ACGME-accredited Medical Microbiology Fellowship

The ACGME-accredited one year fellowship program in clinical microbiology provides advanced training for MD or DO physicians who have completed either a pathology residency, or an internal medicine residency, or an infectious diseases fellowship and wish to subspecialize in clinical microbiology.

The program is hosted by the Indiana University School of Medicine’s Department of Pathology and Laboratory Medicine. ACGME fellows also train side-by-side with CPEP clinical microbiology fellows in the CPEP-accredited Medical Microbiology Fellowship program.

Comprehensive training is provided in the Division of Clinical Microbiology in bacteriology, antimicrobial susceptibility testing (AST), anaerobic bacteriology, molecular diagnostics, mycobacteriology, mycology, parasitology, serology/immunology, and virology. Fellows actively participate in diagnostic and testing activities in each laboratory section. Fellows also have the opportunity to lead weekly laboratory plate rounds on an alternating schedule with CPEP microbiology fellows and participate in bi-weekly microbiology case conferences. Laboratory rounds also serve as in-laboratory education for medical students, pathology residents, and external fellows, i.e. pathology, infectious diseases (ID), and ID pharmacy. Fellows also have the opportunity to participate in teaching rounds and conferences in the Division of Clinical Microbiology and Department of Pathology and Laboratory Medicine and in various Infectious Diseases Services in the Departments of Medicine, Pediatrics, and Infection Control. Fellows routinely participate in laboratory management activities, provider consultations concerning the use of the laboratory and interpretation of test results, assist with diagnostic assay verifications and validations, attend weekly ID Clinical Conferences, and prepare for board examinations.

Fellowship trainees initially work alongside medical laboratory scientists during daily bench rotations to gain fundamental knowledge and experience in microbial pathogen isolation, recognition, identification, and AST. Following each bench rotation, the fellow’s technical proficiency is assessed by formal examinations. Fellows also can attend hospital-based clinical rotations and patient rounds (interacting with infectious diseases physicians, pharmacists, and infection control/prevention practitioners).

During fellowship training, fellows are expected to pursue research projects. Research interest areas include, but are not limited to, enteric and anaerobic bacterial diseases, antimicrobial susceptibility testing (AST), infections in immunocompromised patients, fungal infections, free-living amoebae, and rapid methods and instrumentation for infectious diseases, molecular diagnostics (including microbial identification by nucleic acid amplification including 16S rRNA gene sequencing and real-time PCR, molecular methods for detection of antimicrobial resistance, bacterial strain typing, HPV DNA-typing, and viral load testing and genotyping of various viruses such as HIV and HCV). Fellows are expected to present their 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.

Candidates must be qualified for certification or certified in clinical pathology or combined anatomic pathology-clinical pathology or infectious diseases. They must hold (or be eligible for) a permanent license to practice medicine in the State of Indiana. If candidates are not citizens of the US, they must hold a valid visa. Stipends are commensurate with the year of postgraduate training in pathology.

To apply, applicants should complete the CAP Standard Fellowship application and email it, along with their CV and personal statement, to Noel Stewart, fellowship coordinator. Letters of recommendation should be addressed to:

Christopher Emery, MD 
IU Health Pathology Laboratory
350 W 11th Street, Rm 6027
Indianapolis, IN 46202

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, a centralized reference laboratory for 17 IU Health hospitals and numerous non-IU Health clients, located in Indianapolis, Indiana. Fellows may also rotate within clinical microbiology laboratories at the Sidney & Lois Eskenazi Hospital (which is part of the community-based Eskenazi Health system based in Marion County, Indiana). Public health laboratory experience is gained through rotations at the Indiana Department of Health 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 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 AST. In addition, fellows are trained in classical virus and parasite detection methods by culture and microscopic analysis, respectively.

Fellows have full access to 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, pharmacy fellows, medical students and clinical laboratory science students, enabling cross-discipline collaboration and learning.