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CPEP-accredited Medical Microbiology Fellowship

Indiana University School of Medicine’s Medical and Public Health Laboratory Microbiology Fellowship is a two year post-doctoral training program designed to prepare trainees to direct clinical and public health microbiology laboratories. The program is hosted by the Department of Pathology and Laboratory Medicine and is accredited by the American Society for Microbiology’s Subcommittee on Postgraduate Educational Programs (CPEP).

The program accepts one doctoral-level scientist (PhD) or other doctoral-level professional (MD, MD/PhD, etc.) each year. Throughout the first year of training, fellows spend most of their time (~70%) working alongside medical laboratory scientists during daily bench rotations to gain fundamental knowledge and experience in microbial pathogen isolation, recognition, identification, and antimicrobial susceptibility testing.

Following each bench rotation, the fellow’s technical proficiency is assessed by formal examinations. Fellows will also lead weekly laboratory rounds on an alternating schedule, which serves as in-laboratory education for medical students, pathology residents, and external fellows (i.e. pathology, infectious diseases, ID pharmacy). When fellows are not rotating in the clinical laboratory, time is spent preparing lectures for bi-weekly microbiology case conferences and teaching rounds, consulting with patient care providers, assisting with diagnostic assay verifications and validations, attending weekly Infectious Disease Clinical Conferences, and preparing for board examinations.

The second year of training is largely dedicated to hospital-based clinical rotations and patient rounds (interacting with infectious diseases physicians, pharmacists, and infection control/prevention practitioners), research, public health laboratory microbiology training, and clinical consultation for laboratory testing. Fellows also continue to participate in microbiology laboratory case conferences and rounds.

Areas of Focus

The CPEP-accredited Medical and Public Health Laboratory Microbiology Fellowship Program adheres to CPEP Essentials and Guidelines of an Accredited Postgraduate Fellowship Program in Medical and Public Health Laboratory Microbiology, and as such, fellows receive comprehensive training in:

  • Aerobic and anaerobic bacteriology
  • Antimicrobial susceptibility testing, utilization, and stewardship
  • Biothreat agent detection and identification
  • Clinical consultation
  • Clinical infectious diseases
  • Infection prevention and control
  • Infectious disease immunology and serology
  • Infectious disease pathology
  • Laboratory directorship and management
  • Molecular microbiology
  • Mycobacteriology
  • Mycology
  • Outbreak response
  • Parasitology
  • Public health laboratory microbiology
  • Virology

Fellows are presented opportunities throughout their training to participate in applied and basic research projects centered around the development of novel antimicrobial drug susceptibility testing methods, development and evaluation of diagnostic devices, emerging zoonotic viruses, and industry-sponsored investigator-initiated studies through the In Vitro Diagnostics Development and Clinical Trials group of the Department of Pathology and Laboratory Medicine. Fellows are expected to present research findings via publication in peer-refereed journals and/or at scientific conferences, including the ASM Clinical Virology Symposium, ASM Microbe, the South Central Association for Clinical Microbiology, the Pan-American Society for Clinical Virology, and the Association for Molecular Pathology, among others.

Facilities and Resources

Clinical and molecular microbiology rotations occur primarily within the Indiana University Health Divisions of Clinical Microbiology and Molecular Pathology at the IU Health Pathology Laboratory (IUHPL), a centralized reference laboratory for 18 IU Health hospitals and numerous non-IU Health clients, located in Indianapolis, IN. Fellows also rotate within the clinical microbiology laboratories of the Sidney & Lois Eskenazi Hospital (which is part of the community-based Eskenazi Health system based in Marion County, IN) and the Richard L. Roudebush VA Medical Center. Public health laboratory experience is gained through rotations at the Indiana Department of Health (IDOH) Laboratories. Clinical rotations, including clinical infectious diseases, infectious disease pharmacy and antimicrobial stewardship, and infection prevention and control, occur at various IU Health hospitals, including the Riley Hospital for Children, Methodist Hospital, University Hospital, and also at the Sidney & Lois Eskenazi Hospital. All participating institutions are located within a  one mile radius of each other in downtown Indianapolis.

Each laboratory facility uses state-of-the-art laboratory testing methods and instrumentation to detect, identify, and characterize common and esoteric pathogens isolated from diverse patient populations. Fellows gain experience using the latest methods for microbial pathogen identification and characterization such as mass spectrometry, rapid nucleic acid amplification testing, nucleotide sequencing, and automated antimicrobial susceptibility testing. In addition, fellows are trained in classical methods of virus and parasite detection by culture and microscopic analysis, respectively.

Fellows have full access to all training materials, including published references, completed proficiency testing survey materials, training slide sets, and archived lectures, throughout their training. In addition, fellows regularly interact with trainees from other disciplines, including pathology residents, infectious diseases fellows, infectious diseases pharmacy fellows, medical students, and clinical laboratory science students, which enables cross-discipline collaboration and learning.

Moreover, ordinarily, the fellows in this CPEP-accredited fellowship train side-by-side with a fellow in the Accreditation Council for Graduate Medical Education (ACGME)-accredited Medical Microbiology fellowship program, which is also hosted by IU School of Medicine within the same divisions. The latter fellow is an MD or DO who has completed either a pathology residency or an internal medicine residency and an infectious diseases fellowship. The daily interaction of trainees in these parallel fellowship programs enables valuable peer-to-peer educational opportunities. For instance, the fellows in the CPEP-accredited program often possess in-depth knowledge of investigative methods and experimental design strategies acquired from prior laboratory experiences, whereas the fellows in the ACGME-accredited program typically bear extensive experience with clinical medicine and the implementation of diagnostic approaches. This arrangement is ripe for cross-pollination between fellows and is a key strength of the IU School of Medicine program as not all institutions offering advanced diagnostic microbiology training concomitantly host individuals from both backgrounds.


Fellows are paid a competitive annual salary and are provided with healthcare benefits. In addition, fellows receive an annual stipend to cover the costs of books and travel to conferences.

Current Fellows

Portrait photo of Dr. Franco

Lauren Franco, PhD

Senior Fellow

PhD: 2017, Montana State University

Portrait photo of Dr. Kendra

Christopher Kendra, PhD

Junior Fellow

PhD: 2023, Penn State University College of Medicine

Former Fellows

Since its inauguration in 2013, the program has graduated nine fellows who currently serve community health care organizations, academic medical centers, the pharmaceutical industry, the biotech industry, and the U.S. military.

Applying to the program

Applications are accepted each year from July 1–September 30, and applicants are notified by mid-January that they have been selected for an interview for a position starting on July 1 of that year. Please note that IU School of Medicine does not reimburse candidates for interview-related expenses such as travel or room and board.

To apply, interested individuals must first complete the online CPEP program application. Preliminary applications are reviewed after the November 30 deadline, and selected applicants will be contacted and asked to complete an institution-specific program application. A complete application package includes:

  1. Completed IU School of Medicine CPEP program application
  2. Up-to-date CV
  3. Personal statement

  4. Three professional letters of recommendation

All required documents must be compiled into a single PDF document and emailed to Aleah La Neve, fellowship and clinical education coordinator, at Letters of recommendation must be submitted separately by referees via e-mail to Aleah La Neve.

Committed to diversity, equity and inclusion

The CPEP-accredited Medical and Public Health Laboratory Microbiology Fellowship program is committed to creating and sustaining a diverse, equitable, and inclusive environment to train future medical and public health microbiologists. We invite all eligible applicants to apply.

Please review eligibility requirements on the American Society for Microbiology’s CPEP website or contact the program coordinator for more information.

American Society for Microbiology CPEP

Email Aleah La Neve

Program Faculty

21552-Relich, Ryan

Ryan F. Relich, PhD

Associate Professor of Clinical Pathology & Laboratory Medicine

Program Director

Read Bio Ryan F. Relich, PhD

27663-Emery, Christopher

Christopher L. Emery, MD

Professor of Clinical Pathology & Laboratory Medicine

Program Associate Director

Read Bio Christopher L. Emery, MD

1779-Beeler, Cole

Cole Beeler, MD

Associate Professor of Clinical Medicine

Read Bio Cole Beeler, MD

15157-Christenson, John

John C. Christenson, MD

Professor of Clinical Pediatrics

Read Bio John C. Christenson, MD

13549-Davis, Thomas

Thomas E. Davis, MD, PhD

Professor of Pathology & Laboratory Medicine

Read Bio Thomas E. Davis, MD, PhD

60670-Gavina, Kenneth

Kenneth Gavina, PhD

Assistant Professor of Clinical Pathology & Laboratory Medicine

Read Bio Kenneth Gavina, PhD

60649-Hiles, Jon

Jon Hiles, PharmD

Adjunct Clinical Assistant Professor of Medicine

Read Bio Jon Hiles, PharmD

44590-Hursh, Rachel

Rachel L. Hursh, MPH

Assistant Professor of Clinical Pathology & Laboratory Medicine

Read Bio Rachel L. Hursh, MPH

44432-Lavik, John-Paul

John-Paul Lavik, PhD, MD

Assistant Professor of Clinical Pathology & Laboratory Medicine

Read Bio John-Paul Lavik, PhD, MD

5065-Kressel, Amy

Amy B. Kressel, MD

Professor of Clinical Medicine

Read Bio Amy B. Kressel, MD