Dustin Daniel Flannery, DO, MSCE, is an attending physician at Children’s Hospital of Philadelphia (CHOP) and CHOP Newborn Care at Pennsylvania Hospital, an Assistant Professor of Pediatrics at the Perelman School of Medicine at the University of Pennsylvania, and a core faculty member in the CHOP Center for Pediatric Clinical Effectiveness (CPCE). He is a graduate of the Pediatric Hospital Epidemiology and Outcomes Research Training (PHEOT) program managed by the CPCE, and the Master of Science in Clinical Epidemiology (MSCE) program at the University of Pennsylvania.

Dr. Flannery received a Doctor of Osteopathic Medicine (DO) degree from the Philadelphia College of Osteopathic Medicine and a Bachelor of Science (BS) with Honors from Virginia Tech. After completing a residency and chief residency in Pediatrics at Alfred I. DuPont Hospital for Children/Thomas Jefferson University Hospital, he completed a fellowship in Neonatal-Perinatal Medicine at CHOP. His research interests are neonatal infectious diseases and antimicrobial stewardship. His current research projects involve 1) analyzing antimicrobial resistance patterns in neonatal intensive care units across the country; 2) analyzing contemporary maternal and neonatal seroepidemiology; and 3) identifying meaningful metrics of neonatal antibiotic use for more accurate inter-hospital comparison. He has received research funding from CHOP, National Institute of Child Health and Human Development (T32), Agency for Healthcare Research and Quality (K08), and Centers for Disease Control and Prevention.

Education and Training

Medical School

DO - Philadelphia College of Osteopathic Medicine, Philadelphia, PA


Pediatrics - Nemours Alfred I duPont Hospital for Children/Thomas Jefferson University, Philadelphia, PA


Pediatrics - Nemours Alfred I duPont Hospital for Children/Thomas Jefferson University, Philadelphia, PA (Chief Resident)


Neonatal-Perinatal Medicine - Children's Hospital of Philadelphia, PA (Chief Fellow)

Board Certification

Neonatal-Perinatal Medicine – American Board of Pediatrics
Pediatrics – American Board of Pediatrics

Graduate Degree

MS in Clinical Epidemiology (MSCE) - University of Pennsylvania Perelman School of Medicine, Philadelphia, PA

Titles and Academic Titles

Attending Neonatologist

Assistant Professor of Pediatrics, University of Pennsylvania Perelman School of Medicine

Departments and Services




Flannery, D.D., Zevallos Barboza, A., Pfeifer, M.R. et al. Perinatal COVID-19 maternal and neonatal outcomes at two academic birth hospitals. J Perinatol (2022).

Flannery DD, Puopolo KM, Hansen NI, Gerber JS, Sánchez PJ, Stoll BJ, for the Eunice Kennedy Shriver National Institute of Child Health and Human Development Neonatal Research Network. Antimicrobial Susceptibility Profiles Among Neonatal Early-Onset Sepsis Pathogens. Pediatr Infect Dis J. March 2022 Mar; 41(3):263-271/ PMID: 34862339; PubMed Central PMCID: PMC8831448

Flannery DD, Mukhopadhyay S, Morales KH, Dhudasia MB, Passarella M, Gerber JS, Puopolo KM. Delivery Characteristics and the Risk of Early-Onset Neonatal Sepsis. Pediatrics. 2022;149(2):e2021052900. PubMed PMID: 35022750; PubMed Central PMCID: pending doi: 10.1542/peds.2021-052900. Online ahead of print.

Flannery DD, Chiotos K, Gerber JS, Puopolo KM. Neonatal multidrug resistant gram-negative infection: epidemiology, mechanisms of resistance, and management. Pediatr Res. 2022; 91(2):380-391.  PubMed PMID: 34599280; PubMed Central PMCID: PMC8819496

Flannery DD, Passarella M, Mukhopadhyay S, Dhudasia MB, Gerber JS, Lorch SA, Hennessy S, Puopolo KM. Early Childhood Antibiotic Utilization for Infants Discharged from the Neonatal Intensive Care Unit. J Perinatol. 2022. In press.

O'Leary EN, Edwards JR, Srinivasan A, Neuhauser MM, Soe MM, Webb AK, Edwards EM, Horbar JD, Soll RF, Roberts J, Hicks LA, Wu H, Zayack D, Braun D, Cali S, Edwards WH, Flannery DD, Fleming-Dutra KE, Guzman-Cottrill JA, Kuzniewicz M, Lee GM, Newland J, Olson J, Puopolo KM, Rogers SP, Schulman J, Septimus E, Pollock DA. National Healthcare Safety Network 2018 Baseline Neonatal Standardized Antimicrobial Administration Ratios. Hosp Pediatr. 2022 Feb 1;12(2):190-198. doi: 10.1542/hpeds.2021-006253. PubMed PMID: 35075483; PubMed Central PMCID: pending

Mukhopadhyay S, Briker SM, Flannery DD, Dhudasia MB, Coggins SA, Woodford E, Walsh EM. Li S, Puopolo KM, Kuzniewicz MW. Time to Positivity of Blood Cultures in Neonatal Late-Onset Bacteremia. Arch Dis Child – Fetal Neonat Ed. Published Online First: 10 March 2022. doi: 10.1136/archdischild-2021-323416

Burris HH, Mullin AM, Dhudasia MB, Flannery DD, Mukhopadhyay S, Pfeifer MR, Woodford EC, Briker SM, Triebwasser JE, Morris JS, Montoya-Williams D, Gouma S, Hensley SE, Puopolo KM. Neighborhood Characteristics and Racial Disparities in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Seropositivity in Pregnancy. Obstet Gynecol. 2022. In press.

Puopolo KM, Mukhopadhyay S, Hansen NI, Flannery DD, Greenberg RG, Sanchez PJ, Bell EF, DeMauro SB, Wyckoff MH, Eichenwald EC, Stoll BJ, for the Eunice Kennedy Shriver National Institute of Child Health and Human Development Neonatal Research Network. Group B Streptococcal Infection in Extremely Preterm Neonates and Neurodevelopmental Outcomes at 2 Years. Clin Infect Dis. March 2022. PubMed PMID: pending; PubMed Central PMCID: pending. doi:10.1093/CID/CIAC222. Online ahead of print.

Triebwasser JE, Dhudasia MB, Mukhopadhyay S, Flannery DD, Gouma S, Hensley SE, Puopolo KM. Assessment of SARS-CoV-2 serostatus and hypertensive disorders of pregnancy. Am J Obstet Gynecol. 2022 Oct;227(4):664-666.e1. doi: 10.1016/j.ajog.2022.06.012. PubMed PMID: 35718110; PubMed Central PMCID: PMC9212257

Flannery DD, Puopolo KM. The imperfect science of neonatal sepsis. Pediatr Res. Pediatr Res. 2022 Mar;91(4):733-734. doi: 10.1038/s41390-021-01863-2. Epub 2021 Nov 20. PubMed PMID: 34802037

Flannery DD, Puopolo KM, Hansen NI, Sánchez PJ, Stoll BJ; Eunice Kennedy Shriver National Institute of Child Health and Human Development Neonatal Research Network. Neonatal infections: Insights from a multicenter longitudinal research collaborative. Semin Perinatol. 2022 Nov;46(7):151637. doi: 10.1016/j.semperi.2022.151637. Epub 2022 Jun 10. PubMed PMID: 35864010

Flannery DD, Puopolo KM. Neonatal Early-Onset Sepsis. Neoreviews, American Academy of Pediatrics. 2022 Nov 1;23(11):756-770. doi: 10.1542/neo.23-10-e756. PubMed PMID: 36316253

Flannery DD, Edwards EM, Coggins SA, Horbar JD, Puopolo KM. Late-onset sepsis among very preterm infants. Pediatrics. 2022. doi: 10.1542/peds.2022-058813.

Flannery DD, Gouma S, Dhudasia MB, Mukhopadhyay S, Pfeifer MR, Woodford EC, Briker SM, Triebwasser JE, Gerber JS, Morris JS, Weirick ME, McAllister CM, Hensley SE, Puopolo KM. Comparison of Maternal and Neonatal Antibody Levels After COVID-19 Vaccination vs SARS-CoV-2 Infection. JAMA Netw Open. 2022;5(11):e2240993. PubMed PMID: 36350652.

Flannery DD, Edwards EM, Coggins SA, Horbar JD, Puopolo KM. Late-Onset Sepsis Among Very Preterm Infants. Pediatrics. 2022;150(6):e2022058813. PubMed PMID: 36366916.


Flannery DD, Edwards EM, Puopolo KM, Horbar JH. Early-Onset Sepsis Among Very Preterm Infants. Pediatrics. 2021 Oct;148(4):e2021052456. PubMed PMID: 34493539; PubMed Central PMCID: pending

Flannery DD, Gouma S, Dhudasia MB, Mukhopadhyay S, Pfeifer MR, Woodford EC, Triebwasser JE, Gerber JS, Morris JS, Weirick ME, McAllister CM, Bolton MJ, Arevalo CP, Anderson EM, Goodwin EC, Hensley SE, Puopolo KM. Assessment of Maternal and Neonatal Cord Blood SARS-CoV-2 Antibodies and Placental Transfer Ratios. JAMA Pediatr. 2021 Jun 1;175(6):594-600. PubMed PMID: 33512440; PubMed Central PMCID: PMC7846944.

Flannery DD, Akinboyo IC, Mukhopadhyay S, Tribble AC, Song L, Chen F, Li Y, Gerber JS, Puopolo, KM. Antibiotic Susceptibility of Escherichia coli Among Infants Admitted to Neonatal Intensive Care Units Across the US from 2009 to 2017. JAMA Pediatr. 2021 Feb 1;175(2):168-175. PubMed PMID: 33165599; PubMed Central PMCID: PMC7653538.

Flannery DD, Wade KC. Immunization in the Neonatal Intensive Care Unit. Clin Perinatol. 2021 Jun;48(2):393-412. PubMed PMID: 34030821.

Flannery DD, Puopolo KM. The imperfect science of neonatal sepsis. Pediatr Res. 2021 Nov 20. PubMed PMID: 34802037; doi: 10.1038/s41390-021-01863-2. Online ahead of print.

Flannery DD, Puopolo KM. Perinatal COVID-19: guideline development, implementation, and challenges. Curr Opin Pediatr. 2021 Apr 1;33(2):188-194. PubMed PMID: 33534424. PMCID: PMC8048376

Flannery DD, Jensen EA, Tomlinson LA, Yu Y, Ying GS, Binenbaum G. Poor postnatal weight growth is a late finding after sepsis in very preterm infants. Arch Dis Child Fetal Neonatal Ed. 2021 May;106(3):298-304. PubMed PMID: 33148685; PubMed Central PMCID: PMC8291375.

Dhudasia MD, Flannery DD, Pfeifer MR, Puopolo KM. Updated Guidance: Prevention and Management of Perinatal Group B Streptococcus Infection. American Academy of Pediatrics NeoReviews 2021 Mar;22(3):e177-e188. PubMed PMID: 33649090.

Garber SJ, Dhudasia MB, Flannery DD, Passarella MR, Puopolo KM, Mukhopadhyay S. Delivery-based criteria for empiric antibiotic administration among preterm infants. J Perinatol. 2021 Feb;41(2):255-262. PubMed PMID: 32792629; PubMed Central PMCID: PMC7881045.

Montoya-Williams D, Mullin AM, Handley SC, Flannery DD, Lorch SA, Elovitz MA, Burris HH. Disparities in SARS-CoV-2 positivity among pregnant patients with limited English proficiency. J Perinatol. 2021 Oct;41(10):2564-2565.  PubMed PMID: 34497337; PubMed Central PMCID: PMC8425017.


Flannery DD, Horbar JD. Metrics of Neonatal Antibiotic Use. Semin Perinatol. 2020 Dec;44(8):151329.

Flannery DD, Gouma S, Dhudasia MB, Mukhopadhyay S, Pfeifer MR, Woodford EC, Gerber JS, Arevalo CP, Bolton MJ, Weirick ME, Goodwin EC, Anderson EM, Greenplate AR, Kim J, Han N, Pattekar A, Dougherty J, Kuthuru O, Mathew D, Baxter AE, Vella LA, Weaver J, Verma A, Leite R, Morris JS, Rader DJ, Elovitz MA, Wherry EJ, Puopolo KM, Hensley SE. SARS-CoV-2 seroprevalence among parturient women in Philadelphia. Sci Immunol. 2020 Jul 29;5(49): eabd5709. PubMed PMID: 32727884.

Flannery DD, Mukhopadhyay S, Jensen EA, Gerber JS, Passarella MR, Dysart K, Aghai ZH, Greenspan J, Puopolo KM. Influence of Patient Characteristics on Antibiotic Use Rates Among Preterm Infants. J Pediatric Infect Dis Soc. 2020 Mar 14. pii: piaa022. doi: 10.1093/jpids/piaa022. PMID: 32170951

Bamat NA, Ekhaguere OA, Zhang L, Flannery DD, Handley SC, Herrick HM, Ellenberg SS. Protocol adherence rates in superiority and noninferiority randomized clinical trials published in high impact medical journals. Clin Trials. 2020 Jul, online ahead of print. PMID: 32666826.

Gordon SM, Srinivasan L, Taylor DM, Master SR, Tremoglie MA, Hankeova A, Flannery DD, Abbasi S, Fitzgerald JC, Harris MC. Derivation of a metabolic signature associated with bacterial meningitis in infants. Pediatr Res. 2020 Aug;88(2):184-191. PubMed PMID: 32120377.


Sloane A, Flannery DD, Lafferty M, Jensen E, Dysart K, Cook A, Greenspan J, Aghai Z. Hypertensive Disorders During Pregnancy Are Associated with Reduced Severe Intraventricular Hemorrhage in Very Low Birth Weight Infants. J Perinatol, Epub ahead of print, July 1, 2019

Dhudasia MB, Flannery DD, Mukhopadhyay S. Early limited formula for breastfeeding infants: too much or just enough? J Perinatol, Epub ahead of print, June 9, 2019


Flannery DD, Dysart K, Cook A, Greenspan J, Aghai ZH, Jensen EA. Association Between Early Antibiotic Exposure and Bronchopulmonary Dysplasia or Death. J Perinatol, Epub ahead of print, June 13, 2018. doi:10.1038/s41372-018-0146-3

Flannery DD, Ross RK, Mukhopadhyay S, Tribble AC, Puopolo KM, Gerber JS. Temporal Trends and Center Variation in Early Antibiotic Use Among Premature Infants. JAMA Network Open. 2018;1(1):e180164. doi:10.1001/jamanetworkopen.2018.0164

Flannery DD, Puopolo KM. Neonatal Antibiotic Use: How Much is Too Much? Pediatrics. 2018; 142(3):e20181942.

Flannery DD, Puopolo KM. Neonatal Antibiotic Use: What Are We Doing and Where Shall We Go? Neoreviews, American Academy of Pediatrics. 2018;19(9):e516-525.


Flannery DD, Brandsma E, Saslow J, Mackley AB, Paul DA, Aghai ZA. Do infants in the neonatal intensive care unit diagnosed with urinary tract infection need a routine voiding cystourethrogram? J Matern Fetal Neonatal Med. 2017 Dec 10:1-121 [Epub ahead of print]. doi: 10.1080/14767058.2017.1416352

Flannery DD, Foglia EE. Critical appraisal of: [Patel RM, Knezevic A, Shenvi N, Hinkes M, Keene S, Roback JD, et al. Association of Red Blood Cell Transfusion, Anemia, and Necrotizing Enterocolitis in Very Low-Birth-Weight Infants. JAMA. 2016;315(9):889-897] J Perinatol 2017, 37: 626-628.

Hay S, Zupancic JA, Flannery DD, Kirpalani H, Dukhovny D. Should We Believe in Transfusion-Associated Necrotizing Enterocolitis? Applying a GRADE to the Literature. Semin Perinatol 2017, 41(1): 80-91

Flannery DD, Foglia EE. The contributions of red blood cell transfusion and severe anemia in necrotizing enterocolitis: causes or confounders? J Perinatol. 2017 Mar 23. [Epub ahead of print]


Flannery DD, Stephens CL, Thompson AD. The Impact of High-Profile Sexual Abuse Cases in the Media on a Pediatric Emergency Department. J Child Sex Abus 2016, 25(6): 627-635

Flannery DD, O’Donnell E, Kornhauser M, Dysart K, Greenspan J, Aghai ZH. Continuous Positive Airway Pressure versus Mechanical Ventilation on the First Day of Life in Very Low Birth Weight Infants. Am J Perinatol 2016, 33(10): 939-944


Flannery DD, Chan S, Swami SK, Eppes SC. Prescriber Perceptions of a Pediatric Antimicrobial Stewardship Program. Clin Pediatr 2014, 53(8): 743-746


Flannery DD, Akinboyo I, Ty JM, Averill LW, Freedman A. Septic Arthritis and Concern for Osteomyelitis in a Child with Rat Bite Fever. J Clin Microbiol 2013, 51(6): 1987-1989

Awards and Honors

2021, Relationship Based Care Physician Award, Shared Governance Advisory Council and Nursing Leadership, Pennsylvania Hospital

2020, Neonatal Abstinence Syndrome Quality Care Subaward: Pennsylvania Hospital Newborn Medicine, Pennsylvania Perinatal Quality Collaborative

2019, Alumni Professional Development Grant Award, Philadelphia College of Osteopathic Medicine Alumni Association

2019, Trainee Travel Grant Award, Pediatric Academic Societies Meeting

2019, Young Investigator Coaching Program (Coach: Dr. Thomas Newman), Society for Pediatric Research

2018, Thomas Boggs Perinatal-Neonatal Fellow Research Award Finalist, Philadelphia Perinatal Society

2017, Excellence in Clinical Research Award, Children’s Hospital of Philadelphia Research Institute

2017, Trainee Travel Grant Award, Eastern Society for Pediatric Research Meeting

2016, Quality and Patient Safety Honorable Mention: Supporting Premature Infant Nutrition (SPIN), Penn Medicine Clinical Effectiveness and Quality Improvement Initiative

2016, Antimicrobial Stewardship Fellowship Award, Pediatric Infectious Diseases Society

2015, Section on Infectious Diseases Travel Grant Award, American Academy of Pediatrics

2014, Rosenblum Award for Excellence (Outstanding Senior Resident), Alfred I. duPont Hospital for Children

2014, Bambi Taylor, M.D. Pediatric Emergency Medicine Award, Alfred I. duPont Hospital for Children

Editorial and Academic Positions

Editorial Positions

Ad Hoc Reviewer

2022-present, GERMS
2021-present, JAMA Network Open
2021-present, Journal of Pediatrics
2021-present, The American Journal of Obstetrics & Gynecology (AJOG)
2021-present, Pediatric Pulmonology
2020-present, Archives of Disease in Childhood
2020-present, Lancet Infectious Diseases
2020-present, Scientific Reports
2020-present, BMJ Paediatrics Open
2019-present, Journal of Perinatology
2017-present, The Pediatric Infectious Disease Journal
2017-present, Journal of the Pediatric Infectious Diseases Society
2016-present, Virulence
2016-present, American Journal of Perinatology
2015-present, Pediatrics

Invited Reviewer

2022, Proposal Peer Reviewer, United Kingdom Research and Innovation Medical Research Council
2021, Proposal Peer Reviewer, Thrasher Research Fund
2019, Reviewer, Pediatric Infectious Diseases Society Antimicrobial Stewardship Fellowship Award
2019, Judge, Philadelphia College of Osteopathic Medicine Research Poster Day
2019, Abstract Reviewer, American Academy of Pediatrics National Conference and Exhibition
2016-present, Abstract Reviewer, Pediatric Academic Societies Annual Meeting Scientific

Academic and Institutional Committees

2022-present, Coworker Observation Reporting System (CORS) Group, Pennsylvania Hospital
2019-present, Neonatology Scientific Review Committee, Children’s Hosp. of Philadelphia
2019-present, Pediatric Sepsis Program, Children’s Hosp. of Philadelphia
2018-present, UTI Management Pathway Development Team, Children’s Hosp. of Philadelphia
2017-present, Neonatology Fellowship Selection Committee

Leadership and Memberships

Memberships in Professional Organizations


2018-present, International Society of Evidence-Based Neonatology (EBNEO)


2018-present, Society for Healthcare Epidemiology of America
2018-present, PIDS Pediatric Committee on Antimicrobial Stewardship
2018-present, CDC/VON Antimicrobial Stewardship Special Interest Group
2016-2018, Liaison, AAP Section on Breastfeeding/Section on Pediatric Trainees
2015-present, Society for Pediatric Research (SPR)
2013-present, Pediatric Infectious Diseases Society (PIDS)
2013-present, Academic Pediatric Association (APA)
2011-present, American Academy of Pediatrics (AAP)