Gastroenteritis is the mild-to-severe inflammation of the stomach and intestines caused by a virus, bacterium, or parasite. The purpose of this lab is to identify and discuss common gastroenteritis pathogens, practice working with mixed cultures, and learn basic epidemiological source tracking skills.
In this lab, a multi-state diarrhea outbreak has occurred. Students will receive a case study patient with a simulated diarrheal sample and a list of foods consumed between 48 and 72 hours prior to the onset of symptoms. They will be tasked with determining if your patient’s symptoms are caused by the outbreak strain or some other pathogen. Additionally, the class will compile data to determine the source of the contamination.
Objectives
After completing this lab, students will be able to:
identify the common causes of gastroenteritis
interpret the results of common biochemical and morphological tests used to diagnose bacterial gastroenteritis
isolate and identify bacteria from mixed cultures
quantify bacteria using the spread plate technique
Skin and soft tissue infections (SSTIs) occur when pathogens invade and reproduce in damaged skin and soft tissues. The purpose of this lab is to become familiar with common SSTI pathogens, develop skills required to work with mixed cultures, and to learn how to test pathogens for antibiotic resistance.
Students receive a case study patient with a simulated wound exudate sample containing an unknown pathogen and two non-pathogenic skin colonizers. They have four lab periods to determine which pathogen is causing the infection. they will then test that pathogen for resistance to their first-line antibiotic treatments.
Objectives
After completing this lab, you will be able to:
identify the common causes of SSTI infections
isolate and identify bacteria from mixed cultures
Interpret the results of common biochemical and morphological tests used to diagnose SSTIs
Bacteremia is the presence of bacteria in the bloodstream. The purpose of this lab is to isolate, identify, and discuss common bacteremia pathogens using common biochemical and morphological tests.
Students receive a case study patient with a simulated blood sample containing an unknown pathogen. These eight patients will be infected by one of eight possible pathogens.
Objectives
After completing this lab, students will be able to:
Identify the common bacterial bacteremia pathogens
Interpret the results of common biochemical and morphological tests used to diagnose bacteremia
Use an enrichment culture to improve the isolation of pathogens from dilute samples
Pneumonia is an infection that causes inflammation in the lungs. The purpose of this lab is to isolate, identify, and discuss bacterial pneumonia pathogens using common biochemical and morphological tests.
Students receive a case study patient with a simulated sputum sample containing two unknown organisms, one of which will be a common pneumonia pathogen. These eight patients will be infected by one of six possible pathogens.
Objectives
After completing this lab, you will be able to:
Isolate and identify bacteria from mixed cultures
Identify the common bacterial pneumonia pathogens
Interpret the results of common biochemical and morphological tests used to diagnose pneumonia
Assess bacterial load from a sputum sample using a semiquantitative quadrant streak
Assess bacterial load from a sputum sample using a semiquantitative Gram stain
In this lab, students will learn how to diagnose Urinary Tract Infections. Urinary tract infections (UTIs) are a common cause of morbidity around the world. The purpose of this lab is to isolate, identify, and discuss common UTI pathogens using common biochemical and morphological tests.
In this lab, students receive a urine sample containing their first unknown bacterial culture. These eight patients will be infected by one of six possible pathogens.
Objectives
After completing this lab, students will be able to:
identify the common causes of urinary tract infections
interpret the results of common biochemical and morphological tests used to diagnose urinary tract infections
isolate bacteria from a urine sample
quantify bacteria in a urine sample using a semiquantitative streak
In this lab, students will explore how the principles of antibody-based human immunity apply to a common laboratory test called an ELISA (enzyme-linked immunosorbent assay). ELISA is commonly used to identify disease-causing pathogens, such as viruses and bacteria. This assay diagnoses an infection by directly screening for the presence of pathogen-specific antigens or indirectly screening for the presence of pathogen-specific antibodies.
Student teams will work to diagnose six patients at risk of HIV infection using a simulation of an indirect ELISA. This kit is a simulated ELISA and does not include actual HIV; thus, there is no risk of infection from the materials included in this lab.
Objectives
After completing this lab, you will be able to:
apply the basic principles of antibody-mediated immunity
describe how an ELISA can be used as a diagnostic tool
diagnose and treat a patient given the results of an ELISA test
The purpose of this exercise is to familiarize the students with the lab safety features and to refresh skills learned in introductory microbiology. They will be practicing aseptic transfer, quadrant streaks, and the Gram stain.
After reviewing the laboratory safety rules, students should receive a mixed culture of Escherichia coli and Staphylococcus aureus. Using that culture, they will practice Gram staining, aseptic transfer, and the quadrant streak. These three skills will be required for the skills test and will be used for nearly every experiment this semester.
Microscopy is the single biggest challenge for students coming into my Pathogenic Microbiology laboratory, despite its regular use in multiple prerequisite classes. Each semester, I ask my students to complete a quick self-assessment on the first day of lab, and the vast majority of students “strongly agree” that they are able to use brightfield microscopy…until I ask them to prove it.
Student perceptions of their ability to use brightfield microscopy at the beginning (pre-class) and end (post-class) of my Pathogenic Microbiology laboratory. As part of the post-class assessment, students are asked to re-rank their abilities from the beginning of the semester (reflection).
Immediately following the self-assessment, I ask my students to Gram stain a mixed culture of E. coli and S. aureus; however, only 59% of students are able to find cells on the microscope. Of the other 41%, some blame the equipment or decide their failure was a fluke, but many hide their inability out of embarrassment or apathy. Very few ask for help.
It isn’t until they start trying to identify unknown bacterial cultures that the students find themselves in the Dunning-Kruger Valley of Despair. Their ability to Gram stain becomes frustratingly inconsistent; some days, everything works perfectly. Other days…not so much.
The Problem
I suspect that the perceived intuitiveness of microscopy is the greatest contributor to microscopy difficulties in teaching laboratories. If somebody cannot find an image, it couldn’t possibly be due to inexperience, right? After all, light microscopes are simple in operation- you place a microscope slide on the stage, look through the ocular lens, and adjust a knob until you see something.
The first student response to microscopy failure is to blame the equipment. Students have an undeserved reputation for being excessively hard on microscopes, while many departments have a well-deserved reputation for not maintaining or replacing their equipment (not mine, btw). Over time, students, TAs, and even instructors can find themselves blaming the equipment, but teaching microscopes are difficult to actually break. More commonly, somebody has naively moved the diaphragm outside of its workable range or inadvertently turned the stage-height safety thumb screw, preventing the stage from ever moving the specimen into the plane of focus. Every semester, I sort through the microscopes labeled “broken” and find that the majority are perfectly functional with minor readjustment.
The second (and worst) student response is to hide in embarrassment. Imposter syndrome sets in quickly when somebody fails to do something they think is simple, and microscopy is actually more complicated than they realize. This problem culminated one semester when, during the final week of the semester, a defeated student admitted they have not been able to use the microscope all semester, and instead relied entirely on their neighbors. It may be (re: is) unhealthy, but I took it as a personal failure- I didn’t effectively communicate one of the most fundamental skills in microbiology, nor did I notice until it was too late.
My Solution
My new approach to teaching microscopy is to “break” the microscopes. Before the second day of class, I crank every knob and dial on each of the microscopes to the extremes. When the students come in, I tell the students that I have “broken” every single microscope in the room. I then challenge the students to fix them using this troubleshooting guide, video tutorials, active demonstrations, their prior knowledge, and a prepared Gram stain slide. I haven’t quantified this exercise yet, but it already seems to be much more effective than the traditional method of teaching them how to really use a microscope. It also gives them a toolbox to refer to the next time they struggle with a microscope.
The purpose of this assignment is to help students build a conceptual model of the application review process. Students will use that model to design application materials that better communicate their qualifications in a meaningful context.
The best professional applications are intentionally designed to communicate evidence that a candidate is qualified for a job, scholarship, graduate program, etc. However, effectively communicating those qualities is not intuitive, especially during the early stages of a career.
Most people believe that they know how to create effective application materials, but that isn’t true. Consider these statistics:
~50% of job applications are rejected because they do not meet the minimum qualifications
~75% of job applications are rejected within 15 seconds of review
In other words, roughly 1 in 4 applications are from qualified individuals whose application materials are so ineffective that they are rejected as quickly as an applicant that didn’t meet the minimum requirements for the job.
Objectives
Each group will review the application materials of 20 applicants for an imaginary quality control lab manager position at McGuffin Eats, a fake food manufacturer. From those candidates, you will choose three to bring in for an interview. Your goal is to hire the most qualified individuals; however, the most qualified candidates may not write the most effective application materials. For your selections, assume that all the applicants are 100% truthful.
As students review these applications, remind them to pay attention to design elements that help them make quick decisions (positive or negative) and those that make the review more difficult.
Approach
Reading and ranking 20 applications is not a trivial task; however, a logical, methodical screening approach can simplify the process and save you time.
Do not start by completely reviewing each application in detail. Instead, identify criteria that can quickly reduce the number of candidates. For example:
Did the applicant submit all the required materials (~1 second per application)?
Yes: Move the application to the next step.
No: Discard the application. If they weren’t able to follow those instructions, how likely are they to appropriately complete their job duties?
Does the applicant have the minimum educational requirement (~3 seconds per application)?
Yes: Move the application to the next step.
No: Discard the application. The minimum education was included for a reason.
Not sure: Discard the application. Clear communication is important.
Does the applicant have relevant experience (~3 seconds per application)?
Yes: Move the application to the next step.
No: Discard the application. They aren’t qualified for the position.
Not sure: Discard the application. If it isn’t included, it doesn’t exist.
Continue with simple, quick screening questions until your pool of candidates is reduced to those that meet all the minimum requirements. Once you have finished eliminating applicants that don’t meet the requirements, you are ready to start ranking the other candidates. For this phase, focus on the strength of the evidence that each applicant provides. For each application, ask yourself these questions:
What evidence does this candidate provide that demonstrates their qualifications?
What are this candidate’s strengths?
How confident am I that this candidate will be successful? Why?
As you review each application, sort them into three categories:
Qualified and Distinguished: The evidence is clear that these candidates would be successful. They would likely be able to complete their job duties with little-to-no training or direct supervision. These candidates should get your full attention.
Qualified and Competitive: These applicants are qualified and would likely be successful, but they would require some training and direct supervision. Depending on the number of qualified and distinguished candidates, you may need to revisit these applications.
Qualified, but not Competitive: These candidates are qualified and might be successful, but the other applicants are obviously better suited. They would need significant training before they would be able to complete their job duties without direct supervision. If groups one and two have plenty of viable candidates, discard this group.
A few weeks ago, I created and tested a single-use, scratch-off mini-case study for my parasitology class. The students absolutely loved the idea, and as I watched them work, it became clear that this could be an incredibly effective tool.
Using scratch-offs isn’t exactly a new idea, and the approach comes with several benefits. First, scratch-offs give students immediate feedback. If they get an answer wrong, they must continue to work on the problem until they get the right answer.
Second, something about scratch-offs is inherently more engaging than a clicker quiz, even though they are functionally similar. With scratchers, you use every resource and debate every option to get the correct answer and keep the “perfect” card. Suspense builds as you scratch to reveal hidden knowledge, especially if you are working against the clock. You feel empowered when the correct answer is revealed and double your efforts when you’re wrong. Don’t get me wrong, digital classroom response systems are still excellent, effective, and easy tools, but the occasional scratcher mini-case creates engagement that excites.
Creating a Mini-Case Study
Designing these mini-cases can be a substantial time investment, but once the design is completed, printing and assembling the scratchers only takes about 15-minutes of prep time for my class of 70 students.
Space is limited on the card, so keep it simple. Include enough details so the students can diagnose the patient, such as clinical signs and symptoms, microscope images, patient behaviors, location, and other risk factors. If you are going to include images directly to the card, you’ll only be able to fit 50-100 words on my template. If you need to add more details, you can free up space by projecting images using PowerPoint.
After you write the case, pick nine possible answers, randomize their order, and arrange them in the 3×3 table on the scratch-off sticker template. Font size 7 seems to work the best with my template, but you may have to abbreviate or use a smaller font on some long scientific names. I print the stickers on my office printer (Lexmark MC2425) and it usually works smoothly.
Copy and paste your scratch-off answers into the table on the card back. Add “correct” or “incorrect” under the scientific name and add a strikethrough on incorrect answers. Once you’ve printed the back, put the scratch-off sticker over the answers, separate the cards, and you’re ready to go.
Game Day
I pass out the cards before class and give the students the first two minutes of class to solve the case. I almost always throw some sort of secondary challenge on the back; for example, describe the life cycle, draw the infectious and/or diagnostic stages and label important structures, a second scratch-off case, or using the chain of infection to describe three ways to prevent the spread of the parasite.
I’m still designing and testing the game aspects of this exercise. Teams are scored using golf rules, earning one “stroke” for each square they scratch. If a team does not turn in a card, they earn the maximum score for that card. Scores are updated and tracked using keepthescore.co. The game component of this won’t be implemented until the Spring of 2023, so I’ll create an update post later.
My Scratch-Offs
I started creating these mini-cases towards the end of the 2022 Spring semester. I’m not teaching this class again until the Spring of 2023, so there likely won’t be a complete set for parasitology until then, but you can download and print my scratchers here.
Student Feedback
Student feedback has been overwhelmingly positive towards this exercise. We’ve tested multiple formats for the exercise (individuals, pairs, and small groups). My students preferred to work in pairs or groups of three (which also helps cut down costs and prep time).
