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Introduction to bacteria

Bacterial structure and functions

Gram positive bacteria

Staphylococcus epidermidis

Staphylococcus aureus

Staphylococcus saprophyticus

Streptococcus viridans

Streptococcus pneumoniae

Streptococcus pyogenes (Group A Strep)

Streptococcus agalactiae (Group B Strep)


Clostridium perfringens

Clostridium botulinum (Botulism)

Clostridium difficile (Pseudomembranous colitis)

Clostridium tetani (Tetanus)

Bacillus cereus (Food poisoning)

Listeria monocytogenes

Corynebacterium diphtheriae (Diphtheria)

Bacillus anthracis (Anthrax)


Actinomyces israelii

Gram negative bacteria

Escherichia coli

Salmonella (non-typhoidal)

Salmonella typhi (typhoid fever)

Pseudomonas aeruginosa


Klebsiella pneumoniae


Proteus mirabilis

Yersinia enterocolitica

Legionella pneumophila (Legionnaires disease and Pontiac fever)

Serratia marcescens

Bacteroides fragilis

Yersinia pestis (Plague)

Vibrio cholerae (Cholera)

Helicobacter pylori

Campylobacter jejuni

Neisseria meningitidis

Neisseria gonorrhoeae

Moraxella catarrhalis

Francisella tularensis (Tularemia)

Bordetella pertussis (Pertussis/Whooping cough)


Haemophilus influenzae

Haemophilus ducreyi (Chancroid)

Pasteurella multocida


Mycobacterium tuberculosis (Tuberculosis)

Mycobacterium leprae

Mycobacterium avium complex (NORD)

Other bacteria

Mycoplasma pneumoniae

Chlamydia pneumoniae

Chlamydia trachomatis

Borrelia burgdorferi (Lyme disease)

Borrelia species (Relapsing fever)


Treponema pallidum (Syphilis)

Rickettsia rickettsii (Rocky Mountain spotted fever) and other Rickettsia species

Coxiella burnetii (Q fever)

Ehrlichia and Anaplasma

Gardnerella vaginalis (Bacterial vaginosis)



USMLE® Step 1 questions

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High Yield Notes

17 pages


USMLE® Step 1 style questions USMLE

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A 16-year-old boy is brought to urgent care for evaluation of crampy abdominal pain and diarrhea. The patient has noticed bright red blood and mucus mixed with stool. Temperature is 38.4 °C (101.3 °F), blood pressure is 103/76 mmHg, pulse is 108/min and respirations are 16/min. Physical examination shows dry mucous membranes. There is mild diffuse abdominal tenderness to palpation. Stool cultures show an immotile Gram-negative organism that produces a toxin capable of inhibiting the 60S ribosomal subunit. Which of the following statements is true regarding the pathogen responsible for this patient’s symptoms?  

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Shigella is a Gram-negative bacterium that belongs to the Enterobacteriaceae family.

There are 4 species of Shigella:

S. dysenteriae, S. flexneri; S. boydii; and S. sonnei, and each has its own serotypes.

In humans these species can all cause Shigellosis, which is a contagious infection of the intestines, particularly the colon.

And shigellosis can progress to dysentery, which is when the infection causes inflammation of the colon, resulting in severe abdominal pain and diarrhea.

Now, Shigella is a gram-negative, rod shaped bacterium, meaning it looks like a little red or pink stick on a gram stain.

And it’s a facultative anaerobe, so it can survive with or without oxygen in the environment.

It has no flagellum, making it nonmotile; and it doesn’t form spores.

It’s also a non-lactose fermenter, so it doesn’t ferment lactose; and it’s urease and oxidase-negative, meaning it doesn’t produce these enzymes.

Finally, it doesn’t produce hydrogen sulfide gas either, and this can be used to selectively identify Shigella on special culture mediums like MacConkey agar.

On this medium, Shigella mostly forms white, non-lactose fermenting, non-hydrogen sulfide-producing colonies

Now, once Shigella is ingested, it multiplies in the small intestine, and then passes into the colon.

There, it targets the epithelial layer of the mucosal lining where it infects colonic enterocytes and microfold cells, or M-cells.

And these M-cells phagocytose, which means they eat the bacteria from the intestinal lumen, and then spit it out into the underlying mucosa-associated lymphoid tissues, or MALTs.

MALTs are a type of mucosal immune tissue that extends into the submucosa, and contains plenty of immune cells like macrophages.

The macrophages gobble up Shigella to neutralize the pathogen, but the bacterium induces apoptosis, or programmed cell death, in the macrophage.


Shigella is a genus of bacteria known to cause a contagious form of gastroenteritis known as shigellosis. Shigellosis is characterized by an inflammation of the gastrointestinal tract, which causes destruction and inflammation of the epithelium, leading to dysentery with symptoms like severe abdominal and rectal cramping and pain, a fever, and watery diarrhea with mucous with or without blood or pus. Shigella is transmitted through the fecal-to-oral route, mainly through fingers, food, and flies. It's diagnosed with a fecal sample and treatment centers around fluid and electrolyte replenishment and antibiotics.


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