About

Dustin Daniel Flannery, DO, MSCE, is an Assistant Professor of Pediatrics specializing in Neonatology and Newborn Services at the Children's Hospital of Philadelphia. He holds a BS in Nutritional Biochemistry from Virginia Polytechnic Institute and State University, a DO from Philadelphia College of Osteopathic Medicine, and an MSCE in Clinical Epidemiology from the University of Pennsylvania School of Medicine. His professional roles include Attending Physician at Penn Presbyterian Medical Center, Hospital of the University of Pennsylvania, Pennsylvania Hospital, and Children's Hospital of Philadelphia, as well as Core Faculty at Children’s Hospital of Philadelphia's Clinical Futures program. He is also the Director of Pediatric Trainee Education at Pennsylvania Hospital and the Associate Program Director for the Neonatal-Perinatal Medicine Fellowship at Children’s Hospital of Philadelphia. His research and clinical interests focus on neonatal infectious diseases, antibiotic susceptibility, maternal and neonatal immune responses, and perinatal COVID-19, contributing to guidelines and understanding in these areas.

Research topics

• Medicine
• Pediatrics
• Intensive care medicine
• Obstetrics
• Immunology

Selected publications

• Anti-cytomegalovirus medications among very low birth weight infants in the United States from 2016 to 2023

  Journal of Perinatology · 2026-04-20

  articleOpen accessSenior author
  PublisherOA PDFDOI

• Long-term sustainability and safety of a delivery-based early-onset sepsis evaluation strategy for very low birth weight infants

  Journal of Perinatology · 2026-03-13

  articleOpen accessSenior author
  PublisherOA PDFDOI

• Placental Vascular Pathology Associated with Congenital Lymphocytic Choriomeningitis Virus Infection, Philadelphia, Pennsylvania, USA

  Emerging infectious diseases · 2026-05-01

  articleOpen access

  Congenital lymphocytic choriomeningitis virus (LCMV) infection is associated with major neurologic malformations and fetal demise. We report 2 cases of probable congenital LCMV infection and chorioretinitis, cerebral ventriculomegaly, and placental histopathology in Philadelphia, Pennsylvania, USA. Clinicians who suspect congenital LCMV infection should screen for chorioretinitis, LCMV antibodies, and evidence of placental pathology.

  PublisherDOI

• Infants ≤24 weeks are not just smaller extremely preterm infants

  Journal of Perinatology · 2026-02-23

  articleOpen accessSenior author

  Among the most pressing topics in neonatal-perinatal medicine today is intensive care for infants born at ≤24 weeks' gestation. Infants born at 22-24 weeks comprise ~1 in 500 live births, with ~7500 liveborn infants annually in the U.S.-more common than Down syndrome or critical congenital heart disease-and make up 1 in 5 U.S. infant deaths. Major uncertainties exist about clinical decisions, including regarding obstetric care, delivery room procedures, incubator management, nutrition, respiratory support, and the optimal developmental environment. Partnering with families, we can develop a sound basis for safe and effective medical care of pregnant women and infants affected by birth at ≤24 weeks.

  PublisherOA PDFDOI

• Bacterial and fungal infections in infants born before 24 weeks’ gestation: a review

  Journal of Perinatology · 2026-02-16

  articleOpen access1st authorCorresponding

  Infants born before 24 weeks' gestational age face unique challenges compared to more mature preterm infants. This includes a higher risk of infection, which remains a leading cause of morbidity and mortality. Over the last two decades, advancements in neonatal care have resulted in higher rates of survival. However, invasive bacterial and fungal infections continue to pose significant threats. This narrative review highlights the epidemiology, microbiology, and related outcomes of bacterial and fungal infections in infants born before 24 weeks' gestational age. This review also discusses major knowledge gaps in infection epidemiology, prevention, and management, highlighting the need for more robust international data and innovative strategies to address the unique vulnerabilities of these infants.

  PublisherOA PDFDOI

• Health Care–Associated Infections Among Neonates During the COVID-19 Pandemic

  JAMA Network Open · 2026-01-28

  articleOpen access

  Importance: Neonatal intensive care units (NICUs) implemented enhanced infection prevention measures during the COVID-19 pandemic to interrupt viral transmission. It was hypothesized that these measures would also reduce nonviral health care-associated infections (HAIs). Objective: To compare rates of viral and bacterial or fungal HAIs in infants admitted to the NICU before and during the pandemic. Design, Setting, and Participants: This cohort study was conducted at 12 level 3 or level 4 NICUs in the US and Canada. Participants were inborn and outborn infants admitted from March 1, 2018, to July 31, 2022, for at least 1 overnight stay at participating NICUs. Data analyses were performed from September 1, 2023, to July 28, 2025. Exposure: The viral and bacterial or fungal HAI rates during the pandemic (April 1, 2020, to July 31, 2022) were compared with those before the pandemic (March 1, 2018, to March 31, 2020). Main Outcomes and Measures: HAI incidence before and during the pandemic was expressed as episodes per 1000 patient-days and compared using pre-post and time series analysis with Poisson regression. HAI was defined as an infection diagnosed 3 or more days after admission and was confirmed using molecular diagnostics for viruses and culture of blood, cerebrospinal fluid, or urine for bacteria or fungal pathogens. Results: The full cohort comprised 48 475 infants, grouped into the viral HAI or bacterial or fungal HAI subpopulations. Among 41 889 infants with 966 025 patient-days admitted at 11 NICUs, 231 (mean [SD] gestational age, 30.5 [5.3] weeks; 147 males [63.6%]) had 241 episodes of viral HAI. Viral HAI rates decreased from 0.35 to 0.16 per 1000 patient-days with an adjusted rate ratio (aRR) of 0.45 (95% CI, 0.34-0.59). Reduced rates persisted during the later pandemic period (April 1, 2021, to July 31, 2022) compared with the corresponding period before the pandemic (aRR, 0.58; 95% CI, 0.42-0.80), even as viral infections in the community increased. Among 48 475 infants with 1 130 038 patient-days at 12 study NICUs, 1537 (mean [SD] gestational age, 29.4 [5.2] weeks; 930 males [60.5%]) had 1969 episodes of bacterial or fungal HAI. Bacterial or fungal HAI rates did not decrease from before to during the pandemic (1.70 to 1.78 per 1000 patient-days; aRR, 1.04; 95% CI, 0.95-1.14). At the site level, changes in bacterial or fungal HAI rates did not correlate with viral HAI rates. Conclusions and Relevance: This cohort study found that viral HAIs decreased significantly during the pandemic, while bacterial or fungal HAIs did not. These findings suggest that the enhanced infection prevention measures used during the pandemic may be beneficial during periods of high viral activity but offer limited additional benefit for preventing bacterial or fungal HAI.

  PublisherDOI

• Lymphocytic Choriomeningitis Virus Seroprevalence among Urban Pregnant Women and Newborns, Philadelphia, Pennsylvania, USA, 2021

  Emerging infectious diseases · 2026-02-25 · 1 citations

  articleOpen access1st authorCorresponding

  Lymphocytic choriomeningitis virus (LCMV) is a globally distributed rodentborne pathogen that can cause severe congenital infections. We conducted a retrospective cross-sectional seroepidemiologic study using remnant serum samples from pregnant women and newborns at 2 hospitals in Philadelphia, Pennsylvania, USA. We tested samples for LCMV IgG and IgM in 3 phases: a high-risk group determined by neighborhood deprivation index scores, a random sample of all birthing women, and a group with prenatally diagnosed neurologic malformations. We found LCMV IgG seroprevalence was 2.4% among 700 high-risk and 2.7% among 300 randomly selected pregnant women. Seroprevalence varied by hospital site, maternal race or ethnicity, and neighborhood deprivation level. All seropositive maternal samples were IgM-negative. Thirty-seven pregnant women carrying fetuses with neurologic malformations were seronegative. Our findings highlight the risk for LCMV exposure in urban settings and emphasize the need for pregnant women to avoid contact with rodents to prevent this rare but serious congenital infection.

  PublisherDOI

• Late-Onset Sepsis Among Extremely Preterm Infants During the COVID-19 Pandemic

  PEDIATRICS · 2025-01-23 · 5 citations

  articleOpen access

  OBJECTIVES: To compare incidence of late-onset sepsis (LOS) among extremely preterm infants before and during the COVID-19 pandemic. METHODS: Multicenter cohort study of infants with birthweight 401 to 1000 g or gestational age 22 to 28 weeks. LOS was defined as a bacterial or fungal pathogen isolated from blood or cerebrospinal fluid culture obtained after 72 hours of age. Primary outcome was LOS incidence calculated as incidence proportion (LOS cases among all admissions) and incidence rate (LOS events/1000 patient days). A multivariable Poisson regression model was used to compare the adjusted risk of LOS incidence proportion before (1/1/18-3/31/20) and during the pandemic (4/1/20-12/31/21). An interrupted time series analysis using a generalized linear mixed model with center as a random effect was used to compare LOS incidence rates during the 2 periods. RESULTS: Among 6509 eligible infants, LOS incidence proportion was not different before (18.2%) and during the pandemic (16.9%; P = .18). The adjusted relative risk (95% CI) for LOS was 0.93 (0.82-1.05) and for LOS or mortality was 0.98 (0.88-1.08) during the pandemic compared to the period before the pandemic. In the interrupted time series analysis, there was no significant change in LOS incidence rates at the start of the pandemic (0.219, 95% CI, -0.453 to 0.891) or microbiology of LOS, and change in trends of LOS incidence rates before and during the pandemic was not significant (-0.005, 95% CI, -0.025 to 0.015). CONCLUSIONS: In a large multicenter study of extremely preterm infants, rates of LOS remained unchanged during the pandemic.

  PublisherOA PDFDOI

• Comparison of metrics of neonatal intensive care unit antibiotic use

  Infection Control and Hospital Epidemiology · 2025-08-19

  articleOpen accessSenior authorCorresponding

  OBJECTIVE: To compare temporal trends, variation, and correlations between antibiotic use metrics across U.S. neonatal intensive care units (NICUs) and assess associations with mortality. METHODS: We conducted a retrospective cohort study of 438,156 infants admitted to 272 NICUs from 2017 to 2021 using the Premier Health Database. Antibiotic use rate (AUR), days of therapy (DOT), and antibiotic spectrum index (ASI) per 1,000 patient or therapy days were calculated both cumulatively by year and at the center level. Mixed-effects models adjusted for center-level characteristics were used for all analyses. RESULTS: < 0.001). None were significantly associated with center-level mortality. ASI had the least variability, indicating more uniform antibiotic selection and lower center-level discriminatory value. CONCLUSIONS: DOT and AUR were comparable measures of antibiotic consumption, both showing significant declines. ASI exhibited the least variability, reflecting more consistency in antibiotic selection. The similarity in dispersion and decline between AUR and DOT suggests that neonatal antibiotic exposure is primarily influenced by initiation and discontinuation decisions rather than regimen complexity. Given its ease of calculation, AUR may be the most practical metric for evaluating the impact of antibiotic stewardship interventions at the center level.

  PublisherDOI

• Antibiotic exposure and infection epidemiology among newborns with congenital diaphragmatic hernia

  Journal of Perinatology · 2025-08-18

  articleSenior author
  PublisherDOI

Recent grants

• Identifying Meaningful Metrics of Neonatal Antibiotic Use

  NIH · $719k · 2020–2025

Frequent coauthors

• Karen M. Puopolo

  Children's Hospital of Philadelphia

  158 shared

• Sagori Mukhopadhyay

  113 shared

• Jeffrey S. Gerber

  Children's Hospital of Philadelphia

  98 shared

• Miren B. Dhudasia

  Children's Hospital of Philadelphia

  45 shared

• Madeline R. Pfeifer

  31 shared

• Sarah A. Coggins

  24 shared

• Emily C. Woodford

  Children's Hospital of Philadelphia

  23 shared

• Scott E. Hensley

  University of Pennsylvania

  21 shared

Education

• D.O.

  Philadelphia College of Osteopathic Medicine

  2011

• B.S.

  Virginia Polytechnic Institute and State University

  2007