Reflections of a Board-Certified Medical Microbiologist

Sept. 7, 2022

An ABMM-certified medical microbiology laboratory director is medically, scientifically and administratively responsible for all that happens in the laboratory. Responsibilities include, but are not limited to:

  • Clinical consultation: Guiding health care providers on the optimal diagnostic tools and treatment choices for their patients.
  • Quality: Serving as leaders of clinical microbiology laboratories to ensure adherence to best practices and regulatory compliance.
  • Leadership: Oversight of large, diverse teams of laboratory scientists and implementation of cutting-edge technologies to improve the practice of laboratory medicine.
  • Education: Educate and train medical students, residents, fellows, medical laboratory scientists/technicians and other health care team members to contribute to the medical and laboratory workforce.
  • Scientific literacy: Quickly evaluate the science around novel infectious diseases and rapidly develop tools to diagnose and treat them at the local level.
  • Community outreach and engagement: Advocate for funding, public policy changes and communicate with the public.
Ready for duty.
Peter Gilligan, Ph.D., D(ABMM), F(AAM)

Peter H Gilligan D(ABMM) emeritus and F(AAM) was a clinical microbiologist at UNC Health for 35 years and led its Committee on Post-doctoral Educational Programs (CPEP) in Medical Microbiology for 31 years. He was also the initial chair (2011-17) of ASM's Professional Practice Committee (now Clinical and Public Health Microbiology Committee). Here, he answers questions about the experience and impact of his career as an ABMM-certified medical microbiologist.

How have you seen the complexity of microbiology change over your career?

When I began my fellowship training in the late 1970s, Pasteur would have been very comfortable working alongside me. The main tools I used in the clinical microbiology lab included a microscope, inoculating loops, agar plates and broth blood cultures in glass bottles that were little changed from when first used during Pasteur’s lifetime.

Blood culture in glass bottles.
Blood culture in glass bottles.
Source: Peter Gilligan, Ph.D., D(ABMM), F(AAM)
By the 1990s, automation of blood cultures, organism identification and antibiotic susceptibility testing had replaced manual methods of identification. More importantly, the 1990s ushered in nucleic acid amplification tests, primarily using polymerase chain reaction (PCR). PCR introduced the power of genetics and has since become an essential tool to clinical microbiology. It has also made many of the tools used early in my career obsolete, while opening amazing new vistas such as metagenomics for pathogen discovery, whole genome sequencing for outbreak analysis and microbiome analysis to better understand disease processes.

Over the past 10 years, the application of proteomics using matrix-assisted laser desorption-ionization time-of-flight mass spectroscopy (MALDI-TOF MS) has further revolutionized the identification of almost all bacteria and many fungi encountered in clinical specimens. It changed a process that once took hours to days, or even weeks, to complete, to one that takes minutes and provides significant cost savings.

Robotics, in the guise of total laboratory automation, has removed the repetitive task of processing and organizing culture plates in many laboratories, freeing laboratorians to perform high complexity tasks. Artificial intelligence may soon allow the initial screening of these plates by robots as well. Needless to say, Pasteur would not have recognized the 21st century clinical microbiology laboratory.

Describe some specific examples of how the healthcare institution benefits from the expertise of a board-certified medical microbiologist.

Health Care Economics and Stewardship

The scientific and technological evolution of the clinical microbiology laboratory has been dependent, in part, on the willingness of institutions to invest in increasingly more expensive technology—from MALDI-TOF MS, costing $100,000s, to Total Laboratory Automation, requiring investments costing well over $1 million. Being able to justify this expense by cost analysis and patient outcome studies is an important role that ABMM diplomates play in health care economics. Test stewardship, (performing only necessary tests in the most cost-efficient manner) is yet another way that ABMM diplomates are good shepherds of institutional resources.


A significant majority of ABMM diplomates are CPEP program graduates. Part of that training involves recognition of agents of bioterrorism. When the 2001 anthrax attack occurred, we had a protocol in place to rule out Bacillus anthracis. This was very reassuring to our medical staff and hospital administration during uncertain times.

Solving Institutional Problems and Addressing Patient Safety Issues

Participating in hospital-wide committees to solve institutional problems is an important role that ABMM microbiologists can play. I served with 21 other individuals from a variety of health care disciplines, including nursing, infection prevention, patient safety, pharmacy, adult and pediatric infectious diseases, patient equipment, environmental services and hospital administration, tasked with reducing high rates of Clostridium difficile infection, an important patient safety issue. Here are the results of that effort:

Health Care Facility-Onset C. difficile Rates and Novel Interventions

Health care facility-onset C. difficile LabID rates and novel interventions, 2015 to 2017.
Health care facility-onset C. difficile LabID rates and novel interventions, 2015 to 2017.

Describe your interactions with other medical specialties.

Inside the Laboratory

Health care systems are exceedingly complex and depend upon the teamwork of a variety of people with unique, highly-specialized expertise to provide the best possible care to their patients. As a result, clinical microbiologists work with a wide array of medical specialties. We assist anatomic pathologists to differentiate Histoplasma from Pneumocystis, Aspergillus from zygomycetes, and Cryptococcus from Candida in tissue and cytopathology specimens. We also assist our blood bank colleagues in determining if a transfusion reaction is due to a contaminated blood product.

Outside the Laboratory

Outside the walls of the laboratory, my infectious disease-ICU attending wife advised me, "If you want to know what is happening in a hospital, listen to the nurses." Many a morning I would arrive at my office with a nurse waiting at my door to describe an issue that they believed was a barrier to the care of their patient. Some of those meetings led to changes in laboratory policies, which improved patient care.

Our most important allies are the adult and pediatric infectious disease physicians, infectious disease pharmacists (PharmDs) and the infection preventionists. These colleagues investigate unusual service requests, help solve conflicts with unhappy clinicians and provide essential feedback, especially, and most importantly, when shortcomings in our service to their patients exist. Any major changes in laboratory services are discussed with 2 infectious disease services prior to implementation.

What impact have individual patients had on your career?


A person with cystic fibrosis who we saw during weekly pediatric ID rounds changed my scientific career. He was infected with an organism now known to belong to the Burkholderia cepacia complex. I knew nothing about the organism, and it turned out, neither did any of the infectious disease or cystic fibrosis physicians at our institution, nor was there any scientific literature at the time to guide us. This encounter led to a 20-plus-year-journey to understand the organism and its impact on patients.

Career Path

In early summer 2003, UNC had 1 of only 9 SARS-CoV-1cases that occurred in the U.S. The patient was estimated to have potentially exposed up to 300 other people, but without access to diagnostic testing, we had no way of knowing if there were secondary cases.

Our hospital challenged us to develop a SARS test by November of that year, reasoning that this virus might spread during the next respiratory virus season. Test development was put in the hands of our CPEP fellow at this time, Dr. Melissa Miller. Working in the lab of one of our CPEP program graduates, Dr. Rick Hodinka, an early pioneer of molecular diagnosis of viral agents, Miller had a test ready for use by August. Though the test never left the freezer, it prepared Miller to develop numerous laboratory-developed tests, including for Influenza A H1N1 2009, Zika virus, SARS-CoV-2 and now mpox (formerly called monkeypox). Today, she is a nationally recognized leader in molecular viral diagnostics.

Job Satisfaction

‚Äč"Choose a job you love, and you will never have to work a day in your life." 
— Confucius

I was privileged to know that every day when I went to work, I had the opportunity to impact a person’s life in a critical way. I have personally been told, "Thank you for saving the life of my patient," knowing that the "you" referred to all the people I had the privilege of working with in the laboratory.

What value does a board-certified medical microbiologist bring to education for medical students, fellows and residents?

A conversation with my wife, Lynn, in the mid-1980s changed the way I thought about teaching medical students, fellows and residents. She was bemoaning the fact that the medical students she had on clinical service often knew little microbiology. This was painful to hear because I was one of the people teaching microbiology to those students. I asked her why she thought they were deficient. She suggested that they did not understand the relevance of what we were teaching to their medical careers.

Introducing Case Studies as a Teaching Method

I saw an opportunity to increase the clinical relevance by introducing case studies into their microbiology course. The microbiology faculty, few of whom were clinicians, were reluctant, but I promised I would teach them enough clinical knowledge during our faculty review of the cases that they would be effective at teaching them. My CPEP fellowship and infectious disease rounding as a practicing medical microbiologist gave me sufficient competency to do this, while also providing novel teaching materials and experiences.

The students worked enthusiastically through the clinical problems of the presented patients. Nothing was more satisfying than the numerous times a student on a clinical rotation would stop and tell me, "I saw a patient today just like the one you taught us about in class. I learned so much from those clinical cases."

The success of these case histories led Lynn and me, with the able assistance of one of our former ID and Microbiology Fellows, Dr. Dan Shapiro, to write 3 editions of Cases in Medical Microbiology and Infectious Diseases, published by ASM Press. Melissa Miller replaced Lynn on the 4th edition.

Improved Resident In-Service Examination (RISE) and ABMM Scores

We took particular pride in the fact that microbiology became the highest scored subsection of the annual RISE (Resident In-Service Examination), as performance on that exam is a strong predictor of success on the American Board of Pathology examination.

The combination of case-based learning, daily contact with our infectious disease clinicians, strong bench training by our technical staff and management training by our supervisory staff led to the continuing success our fellows have in passing the ABMM Examination.

What is your advice to a future ABMM Diplomate?

Learn to Manage Up

From the Director of the Clinical Laboratories and its Chief Administrator, to the CEO of the Health Care System, I had a cordial, first name working relationship with many influential people at my hospital. Many of those relationships were born in a crisis, or for the simple reason that I saw them often in a shared parking lot and would walk with them to the hospital. They came to know that I was a good and dependable teammate. Those relationships allowed me to be heard when I needed to advocate for my teammates in the clinical microbiology laboratory.

Celebrate Your Colleagues

I am quick to write congratulatory emails to my colleagues for an accomplishment that is important to them, such as a new position, a promotion, publication of a well-done paper, an award or retirement. Within the laboratory, our special celebratory tradition was to sing "Happy Birthday" to everyone. Establish your tradition.

ASM Microbe NOLA
ASM Microbe 2017 in New Orleans. Pictured are Peter Gilligan, lead technologist Melissa Jones and CPEP fellow, Rong Pong Plongla.
Source: Peter Gilligan, Ph.D., D(ABMM), F(AAM)

Say "Yes" to People

The most precious thing I have is time. I am careful how I spend it. However, I try to say "yes" to people who ask for my help on their life journey. I have mentored literally hundreds of young people. I tell them "I walk this journey with you." Some of those journeys have been ongoing for decades. Doing this has allowed me to find my best self.

But Don’t Be Reluctant to Say "No"

Sometimes I was so busy building my career, I forgot to take care of myself. Commit to those things that bring you joy or satisfaction, not things that feel only like an obligation.

Have An "I Am Wonderful" File

Particularly during the pandemic, many of my colleagues have had "dark" days. Save mementoes of your accomplishments as a reminder of good days in the past, and that there will be good days in the future.

Prepare For the Next Pandemic

During my career there have been 2 pandemics, HIV and SARS-CoV-2, that have cost millions of lives. Global warming, increasing urbanization and mass migrations will impact the human relationship with the microbial world in ways that we cannot predict. However, it is important that we think in terms of One Health and apply lessons learned from previous pandemics to be prepared for the next one.

Author: Ashley Hagen, M.S.

Ashley Hagen, M.S.
Ashley Hagen, M.S. is the Scientific and Digital Editor for the American Society for Microbiology and host of ASM's Microbial Minutes.

Author: Peter Gilligan, Ph.D., D(ABMM), F(AAM)

Peter Gilligan, Ph.D., D(ABMM), F(AAM)
Peter Gilligan, Ph.D., D(ABMM), F(AAM) is the former Director of the Clinical Microbiology-Immunology Laboratories at the University of North Carolina Hospitals.