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Now, That’s What I Call High Yield: Microbiology Part 2

Despite our best efforts, the entirety of microbiology for Step 1 could not be condensed into a single post. Even compressing things down into two posts was difficult. We felt tremendous guilt leaving out information which seemed crucial, but there simply isn’t enough space when we are only trying to get the highest yield information together. Forgive us for this second post, and enjoy the information contained therein. If you are just joining us, start on Micro Part 1 of the 2 part series.

Diarrhea (7.5)

A medical condition that everyone is afflicted with at some point or another, with excellent overlap to pediatrics. Know your ETEC from your EHEC, and be able to categorize pathogens as causing bloody vs. watery diarrhea. As a caveat, remember not all diarrhea has infectious etiology (think osmotic diarrhea, inflammatory bowel disease, intoxicant ingestion/withdrawal).

Pneumonias (8)

One of the most classic pathologies! We can guarantee pneumonia will show up on your Step 1 exam, and on your medicine rotation. Get familiar with clinical severity and chest X-ray findings (virulent with lobar opacities for Strep pneumo, and more indolent presentation with diffuse bilateral infiltrates for atypicals). Know how to cover for particular pathogens. Respiratory fluoroquinolones or macrolides work well for outpatient treatment (e.g., levofloxacin, azithromycin). Inpatients deserve a hearty IV antibiotic to cover S. pneumo (often ceftriaxone), alongside some atypical coverage like azithromycin. If pseudomonas is a concern (as it is in ventilator-associated pneumonia), make sure you have Pseudomonal coverage!

Vaginal infections (7)

The unholy triumvirate of bacterial vaginosis, Trichomonas, and Candida will likely appear on your test. The takeaways here are symptoms/discharge type, and treatment (metronidazole for BV and Trich, -azoles for the fungal Candida). Don’t get too hung up on pH findings. The microscopic findings are important, yet self-explanatory.

TOrCHES infections (7)

This collection of infections can transmit vertically from mother to fetus, and are often the causes of congenital issues. If confronted with a newborn suffering from growth retardation, hepatosplenomegaly, or jaundice, keep these in your differential. Because there are so many overlapping symptoms between the infections, let history be your guide. A pearl for each: Toxoplasmosis from cat feces or raw meat, rubella causing cataracts, deafness, and cardiac issues, CMV causing periventricular calcifications in the brain, HIV presenting with generalized immunodeficiency, herpes from vaginal lesions, and syphilis with facial abnormalities, saddle nose, and maxillary shortening.

Antibiotics/Anti-infectives (10)

This one is a doozy. One of the most common questions that students come to us with is how to memorize all that needs to be known about antibiotics. The short answer is through flashcards and spaced repetition, in addition to dogged studying. Short of that, we can spend a bit of timing trying to tease out what antimicrobials are most important. Because the line must be drawn somewhere, this will be rapid fire run down in 1-3 sentences of the most important antibiotics from each class.

Penicillin (PCN) is worth knowing, as it stands as the prototypical, seminal antibiotic. Also, while penicillin proper isn’t utilized terribly often in the hospital, many of its analogues and cousins are.

Antipseudomonal PCNs, piperacillin and ticarcillin, are famous for the their Pseudomonal coverage.

Cephalosporins are wildly important. First generation (cefazolin) are great for S. Aureus (skin flora) protection in the perioperative period. Third generation extend to include more gram negative coverage (e.g., ceftriaxone), including some, like ceftazidime, that cover Pseudomonas. The only 4th generation cef- drug to know is cefepime, also known for its Pseudomonal coverage.

Carbapenems are part of your arsenal of “big guns.” Very broad spectrum and saved for highly resistant organisms.

Vancomycin is a classic and powerful antibiotic utilized for gram POSITIVE coverage, especially MRSA.

As far as aminoglycosides, the one to know best here is gentamicin. Excellent for gram NEGATIVES, but can ravage the kidneys.

The tetracyclines, of which doxycycline is the one you’ll see most, are most often used for intracellular organisms like Chlamydia, Borrelia, and Rickettsia.

Macrolides (most clinically used is azithromycin) also cover intracellular organisms, and are often used for atypical pneumonias.

Metronidazole is fantastic for anaerobes (below the diaphragm) and GI/vaginal bugs. Use it for C. Diff, Giardia, Trichomonas, and Gardnerella (BV).

If you remember nothing else about antifungals, remember azoles. They take care of non-life threatening fungal infections. Amphotericin, which is not an azole, is your last ditch effort ultra-powerful possibly devastating to your patient antifungal choice.

Antivirals are not as important as their antibiotic neighbors. To triage them, hang onto the cyclovirs for treatment of herpes viruses. It’s also a good idea to be familiar with some of the prototypical drugs used for HIV treatment.


Again, it feels like a disservice to pack so much information into so little space, like we barely scratched the surface. Stay tuned for a much deeper look at antimicrobials, when time and space permit.