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Now, That’s What I Call High Yield: Microbiology Part 1

As I thumb through the microbiology section of First Aid, it makes me a little nauseous. I’m sure many others feel the same. It’s LONG. Over eighty pages long. To make matters worse, the proper title of the chapter is “High-yield principles in microbiology.” These 80 pages are already the condensed version of high-yield information. We have no choice but to condense this further into the HIGHEST-yield principles of microbiology for USMLE preparation.

Remember, this is by no means comprehensive. That 1000 page textbook on microbiology is comprehensive. This is just a start. In your approach to gargantuan chapters like this, do what you can to scratch one level deeper with each pass through the material. First time through, build the framework. Next time, put some more facts into the framework. Microbiology has so many little facts that it will necessitate multiple passes over time. Those singular facts are also easier to internalize with spaced repetition (flashcards!) like Memorang. The fact that Enterococcus grows in 6.5% NaCl media, or that Strep bovis is related to colon cancer will not get you too far. This primer will help you go after the low-hanging fruit of the material to give you a strong knowledge base.

Bacterial taxonomy (9)

The takeaway here is knowledge of which bacteria are gram positive, gram negative, spirochetes, and atypicals. An age-old gram positive mnemonic – Corny Actors Knock Back Listerine in the Closet. (Corynebacterium, Actinomyces, Nocardia, Bacillus, Listeria, Clostridium). Don’t forget the unforgettables, Staph and Strep. Knowledge of encapsulated bacteria fits in here as well. Thanks, spleen, for clearing those pesky opsonized SHiN organisms (Strep, H. influenzae, Neisseria).

 Endotoxin (6)

More important than the knowledge of endotoxin structure itself is the gestalt of all the terrible things that can happen when your patient is bacteremic (i.e., endotoxin-laden bloodstream). Gram negatives have nasty LPS on their outer membranes, and its presence in appreciable quantity in the bloodstream really, really angers your immune system. Remember from immunology (***link to previous NTWICHY-immuno***), the correct answer to every question is “cytokines.” A shower of IL-1, IL-6, and TNF-α, alongside other “inflammatory mediators,” lead to fever, hypotension, septic shock, coagulation issues, and the feeling of total crumminess.

Staph & Strep (8)

The most classic of gram positive bacteria, these two are incredibly clinically relevant, and we are literally covered in them! Of the staphylococci, S. aureus is undoubtedly most important. It cause skin infections, acute endocarditis, toxic shock syndrome, food poisoning (rapid onset from preformed exotoxin), and MRSA. Get used to blood cultures coming back as “gram positive cocci in clusters.” That’s staph, from the greek staphule, meaning grape.

Knowledge of Streptococci is also super high-yield. Strep pyogenes lives up to its name and causes pyogenic (pus-forming) infections. The most common are pharyngitis (“Strep throat”), cellulitis, and impetigo. These can lead to downstream glomerulonephritis (PSGN) and rheumatic fever. Other pathologies to relate to pyogenes are scarlet fever and necrotizing fasciitis. All that from a single species. The other major Strep, Strep agalactiae, has clinical relevance for parturients, and can cause neonatal meningitis and sepsis, as the defenseless fetus passes through the birth canal.

Clostridium (7)

Collectively, the clostridium (from the Greek kloster, for spindle), cause a number of virulent diseases. They are all toxin related. The pathophysiology of both tetanus and botulism are worth knowing because of their cell biology roots. C. perfringens can cause gas gangrene, and one of the greatest nosocomial villains, C. diff causes…you guessed it…C. Diff Colitis.

Tuberculosis (8)

There is a load of testable information on TB. Everything from CXR findings to the cutoffs for your PPD diameters for a positive test result. Be familiar with the natural course of the disease (progressive primary vs. healing and reactivation), histologic findings of caseating granulomas, and Ghon’s complexes and cavitary lesions on chest X-ray. Treatment paradigms are also important, but we will get to the them on the anti-infectives section.

Pseudomonas (8)

Another nosocomial nuisance that will come up again and again. Pseudomonas aeruginosa (PsA) causes nasty pneumonias, UTIs, wound infections, and more, and is difficult to eradicate because of its polysaccharide capsule. Much of the must-known material is regarding its treatment. You will often find yourself on rounds asking “What will we use for Pseudomonal coverage?” Common options include piperacillin-tazobactam, 3rd and 4th generation cephalosporins (cefepime, ceftazidime), levofloxacin, and carbapenems.

Syphilis (7.5)

The thing that makes syphilis…wonderful?…is that it can have so many different clinical manifestations, and has good overlap to other systems (male & female reproductive, neuro, cardiology, etc.). Be familiar with what primary, secondary, and tertiary syphilis all look like.

Malaria (7)

The dreaded Plasmodium. More than matching cycles to species, realize that this mosquito-borne illness can present with cycling fever and headache. RBCs will often get lysed, and micro-organisms can be found inside RBCs on blood smear. Treat with mefloquine.

Herpes (8)

The collection of herpesviruses cover many pathologies including genital warts, encephalitis, chickenpox & shingles, mononucleosis, roseola, and Kaposi’s sarcoma. Be able to make a diagnosis based on history and physical.

Hepatitis (9)

Hep A through E…five diseases in one! Understand transmission, natural course of the disease including prognosis, and clinical findings of the afflicted. Also wildly important is the immunologic response to Hepatitis infection. Spend some time getting comfortable with all of the serologic markers for Hepatitis A and B. There’s so much to be learned from the different hepatitis B markers. A solid foundation in immunology will make this easier, and working through our bodies’ reactions to HBV will strengthen your immunology knowledge. A delightful cycle.

HIV (8)

So so much important stuff to know about HIV. Start with how reverse transcriptase works, and know the presentation of acute retroviral/HIV illness. Also know the opportunistic organisms involved, and the CD4 counts at which they strike.


There lies part 1. We will round out the rest of micro, including anti-infectives, in part 2. Don’t get bogged down by the factoids. Remember: start from a bottom-up approach. Build the framework of understanding the big picture first, and fill the tiny facts in over time.