review of Fecal Microbiota Transplantation for Clostridium difficile Infection |
Chest |
10.1016/j.chest.2017.09.002 |
| 2018 |
Kelly, Brendan J.; Lautenbach, Ebbing; Nachamkin, Irving; Coffin, Susan E.; Gerber, Jeffrey S.; Fuchs, Barry D.; Garrigan, Charles; Han, Xiaoyan; Bilker, Warren B.; Wise, Jacqueleen; Tolomeo, Pam; Han, Jennifer H. |
Combined Biomarkers Predict Acute Mortality Among Critically Ill Patients With Suspected Sepsis* |
Critical Care Medicine |
10.1097/CCM.0000000000003137 |
| 2018 |
Knecht, Vincent R.; McGinniss, John E.; Shankar, Hari M.; Clarke, Erik L.; Kelly, Brendan J.; Imai, Ize; Fitzgerald, Ayannah S.; Bittinger, Kyle; Bushman, Frederic D.; Collman, Ronald G. |
Molecular analysis of bacterial contamination on stethoscopes in an intensive care unit |
Infection Control & Hospital Epidemiology |
10.1017/ice.2018.319 |
| 2018 |
Agarwal, R.; Bartsch, S.M.; Kelly, B.J.; Prewitt, M.; Liu, Y.; Chen, Y.; Umscheid, C.A. |
Newer glycopeptide antibiotics for treatment of complicated skin and soft tissue infections: systematic review, network meta-analysis and cost analysis |
Clinical Microbiology and Infection |
10.1016/j.cmi.2017.08.028 |
| 2016 |
Kelly, Brendan J.; Lautenbach, Ebbing; Nachamkin, Irving; Coffin, Susan E.; Gerber, Jeffrey S.; Fuchs, Barry D.; Garrigan, Charles; Han, Xiaoyan; Bilker, Warren B.; Wise, Jacqueleen; Tolomeo, Pam; Han, Jennifer H. |
Combined biomarkers discriminate a low likelihood of bacterial infection among surgical intensive care unit patients with suspected sepsis |
Diagnostic Microbiology and Infectious Disease |
10.1016/j.diagmicrobio.2016.01.003 |
| 2016 |
Kelly, Brendan J.; Imai, Ize; Bittinger, Kyle; Laughlin, Alice; Fuchs, Barry D.; Bushman, Frederic D.; Collman, Ronald G. |
Composition and dynamics of the respiratory tract microbiome in intubated patients |
Microbiome |
10.1186/s40168-016-0151-8 |
| 2015 |
Kelly, Brendan J.; Gross, Robert; Bittinger, Kyle; Sherrill-Mix, Scott; Lewis, James D.; Collman, Ronald G.; Bushman, Frederic D.; Li, Hongzhe |
Power and sample-size estimation for microbiome studies using pairwise distances and PERMANOVA |
Bioinformatics |
10.1093/bioinformatics/btv183 |
| 2013 |
Brady, Troy; Kelly, Brendan J.; Male, Frances; Roth, Shoshannah; Bailey, Aubrey; Malani, Nirav; Gijsbers, Rik; O’Doherty, Una; Bushman, Frederic D. |
Quantitation of HIV DNA integration: Effects of differential integration site distributions on Alu-PCR assays |
Journal of Virological Methods |
10.1016/j.jviromet.2013.01.004 |
| 2010 |
Khiabanian, Hossein; Holmes, Antony B.; Kelly, Brendan J.; Gururaj, Mrinalini; Hripcsak, George; Rabadan, Raul |
Signs of the 2009 Influenza Pandemic in the New York-Presbyterian Hospital Electronic Health Records |
PLoS ONE |
10.1371/journal.pone.0012658 |
| 2008 |
Yu, Min; Kumar, T.R. Santha; Nkrumah, Louis J.; Coppi, Alida; Retzlaff, Silke; Li, Celeste D.; Kelly, Brendan J.; Moura, Pedro A.; Lakshmanan, Viswanathan; Freundlich, Joel S.; Valderramos, Juan-Carlos; Vilcheze, Catherine; Siedner, Mark; Tsai, Jennifer H.-C.; Falkard, Brie; Sidhu, Amar bir Singh; Purcell, Lisa A.; Gratraud, Paul; Kremer, Laurent; Waters, Andrew P.; Schiehser, Guy; Jacobus, David P.; Janse, Chris J.; Ager, Arba; Jacobs, William R.; Sacchettini, James C.; Heussler, Volker; Sinnis, Photini; Fidock, David A. |
The Fatty Acid Biosynthesis Enzyme FabI Plays a Key Role in the Development of Liver-Stage Malarial Parasites |
Cell Host & Microbe |
10.1016/j.chom.2008.11.001 |