Matthew Kelly | Scholars@Duke

Matthew Kelly
Assistant Professor of Pediatrics

My research is broadly focused on elucidating the complex interactions that exist between the host microbiome and exogenous pathogens that cause infections in children. We have several ongoing projects evaluating: 1) the impact of the upper respiratory microbiome on the risk of colonization and invasion by bacterial respiratory pathogens among infants in Botswana; 2) associations between the gut microbiome of pediatric stem cell transplant recipients and the risk of infections (bloodstream infection, C. difficile infection) and graft-versus-host disease; and 3) the role of the gut and respiratory microbiomes in mediating COVID-19 infection susceptibility and disease severity in children. Ultimately, I aim to develop strategies that use targeted modification of the microbiome for the prevention of infections in children.

Current Research Interests

As a pediatrician with specialty training in infectious diseases and global health, my career goal is to develop strategies that use targeted manipulation of the microbiome for the prevention and treatment of infections in children. My current research focuses on elucidating the complex relationships that exist between sociodemographic factors, the upper respiratory microbiome, and colonization by pneumonia pathogens among infants in Botswana. Ultimately, we aim to develop microbiome therapeutics that effectively prevent pneumonia and other respiratory infections in children.

Current Appointments & Affiliations

Assistant Professor of Pediatrics, Pediatrics, Infectious Diseases, Pediatrics 2016
Assistant Research Professor of Global Health, Duke Global Health Institute, University Institutes and Centers 2019

Contact Information

2301 Erwin Rd, Durham, NC 27710
2301 Erwin Road, T915 Chc, Durham, NC 27710
msk37@dm.duke.edu (919) 684-6335

Background
Education, Training, & Certifications
- Pediatric Infectious Diseases Fellowship, Pediatrics, Duke University School of Medicine 2013 - 2016
- David N. Pincus Pediatric Global Health Fellowship, Pediatrics, Children's Hospital of Philadelphia 2011 - 2013
- Internship/Residency, Pediatrics, Children's Hospital Boston 2007 - 2010
- M.D., Harvard Medical School 2007
- M.P.H., Harvard University 2007
Medical Licensure
- 194411. North Carolina. 2021
Leadership & Clinical Positions at Duke
- Program Director, Pediatric Infectious Diseases Fellowship Program, Duke University (2018 -
  Assistant Director, Duke Pediatric Research Scholars Program (2018 -
  Associate Director of Physician-Scientist Development, Office of Pediatric Education, Duke University (2018 -
Recognition
In the News
- FEB 26, 2018 Children's Hospital of Philadelphia
  
  Advancing Pneumonia Research and Care Delivery in Botswana
Research
Selected Grants
- Unified Program for Therapeutics in Children awarded by National Institutes of Health 2019 - 2024
- Clinical and gut microbial risk factors for Gram-negative bacterial late-onset sepsis among premature infants in Singapore awarded by KK Women's and Children's Hospital 2020 - 2023
- Nasopharyngeal Microbiome and Risk of Bacterial Pathogen Colonization in Infants awarded by National Institutes of Health 2018 - 2023
- PTN 2.0 Task Order 7 HIV Lactation awarded by Eunice Kennedy Shriver National Institute of Child Health and Human Development 2020 - 2022
- A Randomized, Double-Blind, Placebo-Controlled Clinical Trial to Evaluate the Safety, Tolerability, Pharmacokinetics, and Efficacy of a Single Infusion of Bezlotoxumab (MK-6072, Human Monoclonal Antibody to C. difficile Toxin B) in Children Aged 1 to awarded by Merck Sharp & Dohme 2018 - 2022
- LOC-IMPAACT Leadership Group-IMPAACT 2018 Protocol Co-Vice Chair awarded by Johns Hopkins University 2017 - 2021
- Gene expression profiling of children with SARS-CoV-2 infection or exposure awarded by Merck & Co., Inc. 2021
- The serotype epidemiology and antibiotic resistance of Streptococcus pneumoniae in Botswana following introduction of 13-valent pneumococcal conjugate vaccine awarded by Merck 2019 - 2021
- VTEU Task C Option 2 Protocol 14-0079.B1C1.0028 awarded by National Institutes of Health 2017 - 2021
- A Phase 1b, Open-label Single dose study to Evaluate the Pharmacokinetics, Safety and Tolerability of MK-7655A in Pediatric Subjects from Birth to less than 18 years of Age with Confirmed or Suspected Gramnegative Infections awarded by Merck Sharp & Dohme 2017 - 2020
- The effect of household air pollution on the health outcomes of infants in Botswana awarded by Thrasher Research Fund 2018 - 2020
- The impact of HIV infection or exposure on the upper respiratory microbiome of children in Botswana awarded by Vanderbilt University Medical Center 2019 - 2020
- Fungal biomarkers for diagnosis and response to therapy for pediatric candidemia awarded by Duke University 2016 - 2020
- LOC-IMPAACT Leadership Group-IMPAACT 2018 Protocol Vice Chair support awarded by Johns Hopkins University 2017 - 2018
- RFTP 2016 CISA 03 - Option 1 - Fever after Simultaneous Vaccination (Lead) awarded by Centers for Disease Control and Prevention 2017 - 2018
- American Society of Tropical Medicine and Hygiene awarded by Burroughs Wellcome Fund 2016 - 2018
- Multi-center studies to improve diagnosis and treatment of pediatric candidiasis awarded by Duke University 2016 - 2018
- VTEU Task C Option 1 Protocol 14-0079.B1C1.0028 awarded by National Institutes of Health 2016 - 2018
- RFTP 2016 CISA 03 - Base - Fever after simultaneous vaccination (Lead) awarded by Centers for Disease Control and Prevention 2016 - 2017
- VTEU Task B Base Protocol 14-0079.B1C1.0028 awarded by National Institutes of Health 2015 - 2016
- The Effect of In Utero Exposure to HIV and Antiretroviral Therapy on the Microbiology and Outcomes of Severe Pneumonia awarded by International AIDS Society 2013 - 2016
External Relationships
- Adagio Therapeutics, Inc.
- Merck Sharpe & Dohme (Merck & Co, USA)
Publications & Artistic Works
Selected Publications
- Academic Articles
  - McClain, Micah T., Florica J. Constantine, Ricardo Henao, Yiling Liu, Ephraim L. Tsalik, Thomas W. Burke, Julie M. Steinbrink, et al. “Dysregulated transcriptional responses to SARS-CoV-2 in the periphery.” Nat Commun 12, no. 1 (February 17, 2021): 1079. https://doi.org/10.1038/s41467-021-21289-y.
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  - Singh, Tulika, Sarah M. Heston, Stephanie N. Langel, Maria Blasi, Jillian H. Hurst, Genevieve G. Fouda, Matthew S. Kelly, and Sallie R. Permar. “Lessons From COVID-19 in Children: Key Hypotheses to Guide Preventative and Therapeutic Strategies.” Clin Infect Dis 71, no. 8 (November 5, 2020): 2006–13. https://doi.org/10.1093/cid/ciaa547.
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  - Hurst, Jillian H., Sarah M. Heston, Hailey N. Chambers, Hannah M. Cunningham, Meghan J. Price, Lilianna Suarez, Carter G. Crew, et al. “SARS-CoV-2 Infections Among Children in the Biospecimens from Respiratory Virus-Exposed Kids (BRAVE Kids) Study.” Clin Infect Dis, November 3, 2020. https://doi.org/10.1093/cid/ciaa1693.
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  - Heston, Sarah M., Rebecca R. Young, Hwanhee Hong, Ibukunoluwa C. Akinboyo, John S. Tanaka, Paul L. Martin, Richard Vinesett, et al. “Microbiology of Bloodstream Infections in Children After Hematopoietic Stem Cell Transplantation: A Single-Center Experience Over Two Decades (1997-2017).” Open Forum Infect Dis 7, no. 11 (November 2020): ofaa465. https://doi.org/10.1093/ofid/ofaa465.
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  - Tanaka, John S., Rebecca R. Young, Sarah M. Heston, Kirsten Jenkins, Lisa P. Spees, Anthony D. Sung, Kelly Corbet, et al. “Anaerobic Antibiotics and the Risk of Graft-versus-Host Disease after Allogeneic Hematopoietic Stem Cell Transplantation.” Biol Blood Marrow Transplant 26, no. 11 (November 2020): 2053–60. https://doi.org/10.1016/j.bbmt.2020.07.011.
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  - Hurst, Jillian H., Sarah M. Heston, Hailey N. Chambers, Hannah M. Cunningham, Meghan J. Price, Liliana Suarez, Carter G. Crew, et al. “SARS-CoV-2 Infections Among Children in the Biospecimens from Respiratory Virus-Exposed Kids (BRAVE Kids) Study.” Medrxiv, September 1, 2020. https://doi.org/10.1101/2020.08.18.20166835.
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  - McClain, Micah T., Florica J. Constantine, Ricardo Henao, Yiling Liu, Ephraim L. Tsalik, Thomas W. Burke, Julie M. Steinbrink, et al. “Dysregulated transcriptional responses to SARS-CoV-2 in the periphery support novel diagnostic approaches.” Medrxiv, July 26, 2020. https://doi.org/10.1101/2020.07.20.20155507.
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  - Patel, Sweta M., Sabelle Jallow, Sefelani Boiditswe, Shabir A. Madhi, Kristen A. Feemster, Andrew P. Steenhoff, Tonya Arscott-Mills, et al. “Placental Transfer of Respiratory Syncytial Virus Antibody Among HIV-Exposed, Uninfected Infants.” J Pediatric Infect Dis Soc 9, no. 3 (July 13, 2020): 349–56. https://doi.org/10.1093/jpids/piz056.
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  - Congdon, Morgan, Hwanhee Hong, Rebecca R. Young, Coleen K. Cunningham, Leslie A. Enane, Tonya Arscott-Mills, Francis M. Banda, et al. “Effect of Haemophilus influenzae type b and 13-valent pneumococcal conjugate vaccines on childhood pneumonia hospitalizations and deaths in Botswana.” Clin Infect Dis, July 8, 2020. https://doi.org/10.1093/cid/ciaa919.
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  - Young, Rebecca R., Kirsten Jenkins, Felix Araujo-Perez, Patrick C. Seed, and Matthew S. Kelly. “Long-term stability of microbiome diversity and composition in fecal samples stored in eNAT medium.” Microbiologyopen 9, no. 7 (July 2020): e1046. https://doi.org/10.1002/mbo3.1046.
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  - Fawole, Oluwatunmise A., Matthew S. Kelly, Andrew P. Steenhoff, Kristen A. Feemster, Eric J. Crotty, Mantosh S. Rattan, Thuso David, et al. “Interpretation of pediatric chest radiographs by non-radiologist clinicians in Botswana using World Health Organization criteria for endpoint pneumonia.” Pediatr Radiol 50, no. 7 (June 2020): 913–22. https://doi.org/10.1007/s00247-020-04625-0.
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  - Liang, Guanxiang, Chunyu Zhao, Huanjia Zhang, Lisa Mattei, Scott Sherrill-Mix, Kyle Bittinger, Lyanna R. Kessler, et al. “The stepwise assembly of the neonatal virome is modulated by breastfeeding.” Nature 581, no. 7809 (May 2020): 470–74. https://doi.org/10.1038/s41586-020-2192-1.
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  - Akinboyo, Ibukunoluwa C., Rebecca R. Young, Lisa P. Spees, Sarah M. Heston, Michael J. Smith, Yeh-Chung Chang, Lauren E. McGill, et al. “Microbiology and Risk Factors for Hospital-Associated Bloodstream Infections Among Pediatric Hematopoietic Stem Cell Transplant Recipients.” Open Forum Infectious Diseases 7, no. 4 (April 2020): ofaa093. https://doi.org/10.1093/ofid/ofaa093.
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  - Weimer, Kristin E. D., Matthew S. Kelly, Sallie R. Permar, Reese H. Clark, and Rachel G. Greenberg. “Association of Adverse Hearing, Growth, and Discharge Age Outcomes With Postnatal Cytomegalovirus Infection in Infants With Very Low Birth Weight.” Jama Pediatr 174, no. 2 (February 1, 2020): 133–40. https://doi.org/10.1001/jamapediatrics.2019.4532.
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  - Abu-Raya, Bahaa, David M. Goldfarb, Marek Smieja, Kathy Luinstra, Melissa Richard-Greenblatt, Andrew P. Steenhoff, Kristen A. Feemster, et al. “The prevalence and clinical characteristics of pertussis-associated pneumonia among infants in Botswana.” Bmc Pediatr 19, no. 1 (November 16, 2019): 444. https://doi.org/10.1186/s12887-019-1820-0.
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  - Patel, Sweta M., Lisa Spees, Marek Smieja, Kathy Luinstra, Andrew P. Steenhoff, Kristen A. Feemster, Tonya Arscott-Mills, et al. “Predictors of Poor Outcomes Among Infants With Respiratory Syncytial Virus-associated Acute Lower Respiratory Infection in Botswana.” Pediatr Infect Dis J 38, no. 5 (May 2019): 525–27. https://doi.org/10.1097/INF.0000000000002168.
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  - Spees, Lisa P., Paul L. Martin, Joanne Kurtzberg, Andre Stokhuyzen, Lauren McGill, Vinod K. Prasad, Timothy A. Driscoll, et al. “Reduction in Mortality after Umbilical Cord Blood Transplantation in Children Over a 20-Year Period (1995-2014).” Biol Blood Marrow Transplant 25, no. 4 (April 2019): 756–63. https://doi.org/10.1016/j.bbmt.2018.11.018.
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  - Kelly, Matthew S., Jiayin Zheng, Sefelani Boiditswe, Andrew P. Steenhoff, Kristen A. Feemster, Tonya Arscott-Mills, Boitshepe Seme, et al. “Investigating Mediators of the Poor Pneumonia Outcomes of Human Immunodeficiency Virus-Exposed but Uninfected Children.” J Pediatric Infect Dis Soc 8, no. 1 (March 28, 2019): 13–20. https://doi.org/10.1093/jpids/pix092.
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  - Kelly, Matthew S., Michael G. Surette, Marek Smieja, Laura Rossi, Kathy Luinstra, Andrew P. Steenhoff, David M. Goldfarb, et al. “Pneumococcal Colonization and the Nasopharyngeal Microbiota of Children in Botswana.” Pediatr Infect Dis J 37, no. 11 (November 2018): 1176–83. https://doi.org/10.1097/INF.0000000000002174.
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  - Kelly, Matthew S., Lisa Spees, Richard Vinesett, Andre Stokhuyzen, Lauren McGill, Alan D. Proia, Kirsten Jenkins, Mehreen Arshad, Patrick C. Seed, and Paul L. Martin. “Utility of Autopsy among Pediatric Allogeneic Hematopoietic Stem Cell Transplant Recipients: One Last Chance to Learn?” Biol Blood Marrow Transplant 24, no. 9 (September 2018): 1861–65. https://doi.org/10.1016/j.bbmt.2018.05.030.
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  - Kelly, Matthew S., Michael G. Surette, Marek Smieja, Jeffrey M. Pernica, Laura Rossi, Kathy Luinstra, Andrew P. Steenhoff, et al. “The Nasopharyngeal Microbiota of Children With Respiratory Infections in Botswana.” Pediatr Infect Dis J 36, no. 9 (September 2017): e211–18. https://doi.org/10.1097/INF.0000000000001607.
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  - Salerno, Sara, Christoph P. Hornik, Michael Cohen-Wolkowiez, P Brian Smith, Lawrence C. Ku, Matthew S. Kelly, Reese Clark, Daniel Gonzalez, and Daniel Best Pharmaceuticals for Children Act–Pediatric Trials Network Steering Committee. “Use of Population Pharmacokinetics and Electronic Health Records to Assess Piperacillin-Tazobactam Safety in Infants.” Pediatr Infect Dis J 36, no. 9 (September 2017): 855–59. https://doi.org/10.1097/INF.0000000000001610.
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  - Wynn, James L., Matthew S. Kelly, Daniel K. Benjamin, Reese H. Clark, Rachel Greenberg, and P Brian Smith. “Timing of Multiorgan Dysfunction among Hospitalized Infants with Fatal Fulminant Sepsis.” Am J Perinatol 34, no. 7 (June 2017): 633–39. https://doi.org/10.1055/s-0036-1597130.
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  - Pernica, Jeffrey M., Andrew P. Steenhoff, Margaret Mokomane, Banno Moorad, Kwana Lechiile, Marek Smieja, Loeto Mazhani, et al. “Rapid enteric testing to permit targeted antimicrobial therapy, with and without Lactobacillus reuteri probiotics, for paediatric acute diarrhoeal disease in Botswana: A pilot, randomized, factorial, controlled trial.” Plos One 12, no. 10 (2017): e0185177. https://doi.org/10.1371/journal.pone.0185177.
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  - Kelly, Matthew S., Eric J. Crotty, Mantosh S. Rattan, Kathleen E. Wirth, Andrew P. Steenhoff, Coleen K. Cunningham, Tonya Arscott-Mills, et al. “Chest Radiographic Findings and Outcomes of Pneumonia Among Children in Botswana.” Pediatr Infect Dis J 35, no. 3 (March 2016): 257–62. https://doi.org/10.1097/INF.0000000000000990.
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  - Kelly, Matthew S., Daniel K. Benjamin, Karen M. Puopolo, Matthew M. Laughon, Reese H. Clark, Sagori Mukhopadhyay, P Brian Smith, and Sallie R. Permar. “Postnatal Cytomegalovirus Infection and the Risk for Bronchopulmonary Dysplasia.” Jama Pediatr 169, no. 12 (December 2015): e153785. https://doi.org/10.1001/jamapediatrics.2015.3785.
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  - Kelly, Matthew S., Kathleen E. Wirth, Andrew P. Steenhoff, Coleen K. Cunningham, Tonya Arscott-Mills, Sefelani C. Boiditswe, Mohamed Z. Patel, et al. “Treatment Failures and Excess Mortality Among HIV-Exposed, Uninfected Children With Pneumonia.” J Pediatric Infect Dis Soc 4, no. 4 (December 2015): e117–26. https://doi.org/10.1093/jpids/piu092.
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  - Kelly, M. S., K. E. Wirth, J. Madrigano, K. A. Feemster, C. K. Cunningham, T. Arscott-Mills, S. Boiditswe, S. S. Shah, R. Finalle, and A. P. Steenhoff. “The effect of exposure to wood smoke on outcomes of childhood pneumonia in Botswana.” Int J Tuberc Lung Dis 19, no. 3 (March 2015): 349–55. https://doi.org/10.5588/ijtld.14.0557.
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  - Kelly, Matthew S., Daniel K. Benjamin, and P Brian Smith. “The epidemiology and diagnosis of invasive candidiasis among premature infants.” Clin Perinatol 42, no. 1 (March 2015): 105–ix. https://doi.org/10.1016/j.clp.2014.10.008.
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  - Kelly, Matthew S., Marek Smieja, Kathy Luinstra, Kathleen E. Wirth, David M. Goldfarb, Andrew P. Steenhoff, Tonya Arscott-Mills, et al. “Association of respiratory viruses with outcomes of severe childhood pneumonia in Botswana.” Plos One 10, no. 5 (2015): e0126593. https://doi.org/10.1371/journal.pone.0126593.
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  - Kelly, Matthew S., Margaret Conway, Kathleen E. Wirth, Gail Potter-Bynoe, Amy L. Billett, and Thomas J. Sandora. “Microbiology and Risk Factors for Central Line–Associated Bloodstream Infections Among Pediatric Oncology Outpatients.” Journal of Pediatric Hematology/Oncology 35, no. 2 (March 2013): e71–76. https://doi.org/10.1097/mph.0b013e3182820edd.
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  - Kelly, Matthew, Margaret Conway, Kathleen Wirth, Gail Potter-Bynoe, Amy L. Billett, and Thomas J. Sandora. “Moving CLABSI Prevention beyond the Intensive Care Unit: Risk Factors in Pediatric Oncology Patients.” Infection Control & Hospital Epidemiology 32, no. 11 (November 2011): 1079–85. https://doi.org/10.1086/662376.
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  - Xiang, Zhou, Ronglih Liao, Matthew S. Kelly, and Myron Spector. “Collagen?GAG Scaffolds Grafted onto Myocardial Infarcts in a Rat Model: A Delivery Vehicle for Mesenchymal Stem Cells.” Tissue Engineering 0, no. 0 (n.d.): 060913044658014–060913044658014. https://doi.org/10.1089/ten.2006.12.ft-197.
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- Conference Papers
  - Patel, S., L. Spees, M. Smieja, K. Luinstra, D. M. Goldfarb, A. P. Steenhoff, C. K. Cunningham, et al. “Predictors of Treatment Failure Among Infants with Acute Lower Respiratory Infection Due to Respiratory Syncytial Virus in Botswana.” In American Journal of Respiratory and Critical Care Medicine, Vol. 197. AMER THORACIC SOC, 2018.
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Education, Training, & Certifications

Medical Licensure

Leadership & Clinical Positions at Duke

In the News

Selected Grants

External Relationships

Selected Publications

Academic Articles

Conference Papers