Scholarship | ID Fellowship

Research opportunities

Fellow Lauren Fontana, DO, in the lab.

Through a mentored relationship with one or more of the faculty of the ID Division and/or collaborating programs, fellows develop an original research project. Mentor-fellow arrangements are made early during the first year, after sufficient time has elapsed to become acquainted with the faculty and ongoing research opportunities. Fellows receive support for the development and execution of their scholarly work from Program leadership and by a formal Research Advisory Committee. Our fellows receive funding to attend a national scientific meeting each year, where they are expected to present the results of their research. All fellows are encouraged and supported to submit their work for peer-reviewed publication.

The total time devoted to research activities will depend on long-term career objectives, but is at least eleven months in duration. Our fellows often (roughly one fellow every year or two) pursue a third year of fellowship training as research third. Funding for the third year is typically obtained from mentor support, grants or program awards and/or through ID Division foundation funding.

Current research interests of the ID faculty and associated program faculty are broad and include but are not limited to the following:

  • molecular pathogenesis, treatment and epidemiology of a wide range viral and bacterial infections
  • basic science and clinically based HIV research
  • hospital epidemiology and healthcare-associated infections
  • epidemiology and mechanisms of antiviral and antibiotic resistance
  • pharmacokinetics and toxicity of antimicrobial agents
  • clinical evaluation of new antimicrobial agents

Recent Fellow Research

Active Research Projects

Differences in Laboratory Abnormalities between Patients with Pulmonary Mycobacterium avium complex Infections and Bronchiectasis

  • Role: Protocol development, epidemiologist, statistician
  • August 2019 - present
  • Mentor: Kevin Winthrop
  • Status: Protocol development

 Patients with Corynebacterium Striatum Prosthetic Joint Infections: A Case Series

  • Role: Protocol development, epidemiologist, statistician
  • July 2019 - present
  • Mentor: Monica Sikka, James Lewis
  • Status: Protocol development, data collection; submitted for publication

The Brief Case: Persistent Bacteremia and Psoas Abscess Caused by a lethal toxin-deficient Clostridium sordellii

  • Role: scientific writing
  • February 2019 - present
  • Mentor: John Townes
  • Status: manuscript preparation

Missed opportunities for HIV screening and diagnosis

  • Role: Data analysis, protocol modification, data collection
  • January 2019 - present
  • Mentor: Kristine Simpson, Marcel Curlin, Timothy Menza
  • Status: Additional year of data collection, data analysis, presented at 51st Annual Primary Care Review, Portland, OR. February 2020

Laboratory Abnormalities among Patients with Pulmonary Mycobacterium avium complex Infections.

  • Role: Data analysis, abstract preparation
  • November 2018 - present
  • Mentor: Kevin Winthrop
  • Status: abstract presented at Infectious Diseases Society of America: IDWeek 2019.  Washington, DC. October 2019

 Mycobacterium gordonae isolation in Oregon, 2007-2012

  • Role: Primary author, epidemiologist, statistician
  • December 2016 – present
  • Mentor: Kevin Winthrop
  • Status: Manuscript preparation

Validating the Clinical Case Definition for Lassa Fever

  • Role: Epidemiologist, statistician, data entry and management
  • March 2016 - present
  • Mentor: John Schieffelin
  • Status: Manuscript submitted

Publications

Streifel A, Varley CD, Ham YY, Sikka M, Lewis J. Corynebacterium Striatum, Not Your Mother’s Contaminant. Journal of Clinical Microbiology. (Submitted).

Varley CD, Winthrop KL. Practical Management of the Pregnant Patient with Rheumatic Disease: Vaccination before or during pregnancy. Oxford Medical Handbook. (Pending publication, available for preorder)

Schieffelin JS, Varley CD, Samuels R, Goba A, Alhasan, Demby J, Gbakie M, Kanneh L, Karoma V, Momoh M, Bond N, Chiosi J, Engel E, McLaughlin A, Nelson MD, Roberts N, Boisen M, Branco L, Shaffer JG, Bausch DG, Garry RF, Grant DS. Clinical and Laboratory Predictors of Lassa Virus Infection in a Highly Endemic Region of Sierra Leone. (Submitted).

Conference Presentations

Varley CD, Curlin M, Menza TW, Skrypkar D, Simpson K. Missed Opportunities for HIV Screening and Diagnosis. 51st Annual Primary Care Review, Portland, OR. February 2020. (oral presentation)

Varley CD, Henkle E, Ku JH, Strnad L, Brunton A, Winthrop KL. Laboratory Abnormalities among Patients with Pulmonary Mycobacterium avium complex Infections. Infectious Diseases Society of America: IDWeek 2019.  Washington, DC. October 2019.

Primary Fellowship Research Projects

Diagnostic stewardship of urine and C. difficile testing
Mentor: Christopher Pfeiffer, MD
Collaborated with Oregon Health Authority to deploy and analyze statewide surveys of microbiology labs and acute care hospitals; reported on statewide approaches to stewardship of diagnostic tests. 

Curriculum development and analysis in infection control simulation lab
Mentor: Erin Bonura, MD
Wrote an innovation report describing simulation lab curriculum, developed and piloted a new simulation lab case for medical students, created a virtual curriculum for remote learning, designed a study to compare the efficacy of virtual and in-person simulation lab experiences.

Publications

Villamagna A.H. and Bonura, E.M. Infectious Diseases Simulation for Medical Students: Experiential Instruction on Personal Protective Equipment. MedEd Portal. (Submitted.)

Villamagna A.H., Tran D., Williams H., and Pfeiffer C.D. Tracking MDROs across systems. Current Infectious Disease Reports. (Manuscript in preparation.)

Accepted Abstracts and Posters

VillamagnaA.H., Cassidy P.M., Pierce R, Tran D, Tammer R, Iguchi C, Zhang A, Pfeiffer C.D. Is the Vertical Approach to Multidrug-Resistant Organism Prevention Dead? A Survey of Oregon Hospital Surveillance Practices. Poster presentation, SHEA/CDC Decennial International Conference on Healthcare Associated Infections, March 2020 (Cancelled due to COVID-19)

VillamagnaA.H., Cassidy P.M., Pierce R, Tran D, Tammer R, Iguchi C, Zhang A, Pfeiffer C.D. Has UTI and C. difficile testing and treatment stewardship diffused into Oregon hospitals? A survey of the current state. Poster presentation, SHEA/CDC Decennial International Conference on Healthcare Associated Infections, March 2020 (Cancelled due to COVID-19)

Villamagna A.H., Cassidy P, Pierce R, Tran D, Nix C, Pfeiffer C.D. Survey of urine culturing and C. difficile testing practices amongst Oregon microbiology labs. Poster Presentation, ID Week, October 2019, Washington D.C.

Abstracts and Posters

Gore S, Strnad L, Englander H, Gregg J, Sikka M. Outcomes of Multidisciplinary Care Conferences for Patients with Substance Use Disorders Requiring Prolonged Antimicrobial Therapy for Severe Infections.  Poster, IDWeek 2019, Washington, DC

Strnad L, Douglass A, Young K, Mayer H, Brown J, Mahoney S, Dellabough-Gormley E, Gore S, Englander H, Gregg J, Sikka M. The Development, Implementation, and Feasibility of Multidisciplinary Treatment Planning Conference for Individuals with Unstable Substance Use Disorders and Active Infectious Requiring Prolonged Antimicrobial Therapy: the OPTIONS-DC Model.  Poster, IDWeek 2019, Washington, DC

Holmer H, McCracken C, Tallman G, Gore S, Shan T, Yu D, Bearden D, McGregor J. Automating Assessments of Vancomycin Appropriateness.  Poster, IDWeek 2019, Washington, DC

Peer-Reviewed Publications

Gore S and Forrest G. Cryptococcosis in Liver Transplant Candidates and Recipients. Current Fungal Infection Reports. DOI: 10.1007/s12281-020-00399-y.

Grants

Early Clinical Investigators Grant, Medical Research Foundation of Oregon

Project: Carbapenem-Resistant/Fluoroquinolone-Resistant Pseudomonas aeruginosa in Patients with a Hematologic Malignancy and Hematopoietic Stem Cell Transplant Recipients: The Impact of Infection Control Measures on Transmission from Waster Water Drain Sites

Funding period 9/1/2019 through 8/31/2020

Research Projects

Carbapenem-Resistant/Fluoroquinolone-Resistant Pseudomonas aeruginosa in Patients with a Hematologic Malignancy and Hematopoietic Stem Cell Transplant Recipients: The Impact of Infection Control Measures on Transmission From Waste Water Drain Sites

  • Mentors: Lynne Strasfeld, MD, Morgan Hakki, MD, William Messer, PhD, MD
  • Role: Trainee Principal investigator, IRB and IBC submission, grant writing, procurement of patient and environmental samples, execution and oversight of microbiology lab procedures
  • Project: Prospective study, determining the impact of an intervention to limit contamination from waste water drain sites on colonization and infection with carbapenem-resistant/fluoroquinolone-resistant Pseudomonas aeruginosa in patients with a hematologic malignancy and hematopoietic stem cell transplant recipients         

Emergence of Resistance and Associated Mortality during Persistent Pseudomonas aeruginosa Bacteremia

  • Mentor: Morgan Hakki, MD
  • Role: study design, data abstraction, data analysis, manuscript preparation
  • Project: Retrospective study, determine number of persistent bacteremia episodes amongst patients with hematologic malignancies and hematopoietic stem cell transplant recipients compared to the general hospital patient population. Evaluated for risk factors that contribute to emergence of resistance and mortality rates.         

Isavuconazole Prophylaxis in Patients with Hematologic Malignancies and Hematopoietic Stem Cell Transplant Recipients

  • Mentor: Morgan Hakki, MD
  • Role: study design, data abstraction, data analysis, manuscript preparation
  • Project: Retrospective study, evaluating the incidence and characteristics of breakthrough fungal infections in high-risk patients with hematologic malignancies and hematopoietic stem cell transplant recipients while on isavuconazole prophylaxis

Quality Improvement Projects

Utilization of MRSA Nasal PCR Screen: An Antibiotic Stewardship Tool to Decrease Use of Empiric Vancomycin for Treatment of Pneumonia in the MICU at OHSU

  • Mentor: Ellie Sukerman, MD
  • Project: Utilizing MRSA nasal screens to guide de-escalation of empiric anti-Staphylococcus coverage in patients with pneumonia in the MICU

Peer Reviewed Publications

Fontana L, Perlin DS, Zhao Y, Noble BN, Lewis JS, Strasfeld L, Hakki M. Isavuconazole prophylaxis in patients with hematologic malignancies and hematopoietic-cell transplant recipients. Clin Infect Dis. 2019. Epub 2019/04/09. doi: 10.1093/cid/ciz282. PubMed PMID: 30958538.

Fontana L, Bonura E, Lyski Z, Messer W. The Brief Case: Klebsiella variicola-Identifying the Misidentified. J Clin Microbiol. 2019;57(1). Epub 2019/01/04. doi: 10.1128/JCM.00826-18. PubMed PMID: 30602547; PMCID: PMC6322460.

Fontana L, Bonura E, Lyski Z, Messer W. Closing the Brief Case: Klebsiella variicola-Identifying the Misidentified. J Clin Microbiol. 2019;57(1). Epub 2019/01/04. doi: 10.1128/JCM.00825-18. PubMed PMID: 30602546; PMCID: PMC6322464.

Electronic Publications

Fontana L, Bonura E, Hakki, M. Vision Loss in a Man with a Stem Cell Transplant. Partners Infectious Disease Images eMicrobes Digital Library. http://www.idimages.org/idreview/case/?CaseID=562. Published March 2019. Accessed March 09, 2019. (Invited oral presentation ID week 10/2018)

Book Chapters

Fontana L, Strasfeld L. Respiratory Virus Infections of the Stem Cell Transplant Recipient and the Hematologic Malignancy Patient. Infect Dis Clin North Am. 2019. Epub 2019/04/04. doi: 10.1016/j.idc.2019.02.004. PubMed PMID: 30940462.
Editor: Jo-Anne H Young

Invited National Presentations

Oral Presentation, Case Report: Vision Loss in a Man with a Stem Cell Transplant.
Contributing Authors: Erin Bonura and Morgan Hakki
ID Week, 2018, San Francisco, CA

Abstracts Presentations at Professional Meetings

Fontana, L and Hakki, M. Emergence of Resistance and Associated Mortality during Persistent Pseudomonas aeruginosa Bacteremia.
Poster presentation, ID Week, 2019, Washington D.C.

Fontana L, Perlin DS, Zhao Y, Noble BN, Lewis JS, Strasfeld L, Hakki M.  Isavuconazole prophylaxis in patients with hematologic malignancies and hematopoietic-cell transplant recipients.
Poster presentation, 3rd Symposium on Infectious Diseases in the Immunocompromised Host, 2019, Seattle, WA

Fontana L, J Lewis, Hakki, M. Breakthrough Invasive Pulmonary Aspergillosis during Isavuconazole Prophylaxis in Patients with Hematologic Malignancies: A Singe Center Experience.
Poster Presentation, ID Week, 2018, San Francisco, CA