Life as an ASM CPEP Fellow: Advancing Clinical Microbiology

Oct. 26, 2021

2018–2020 CPEP Fellows at Clinical Virology Symposium 2019 in Savannah, Ga.
2018–2020 CPEP Fellows at Clinical Virology Symposium 2019 in Savannah, Ga.
Source: American Society for Microbiology
Less than 2 years ago, I was a Committee on Postgraduate Educational Programs (CPEP) fellow in medical and public health microbiology at the University of California, Los Angeles (UCLA). As a fellow from 2018–2020, I had the unique experience of being trained both pre-pandemic and during the pandemic. I witnessed the inner workings of a clinical microbiology lab with, and without, SARS-CoV-2 and facilitated coordination of confirmatory testing of a variety of pathogens with our public health entities. I actively contributed to improving patient care through evaluation of new assays, participating on committees and answering thousands of clinical questions throughout those 2 short years. The experience I gained during my fellowship has profoundly impacted my career trajectory and research interests, as well as prepared me to pursue a career as a clinical microbiology laboratory director. As the requirements for each program can be found online, the most common question I am asked by potential CPEP applicants is, “What is life like as a fellow?”

A Day in the Life of a CPEP Fellow

From the very first day, I was fully immersed in all aspects of clinical microbiology, from being on the bench, to participating in management meetings and shadowing the senior fellows responding to their pages and clinical consults. All CPEP fellowships can be divided into several key focuses: bench experience and other educational activities, clinical service, public health lab rotation, clinical rotations and research.

Bench Experience & Other Educational Activities

CPEP fellows rotate through bacteriology, virology, parasitology, acid fast bacilli, mycology, molecular diagnostics, accessioning and antimicrobial susceptibility testing, spending weeks to months in each section. I was trained by expert medical laboratory professionals and learned traditional methods for identification (biochemical tests), modern methods (MALDI-TOF) and up-and-coming technologies (next-generation sequencing). This bench training translated directly into clinical care, as we continually connected each organism back to the patient and specific case. I was even able to sit for the technologist in microbiology (M(ASCP)) exam, as a result of my bench experience during fellowship.

We also had daily rounds with the directors where we discussed interesting cases or focused on specific disease etiologies. Throughout the week, we attended lectures and case conferences with infectious diseases teams, which further improved our clinical knowledge base. I particularly enjoyed our weekly case conferences with the pediatric infectious diseases team because those conferences allowed for ongoing collaboration and discussion of cases in real time with the treating team. I was also able to actively participate in several committees, including antimicrobial stewardship.

UCLA offered hands-on experience with laboratory management including regular meetings to discuss new assays, review of new laboratory information services and discussion of quality metrics. Some programs offer lab management courses, either onsite (in the case of University of North Carolina (UNC)) or online (in the case of UCLA). Fellows partake in regulatory inspections, including College of American Pathologists (CAP) inspections.

Additionally, CPEP fellowships offer many opportunities for teaching. During my first year, I co-led the laboratory section of the microbiology course for medical students. I also presented cases at case conferences and developed lectures for residents and other trainees. These teaching experiences reinforced my clinical microbiology knowledge and improved my science communication skills. At Memorial Sloan Kettering Cancer Center, CPEP fellows lead the lab scholars program review course to prepare future medical laboratory professionals to sit for their American Society for Clinical Pathology (ASCP) exam. At the University of Utah, CPEP fellows prepare lectures for the medical laboratory sciences (MLS) program.

Clinical Service & Rotations

Once we completed our bench training and settled into the fellowship, we started our on-call clinical service. During that time, we carried a pager and were responsible for answering all questions from providers related to infectious diseases testing. Those questions ranged from “What sample should I collect, and what test should I order if my patient has meningitis symptoms?” to “What does this result mean, and what follow-up testing should be performed?” On-call service was my favorite part of fellowship; the frequency of interactions with clinicians and the variety of cases I consulted on solidified my knowledge base and prepared me to be a director. Transplant, oncology, pediatrics, OB/GYN, neurology, surgery, allergists, cardiology—I can’t name an area of medicine that I did not work with directly during my fellowship.

During my second year, I rotated on the floors with the infectious diseases teams at the children’s hospital, adult inpatient units and veteran’s hospital, as well as with the infection control team. Seeing the patients and participating in the rounds invigorated me. I was able to see firsthand the diagnostic process and contribute my clinical microbiology recommendations for testing. I spent 3 weeks at Los Angeles County Department of Public Health, where I learned about water and food testing, bacterial serotyping for outbreak investigation and public health initiatives. While on clinical service, I often coordinated sending a variety of samples to Los Angeles County for confirmatory testing. However, I had never spent time in a public health lab, and experiencing the processes therein piqued my interest in public health.


Clinical and translational research is also a focus of CPEP fellowships. Unlike most graduate school research, clinical research focuses on directly improving patient care through developing, comparing and implementing new assays. Typically, this research has a direct link to quality improvement initiatives and supports the assessment of the patient's clinical outcomes, as well as costs associated with diagnostic testing and patient care. For example, during my fellowship, I developed a protocol for sequencing fungi directly from formalin-fixed paraffin-embedded tissues, which directly aids in diagnosing invasive fungal infections, particularly in the immunocompromised patient population. I compared this method to existing assays used for fungal diagnostics to assess potential impact on patient care. Fellows present their research at national and international conferences, publish in high-impact journals and become recognized in their field for their fellowship projects. CPEP fellows also participate in quality assurance projects and publish interesting case reports.

Unique Opportunities

In addition to covering the core areas, each CPEP Fellowship offers unique opportunities and experiences. The CPEP fellowship programs at the Mayo Clinic and the University of Utah allow fellows to experience clinical microbiology at large reference laboratories. Others, like Washington University in St. Louis, offer “away” rotations at other institutions. These “away” rotations allow fellows to experience clinical microbiology in other settings, which diversifies fellow experiences and allows fellows to identify lab settings or career paths that most interest them.
2018 – 2020 CPEP Fellows at ASM Microbe 2019 in San Francisco, Calif.
2018 – 2020 CPEP Fellows at ASM Microbe 2019 in San Francisco, Calif.
Source: American Society for Microbiology

Career Options

CPEP fellowships prepare fellows for a wide variety of career options. My experience as a fellow at UCLA solidified my decision to pursue a director position at a large hospital system, where my daily responsibilities focus on teaching, research and clinical service, with strong collaboration across the medical field and ongoing relationship with public health entities. I am now the Director of Molecular Microbiology and Associate Director of Clinical Microbiology at NorthShore University HealthSystem in Evanston, Ill. Following my research during the CPEP fellowship, I continue to pursue development of fungal diagnostics for immunocompromised individuals, while expanding my research interests into other molecular areas, including SARS-CoV-2 sequencing. I am also a Clinical Assistant Professor at the University of Chicago Pritzker School of Medicine, which allows me to continue to educate the next generation of healthcare on medical microbiology and infectious diseases.

Other fellows are directors at public health laboratories, community hospitals, academic medical institutions, reference laboratories or private practices. Leadership positions in industry and diagnostic companies, where clinical microbiology knowledge and experience aids in the development and implementation of novel diagnostic assays, are also common career paths for CPEP fellows. Other CPEP graduates have focused on global and public health initiatives and go on to complete additional fellowships including the laboratory leadership service (LLS) at the Centers for Disease Control and Prevention (CDC).

Beyond the Lab

The role of clinical microbiologists extends far beyond the lab. Clinical microbiologists have profound and lasting impacts on the healthcare system. In our leadership positions, we select which assays to evaluate and bring into the labs (and then monitor their impacts on patient care and finances), serve as active members of the infection control teams, design algorithms for testing of various pathogens and constantly communicate with the treating team. We work with other institutions and industry partners to lead clinical research and trials, while also serving as liaisons to public health entities.

Clinical microbiologists play a leading role in teaching the next generation of clinical microbiologists, pathologists and lab professionals, both within their own institution and outside of it. Many of us contribute to online educational materials that are widely accessible to a large trainee audience. Dr. Richard Davis (University of Utah fellow), Dr. Phyu Thwe (University of Texas Medical Branch fellow), Dr. Erin McElvania (Washington University in St. Louis fellow) and I contribute regularly to the ASCP Lablogatory, where we often work with trainees to describe the diagnostic practices behind real-life cases. Other previous CPEP fellows, including Dr. Peera Hemarajata (UCLA fellow ), are regular ASM contributors.

Leadership extends beyond medicine. Former CPEP fellows, including Dr. Melissa Miller (UNC fellow), have advocated for clinical microbiology and science policy with Congress both through letters and during ASM Hill Day. During the pandemic, many of us were interviewed by journalists to explain SARS-CoV-2 testing to the general public, including Dr. Omai Garner (UCLA fellow), Dr. Susan Butler-Wu (University of Washington fellow), Dr. Amanda Harrington (University of Washington fellow) and countless others.

Prior fellows are also internationally recognized in the medical field. Dr. Karissa Culbreath (UNC fellow) was named to the 2021 Pathologist Powerlist. Dr. Esther Babady (Mayo fellow) was elected into the 2021 American Academy of Microbiology (AAM). Dr. Elitza Theel (Mayo fellow) was named as one in Business Insider’s list of 30 under 40 working to transform healthcare. Previous fellows are editors of world-renowned journals and sit on various committees including the Clinical and Laboratory Standards Institution (CLSI) expert panels. For example, I am a member of the Association for Molecular Pathology (AMP) training and education (T&E) committee, ASM Subcommittee for Postgraduate Education Programs, ASM ABMM exam subvalidation committee, South Central Association for Clinical Microbiology (SCACM) program planning committee and several others. Needless to say, previous CPEP fellows are involved in all areas of clinical microbiology.

How to Prepare for a CPEP Fellowship

With the increase in novel pathogens, expansion of patient populations and ongoing public health efforts, trained clinical microbiology directors and leaders are essential. CPEP fellowships offer the education and training that is necessary to become a director and are open to postdoctoral-level candidates (Ph.D., M.D., Sc.D., etc). Following completion of the 2 year fellowship, fellows are eligible to sit for the American Board in Medical Microbiology (ABMM) exam, qualifying them to serve as CLIA director of a high complexity lab. More details on the programs were recently discussed by Dr. Peter Gilligan.

There is no one right pathway to the CPEP fellowship—some fellows have worked as medical laboratory professionals or clinical laboratory scientists, completed postdocs in public health or microbiology, served in the military or had clinical microbiology experience during graduate school. Acceptance into any program is competitive, and aside from meeting the requirements, clinical microbiology experience is highly desirable. I completed my Experimental Pathology Ph.D. at the University of Virginia (UVA) School of Medicine, which required rotations in clinical pathology areas, including clinical microbiology. This provided me the opportunity to be exposed to clinical microbiology early in my education with the continued ability to participate in clinical microbiology rounds and perform research within that lab throughout my time at UVA. However, if interested in expanding clinical microbiology exposure, there are many ways to do so:
  • Reach out to directors at local clinical microbiology laboratories about the availability of shadowing staff or attending rounds.
  • Attend local, regional or national microbiology conferences to meet clinical microbiologists and keep up to date with exciting progress in the field. ASM Microbe and Clinical Virology Symposium bring together clinical microbiologists from around the world. If a large national meeting is not feasible, local microbiology branches offer smaller conference and networking opportunities.
  • Set up virtual meetings with directors and CPEP fellows to better understand the programs and career paths.
  • Attend Clinical Microbiology Virtual Journal Club to keep up to date with exciting progress and recent literature in the field.
  • Connect with clinical microbiologists on Twitter.

Author: Paige M.K. Larkin, Ph.D., D(ABMM), M(ASCP)

Paige M.K. Larkin, Ph.D., D(ABMM), M(ASCP)
Paige M.K. Larkin, Ph.D., D(ABMM), M(ASCP) is the ASM CPHM program officer. Her interests include molecular microbiology, laboratory practices, coding/reimbursement, lab equity, policy and advocacy.