Bio

Clinical Focus


  • Cystic Fibrosis
  • Pediatric Pulmonary

Academic Appointments


Professional Education


  • Board Certification: American Board of Pediatrics, Pediatric Pulmonary (2018)
  • Board Certification, American Board of Pediatrics, Pediatric Pulmonology (2018)
  • Fellowship: Stanford University Pediatric Pulmonary Fellowship (2018) CA
  • Residency: Stanford University Pediatric Residency (2015) CA
  • Board Certification: American Board of Pediatrics, Pediatrics (2014)
  • Medical Education: Joe and Teresa Lozano Long School of Medicine at UT San Antonio (2011) TX

Research & Scholarship

Current Research and Scholarly Interests


Patients with cystic fibrosis suffer from chronic infection in their airways. Pseudomonas aeruginosa is the most common bacteria found in their lungs and is associated with faster decline in lung function and earlier death. We recently discovered a bacteriophage (virus) that infects Pseudomonas, Pf bacteriophage. This virus turns sputum into a thick goop of molecules called a biofilm that makes infection very difficult to treat. In the laboratory we know that Pf phage makes biofilms more viscous, more adherent, and it helps protect Pseudomonas from both antibiotics and immune cells. I am currently studying the role of Pf phage in patients with cystic fibrosis. Pf phage is associated with chronic infection, older age and increased antibiotic resistance in patients with cystic fibrosis.

Publications

All Publications


  • Area Under the Curve Achievement of Once Daily Tobramycin in Children with Cystic Fibrosis during Clinical Care. Pediatric pulmonology Brockmeyer, J. M., Wise, R. T., Burgener, E. B., Milla, C., Frymoyer, A. 2020

    Abstract

    BACKGROUND: The area under the concentration-time curve over 24 hours (AUC24 ) is frequently utilized to monitor tobramycin exposure in children with cystic fibrosis (CF). An understanding of exposure target achievement during clinical implementation of an AUC24 based approach in children is limited.METHODS: A retrospective chart review was performed in children with CF treated with once daily tobramycin and drug concentration monitoring at a pediatric CF center. During clinical care AUC24 was estimated using a traditional log-linear regression approach (LLR). AUC24 was also estimated retrospectively using a pharmacokinetic model-based Bayesian forecasting approach (BF). AUC24 achievement after both approaches were compared.RESULTS: In 77 treatment courses (mean age 12.7 5.0 years), a target AUC24 100-125 mg*h/L was achieved after starting dose in 21 (27%) and after initial dose adjustment in 35 (45%). In the first 7 days of treatment, 24 (32%) required ?3 dose adjustments, and the mean number of drug concentrations measured was 7.1 3.2. Examination of a BF approach demonstrated adequate prediction of measured tobramycin concentrations (median bias -2.1% [95% CI -3.1 to -1.4]; median precision 7.6% [95% CI 7.1 to 8.2%]). AUC24 estimates utilizing the BF approach were higher than the LLR approach with a mean difference of 6.4 mg*h/L (95% CI 4.8 to 8.0 mg*h/L).CONCLUSIONS: Achievement of a narrow AUC24 target is challenging during clinical care, and dose individualization is needed in most children with CF. Implementing a BF approach for estimating AUC24 in children with CF is supported. This article is protected by copyright. All rights reserved.

    View details for DOI 10.1002/ppul.25037

    View details for PubMedID 32827334

  • Methods for Extraction and Detection of Pf Bacteriophage DNA from the Sputum of Patients with Cystic Fibrosis. PHAGE (New Rochelle, N.Y.) Burgener, E. B., Secor, P. R., Tracy, M. C., Sweere, J. M., Bik, E. M., Milla, C. E., Bollyky, P. L. 2020; 1 (2): 100?108

    Abstract

    Background: There is increasing interest in the pulmonary microbiome's bacterial and viral communities, particularly in the context of chronic airway infections in cystic fibrosis (CF). However, the isolation of microbial DNA from the sputum from patients with CF is technically challenging and the optimal protocols for the analysis of viral species, including bacteriophage, from clinical samples remains difficult. Materials and Methods: In this study, we evaluate a set of methods developed for processing and analyzing sputum from patients with CF with the goal of detecting Pf bacteriophage virion-derived nucleic acid. We evaluate the impact of bead beating, deoxyribonuclease digestion, and heating steps in these protocols focusing on the quantitative assessment of Pseudomonas aeruginosa and Pf bacteriophage in sputum. Results: Based on these comparative data, we describe an optimized protocol for processing sputum from patients with CF and isolating DNA for polymerase chain reaction or sequencing-based studies. Conclusion: These studies demonstrate the assessment of a specific bacteriophage and bacteria in sputum from patients with CF.

    View details for DOI 10.1089/phage.2020.0003

    View details for PubMedID 32626852

    View details for PubMedCentralID PMC7327540

  • Pf Bacteriophage and Their Impact on Pseudomonas Virulence, Mammalian Immunity, and Chronic Infections. Frontiers in immunology Secor, P. R., Burgener, E. B., Kinnersley, M., Jennings, L. K., Roman-Cruz, V., Popescu, M., Van Belleghem, J. D., Haddock, N., Copeland, C., Michaels, L. A., de Vries, C. R., Chen, Q., Pourtois, J., Wheeler, T. J., Milla, C. E., Bollyky, P. L. 2020; 11: 244

    Abstract

    Pf bacteriophage are temperate phages that infect the bacterium Pseudomonas aeruginosa, a major cause of chronic lung infections in cystic fibrosis (CF) and other settings. Pf and other temperate phages have evolved complex, mutualistic relationships with their bacterial hosts that impact both bacterial phenotypes and chronic infection. We and others have reported that Pf phages are a virulence factor that promote the pathogenesis of P. aeruginosa infections in animal models and are associated with worse skin and lung infections in humans. Here we review the biology of Pf phage and what is known about its contributions to pathogenesis and clinical disease. First, we review the structure, genetics, and epidemiology of Pf phage. Next, we address the diverse and surprising ways that Pf phages contribute to P. aeruginosa phenotypes including effects on biofilm formation, antibiotic resistance, and motility. Then, we cover data indicating that Pf phages suppress mammalian immunity at sites of bacterial infection. Finally, we discuss recent literature implicating Pf in chronic P. aeruginosa infections in CF and other settings. Together, these reports suggest that Pf bacteriophage have direct effects on P. aeruginosa infections and that temperate phages are an exciting frontier in microbiology, immunology, and human health.

    View details for DOI 10.3389/fimmu.2020.00244

    View details for PubMedID 32153575

    View details for PubMedCentralID PMC7047154

  • Filamentous bacteriophages are associated with chronic Pseudomonas lung infections and antibiotic resistance in cystic fibrosis SCIENCE TRANSLATIONAL MEDICINE Burgener, E. B., Sweere, J. M., Bach, M. S., Secor, P. R., Haddock, N., Jennings, L. K., Marvig, R. L., Johansen, H., Rossi, E., Cao, X., Tian, L., Nedelec, L., Molin, S., Bollyky, P. L., Milla, C. E. 2019; 11 (488)
  • Cystic fibrosis transmembrane conductance regulator modulators: precision medicine in cystic fibrosis CURRENT OPINION IN PEDIATRICS Burgener, E. B., Moss, R. B. 2018; 30 (3): 372?77
  • Pf Phage in Chronic Pseudomonas aeruginosa Wound Infections Bach, M. S., Sweere, J., Burgener, E. B., Bollyky, P. L., Suh, G. A. WILEY. 2018: A5
  • PF BACTERIOPHAGE IN PATIENTS WITH CYSTIC FIBROSIS (CF) IS ASSOCIATED WITH INCREASED SPUTUM ELASTASE AND PSEUDOMONAS AERUGINOSA LOAD Burgener, E. B., Sweere, J. M., Bollyky, P. L., Milla, C. WILEY. 2017: S350
  • Clinical characteristics and outcomes of pediatric patients with CMV DNA detection in bronchoalveolar lavage fluid. Pediatric pulmonology Burgener, E. B., Waggoner, J., Pinsky, B. A., Chen, S. F. 2017; 52 (1): 112-118

    Abstract

    Cytomegalovirus (CMV) infection can cause severe pulmonary disease in immunocompromised patients. There are no standard diagnostic criteria for CMV pulmonary disease beyond histopathology findings on lung tissue, which is challenging to obtain in pediatric patients. Bronchoalveolar lavage (BAL) fluid is easier to obtain. Since CMV remains latent after primary infection and can potentially reactivate due to any inflammatory response, CMV detection in BAL specimen may not indicate acute CMV pulmonary disease. Thus, we describe the clinical manifestations and outcomes of pediatric patients with CMV detection in BAL fluid.We reviewed the clinical, radiologic, and laboratory data of patients <19 years old with a BAL specimen positive for CMV during a 5-year period.Thirty-four encounters in 29 patients were found with CMV detected in their BAL specimen. Half (17/34) of the encounters were in immunocompromised patients. CMV, polymerase chain reaction (PCR) was the most common positive test. Forty-seven percent of the patients had other infections detected in BAL specimens. The majority of patients were never treated for CMV and resolved their acute respiratory illness. Only one patient had probable CMV pulmonary disease.CMV is frequently recovered from BAL specimens but does not usually indicate acute CMV pulmonary disease. We would suggest that other diagnoses be considered first, even if CMV is recovered. Pediatr Pulmonol. 2016; 9999:XX-XX. 2016 Wiley Periodicals, Inc.

    View details for DOI 10.1002/ppul.23494

    View details for PubMedID 27280337

  • Molecular and Culture-Based Bronchoalveolar Lavage Fluid Testing for the Diagnosis of Cytomegalovirus Pneumonitis. Open forum infectious diseases Tan, S. K., Burgener, E. B., Waggoner, J. J., Gajurel, K., Gonzalez, S., Chen, S. F., Pinsky, B. A. 2016; 3 (1): ofv212-?

    Abstract

    Background. ?Cytomegalovirus (CMV) is a major cause of morbidity and mortality in immunocompromised patients, with CMV pneumonitis among the most severe manifestations of infection. Although bronchoalveolar lavage (BAL) samples are frequently tested for CMV, the clinical utility of such testing remains uncertain. Methods. ?Retrospective analysis of adult patients undergoing BAL testing via CMV polymerase chain reaction (PCR), shell vial culture, and conventional viral culture between August 2008 and May 2011 was performed. Cytomegalovirus diagnostic methods were compared with a comprehensive definition of CMV pneumonitis that takes into account signs and symptoms, underlying host immunodeficiency, radiographic findings, and laboratory results. Results. ?Seven hundred five patients underwent 1077 bronchoscopy episodes with 1090 BAL specimens sent for CMV testing. Cytomegalovirus-positive patients were more likely to be hematopoietic cell transplant recipients (26% vs 8%, P < .0001) and less likely to have an underlying condition not typically associated with lung disease (3% vs 20%, P < .0001). Histopathology was performed in only 17.3% of CMV-positive bronchoscopy episodes. When CMV diagnostic methods were evaluated against the comprehensive definition, the sensitivity and specificity of PCR, shell vial culture, and conventional culture were 91.3% and 94.6%, 54.4% and 97.4%, and 28.3% and 96.5%, respectively. Compared with culture, PCR provided significantly higher sensitivity and negative predictive value (P ? .001), without significantly lower positive predictive value. Cytomegalovirus quantitation did not improve test performance, resulting in a receiver operating characteristic curve with an area under the curve of 0.53. Conclusions. ?Cytomegalovirus PCR combined with a comprehensive clinical definition provides a pragmatic approach for the diagnosis of CMV pneumonitis.

    View details for DOI 10.1093/ofid/ofv212

    View details for PubMedID 26885542

  • Eosinophilic Pneumonitis As Initial Presentation Of Acute Lymphoblastic Leukemia Burgener, E. B., Milla, C. E. AMER THORACIC SOC. 2016
  • Index of suspicion. Pediatrics in review Todd, S., Arora, R., Kannikeswaran, N., Allarakhia, I., Sivaswamy, L., Wallenstein, M. B., Burgener, E. B., Klotz, J., Kerner, J. A. 2014; 35 (10): 439-446

    View details for DOI 10.1542/pir.35-10-439

    View details for PubMedID 25274971

  • Case 3 Lactic Acidosis and Cardiovascular Collapse in a Teen With Ulcerative Colitis PEDIATRICS IN REVIEW Wallenstein, M. B., Burgener, E. B., Klotz, J., Kerner, J. A. 2014; 35 (10): 444?46
  • The impact of the central venous catheter on the diagnosis of infectious endocarditis using Duke criteria in children with Staphylococcus aureus bacteremia PEDIATRIC INFECTIOUS DISEASE JOURNAL Bendig, E. A., Singh, J., Butler, T. J., Arrieta, A. C. 2008; 27 (7): 636-639

    Abstract

    Infective endocarditis (IE) is a known complication of Staphylococcus aureus bacteremia in pediatric patients. We sought to evaluate the impact of prolonged bacteremia associated with a retained central venous catheter (CVC) in the diagnosis of IE using Duke criteria.We conducted a 13-year retrospective review of hospitalized patients with blood cultures positive for S. aureus from 1993 to 2005. Subjects were identified from the microbiology database and medical records. To identify patients with IE we retrospectively applied the Duke criteria by recording the number of positive blood cultures, time to sterilization, presence of congenital heart disease, fever >38.5 degrees C, and echocardiographic findings.During the study period, 344 events of S. aureus bacteremia were identified in 316 pediatric patients. S. aureus bacteremia attributable mortality was 1.7% (n = 6), all among patients with comorbid conditions. By applying the Duke criteria to the 206 (60%) patients who received echocardiographic evaluation, 78 (37.9%) patients were given a diagnosis of IE (7 definite; 71 possible). The incidence of definite IE in patients with CVC is 3.4% and the incidence in patients without CVC is 3.4% (P = 0.6305). The incidence of possible IE in patients with CVC is 42.9%, whereas the incidence in patients without CVC is 23% (P = 0.002).Evaluation for IE is inconsistently done. The presence of a CVC may skew the diagnosis of IE by prolonging the bacteremic state. We believe that a major microbiologic criteria should not be assumed unless cultures remain positive after removal of CVC.

    View details for DOI 10.1097/INF.0b013e31816b78c8

    View details for Web of Science ID 000257176600010

    View details for PubMedID 18520969

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