Case Reports: Clinical Microbiology Stories as Teaching Tools

April 12, 2024

Students receiving clinical teaching.
Students receiving clinical teaching.
Source: Flickr
From childhood, we learn about the world through stories—accounts of a series of related events or experiences. Case reports, which detail the signs, symptoms, diagnosis, treatment and follow-up of individual patients, are the stories of clinical microbiology. One of those stories that first captured my imagination, and ultimately led to a career in clinical microbiology, was that of Joseph Meister, a 9-year old boy living in rural France in 1885. Meister was bitten several times by a rabid dog, a sure death sentence at the time. However, Louis Pasteur was simultaneously developing a rabies vaccine, and a physician colleague, Jacques Grancher, pleaded with Pasteur to allow him to administer the vaccine to the boy. Pasteur agreed, against the advice of his physician research colleague, Emile Roux, who reasoned that Pasteur would be risking his scientific career because the vaccine had never been given to humans, was not standardized and the number of doses needed to induce immunity and its safety in humans remained unknown. At the time, Pasteur was a polarizing member in the medical community because he was a chemist and not a physician. Roux suggested that if this treatment failed, Pasteur's career could be over. Meisner survived, and rabies vaccination has become the global standard of care for preventing rabies in vaccinated domestic animals and saving untold lives in people attacked by rabid animals.

There are thousands of case reports resulting in important medical advances. A 1977 paper by Larson and colleagues describing an unknown toxin in the feces of a child with pseudomembranous colitis (PMC) led Bartlett, Onderdonk and colleagues to discover the primary agent of PMC, Clostridium difficile. C. difficile is now recognized as the leading cause of antimicrobial-associated diarrhea and colitis.

Perhaps the most famous microbiology story in the last 4 decades was that of Barry Marshall, who performed self-experimentation, in which he ingested Helicobacter pylori to show that it was the etiologic agent of peptic ulcer disease. This work garnered Marshall and his colleague, Robin Warren, the Nobel Prize in Physiology. Listen to the story of Barry Marshall in his own words below.

Case Reports as a Road to Discovery

On a Wednesday afternoon in the early 1980s, a case I encountered while rounding with the infectious disease team at St. Christopher’s Hospital for Children changed the trajectory of my own clinical microbiology career. The  team consulted on a young person living with cystic fibrosis (pwCF), who in the previous 2 weeks had graduated from high school, an infrequent event for pwCF in the 80s. He had comparatively good lung function for an 18-year-old pwCF, despite a long history of chronic mucoid Pseudomonas aeruginosa pulmonary infection, the most common cause of chronic lung infection in adolescent and adult pwCF.

A petri dish holding an example of mucoid Pseudomonas aeruginosa.
Mucoid Pseudomonas aeruginosa.
Source: Peter Gilligan.

He was admitted with a white blood count of 22,000/ul, increased cough and sputum production and a temperature of 39° C, all common features of pulmonary exacerbation of chronic P. aeruginosa lung infection in pwCF. He received an anti-pseudomonal penicillin and gentamicin, to which his P. aeruginosa was susceptible, and to which he had responded during several previous hospital admissions. But instead of getting better as he had numerous times before, he got worse. He had rapidly declining lung function with increasing pulmonary infiltrates, persistent fevers and elevated white count. He died of pulmonary arrest just 10 days after I first saw him.

At autopsy, he had pus in his airways, along with an organism I had not really considered important in CF lung disease, Pseudomonas cepacia  (subsequently reclassified as Burkholderia cepacia group). I went to the library (no internet at that time) and found very little about this organism. Next, we examined our autopsy data in pwCF, and found that this organism was present in the lungs of approximately 40% of samples. Working with scientists from the CDC, we found additional data that was truly alarming—20% of pwCF who became infected with this organism died within 90 days, while the organism was essentially absent from respiratory tract cultures of children who did not have cystic fibrosis.

A 1980s chart showing cystic fibrosis survival rates.
Survival of people with cystic fibrosis with (cases) and without (controls) P. cepacia. 1983 Grand Round Presentation at Saint Christopher's Hospital for Children.
Source: Peter Gilligan.

These data showed the P. cepacia was highly virulent in a sub-population of pwCF. Other contemporary studies from 2 other CF centers, Toronto and Cleveland, reported similar findings. In the 1980s and 1990s, B. cepacia complex was as feared in the CF community as HIV was in the general population. Subsequent research and infection control measures have controlled, but not eliminated, this organism from pwCF.

Case Reports as an Educational Tool

Perhaps the greatest impact clinical cases have had in my career has been their use as tools for teaching clinical microbiologists and physicians about microorganisms. McMaster University School of Medicine first challenged the practice of lecture-style passive learning techniques in the late 1960s and 1970s, when faculty developed a novel, active learning approach called "problem-based learning." Here, small groups of 6-12 medical students review a clinical case with the help of a faculty preceptor to consider questions about basic science and clinical care. For example, in a case of pneumonia, the students might be asked to interpret a chest radiograph, explain the pathophysiology of hypoxemia, the basic lung anatomy and gas exchange, identify the etiological agent of pneumonia, interpret a Gram stain, discuss antimicrobial resistance in pneumococci and explain the science behind pneumococcal vaccines. The acceptance of problem-based learning was slow, but over the past 2 decades, it has become an important staple of medical education.

My personal journey of using clinical case studies in education began in 1986 when Michael Miller, founder and curator of ASM’s clinical community listserv, Clinmicronet, asked me to give a lecture on pediatric microbiology at the fall 1986 meeting of the Southeastern Association of Clinical Microbiology (SEACM). I wanted to try something different in this presentation, so, I decided to present (as cases that needed to be solved) some of the unique stories of child and adolescent infectious diseases patients to meeting attendees. Notably, this was and still is a standard approach in clinical case conferences in many disciplines in medicine. I gave the outline of the case and then walked around the audience giving them clues and asking them to identify the organism causing the illness. Overall, the evaluations after the presentation were enthusiastic, and numerous invitations to speak to other clinical microbiology groups followed.

Still, I believe the greatest impact of case studies has been in my teaching of pre-medical and medical students, pathology residents and clinical microbiology fellows. In the late 1980s, my wife Lynn Smiley, an infectious disease specialist and I were having lunch on a Saturday afternoon at the local mall. Lynn had just completed ID clinical rounds and was grousing about how the fourth-year medical students "didn’t seem to know any microbiology." This was quickly getting to be an "uncomfortable" conversation because I was one of the core faculty who had taught them microbiology in their second year. We put on our problem-solving hats and talked about how we might help students understand that what they were learning in the classroom was directly relevant to patient care. Like most U.S. medical schools, the McMaster problem-based learning approach would not be applied until 5-10 years (or more) in the future. However, my experience at the fall 1986 SEACM meeting, coupled with additional presentations, all with enthusiastic receptions, suggested that a case-based approach to teaching microbiology would help medical students understand how to apply microbiology information to patient care.

My challenge was to persuade a primarily Ph.D., basic science faculty that this approach would be welcomed by the students—no small task as a junior faculty member. After some convincing, the course director agreed to try it.

The students were given cases with specific questions to answer within their lab sections. Then a group of 5-6 students would present their answers, and the lab preceptors would oversee the process. The response from the students was highly enthusiastic. One of the real pleasures in my career was having numerous medical students stop me in the hospital or on campus to tell me how they had just seen a case "like the one we learned about in the case discussions."

For the next 25 years, case studies became a staple of microbiology teaching at UNC, now supplanted and appropriately so, by problem-based learning using the McMaster model. For decades, until my retirement, I used case-based, active learning to train a generation of pathology residents and clinical microbiology fellows, as well as clinical microbiologists and infectious disease fellows globally.

One of the outgrowths of that fateful Saturday lunch with my wife was the decision to write a new type of textbook, Cases in Medical Microbiology and Infectious Disease. Working with a clinical microbiology/infectious disease fellow, Daniel Shapiro, and the close guidance of Patrick Fitzgerald, then Director of ASM Books, we published the first edition of this text in 1992. Three additional editions have since been published. The fifth edition, co-authored by Melissa Miller, Andrea Prinzi, Kyle Rodino and me, will be published in late 2024 or early 2025.

ASM's New Journal: ASM Case Reports

Recognizing the importance of case reports to the discipline of clinical microbiology, the American Society for Microbiology is initiating a new journal, ASM Case Reports, in 2025 with manuscripts being accepted this summer. The hope is that this journal will be a rich source for understanding novel microbes important in disease processes or organisms that may not yet be recognized or associated with disease processes, but whose importance will emerge because of applications of novel technologies or thought.

Uncover interesting and unusual findings in the microbiology laboratory by browsing ASM case studies. These cases have been shared by clinical and public health microbiology colleagues and can be used as a teaching tool or to further individual knowledge of the field. Plus, if you have a case study of your own that you would like to submit, check out the open position on our volunteer page

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.