USMLE Step 1 First Aid 2021-148-184

Microbiology 
microbiology—Basic Bacteriology SEC TION II 125
Stains
Gram stain First-line lab test in bacterial identification. Bacteria with thick peptidoglycan layer retain crystal
violet dye (gram ⊕); bacteria with thin peptidoglycan layer turn red or pink (gram ⊝) with
counterstain.
These bugs do not Gram stain well (These Little Microbes May Unfortunately Lack Real Color
But Are Everywhere):
Treponema, Leptospira Too thin to be visualized
Mycobacteria Cell wall has high lipid content
Mycoplasma, Ureaplasma No cell wall
Legionella, Rickettsia, Chlamydia, Bartonella, Primarily intracellular; also, Chlamydia lack
Anaplasma, Ehrlichia classic peptidoglycan because of muramic
acid
Giemsa stain Chlamydia, Rickettsia, Trypanosomes A , Clumsy Rick Tripped on a Borrowed
Borrelia, Helicobacter pylori, Plasmodium Helicopter Plastered in Gems
Periodic acid–Schiff Stains glycogen, mucopolysaccharides; used PaSs the sugar
stain to diagnose Whipple disease (Tropheryma
whipplei B )
Ziehl-Neelsen stain Acid-fast bacteria (eg, Mycobacteria C , Auramine-rhodamine stain is more often used
(carbol fuchsin) Nocardia; stains mycolic acid in cell wall); for screening (inexpensive, more sensitive)
protozoa (eg, Cryptosporidium oocysts)
India ink stain Cryptococcus neoformans D ; mucicarmine
can also be used to stain thick polysaccharide
capsule red
Silver stain Fungi (eg, Coccidioides E , Pneumocystis
jirovecii), Legionella, Helicobacter pylori
Fluorescent antibody Used to identify many bacteria, viruses, Example is FTA-ABS for syphilis
stain Pneumocystis jirovecii, Giardia, and
Cryptosporidium
A B C D E
FAS1_2021_03-Microbiology.indd 125 11/9/20 4:28 PM

126 SEC TION II Microbiology 
microbiology—Basic Bacteriology
Properties of growth
media The same type of media can possess both (or neither) of these properties.
Selective media Favors the growth of particular organism while preventing growth of other organisms. Example:
Thayer-Martin agar contains antibiotics that allow the selective growth of Neisseria by inhibiting
the growth of other sensitive organisms.
Indicator (differential) Yields a color change in response to the metabolism of certain organisms. Example: MacConkey
media agar contains a pH indicator; a lactose fermenter like E coli will convert lactose to acidic
metabolites color changes to pink.
Special culture requirements

BUG MEDIA USED FOR ISOLATION MEDIA CONTENTS/OTHER
H influenzae Chocolate agar Factors V (NAD+) and X (hematin)
N gonorrhoeae, Thayer-Martin agar Selectively favors growth of Neisseria by
N meningitidis inhibiting growth of gram ⊕ organisms
with vancomycin, gram ⊝ organisms except
Neisseria with trimethoprim and colistin, and
fungi with nystatin
Very typically cultures Neisseria
B pertussis Bordet-Gengou agar (Bordet for Bordetella) Potato extract
Regan-Lowe medium Charcoal, blood, and antibiotic
C diphtheriae Tellurite agar, Löffler medium
M tuberculosis Löwenstein-Jensen medium, Middlebrook
medium, rapid automated broth cultures
M pneumoniae Eaton agar Requires cholesterol
Lactose-fermenting MacConkey agar Fermentation produces acid, causing colonies to
enterics turn pink
E coli Eosin–methylene blue (EMB) agar Colonies with green metallic sheen
Brucella, Francisella, Charcoal yeast extract agar buffered with The Ella siblings, Bruce, Francis, a
Legionella, Pasteurella cysteine and iron legionnaire, and a pasteur (pastor), built the
Sistine (cysteine) chapel out of charcoal and
iron
Fungi Sabouraud agar “Sab’s a fun guy!”
Aerobes Use an O2-dependent system to generate ATP.

Examples include Nocardia, Pseudomonas aeruginosa, Mycobacterium tuberculosis, and Bordetella
pertussis.
Reactivation of M tuberculosis (eg, after immunocompromise or TNF-α inhibitor use) has a
predilection for the apices of the lung.

Microbiology 
Anaerobes Examples include Clostridium, Bacteroides, Anaerobes Can’t Breathe Fresh Air.
Fusobacterium, and Actinomyces israelii. They Anaerobes are normal flora in GI tract, typically
lack catalase and/or superoxide dismutase pathogenic elsewhere. AminO2glycosides are
and are thus susceptible to oxidative damage. ineffective against anaerobes because these
Generally foul smelling (short-chain fatty antibiotics require O2 to enter into bacterial
acids), are difficult to culture, and produce gas cell.
in tissue (CO2 and H2).
Facultative anaerobes May use O2 as a terminal electron acceptor to Streptococci, staphylococci, and enteric gram ⊝
generate ATP, but can also use fermentation bacteria.
and other O2-independent pathways.
Intracellular bacteria
Obligate intracellular Rickettsia, Chlamydia, Coxiella Stay inside (cells) when it is Really Chilly and
Rely on host ATP Cold
Facultative Salmonella, Neisseria, Brucella, Mycobacterium, Some Nasty Bugs May Live FacultativeLY
intracellular Listeria, Francisella, Legionella, Yersinia pestis
Encapsulated bacteria Examples are Pseudomonas aeruginosa, Please SHiNE my SKiS.

A
Streptococcus pneumoniae A , Haemophilus Are opsonized, and then cleared by spleen.
influenzae type b, Neisseria meningitidis, Asplenics (No Spleen Here) have opsonizing
Escherichia coli, Salmonella, Klebsiella ability and thus risk for severe infections;
pneumoniae, and group B Strep. Their need vaccines to protect against:
capsules serve as an antiphagocytic virulence N meningitidis
factor. S pneumoniae
Capsular polysaccharide + protein conjugate H influenzae
serves as an antigen in vaccines.
Encapsulated bacteria Some vaccines containing polysaccharide Pneumococcal vaccines: PCV13 (pneumococcal
vaccines capsule antigens are conjugated to a carrier conjugate vaccine), PPSV23 (pneumococcal
protein, enhancing immunogenicity by polysaccharide vaccine with no conjugated
promoting T-cell activation and subsequent protein).
class switching. A polysaccharide antigen H influenzae type b (conjugate vaccine).
alone cannot be presented to T cells. Meningococcal vaccine (conjugate vaccine).
Urease-positive Proteus, Cryptococcus, H pylori, Ureaplasma, Pee CHUNKSS.

organisms Nocardia, Klebsiella, S epidermidis,
S saprophyticus. Urease hydrolyzes urea
to release ammonia and CO2 pH.
Predisposes to struvite (magnesium
ammonium phosphate) stones, particularly
Proteus.

Catalase-positive Catalase degrades H2O2 into H2O and bubbles of O2 A before it can be converted to microbicidal
organisms products by the enzyme myeloperoxidase. People with chronic granulomatous disease (NADPH
A
oxidase deficiency) have recurrent infections with certain catalase ⊕ organisms.
Examples: Nocardia, Staphylococci, Serratia, Candida, Listeria, E coli, Burkholderia cepacia,
Pseudomonas, Aspergillus, Helicobacter pylori, Bordetella pertussis.
Pigment-producing Actinomyces israelii—yellow “sulfur” granules, Israel has yellow sand

bacteria which are composed of filaments of bacteria
S aureus—golden yellow pigment Aureus (Latin) = gold
P aeruginosa—blue-green pigment (pyocyanin Aerugula is green
and pyoverdin)
Serratia marcescens—red pigment Think red Sriracha hot sauce
In vivo biofilm- S epidermidis Catheter and prosthetic device infections

producing bacteria Viridans streptococci (S mutans, S sanguinis) Dental plaques, infective endocarditis
P aeruginosa Respiratory tree colonization in patients with
cystic fibrosis, ventilator-associated pneumonia
Contact lens–associated keratitis
Nontypeable (unencapsulated) H influenzae Otitis media

Microbiology 
Spore-forming Some gram ⊕ bacteria can form spores A Examples: B anthracis (anthrax), B cereus (food
bacteria when nutrients are limited. Spores lack poisoning), C botulinum (botulism), C difficile
A metabolic activity and are highly resistant to (pseudomembranous colitis), C perfringens
heat and chemicals. Core contains dipicolinic (gas gangrene), C tetani (tetanus).
acid (responsible for heat resistance). Must
autoclave to kill spores (as is done to surgical
equipment) by steaming at 121°C for 15
minutes. Hydrogen peroxide and iodine-based
agents are also sporicidal.
Bacterial virulence
factors These promote evasion of host immune response.
Protein A Binds Fc region of IgG. Prevents opsonization and phagocytosis. Expressed by S aureus.
IgA protease Enzyme that cleaves IgA, allowing bacteria to adhere to and colonize mucous membranes. Secreted
by S pneumoniae, H influenzae type b, and Neisseria (SHiN).
M protein Helps prevent phagocytosis. Expressed by group A streptococci. Sequence homology with human
tropomyosin and myosin (molecular mimicry); possibly underlies the autoimmune response seen
in acute rheumatic fever.

Bacterial genetics
Transformation Competent bacteria can bind and import short Degraded
uncombined Recipient DNA
pieces of environmental naked bacterial DNA Donor DNA
chromosomal DNA (from bacterial cell
lysis). The transfer and expression of newly
Naked DNA Recipient cell Transformed cell
transferred genes is called transformation.
A feature of many bacteria, especially
S pneumoniae, H influenzae type b, and
Neisseria (SHiN).
Adding deoxyribonuclease degrades naked
DNA, preventing transformation.
Conjugation
F+ × F– F+ plasmid contains genes required for sex pilus Single strand
Sex pilus transferred
and conjugation. Bacteria without this plasmid
are termed F–. Sex pilus on F+ bacterium Plasmid
contacts F− bacterium. A single strand
of plasmid DNA is transferred across the F+ cell F– cell F+ cell F– cell F+ cell F+ cell
conjugal bridge (“mating bridge”). No transfer
of chromosomal DNA.
Hfr × F– F+ plasmid can become incorporated into Plasmid incorporates Transfer and replication
into bacterial DNA of part of the chromosome
bacterial chromosomal DNA, termed high-
frequency recombination (Hfr) cell. Transfer Plasmid
of leading part of plasmid and a few flanking F+ cell F– cell Hfr cell F– cell Hfr cell F– cell Hfr cell Recombinant
F– cell
chromosomal genes. High-frequency
recombination may integrate some of those
bacterial genes. Recipient cell remains F– but
now may have new bacterial genes.
Transduction
Generalized A “packaging” error. Lytic phage infects Lytic
Cleavage of Bacterial DNA packaged
Bacteria bacterial DNA in phage capsids
bacterium, leading to cleavage of bacterial phage
DNA. Parts of bacterial chromosomal DNA
may become packaged in phage capsid. Phage
infects another bacterium, transferring these
genes.
Release of new phage Infects other Genes transferred

from lysed cell bacteria to new bacteria
Specialized An “excision” event. Lysogenic phage infects Viral DNA Viral DNA
Lysogenic incorporates in Phage particles
bacterium; viral DNA incorporates into phage Bacteria bacterial DNA carry bacterial DNA
bacterial chromosome. When phage DNA
is excised, flanking bacterial genes may be
excised with it. DNA is packaged into phage
capsid and can infect another bacterium.
Genes for the following 5 bacterial toxins are
encoded in a lysogenic phage (ABCD’S): Group
A strep erythrogenic toxin, Botulinum toxin,
Release of new phage Infects other Genes different from
Cholera toxin, Diphtheria toxin, Shiga toxin. from lysed cell bacteria donor and recipient

Microbiology 
Bacterial genetics (continued)

Transposition A “jumping” process involving a transposon Plasmid
(specialized segment of DNA), which can copy
and excise itself and then insert into the same
DNA molecule or an unrelated DNA (eg, Integration of genes
Transposon
plasmid or chromosome). Critical in creating
Bacterial
plasmids with multiple drug resistance and DNA
transfer across species lines (eg, Tn1546 with Target site
vanA from Enterococcus to S aureus).
Main features of exotoxins and endotoxins

Exotoxins Endotoxins
SOURCE Certain species of gram ⊕ and gram ⊝ bacteria Outer cell membrane of most gram ⊝ bacteria
SECRETED FROM CELL Yes No
CHEMISTRY Polypeptide Lipid A component of LPS (structural part of
bacteria; released when lysed)
LOCATION OF GENES Plasmid or bacteriophage Bacterial chromosome
TOXICITY High (fatal dose on the order of 1 µg) Low (fatal dose on the order of hundreds of
micrograms)
CLINICAL EFFECTS Various effects (see following pages) Fever, shock (hypotension), DIC
MODE OF ACTION Various modes (see following pages) Induces TNF, IL-1, and IL-6
ANTIGENICITY Induces high-titer antibodies called antitoxins Poorly antigenic
VACCINES Toxoids used as vaccines No toxoids formed and no vaccine available
HEAT STABILITY Destroyed rapidly at 60°C (except Stable at 100°C for 1 hr
staphylococcal enterotoxin and E coli heat-
stable toxin)
TYPICAL DISEASES Tetanus, botulism, diphtheria, cholera Meningococcemia; sepsis by gram ⊝ rods
Exotoxin Endotoxin
TNF, IL-1,
Downstream
IL-6
cellular reaction
Host cell

Bacteria with exotoxins

BACTERIA TOXIN MECHANISM MANIFESTATION
Inhibit protein synthesis
Corynebacterium Diphtheria toxina Pharyngitis with pseudomembranes in throat
diphtheriae and severe lymphadenopathy (bull neck),
Inactivate elongation factor myocarditis
(EF-2)
Pseudomonas Exotoxin A a Host cell death
aeruginosa
Shigella spp Shiga toxina Inactivate 60S ribosome by Damages GI mucosa dysentery
Enterohemorrhagic removing adenine from Enhances cytokine release hemolytic-uremic
E coli rRNA syndrome (HUS; prototypically in EHEC
serotype O157:H7)
Unlike Shigella, EHEC does not invade host
cells
Increase fluid secretion
Enterotoxigenic Heat-labile Overactivates adenylate Watery diarrhea: “labile in the Air (Adenylate
E coli toxin (LT)a cyclase ( cAMP) Cl− cyclase), stable on the Ground (Guanylate
secretion in gut and H2O cyclase)”
efflux Bacteria that cAMP include Cholera,
Heat-stable Overactivates guanylate Anthracis, Pertussis, E coli; “Increase cAMP
toxin (ST) cyclase ( cGMP) with CAPE
resorption of NaCl
and H2O in gut
Bacillus anthracis Anthrax toxina Mimics adenylate cyclase Likely responsible for characteristic edematous
( cAMP) borders of black eschar in cutaneous anthrax
Vibrio cholerae Cholera toxina Overactivates adenylate Voluminous “rice-water” diarrhea
cyclase ( cAMP) by
permanently activating Gs
Inhibit phagocytic ability
Bordetella pertussis Pertussis toxina Inactivates inhibitory G Whooping cough—child coughs on expiration
subunit (Gi) activation and “whoops” on inspiration; can cause
of adenylate cyclase “100-day cough” in adults; associated with
cAMP posttussive emesis
Inhibit release of neurotransmitter
Clostridium tetani Tetanospasmina Toxin prevents release of inhibitory (GABA
Both are proteases that and glycine) neurotransmitters from Renshaw
cleave SNARE (soluble cells in spinal cord spastic paralysis, risus
NSF attachment sardonicus, trismus (lockjaw), opisthotonos
Clostridium Botulinum toxina protein receptor), a set Infant botulism—caused by ingestion of spores
botulinum of proteins required for (eg, from soil, raw honey). Toxin produced in
neurotransmitter release vivo
via vesicular fusion Foodborne botulism—caused by ingestion of
preformed toxin (eg, from canned foods)
a
An AB toxin (aka, two-component toxin [or three for anthrax]) with B enabling Binding and triggering uptake (endocytosis)
of the Active A component. The A components are usually ADP ribosyltransferases; others have enzymatic activities as listed
in chart.

Microbiology 
Bacteria with exotoxins (continued)

BACTERIA TOXIN MECHANISM MANIFESTATION
Lyse cell membranes
Clostridium Alpha toxin Phospholipase (lecithinase) Degradation of phospholipids myonecrosis
perfringens that degrades tissue and (“gas gangrene”) and hemolysis (“double zone”
cell membranes of hemolysis on blood agar)
Streptococcus Streptolysin O Protein that degrades cell Lyses RBCs; contributes to β-hemolysis;
pyogenes membrane host antibodies against toxin (ASO) used to
diagnose rheumatic fever (do not confuse
with immune complexes of poststreptococcal
glomerulonephritis)
Superantigens causing shock
Staphylococcus Toxic shock Cross-links β region of Toxic shock syndrome: fever, rash, shock; other
aureus syndrome toxin TCR to MHC class II toxins cause scalded skin syndrome (exfoliative
(TSST-1) on APCs outside of the toxin) and food poisoning (heat-stable
antigen binding site enterotoxin)
Streptococcus Erythrogenic overwhelming release Toxic shock–like syndrome: fever, rash, shock;
pyogenes exotoxin A of IL-1, IL-2, IFN-γ, and scarlet fever
TNF-α shock
Endotoxin LPS found in outer membrane of gram ⊝ ENDOTOXINS:

bacteria (both cocci and rods). Composed of Edema
O-antigen + core polysaccharide + lipid A (the Nitric oxide
toxic component). DIC/Death
Released upon cell lysis or by living cells by Outer membrane
blebs detaching from outer surface membrane TNF-α
(vs exotoxin, which is actively secreted). O-antigen + core polysaccharide + lipid A
Three main effects: macrophage activation eXtremely heat stable
(TLR4/CD14), complement activation, and IL-1 and IL-6
tissue factor activation. Neutrophil chemotaxis
Shock
IL-1, IL-6 Fever
Macrophage activation TNF-α Fever and hypotension

(TLR4/CD14)
Nitric oxide Hypotension
Histamine release:
C3a
Endotoxin Hypotension and edema
(lipid A component) Complement activation
C5a Neutrophil chemotaxis
Coagulation
Tissue factor activation DIC
cascade

microbiology—Clinical Bacteriology
MICROBIOLOGY—CLINICAL BACTERIOLOGY
``
Gram-positive lab algorithm
Gram (purple/blue)
Branching
Bacilli Cocci
filaments
Aerobic Anaerobic Aerobic Anaerobic
Listeria Clostridium Nocardia Actinomyces

Bacillus Cutibacterium (weakly acid fast) (not acid fast)
Corynebacterium
(formerly
Propionibacterium)
Catalase
(Pairs or Streptococcus (Clusters) Staphylococcus

chains)
Hemolysis Coagulase
α γ
(Partial (Complete
hemolysis,
green)
β hemolysis,
clear)
(No hemolysis,
grows in bile)
S aureus
Novobiocin
Optochin sensitivity Bacitracin sensitivity Growth in 6.5% NaCl sensitivity
and bile solubility and PYR status and PYR Status
Group B Group A S saprophyticus S epidermidis

S agalactiae S pyogenes
Viridans streptococci
(no capsule) Enterococcus
S pneumoniae Nonenterococcus E faecium
S mutans (encapsulated) S bovis
S mitis E faecalis
Important tests are in bold. Important pathogens are in bold italics.

Note: Enterococcus is either α- or γ-hemolytic.
Gram-positive cocci antibiotic tests

Staphylococci Novobiocin—Saprophyticus is resistant; Sapro is a no-go on Novo
epidermidis is sensitive
Streptococci Optochin—Viridans is Resistant; Pneumoniae is OVRPS (overpass)
Sensitive
Bacitracin—group B strep are Resistant; group B-BRAS
A strep are Sensitive

Microbiology 
microbiology—Clinical Bacteriology SEC TION II 135
α-hemolytic bacteria Gram ⊕ cocci. Partial oxidation of hemoglobin causes greenish or brownish color without clearing
A around growth on blood agar A . Include the following organisms:
Streptococcus pneumoniae (catalase ⊝ and optochin sensitive)
Viridans streptococci (catalase ⊝ and optochin resistant)
β-hemolytic bacteria Gram ⊕ cocci. Complete lysis of RBCs pale/clear area surrounding colony on blood agar A .
A Include the following organisms:
Staphylococcus aureus (catalase and coagulase ⊕)
Streptococcus pyogenes—group A strep (catalase ⊝ and bacitracin sensitive)
Streptococcus agalactiae—group B strep (catalase ⊝ and bacitracin resistant)
Staphylococcus aureus Gram ⊕, β-hemolytic, catalase ⊕, coagulase TSST-1 is a superantigen that binds to MHC
⊕ cocci in clusters A . Protein A (virulence II and T-cell receptor, resulting in polyclonal
A
factor) binds Fc-IgG, inhibiting complement T-cell activation and cytokine release.
activation and phagocytosis. Commonly Staphylococcal toxic shock syndrome (TSS)—
colonizes the nares, ears, axilla, and groin. fever, vomiting, diarrhea, rash, desquamation,
Causes: shock, end-organ failure. TSS results in AST,
Inflammatory disease—skin infections, ALT, bilirubin. Associated with prolonged
organ abscesses, pneumonia (often after use of vaginal tampons or nasal packing.
influenza virus infection), endocarditis, Compare with Streptococcus pyogenes TSS (a
septic arthritis, and osteomyelitis. toxic shock–like syndrome associated with
Toxin-mediated disease—toxic shock painful skin infection).
syndrome (TSST-1), scalded skin syndrome S aureus food poisoning due to ingestion of
(exfoliative toxin), rapid-onset food preformed toxin short incubation period
poisoning (enterotoxins). (2–6 hr) followed by nonbloody diarrhea
MRSA (methicillin-resistant S aureus)— and emesis. Enterotoxin is heat stable not
important cause of serious nosocomial and destroyed by cooking.
community-acquired infections. Resistance S aureus makes coagulase and toxins. Forms
due to altered penicillin-binding proteins fibrin clot around itself abscess.
(conferred by mecA gene). Some strains release
Panton-Valentine leukocidin (PVL), which
kills leukocytes and causes tissue necrosis.
Staphylococcus Gram ⊕, catalase ⊕, coagulase ⊝, urease ⊕ cocci in clusters. Novobiocin sensitive. Does not
epidermidis ferment mannitol (vs S aureus).
Normal flora of skin; contaminates blood cultures.
Infects prosthetic devices (eg, hip implant, heart valve) and IV catheters by producing adherent
biofilms.

Staphylococcus Gram ⊕, catalase ⊕, coagulase ⊝, urease ⊕ cocci in clusters. Novobiocin resistant.

saprophyticus Normal flora of female genital tract and perineum.
Second most common cause of uncomplicated UTI in young females (most common is E coli).
Streptococcus Gram ⊕, α-hemolytic, lancet-shaped Pneumococcus is associated with “rusty”

pneumoniae diplococci A . sputum, patients with hyposplenia or asplenia.
A Encapsulated. IgA protease. Optochin No virulence without capsule.
sensitive and bile soluble.
Most commonly causes MOPS:
Meningitis
Otitis media (in children)
Pneumonia
Sinusitis
Viridans group Gram ⊕, α-hemolytic cocci. Optochin resistant Viridans group strep live in the mouth, because
streptococci and bile insoluble. Normal flora of the they are not afraid of-the-chin (op-to-chin
oropharynx. resistant).
Streptococcus mutans and S mitis cause dental Sanguinis = blood. Think, “there is lots of
caries. blood in the heart” (endocarditis).
S sanguinis makes dextrans that bind to fibrin-
platelet aggregates on damaged heart valves,
causing subacute bacterial endocarditis.
Streptococcus Gram ⊕ cocci in chains A . Group A strep “Ph”yogenes pharyngitis can result in
pyogenes (group A cause: rheumatic “phever” and glomerulonephritis.
streptococci) Pyogenic—pharyngitis, cellulitis, impetigo Strains causing impetigo can induce
A (“honey-crusted” lesions), erysipelas glomerulonephritis.
Toxigenic—scarlet fever, toxic shock–like Key virulence factors include DNase,
syndrome, necrotizing fasciitis erythrogenic exotoxin, streptokinase,
Immunologic—rheumatic fever, streptolysin O. ASO titer or anti-DNase
glomerulonephritis B antibodies indicate recent S pyogenes
Bacitracin sensitive, β-hemolytic, pyrrolidonyl infection.
arylamidase (PYR) ⊕. Hyaluronic acid capsule Scarlet fever—blanching, sandpaper-like body
and M protein inhibit phagocytosis. Antibodies rash, strawberry tongue, and circumoral
to M protein enhance host defenses against S pallor in the setting of group A streptococcal
pyogenes but can give rise to rheumatic fever. pharyngitis (erythrogenic toxin ⊕).
Diagnose strep pharyngitis via throat swab,
which can be tested with an antigen detection
assay (rapid, in-office results) or cultured on
blood agar (results in 48 hours).

Microbiology 
Streptococcus Gram ⊕ cocci, bacitracin resistant, β-hemolytic, Group B for Babies!

agalactiae (group B colonizes vagina; causes pneumonia,
streptococci) meningitis, and sepsis, mainly in babies.
Polysaccharide capsule confers virulence.
Produces CAMP factor, which enlarges the
area of hemolysis formed by S aureus. (Note:
CAMP stands for the authors of the test, not
cyclic AMP.) Hippurate test ⊕. PYR ⊝.
Screen pregnant patients at 35–37 weeks’
gestation with rectal and vaginal swabs.
Patients with ⊕ culture receive intrapartum
penicillin/ampicillin prophylaxis.
Streptococcus bovis Gram ⊕ cocci, colonizes the gut. S gallolyticus Bovis in the blood = cancer in the colon.
(S bovis biotype 1) can cause bacteremia and
subacute endocarditis. Patients with S bovis
endocarditis have  incidence of colon cancer.
Enterococci Gram ⊕ cocci. Enterococci (E faecalis and Enterococci are more resilient than
E faecium) are normal colonic flora that are streptococci, can grow in 6.5% NaCl and bile
penicillin G resistant and cause UTI, biliary (lab test).
tract infections, and subacute endocarditis Entero = intestine, faecalis = feces, strepto =
(following GI/GU procedures). Catalase ⊝, twisted (chains), coccus = berry.
PYR ⊕, typically nonhemolytic.
VRE (vancomycin-resistant enterococci) are an
important cause of nosocomial infection.
Bacillus anthracis Gram ⊕, spore-forming rod that produces anthrax toxin (an exotoxin consisting of protective
antigen, lethal factor, and edema factor). Has a polypeptide capsule (poly d-glutamate). Colonies
show a halo of projections, sometimes referred to as “medusa head” appearance.
Cutaneous anthrax Painless papule surrounded by vesicles ulcer with black eschar A (painless, necrotic)
A uncommonly progresses to bacteremia and death.
Pulmonary anthrax Inhalation of spores, most commonly from contaminated animals or animal products, although
also a potential bioweapon flu-like symptoms that rapidly progress to fever, pulmonary
hemorrhage, mediastinitis (CXR may show widened mediastinum), and shock. Also called
woolsorter’s disease. Prophylaxis with ciprofloxacin or doxycycline when exposed.

Bacillus cereus Gram ⊕ rod. Causes food poisoning. Spores survive cooking rice (reheated rice syndrome).
Keeping rice warm results in germination of spores and enterotoxin formation.
Emetic type causes nausea and vomiting within 1–5 hours. Caused by cereulide, a preformed toxin.
Diarrheal type causes watery, nonbloody diarrhea and GI pain within 8–18 hours.
Management: supportive care (antibiotics are ineffective against toxins).
Clostridia Gram ⊕, spore-forming, obligate anaerobic rods. Tetanus toxin and botulinum toxin are proteases
that cleave SNARE proteins involved in neurotransmission.
Clostridium tetani Pathogen is noninvasive and remains localized Tetanus is tetanic paralysis.
to wound site. Produces tetanospasmin, an Prevent with tetanus vaccine. Treat with antitoxin
exotoxin causing tetanus. Tetanospasmin +/− vaccine booster, antibiotics, diazepam (for
spreads by retrograde axonal transport to CNS muscle spasms), and wound debridement.
and blocks release of GABA and glycine from
Renshaw cells in spinal cord.
Causes spastic paralysis, trismus (lockjaw), risus
sardonicus (raised eyebrows and open grin),
opisthotonos (spasms of spinal extensors).
Clostridium botulinum Produces a heat-labile toxin that inhibits ACh Botulinum is from bad bottles of food, juice,
release at the neuromuscular junction, causing and honey.
botulism. In babies, ingestion of spores Treatment: human botulinum immunoglobulin.
(eg, in honey) leads to disease (floppy baby Local botulinum toxin A (Botox) injections used
syndrome). In adults, disease is caused by to treat focal dystonia, hyperhidrosis, muscle
ingestion of preformed toxin (eg, in canned spasms, and cosmetic reduction of facial
food). wrinkles.
Symptoms of botulism (the 5 D’s): diplopia,
dysarthria, dysphagia, dyspnea, descending
flaccid paralysis. Does not present with
sensory deficits.
Clostridium Produces α-toxin (lecithinase, a phospholipase) Perfringens perforates a gangrenous leg.
perfringens that can cause myonecrosis (gas gangrene A ;
A
presents as soft tissue crepitus) and hemolysis.
If heavily spore-contaminated food is cooked
but left standing too long at < 60°C, spores
germinate vegetative bacteria heat-labile
enterotoxin late-onset (10-12 hours) food
poisoning symptoms, resolution in 24 hours.
Clostridioides difficile Produces toxins A and B, which damage Difficile causes diarrhea.
B
enterocytes. Both toxins lead to watery diarrhea Diagnosed by PCR or antigen detection of one or
pseudomembranous colitis B . Often 2° both toxins in stool.
to antibiotic use, especially clindamycin, Treatment: oral vancomycin or fidaxomicin.
ampicillin, cephalosporins, fluoroquinolones; For recurrent cases, consider repeating prior
associated with PPIs. regimen or fecal microbiota transplant.
Fulminant infection: toxic megacolon, ileus,
shock.

Microbiology 
Corynebacterium Gram ⊕ rods occurring in angular Coryne = club shaped (metachromatic granules
diphtheriae arrangements; transmitted via respiratory on Löffler media).
A droplets. Causes diphtheria via exotoxin Black colonies on cystine-tellurite agar.
encoded by β-prophage. Potent exotoxin ABCDEFG:
inhibits protein synthesis via ADP-ribosylation ADP-ribosylation
of EF-2, leading to possible necrosis in β-prophage
pharynx, cardiac, and CNS tissue. Corynebacterium
Symptoms include pseudomembranous Diphtheriae
pharyngitis (grayish-white membrane A ) with Elongation Factor 2
lymphadenopathy (“bull’s neck” appearance). Granules
Toxin dissemination may cause myocarditis, Treatment: diphtheria antitoxin +/–
arrhythmias, neuropathies. erythromycin or penicillin.
Lab diagnosis based on gram ⊕ rods with
metachromatic (blue and red) granules and
⊕ Elek test for toxin.
Toxoid vaccine prevents diphtheria.
Listeria Gram ⊕, facultative intracellular rod; acquired by ingestion of unpasteurized dairy products and
monocytogenes cold deli meats, transplacental transmission, by vaginal transmission during birth. Grows well at
A refrigeration temperatures (“cold enrichment”).
Forms “rocket tails” (red in A ) via actin polymerization that allow intracellular movement and cell-
to-cell spread across cell membranes, thereby avoiding antibody. Characteristic tumbling motility
in broth.
Can cause amnionitis, septicemia, and spontaneous abortion in pregnant patients; granulomatosis
infantiseptica; meningitis in immunocompromised patients, neonates, and older adults; mild, self-
limited gastroenteritis in healthy individuals.
Treatment: ampicillin.
Nocardia vs Both are gram ⊕ and form long, branching filaments resembling fungi.
Actinomyces Nocardia Actinomyces
A Aerobe Anaerobe
Acid fast (weak) A Not acid fast B
Found in soil Normal oral, reproductive, and GI flora
Causes pulmonary infections in Causes oral/facial abscesses that drain through
immunocompromised (can mimic TB but sinus tracts; often associated with dental caries/
with ⊝ PPD); cutaneous infections after extraction and other maxillofacial trauma;
trauma in immunocompetent; can spread to forms yellow “sulfur granules”; can also cause
B
CNS cerebral abscess PID with IUDs
Treat with sulfonamides (TMP-SMX) Treat with penicillin
Treatment is a SNAP: Sulfonamides—Nocardia; Actinomyces—Penicillin

Mycobacteria Acid-fast rods (pink rods, arrows in A ). TB symptoms include fever, night sweats,
A
Mycobacterium tuberculosis (TB, often resistant weight loss, cough (nonproductive or
to multiple drugs). productive), hemoptysis.
M avium–intracellulare (causes disseminated, Cord factor creates a “serpentine cord”
non-TB disease in AIDS; often resistant to appearance in virulent M tuberculosis
multiple drugs). Prophylaxis with azithromycin strains; activates macrophages (promoting
when CD4+ count < 50 cells/mm3. granuloma formation) and induces release of
M scrofulaceum (cervical lymphadenitis in TNF-α. Sulfatides (surface glycolipids) inhibit
children). phagolysosomal fusion.
M marinum (hand infection in aquarium
handlers).
Tuberculosis
Mycobacterium PPD ⊕ if current infection or past exposure.
tuberculosis
Hilar nodes PPD ⊝ if no infection and in
+ immunocompromised patients (especially with
Ghon
complex Ghon focus low CD4+ cell count).
(usually mid/ Interferon-γ release assay (IGRA) has fewer false
lower lobes)
Primary tuberculosis positives from BCG vaccination.
> 90% < 10% Caseating granulomas with central necrosis and
Healing by fibrosis Progressive primary tuberculosis Langhans giant cell (single example in A )
Calcification (AIDS, malnutrition)
(PPD )
are characteristic of 2° tuberculosis. Do not
Reactivation
confuse Langhans giant cell with Langerhans
Progressive
lung disease cell, an APC.
2° tuberculosis
Fibrocaseous
Bacteremia TB reactivation risk highest in
cavitary lesion immunocompromised individuals (eg, HIV,
(usually upper
Miliary
Meninges organ transplant recipients).
lobes)
tuberculosis
A
Vertebrae
(Pott disease)
Localized destructive disease Lymph nodes
Cavity
Caseation Lungs
Caseation
Spleen
Scar
Liver Adrenal
gland
Joints and
long bones

Microbiology 
Leprosy Also called Hansen disease. Caused by Mycobacterium leprae, an acid-fast bacillus that likes cool
A
temperatures (infects skin and superficial nerves—“glove and stocking” loss of sensation A ) and
cannot be grown in vitro. Diagnosed via skin biopsy or tissue PCR. Reservoir in United States:
armadillos.
Leprosy has 2 forms (many cases fall temporarily between two extremes):
Lepromatous—presents diffusely over the skin, with leonine (lion-like) facies B , and is
communicable (high bacterial load); characterized by low cell-mediated immunity with a
largely Th2 response. Lepromatous form can be lethal.
B
Tuberculoid—limited to a few hypoesthetic, hairless skin plaques; characterized by high cell-
mediated immunity with a largely Th1-type response and low bacterial load.
Treatment: dapsone and rifampin for tuberculoid form; clofazimine is added for lepromatous form.
Gram-negative lab algorithm
Gram (pink)
Diplococci Coccobacilli Curved rods
Aerobic Haemophilus influenzae Oxidase

Bordetella pertussis
Maltose fermentation Pasteurella
Brucella
Francisella tularensis Grows in 42°C Grows in alkaline media Produces urease
Acinetobacter baumannii
N gonorrhoeae Campylobacter jejuni Vibrio cholerae Helicobacter pylori
N meningitidis
Moraxella
Bacilli
Lactose fermentation
Oxidase Fast Slow
E coli
Citrobacter
Klebsiella
Pseudomonas Serratia
H2S production Burkholderia
Enterobacter
on TSI agar
Shigella Salmonella
Yersiniaa Proteus
Important tests are in bold. Important pathogens are in bold italics.

a
Pleomorphic rod/coccobacillus

Neisseria Gram ⊝ diplococci. Metabolize glucose N gonorrhoeae is often intracellular (within

A and produce IgA proteases. Contain neutrophils) A .
lipooligosaccharides (LOS) with strong Acid production: meningococci—maltose and
endotoxin activity. glucose; gonococci—glucose.
Gonococci Meningococci
No polysaccharide capsule Polysaccharide capsule
No maltose acid detection Maltose acid detection
No vaccine due to antigenic variation of pilus Vaccine (type B vaccine available for at-risk
B
proteins individuals)
Sexually or perinatally transmitted Transmitted via respiratory and oral secretions.
More common among individuals in close
quarters (eg, army barracks, college dorms)
Causes gonorrhea, septic arthritis, neonatal Causes meningococcemia with petechial
conjunctivitis (2–5 days after birth), pelvic hemorrhages and gangrene of toes B ,
inflammatory disease (PID), and Fitz-Hugh– meningitis, Waterhouse-Friderichsen
Curtis syndrome syndrome (adrenal insufficiency, fever, DIC)
Diagnosed with NAT Diagnosed via culture-based tests or PCR
Condoms sexual transmission, erythromycin Rifampin, ciprofloxacin, or ceftriaxone
eye ointment prevents neonatal blindness prophylaxis in close contacts
Treatment: ceftriaxone + azithromycin (to cover Treatment: ceftriaxone or penicillin G
possible chlamydial coinfection, ceftriaxone-
resistant strains)
Haemophilus Small gram ⊝ (coccobacillary) rod. Aerosol Vaccine contains type b capsular polysaccharide
influenzae transmission. Nontypeable (unencapsulated) (polyribosylribitol phosphate) conjugated
A strains are the most common cause of mucosal to diphtheria toxoid or other protein. Given
infections (otitis media, conjunctivitis, between 2 and 18 months of age.
bronchitis) as well as invasive infections since Does not cause the flu (influenza virus does).
the vaccine for capsular type b was introduced. Treatment: amoxicillin +/− clavulanate for
Produces IgA protease. mucosal infections; ceftriaxone for meningitis;
Culture on chocolate agar, which contains rifampin prophylaxis for close contacts.
factors V (NAD+) and X (hematin) for growth;
can also be grown with S aureus, which
B provides factor V via RBC hemolysis.
Haemophilus causes epiglottitis (endoscopic
appearance in A , can be “cherry red” in
children; “thumb sign” on lateral neck
x-ray B ), meningitis, otitis media, and
pneumonia.
Burkholderia cepacia Gram ⊝ bacilli. Causes pneumonia in and can be transmitted between patients with cystic fibrosis.
complex Often multidrug resistant. Infection is a relative contraindication to undergoing lung transplant
due to its association with poor outcomes.

Microbiology 
Bordetella pertussis Gram ⊝, aerobic coccobacillus. Virulence factors include pertussis toxin (disables Gi), adenylate
cyclase toxin ( cAMP), and tracheal cytotoxin. Three clinical stages:
Catarrhal—low-grade fevers, coryza.
Paroxysmal—paroxysms of intense cough followed by inspiratory “whoop” (“whooping cough”),
posttussive vomiting.
Convalescent—gradual recovery of chronic cough.
Prevented by Tdap, DTaP vaccines.
Treatment: macrolides; if allergic use TMP-SMX.
Brucella Gram ⊝, aerobic coccobacillus. Transmitted via ingestion of contaminated animal products (eg,
unpasteurized milk). Survives in macrophages in the reticuloendothelial system. Can form non-
caseating granulomas. Typically presents with undulant fever, night sweats, and arthralgia.
Treatment: doxycycline + rifampin or streptomycin.
Legionella Gram ⊝ rod. Gram stains poorly—use silver Think of a French legionnaire (soldier) with
pneumophila stain. Grow on charcoal yeast extract his silver helmet, sitting around a campfire
A medium with iron and cysteine. Detected by (charcoal) with his iron dagger—he is missing
presence of antigen in urine. Labs may show his sister (cysteine).
hyponatremia. Legionnaires’ disease—severe pneumonia
Aerosol transmission from environmental water (often unilateral and lobar A ), fever, GI and
source habitat (eg, air conditioning systems, CNS symptoms. Risk factors include older age,
hot water tanks). Outbreaks associated with tobacco smoking, chronic lung disease.
cruise ships, nursing homes. No person-to- Pontiac fever—mild flu-like symptoms.
person transmission.
Treatment: macrolide or quinolone.
Pseudomonas Aeruginosa—aerobic; motile, catalase ⊕, Corneal ulcers/keratitis in contact lens wearers/

aeruginosa gram ⊝ rod. Non-lactose fermenting. minor eye trauma.
A Oxidase ⊕. Frequently found in water. Has a Ecthyma gangrenosum—rapidly progressive,
grape-like odor. necrotic cutaneous lesion B caused by
PSEUDOMONAS is associated with: Pseudomonas bacteremia. Typically seen in
Pneumonia, Sepsis, Ecthyma gangrenosum, immunocompromised patients.
UTIs, Diabetes, Osteomyelitis, Mucoid Treatments:
polysaccharide capsule, Otitis externa Antipseudomonal penicillins in combination
(swimmer’s ear), Nosocomial infections (eg, with β-lactamase inhibitor (eg, piperacillin-
catheters, equipment), Addiction (people tazobactam)
B who inject drugs), Skin infections (eg, hot tub 3rd- and 4th-generation cephalosporins (eg,
folliculitis, wound infection in burn victims). ceftazidime, cefepime)
Mucoid polysaccharide capsule may contribute Monobactams
to chronic pneumonia in patients with cystic Fluoroquinolones
fibrosis due to biofilmformation. Carbapenems
Produces PEEP: Phospholipase C (degrades
cell membranes); Endotoxin (fever, shock);
Exotoxin A (inactivates EF-2); Pigments:
pyoverdine and pyocyanin (blue-green
pigment A ; also generates ROS).

Salmonella vs Shigella Both Salmonella and Shigella are gram ⊝ rods, non-lactose fermenters, oxidase ⊝, and can invade
the GI tract via M cells of Peyer patches.
Salmonella typhi (ty-Vi) Salmonella spp. Shigella
except S typhi
RESERVOIRS Humans only Humans and animals Humans only
SPREAD Hematogenous spread Hematogenous spread Cell to cell; no hematogenous spread
H2S PRODUCTION Yes Yes No
FLAGELLA Yes (salmon swim) Yes (salmon swim) No
VIRULENCE FACTORS Endotoxin; Vi capsule Endotoxin Endotoxin; Shiga toxin (enterotoxin)
(pronounce “tyVi”)
INFECTIOUS DOSE (ID50) High—large inoculum High Low—very small inoculum required;
required; acid-labile acid stable (resistant to gastric acids)
(inactivated by gastric acids)
EFFECT OF ANTIBIOTICS ON FECAL Prolongs duration Prolongs duration Shortens duration
EXCRETION
IMMUNE RESPONSE Primarily monocytes PMNs in disseminated Primarily PMN infiltration
disease
GI MANIFESTATIONS Constipation, followed by Diarrhea (possibly bloody) Crampy abdominal pain tenesmus,
diarrhea bloody mucoid stools (bacillary
dysentery)
VACCINE Oral vaccine contains live No vaccine No vaccine
attenuated S typhi
IM vaccine contains Vi
capsular polysaccharide
UNIQUE PROPERTIES Causes typhoid fever Poultry, eggs, pets, and 4 F’s: fingers, flies, food, feces
(rose spots on abdomen, turtles are common In order of decreasing severity (less
constipation, abdominal sources toxin produced): S dysenteriae,
pain, fever [pulse- Antibiotics not S flexneri, S boydii, S sonnei
temperature dissociation]; indicated Invasion of M cells is key to
later GI ulceration Gastroenteritis is pathogenicity: organisms that
and hemorrhage); treat usually caused by non- produce little toxin can cause disease
with ceftriaxone or typhoidal Salmonella
fluoroquinolone
Carrier state with
gallbladder colonization
Yersinia enterocolitica Gram ⊝ pleomorphic rod/coccobacillus. Usually transmitted from pet feces (eg, cats, dogs),
contaminated milk, or pork. Can cause acute bloody diarrhea, pseudoappendicitis (right lower
abdominal pain due to mesenteric adenitis and/or terminal ileitis), reactive arthritis in adults.
Lactose-fermenting Fermentation of lactose pink colonies McCowkey CEEKS milk.

enteric bacteria on MacConkey agar. Examples include EMB agar—lactose fermenters grow as purple/
Citrobacter, E coli, Enterobacter, Klebsiella, black colonies. E coli grows colonies with a
Serratia. E coli produces β-galactosidase, which green sheen.
breaks down lactose into glucose and galactose.

Microbiology 
Escherichia coli Gram ⊝, indole ⊕ rod. E coli virulence factors: fimbriae—cystitis and pyelonephritis (P pili); K
capsule—pneumonia, neonatal meningitis; LPS endotoxin—septic shock.
STRAIN TOXIN AND MECHANISM PRESENTATION
Enteroinvasive E coli Microbe invades intestinal mucosa and causes EIEC is Invasive; dysentery. Clinical
necrosis and inflammation. manifestations similar to Shigella.
Enterotoxigenic E coli Produces heat-labile and heat-stable ETEC; Traveler’s diarrhea (watery).
enteroToxins. No inflammation or invasion.
Enteropathogenic No toxin produced. Adheres to apical surface, Diarrhea, usually in children (think EPEC and
E coli flattens villi, prevents absorption. Pediatrics).
Enterohemorrhagic O157:H7 is most common serotype in US. Often Dysentery (toxin alone causes necrosis and
E coli transmitted via undercooked meat, raw leafy inflammation).
vegetables. Does not ferment sorbitol (vs other E coli).
Shiga toxin causes hemolytic-uremic EHEC associated with hemorrhage, hamburgers,
syndrome—triad of anemia, thrombocytopenia, hemolytic-uremic syndrome.
and acute kidney injury due to microthrombi
forming on damaged endothelium
mechanical hemolysis (with schistocytes on
peripheral blood smear), platelet consumption,
and renal blood flow.
Klebsiella Gram ⊝ rod; intestinal flora that causes lobar ABCDE’s of Klebsiella:
A pneumonia in patients with alcohol overuse Aspiration pneumonia
and patients with diabetes when aspirated. aBscess in lungs and liver
Very mucoid colonies A caused by abundant “Currant jelly” sputum
polysaccharide capsules. Dark red “currant Diabetes mellitus
jelly” sputum (blood/mucus). EtOH overuse
Also cause of nosocomial UTIs. Associated with
evolution of multidrug resistance (MDR).
Campylobacter jejuni Gram ⊝, comma or S shaped (with polar flagella) A , oxidase ⊕, grows at 42°C (“Campylobacter
A likes the hot campfire”).
Major cause of bloody diarrhea, especially in children. Fecal-oral transmission through person-
to-person contact or via ingestion of undercooked contaminated poultry or meat, unpasteurized
milk. Contact with infected animals (dogs, cats, pigs) is also a risk factor.
Common antecedent to Guillain-Barré syndrome and reactive arthritis.

Vibrio cholerae Gram ⊝, flagellated, comma shaped A , oxidase ⊕, grows in alkaline media. Endemic to
A developing countries. Produces profuse rice-water diarrhea via enterotoxin that permanently
activates Gs, cAMP. Sensitive to stomach acid (acid labile); requires large inoculum (high ID50)
unless host has gastric acidity. Transmitted via ingestion of contaminated water or uncooked
food (eg, raw shellfish). Treat promptly with oral rehydration solution.
Vibrio vulnificus—gram ⊝ bacillus, usually found in marine environments. Causes severe wound
infections or septicemia due to exposure to contaminated sea water. Presents as cellulitis that
can progress to necrotizing fasciitis in high-risk patients, especially those with liver disease (eg,
cirrhosis). Serious wound infection requires surgical debridement.
Helicobacter pylori Curved, flagellated (motile), gram ⊝ rod A that is triple ⊕: catalase ⊕, oxidase ⊕, and urease ⊕
A (can use urea breath test or fecal antigen test for diagnosis). Urease produces ammonia, creating
an alkaline environment, which helps H pylori survive in acidic mucosa. Colonizes mainly
antrum of stomach; causes gastritis and peptic ulcers (especially duodenal). Risk factor for peptic
ulcer disease, gastric adenocarcinoma, and MALT lymphoma.
Most common initial treatment is triple therapy: amoxicillin (metronidazole if penicillin allergy)
+ clarithromycin + proton pump inhibitor; antibiotics cure Pylori. Bismuth-based quadruple
therapy if concerned about macrolide resistance.
Spirochetes Spiral-shaped bacteria A with axial filaments. Little Twirling Bacteria

A
Includes Leptospira, Treponema, and Borrelia.
Only Borrelia can be visualized using
aniline dyes (Wright or Giemsa stain) in
light microscopy due to size. Treponema is
visualized by dark-field microscopy or direct
fluorescent antibody (DFA) microscopy.
Lyme disease Caused by Borrelia burgdorferi, which is A Key Lyme pie to the FACE:
A
transmitted by the Ixodes deer tick A (also Facial nerve palsy (typically bilateral)
vector for Anaplasma spp. and protozoa Arthritis
Babesia). Natural reservoir is the mouse; deer Cardiac block
are essential to tick life cycle but do not harbor Erythema migrans
Borrelia. Treatment: doxycycline (1st line); amoxicillin
Common in northeastern United States. (pregnant patients, children < 8 years old);
Stage 1—early localized: erythema migrans ceftriaxone if IV therapy required
(typical “bulls-eye” configuration B is
B pathognomonic but not always present),
flu‑like symptoms.
Stage 2—early disseminated: secondary lesions,
carditis, AV block, facial nerve (Bell) palsy,
migratory myalgias/transient arthritis.
Stage 3—late disseminated: encephalopathy,
chronic arthritis, peripheral neuropathy.

Microbiology 
Leptospira interrogans Spirochete with hook-shaped ends found in water contaminated with animal urine.
Leptospirosis—flu-like symptoms, myalgias (classically of calves), jaundice, photophobia with
conjunctival suffusion (erythema without exudate). Prevalent among surfers and in tropics (eg,
Hawaii).
Weil disease (icterohemorrhagic leptospirosis)—severe form with jaundice and azotemia from liver
and kidney dysfunction, fever, hemorrhage, and anemia.
Syphilis Caused by spirochete Treponema pallidum. Treatment: penicillin G.

Primary syphilis Localized disease presenting with painless chancre A . Use fluorescent or dark-field microscopy to
visualize treponemes in fluid from chancre B . VDRL ⊕ in ~ 80%.
Secondary syphilis Disseminated disease with constitutional symptoms, maculopapular rash C (including
palms D and soles), condylomata lata E (smooth, painless, wart-like white lesions on genitals),
lymphadenopathy, patchy hair loss; also confirmable with dark-field microscopy.
Serologic testing: VDRL/RPR (nonspecific), confirm diagnosis with specific test (eg, FTA-ABS).
Secondary syphilis = systemic. Latent syphilis (⊕ serology without symptoms) may follow.
Tertiary syphilis Gummas F (chronic granulomas), aortitis (vasa vasorum destruction), neurosyphilis (tabes dorsalis,
“general paresis”), Argyll Robertson pupil (constricts with accommodation but is not reactive to
light).
Signs: broad-based ataxia, ⊕ Romberg, Charcot joint, stroke without hypertension.
For neurosyphilis: test spinal fluid with VDRL, FTA-ABS, and PCR.
Congenital syphilis Presents with facial abnormalities such as rhagades (linear scars at angle of mouth, black arrow
in G ), snuffles (nasal discharge, red arrow in G ), saddle nose, notched (Hutchinson) teeth H ,
mulberry molars, and short maxilla; saber shins; CN VIII deafness.
To prevent, treat patient early in pregnancy, as placental transmission typically occurs after first
trimester.
A B C D
E F G H

Diagnosing syphilis VDRL and RPR detects nonspecific antibody False-Positive results on VDRL with:
that reacts with beef cardiolipin. Quantitative, Pregnancy
inexpensive, and widely available test for Viral infection (eg, EBV, hepatitis)
syphilis (sensitive but not specific). Drugs (eg, chlorpromazine, procainamide)
Rheumatic fever (rare)
Lupus (anticardiolipin antibody) and Leprosy
Serologic testing Direct testing
Nontreponemal Treponemal
Darkfield
(nonspecific) (specific) PCR
microscopy
RPR VDRL FTA-ABS TPPA
Jarisch-Herxheimer Flu-like symptoms (fever, chills, headache, myalgia) after antibiotics are started due to host
reaction response to sudden release of bacterial antigens.
Gardnerella vaginalis A pleomorphic, gram-variable rod involved in Amine whiff test—mixing discharge with 10%
A
bacterial vaginosis. Presents as a gray vaginal KOH enhances fishy odor.
discharge with a fishy smell; nonpainful (vs Vaginal pH >4.5 during infection.
vaginitis). Associated with sexual activity, Treatment: metronidazole or clindamycin.
but not sexually transmitted. Bacterial
vaginosis is also characterized by overgrowth
of certain anaerobic bacteria in vagina (due
to lactobacilli). Clue cells (vaginal epithelial
cells covered with Gardnerella) have stippled
appearance along outer margin (arrow in A ).
Chlamydiae Chlamydiae cannot make their own ATP. They Chlamydial cell wall lacks classic peptidoglycan
A
are obligate intracellular organisms that cause (due to reduced muramic acid), rendering
mucosal infections. 2 forms: β-lactam antibiotics ineffective.
Elementary body (small, dense) Chlamys = cloak (intracellular).
is “enfectious” and enters cell via C psittaci—has an avian reservoir (parrots),
endocytosis; transforms into reticulate body. causes atypical pneumonia.
Reticulate body replicates in cell by fission; Lab diagnosis: PCR, nucleic acid amplification
reorganizes into elementary bodies. test. Cytoplasmic inclusions (reticulate bodies)
Chlamydia trachomatis causes neonatal seen on Giemsa or fluorescent antibody–
and follicular adult conjunctivitis A , stained smear.
nongonococcal urethritis, PID, and reactive Treatment: azithromycin (favored because
arthritis. one-time treatment) or doxycycline. Add
Chlamydophila pneumoniae and Chlamydophila ceftriaxone for possible concomitant
psittaci cause atypical pneumonia; transmitted gonorrhea.
by aerosol.

Microbiology 
Chlamydia trachomatis serotypes

Types A, B, and C Chronic infection, cause blindness due to ABC = Africa, Blindness, Chronic infection.
follicular conjunctivitis in resource-limited
areas.
Types D–K Urethritis/PID, ectopic pregnancy, neonatal D–K = everything else.
pneumonia (staccato cough) with eosinophilia, Neonatal disease can be acquired during vaginal
neonatal conjunctivitis (1–2 weeks after birth). birth if pregnant patient is infected.
Types L1, L2, and L3 Lymphogranuloma venereum—small, painless
ulcers on genitals swollen, painful inguinal
lymph nodes that ulcerate (buboes). Treat with
doxycycline.
Zoonotic bacteria Zoonosis—infectious disease transmitted between animals and humans.

SPECIES DISEASE TRANSMISSION AND SOURCE
Anaplasma spp Anaplasmosis Ixodes ticks (live on deer and mice)
Bartonella spp Cat scratch disease, bacillary angiomatosis Cat scratch
Borrelia burgdorferi Lyme disease Ixodes ticks (live on deer and mice)
Borrelia recurrentis Relapsing fever Louse (recurrent due to variable surface
antigens)
Brucella spp Brucellosis/undulant fever Unpasteurized dairy
Campylobacter Bloody diarrhea Feces from infected pets/animals; contaminated
meats/foods/hands
Chlamydophila psittaci Psittacosis Parrots, other birds
Coxiella burnetii Q fever Aerosols of cattle/sheep amniotic fluid
Ehrlichia chaffeensis Ehrlichiosis Amblyomma (Lone Star tick)
Francisella tularensis Tularemia Ticks, rabbits, deer flies
Leptospira spp Leptospirosis Animal urine in water; recreational water use
Mycobacterium leprae Leprosy Humans with lepromatous leprosy; armadillo
(rare)
Pasteurella multocida Cellulitis, osteomyelitis Animal bite, cats, dogs
Rickettsia prowazekii Epidemic typhus Human to human via human body louse
Rickettsia rickettsii Rocky Mountain spotted fever Dermacentor (dog tick)
Rickettsia typhi Endemic typhus Fleas
Salmonella spp Diarrhea (which may be bloody), vomiting, Reptiles and poultry
(except S typhi) fever, abdominal cramps
Yersinia pestis Plague Fleas (rats and prairie dogs are reservoirs)

Rickettsial diseases
and vector-borne
illnesses Treatment: doxycycline.
RASH COMMON
Rocky Mountain Rickettsia rickettsii, vector is tick. Despite its Classic triad—headache, fever, rash (vasculitis).
spotted fever name, disease occurs primarily in the South Palms and soles rash is seen in Coxsackievirus
Atlantic states, especially North Carolina. A infection (hand, foot, and mouth disease),
Rash typically starts at wrists A and ankles and Rocky Mountain spotted fever, and 2° Syphilis
then spreads to trunk, palms, and soles. (you drive CARS using your palms and soles).
Typhus Endemic (fleas)—R typhi. Rickettsii on the wrists, typhus on the trunk.
Epidemic (human body louse)—R prowazekii.
Rash starts centrally and spreads out, sparing
palms and soles.
RASH RARE
Ehrlichiosis Ehrlichia, vector is tick. Monocytes with MEGA:

morulae B (mulberry-like inclusions) in Monocytes = Ehrlichiosis
cytoplasm. Granulocytes = Anaplasmosis
Anaplasmosis Anaplasma, vector is tick. Granulocytes with
morulae C in cytoplasm.
Q fever Coxiella burnetii, no arthropod vector. Q fever is caused by a Quite Complicated
Bacterium inhaled as aerosols from cattle/ bug because it has no rash or vector and its
sheep amniotic fluid. Presents with headache, causative organism can survive outside in its
cough, influenza-like symptoms, pneumonia, endospore form. Not in the Rickettsia genus,
possibly in combination with hepatitis. but closely related.
Common cause of culture ⊝ endocarditis.
A B C
Mycoplasma Classic cause of atypical “walking pneumonia” Not seen on Gram stain. Pleomorphic A .
pneumoniae (insidious onset, headache, nonproductive Bacterial membrane contains sterols for
A
cough, patchy or diffuse interstitial infiltrate, stability. Grown on Eaton agar.
macular rash). CXR appears more severe than patient
Occurs frequently in those <30 years old; presentation. High titer of cold agglutinins (IgM),
outbreaks in military recruits, prisons, colleges. which can agglutinate RBCs. Mycoplasma gets
Treatment: macrolides, doxycycline, or cold without a coat (no cell wall).
fluoroquinolone (penicillin ineffective since Can cause atypical variant of Stevens-
Mycoplasma has no cell wall). Johnson syndrome, typically in children and
adolescents.

Microbiology 
microbiology—Mycology SEC TION II 151
MICROBIOLOGY—MYCOLOGY
``
Systemic mycoses All of the following can cause pneumonia and can disseminate.
All are caused by dimorphic fungi: cold (20°C) = mold; heat (37°C) = yeast. Only exception is
Coccidioides, which is a spherule (not yeast) in tissue.
Systemic mycoses can form granulomas (like TB); cannot be transmitted person-to-person (unlike TB).
Treatment: fluconazole or itraconazole for local infection; amphotericin B for systemic infection.
DISEASE ENDEMIC LOCATION PATHOLOGIC FEATURES UNIQUE SIGNS/SYMPTOMS NOTES
Histoplasmosis Mississippi and Ohio Macrophage filled Palatal/tongue ulcers, Histo hides (within
A River Valleys with Histoplasma splenomegaly, macrophages)
(smaller than pancytopenia, Associated with bird
RBC) A erythema nodosum or bat droppings
(eg, caves)
Diagnosis via urine/
serum antigen
Blastomycosis Eastern and Central Broad-based budding Inflammatory lung Blasto buds broadly
B US, Great Lakes of Blastomyces (same disease
size as RBC) B Disseminates to bone/
skin (verrucous
lesions, may mimic
SCC).
Coccidioidomycosis Southwestern US, Spherule (much larger Disseminates to bone/ Associated with
C California than RBC) filled skin dust exposure in
with endospores of Erythema nodosum endemic areas
Coccidioides C (desert bumps) or (eg, archeological
multiforme excavations,
Arthralgias (desert earthquakes)
rheumatism)
Can cause meningitis
Para Latin America Budding yeast of Similar to Paracoccidio parasails
coccidioidomycosis Paracoccidioides with blastomycosis, with the captain’s
D “captain’s wheel” males > females wheel all the way to
formation (much Latin America
larger than RBC) D
Histoplasmosis
Blastomycosis
Coccidioidomycosis

microbiology—Mycology
Cutaneous mycoses
Tinea Clinical name for dermatophyte (cutaneous fungal) infections. Dermatophytes include
(dermatophytes) Microsporum, Trichophyton, and Epidermophyton. Branching septate hyphae visible on KOH
preparation with blue fungal stain A . Associated with pruritus.
Tinea capitis Occurs on head, scalp. Associated with lymphadenopathy, alopecia, scaling B .
Tinea corporis Occurs on body (usually torso). Characterized by enlarging erythematous, scaly rings (“ringworm”)
with central clearing C . Can be acquired from contact with infected pets or farm animals.
Tinea cruris Occurs in inguinal area (“jock itch”) D . Often does not show the central clearing seen in tinea
corporis.
Tinea pedis Three varieties (“athlete’s foot”):
Interdigital E ; most common
Moccasin distribution F
Vesicular type
Tinea unguium Onychomycosis; occurs on nails.
Tinea (pityriasis) Caused by Malassezia spp. (Pityrosporum spp.), a yeast-like fungus (not a dermatophyte despite
versicolor being called tinea). Degradation of lipids produces acids that inhibit tyrosinase (involved in
melanin synthesis) hypopigmentation G ; hyperpigmentation and/or pink patches can also
occur due to inflammatory response. Less pruritic than dermatophytes.
Can occur any time of year, but more common in summer (hot, humid weather). “Spaghetti and
meatballs” appearance on microscopy H .
Treatment: selenium sulfide, topical and/or oral antifungal medications.
A B C D
E F G H

Microbiology 
microbiology—Mycology SEC TION II 153
Opportunistic fungal infections

Candida albicans alba = white. Dimorphic; forms pseudohyphae and budding yeasts at 20°C A , germ tubes at
37°C B .
Systemic or superficial fungal infection. Causes oral C and esophageal thrush in
immunocompromised (neonates, steroids, diabetes, AIDS), vulvovaginitis (diabetes, use of
antibiotics), diaper rash, endocarditis (people who inject drugs), disseminated candidiasis
(especially in neutropenic patients), chronic mucocutaneous candidiasis.
Treatment: oral fluconazole/topical azoles for vaginal; nystatin, azoles, or, rarely, echinocandins for
oral; fluconazole, echinocandins, or amphotericin B for esophageal or systemic disease.
Aspergillus Septate hyphae that branch at 45° Acute Angle D E .
fumigatus Causes invasive aspergillosis in immunocompromised patients, especially those with neutrophil
dysfunction (eg, chronic granulomatous disease) because Aspergillus is catalase ⊕.
Can cause aspergillomas F in pre-existing lung cavities, especially after TB infection.
Some species of Aspergillus produce Aflatoxins (associated with hepatocellular carcinoma).
Treatment: voriconazole or echinocandins (2nd-line).
Allergic bronchopulmonary aspergillosis (ABPA)—hypersensitivity response to Aspergillus
growing in lung mucus. Associated with asthma and cystic fibrosis; may cause bronchiectasis and
eosinophilia.
Cryptococcus 5–10 μm with narrow budding. Heavily encapsulated yeast. Not dimorphic.
neoformans Found in soil, pigeon droppings. Acquired through inhalation with hematogenous dissemination
to meninges. Highlighted with India ink (clear halo G ) and mucicarmine (red inner capsule H ).
Latex agglutination test detects polysaccharide capsular antigen and is more sensitive and specific.
Causes cryptococcosis, cryptococcal meningitis, cryptococcal encephalitis (“soap bubble” lesions
in brain), primarily in immunocompromised.
Treatment: amphotericin B + flucytosine followed by fluconazole for cryptococcal meningitis.
Mucor and Rhizopus Irregular, broad, nonseptate hyphae branching at wide angles I .
spp Causes mucormycosis, mostly in patients with DKA and/or neutropenia (eg, leukemia). Inhalation
of spores fungi proliferate in blood vessel walls, penetrate cribriform plate, and enter brain.
Rhinocerebral, frontal lobe abscess; cavernous sinus thrombosis. Headache, facial pain, black
necrotic eschar on face J ; may have cranial nerve involvement.
Treatment: surgical debridement, amphotericin B or isavuconazole.
A B C D E
F G H I J

microbiology—Mycology
Pneumocystis jirovecii Causes Pneumocystis pneumonia (PCP), a diffuse interstitial pneumonia A . Yeast-like fungus
(originally classified as protozoan). Most infections are asymptomatic. Immunosuppression (eg,
AIDS) predisposes to disease. Diffuse, bilateral ground-glass opacities on chest imaging, with
pneumatoceles B . Diagnosed by bronchoalveolar lavage or lung biopsy. Disc-shaped yeast seen on
methenamine silver stain of lung tissue C or with fluorescent antibody.
Treatment/prophylaxis: TMP-SMX, pentamidine, dapsone (prophylaxis as single agent, or
treatment in combination with TMP), atovaquone. Start prophylaxis when CD4+ cell count drops
to < 200 cells/mm3 in people living with HIV.
A B C
Sporothrix schenckii Causes sporotrichosis. Dimorphic fungus. Exists as a cigar-shaped yeast at 37 ºC in the human
A body and as hyphae with spores in soil (conidia). Lives on vegetation. When spores are
traumatically introduced into the skin, typically by a thorn (“rose gardener’s disease”), causes
local pustule or ulcer with nodules along draining lymphatics (ascending lymphangitis A ).
Disseminated disease possible in immunocompromised host.
Treatment: itraconazole or potassium iodide (only for cutaneous/lymphocutaneous).
Think of a rose gardener who smokes a cigar and pot.

Microbiology 
microbiology—Parasitology SEC TION II 155
MICROBIOLOGY—PARASITOLOGY
``
Protozoa—gastrointestinal infections
ORGANISM DISEASE TRANSMISSION DIAGNOSIS TREATMENT
Giardia lamblia Giardiasis—bloating, flatulence, Cysts in water Multinucleated Metronidazole
foul-smelling, nonbloody, trophozoites A or
fatty diarrhea (often seen in cysts B in stool,
campers/hikers)—think fat-rich antigen detection,
Ghirardelli chocolates for fatty PCR
stools of Giardia
Entamoeba Amebiasis—bloody diarrhea Cysts in water Serology, antigen Metronidazole;
histolytica (dysentery), liver abscess testing, PCR, and/ paromomycin or
(“anchovy paste” exudate), RUQ or trophozoites iodoquinol for
pain; histology of colon biopsy (with engulfed asymptomatic cyst
shows flask-shaped ulcers RBCs C in the passers
cytoplasm) or
cysts with up to 4
nuclei in stool D ;
Entamoeba Eats
Erythrocytes
Cryptosporidium Severe diarrhea in AIDS Oocysts in water Oocysts on acid-fast Prevention (by
Mild disease (watery diarrhea) in stain E , antigen filtering city
immunocompetent hosts detection, PCR water supplies);
nitazoxanide in
immunocompetent
hosts
A B C D E

microbiology—Parasitology
Protozoa—CNS infections
Toxoplasma Immunocompetent: Cysts in meat (most Serology, biopsy Sulfadiazine +
gondii mononucleosis-like symptoms, common); oocysts (tachyzoite) B ; pyrimethamine
⊝ heterophile antibody test in cat feces; crosses PCR of amniotic Prophylaxis with
Reactivation in AIDS brain placenta (pregnant fluid for possible TMP-SMX when
abscesses usually seen as patients should intrauterine disease CD4+ cell count
multiple ring-enhancing lesions avoid cats) < 100 cells/mm3
on MRI A
Congenital toxoplasmosis:
classic triad of chorioretinitis,
hydrocephalus, and intracranial
calcifications
Naegleria fowleri Rapidly fatal meningoencephalitis Swimming in warm Amoebas in CSF C Amphotericin B has
freshwater; enters been effective for a
via cribriform plate few survivors
Trypanosoma African sleeping sickness— Tsetse fly, a painful Trypomastigote in Suramin for blood-
brucei enlarged lymph nodes, recurring bite blood smear D borne disease or
fever (due to antigenic variation), melarsoprol for
somnolence, coma CNS penetration
(“I sure am
mellow when I’m
sleeping”)
A B C D

Microbiology 
Protozoa—hematologic infections
Plasmodium Malaria—fever, headache, anemia, Anopheles mosquito Blood smear: Chloroquine (for
P vivax/ovale splenomegaly; hypoglycemia in trophozoite ring sensitive species);
P falciparum severe disease form within if resistant, use
P malariae P vivax/ovale—48-hr cycle (tertian; RBC A , schizont mefloquine or
A includes fever on first day and containing atovaquone/
third day, thus fevers are actually merozoites; red proguanil
48 hr apart); dormant form granules (Schüffner If life-threatening,
(hypnozoite) in liver stippling) B use intravenous
P falciparum—severe; irregular throughout RBC quinidine or
fever patterns; parasitized RBCs cytoplasm seen artesunate (test for
occlude capillaries in brain with P vivax/ovale G6PD deficiency)
B
(cerebral malaria), kidneys, lungs For P vivax/ovale,
P malariae—72-hr cycle (quartan) add primaquine for
hypnozoite (test for
G6PD deficiency)
Babesia Babesiosis—fever and hemolytic Ixodes tick (also Blood smear: ring Atovaquone
C anemia; predominantly in vector for Borrelia form C1 , “Maltese + azithromycin
northeastern and north central burgdorferi and cross” C2 ; PCR
United States; asplenia risk of Anaplasma spp)
severe disease due to inability to
clear infected RBCs

Protozoa—others
Visceral infections
Trypanosoma Chagas disease—dilated Triatomine insect Trypomastigote in Benznidazole
cruzi cardiomyopathy with (kissing bug) bites blood smear A or nifurtimox;
apical atrophy, megacolon, and defecates cruzing in my
megaesophagus; predominantly around the mouth Benz, with a fur
in South America or eyes fecal coat on
Unilateral periorbital swelling transmission into
(Romaña sign) characteristic of bite site or mucosa
acute stage
Leishmania spp Visceral leishmaniasis Sandfly Macrophages Amphotericin B,
(kala-azar)—spiking fevers, containing sodium
hepatosplenomegaly, amastigotes C stibogluconate
pancytopenia
Cutaneous leishmaniasis—skin
ulcers B
Sexually transmitted infections
Trichomonas Vaginitis—foul-smelling, greenish Sexual (cannot exist Trophozoites (motile) Metronidazole
vaginalis discharge; itching and burning; outside human D on wet mount; for patient
do not confuse with Gardnerella because it cannot punctate cervical and partner(s)
vaginalis, a gram-variable form cysts) hemorrhages (prophylaxis; check
bacterium associated with (“strawberry for STI)
bacterial vaginosis cervix”)
A B C D
Nematode routes of Ingested—Enterobius, Ascaris, Toxocara, You’ll get sick if you EATTT these!
infection Trichinella, Trichuris
Cutaneous—Strongyloides, Ancylostoma, These get into your feet from the SANd
Necator
Bites—Loa loa, Onchocerca volvulus, Lay LOW to avoid getting bitten
Wuchereria bancrofti

Microbiology 
Nematodes (roundworms)
ORGANISM DISEASE TRANSMISSION TREATMENT
Intestinal
Enterobius vermicularis Causes anal pruritus (diagnosed by seeing Fecal-oral. Bendazoles, pyrantel
(pinworm) egg A via the tape test). pamoate.
Ascaris lumbricoides May cause obstruction at ileocecal Fecal-oral; knobby-coated, Bendazoles.
(giant roundworm) valve, biliary obstruction, intestinal oval eggs seen in feces
perforation, migrates from nose/mouth. under microscope B .
Migration of larvae to alveoli Löeffler
syndrome (pulmonary eosinophilia).
Strongyloides GI (eg, duodenitis), pulmonary (eg, dry Larvae in soil penetrate skin; Ivermectin or
stercoralis cough, hemoptysis), and cutaneous (eg, rhabditiform larvae seen in bendazoles.
(threadworm) pruritus) symptoms. Hyperinfection feces under microscope.
syndrome caused by autoinfection
(larvae enter bloodstream).
Ancylostoma spp, Cause microcytic anemia by sucking Larvae penetrate skin Bendazoles or pyrantel
Necator americanus blood from intestinal wall. from walking barefoot on pamoate.
(hookworms) Cutaneous larva migrans—pruritic, contaminated beach/soil.
serpiginous rash C .
Trichinella spiralis Larvae enter bloodstream, encyst in Undercooked meat (especially Bendazoles.
striated muscle D myositis. pork); fecal-oral (less likely).
Trichinosis—fever, vomiting, nausea,
periorbital edema, myalgia.
Trichuris trichiura Often asymptomatic; loose stools, Fecal-oral. Bendazoles.
(whipworm) anemia, rectal prolapse in children.
Tissue
Toxocara canis Visceral larva migrans—migration into Fecal-oral. Bendazoles.
blood inflammation of liver, eyes
(visual impairment, blindness), CNS
(seizures, coma), heart (myocarditis).
Patients often asymptomatic.
Onchocerca volvulus Skin changes, loss of elastic fibers, river Female black fly. Ivermectin (ivermectin
blindness (black skin nodules, “black for river blindness).
sight”); allergic reaction possible.
Loa loa Swelling in skin, worm in conjunctiva. Deer fly, horse fly, mango fly. Diethylcarbamazine.
Wuchereria bancrofti, Lymphatic filariasis (elephantiasis)— Female mosquito. Diethylcarbamazine.
Brugia malayi worms invade lymph nodes.
inflammation lymphedema E ;
symptom onset after 9 mo–1 yr.
A B C D E

Cestodes (tapeworms)
Taenia solium A Intestinal tapeworm Ingestion of larvae encysted in Praziquantel
undercooked pork
Cysticercosis, Ingestion of eggs in food Praziquantel; albendazole for
neurocysticercosis (cystic contaminated with human neurocysticercosis
CNS lesions, seizures) B feces
Diphyllobothrium Vitamin B12 deficiency Ingestion of larvae in raw Praziquantel, niclosamide
latum (tapeworm competes for B12 freshwater fish
in intestine) megaloblastic
anemia
Echinococcus Hydatid cysts D (“eggshell Ingestion of eggs in food Albendazole; surgery for
granulosus C calcification”) in liver E ; cyst contaminated with dog feces complicated cysts
rupture can cause anaphylaxis Sheep are an intermediate host
A B C D E
Liver
St
Trematodes (flukes)
Schistosoma Liver and spleen enlargement Snails are intermediate host; Praziquantel
A
( A shows S mansoni egg cercariae penetrate skin of
with lateral spine), fibrosis, humans in contact with
inflammation, portal contaminated fresh water (eg,
hypertension swimming or bathing)
Chronic infection with
B
S haematobium (egg with
terminal spine B ) can lead
to squamous cell carcinoma
of the bladder (painless
hematuria) and pulmonary
hypertension
Clonorchis sinensis Biliary tract inflammation Undercooked fish Praziquantel
pigmented gallstones
Associated with
cholangiocarcinoma

Microbiology 
Ectoparasites
Sarcoptes scabiei Mites burrow into stratum corneum and Common in children, crowded populations
A cause scabies—pruritus (worse at night) and (jails, nursing homes); transmission through
serpiginous burrows (lines) often between skin-to-skin contact (most common) or via
fingers and toes A . fomites.
Treatment: permethrin cream, oral ivermectin,
washing/drying all clothing/bedding, treat
close contacts.
Pediculus humanus/ Blood-sucking lice that cause intense pruritus Body lice can transmit Rickettsia prowazekii
Phthirus pubis with associated excoriations, commonly on (epidemic typhus), Borrelia recurrentis (relapsing
B
scalp and neck (head lice), waistband and fever), Bartonella quintana (trench fever).
axilla (body lice), or pubic and perianal Treatment: pyrethroids, malathion, or ivermectin
regions (pubic lice). lotion, and nit B combing. Children with head
lice can be treated at home without interrupting
school attendance.
Parasite hints ASSOCIATIONS ORGANISM

Biliary tract disease, cholangiocarcinoma Clonorchis sinensis
Brain cysts, seizures Taenia solium (neurocysticercosis)
Hematuria, squamous cell bladder cancer Schistosoma haematobium
Liver (hydatid) cysts, exposure to infected dogs Echinococcus granulosus
Iron deficiency anemia Ancylostoma, Necator
Myalgias, periorbital edema Trichinella spiralis
Nocturnal perianal pruritus Enterobius
Portal hypertension Schistosoma mansoni, Schistosoma japonicum
Vitamin B12 deficiency Diphyllobothrium latum

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Microbiology 

microbiology—Basic Bacteriology SEC TION II 125

FAS1_2021_03-Microbiology.indd 125 11/9/20 4:28 PM

Special culture requirements

Aerobes Use an O2-dependent system to generate ATP.

FAS1_2021_03-Microbiology.indd 126 11/9/20 4:28 PM

Encapsulated bacteria Examples are Pseudomonas aeruginosa, Please SHiNE my SKiS.

Urease-positive Proteus, Cryptococcus, H pylori, Ureaplasma, Pee CHUNKSS.

FAS1_2021_03-Microbiology.indd 127 11/9/20 4:28 PM

Pigment-producing Actinomyces israelii—yellow “sulfur” granules, Israel has yellow sand

In vivo biofilm- S epidermidis Catheter and prosthetic device infections

FAS1_2021_03-Microbiology.indd 128 11/9/20 4:28 PM

FAS1_2021_03-Microbiology.indd 129 11/9/20 4:28 PM

Release of new phage Infects other Genes transferred

FAS1_2021_03-Microbiology.indd 130 11/9/20 4:28 PM

Bacterial genetics (continued)

Main features of exotoxins and endotoxins

FAS1_2021_03-Microbiology.indd 131 11/9/20 4:28 PM

Bacteria with exotoxins

FAS1_2021_03-Microbiology.indd 132 11/9/20 4:28 PM

Bacteria with exotoxins (continued)

Endotoxin LPS found in outer membrane of gram ⊝ ENDOTOXINS:

IL-1, IL-6 Fever

Macrophage activation TNF-α Fever and hypotension

Nitric oxide Hypotension

FAS1_2021_03-Microbiology.indd 133 11/9/20 4:28 PM

Gram-positive lab algorithm

Aerobic Anaerobic Aerobic Anaerobic

Listeria Clostridium Nocardia Actinomyces

(Pairs or Streptococcus (Clusters) Staphylococcus

Group B Group A S saprophyticus S epidermidis

Important tests are in bold. Important pathogens are in bold italics.

Gram-positive cocci antibiotic tests

FAS1_2021_03-Microbiology.indd 134 11/9/20 4:28 PM

FAS1_2021_03-Microbiology.indd 135 11/9/20 4:29 PM

Staphylococcus Gram ⊕, catalase ⊕, coagulase ⊝, urease ⊕ cocci in clusters. Novobiocin resistant.

Streptococcus Gram ⊕, α-hemolytic, lancet-shaped Pneumococcus is associated with “rusty”

FAS1_2021_03-Microbiology.indd 136 11/9/20 4:29 PM

Streptococcus Gram ⊕ cocci, bacitracin resistant, β-hemolytic, Group B for Babies!

FAS1_2021_03-Microbiology.indd 137 11/9/20 4:29 PM

FAS1_2021_03-Microbiology.indd 138 11/9/20 4:30 PM

FAS1_2021_03-Microbiology.indd 139 11/9/20 4:30 PM

FAS1_2021_03-Microbiology.indd 140 11/9/20 4:30 PM

Gram-negative lab algorithm

Diplococci Coccobacilli Curved rods

Aerobic Haemophilus influenzae Oxidase

Oxidase Fast Slow

Important tests are in bold. Important pathogens are in bold italics.

FAS1_2021_03-Microbiology.indd 141 11/9/20 4:30 PM

Neisseria Gram ⊝ diplococci. Metabolize glucose N gonorrhoeae is often intracellular (within

FAS1_2021_03-Microbiology.indd 142 11/9/20 4:30 PM

Pseudomonas Aeruginosa—aerobic; motile, catalase ⊕, Corneal ulcers/keratitis in contact lens wearers/

FAS1_2021_03-Microbiology.indd 143 11/9/20 4:30 PM

Lactose-fermenting Fermentation of lactose  pink colonies McCowkey CEEKS milk.

FAS1_2021_03-Microbiology.indd 144 11/9/20 4:30 PM

FAS1_2021_03-Microbiology.indd 145 11/9/20 4:30 PM

Spirochetes Spiral-shaped bacteria A with axial filaments. Little Twirling Bacteria

FAS1_2021_03-Microbiology.indd 146 11/9/20 4:30 PM

Syphilis Caused by spirochete Treponema pallidum. Treatment: penicillin G.

FAS1_2021_03-Microbiology.indd 147 11/9/20 4:31 PM

Serologic testing Direct testing

RPR VDRL FTA-ABS TPPA

FAS1_2021_03-Microbiology.indd 148 11/9/20 4:31 PM

Lactose-fermenting Fermentation of lactose pink colonies McCowkey CEEKS milk.