Microbiology PDF

124 SEC TION II MICROBIOLOGY
MICROBIOLOGY
`M̀ICROBIOLOGY—BASIC BACTERIOLOGYBACTERIOLOGY
`M̀ICROBIOLOGY—BASIC MICROBIOLOGY `M̀ICROBIOLOGY—BASIC BACTERIOLOGY SEC TION II 125 126 SEC TION II MICROBIOLOGY `M̀ICROBIOLOGY—BASIC BACTERIOLOGY
HIGH-YIELD PRINCIPLES IN MICROBIOLOGY—BASIC BACTERIOLOGY

`` Bacterial taxonomy Stains
MORPHOLOGY Gram ⊕ examples Gram ⊝ examples Gram stain First-line lab test in bacterial identification. Bacteria with thick peptidoglycan layer retain crystal
Microbiology
Bacterial structures violet dye (gram ⊕); bacteria with thin peptidoglycan layer turn red or pink (gram ⊝) with
Spherical (coccus) Staphylococcus (clusters) Moraxella catarrhalis
STRUCTURE CHEMICAL COMPOSITION FUNCTION counterstain.
Streptococcus (chains or pairs) Neisseria
Appendages Enterococcus (pairs or short chains) These bugs do not Gram stain well (These Little Microbes May Unfortunately Lack Real Color
Flagellum Proteins. Motility. But Are Everywhere).
Rod (bacillus) Bacillus Enterics:
Pilus/fimbria Glycoprotein. Mediate adherence of bacteria to cell surface; Clostridium Bacteroides Treponema, Leptospira Too thin to be visualized.
sex pilus forms during conjugation. Corynebacterium Campylobacter Mycobacteria Cell wall has high lipid content.
Specialized structures Gardnerella (gram variable) E coli Mycoplasma, Ureaplasma No cell wall.
Lactobacillus Enterobacter
Spore Keratin-like coat; dipicolinic acid; Gram ⊕ only. Legionella, Rickettsia, Chlamydia, Bartonella, Primarily intracellular; also, Chlamydia lack
“Support bacteria. They’re the only culture some people have.” ` Basic Bacteriology 124 Listeria Fusobacterium
peptidoglycan, DNA. Survival: resist dehydration, heat, chemicals. Anaplasma, Ehrlichia classic peptidoglycan because of muramic
—Steven Wright Mycobacterium (acid fast) Helicobacter
Cell envelope acid.
` Clinical Bacteriology 134 Cutibacterium (formerly Propionibacterium) Klebsiella
“What lies behind us and what lies ahead of us are tiny matters Capsule Organized, discrete polysaccharide layer (except Protects against phagocytosis. Proteus Giemsa stain Rickettsia, Chlamydia, Trypanosomes A , Ricky got Chlamydia as he Tried to Please the
poly-d-glutamate on B anthracis). Pseudomonas Plasmodium, Borrelia Bored “Geisha.”
compared to what lies within us.” ` Mycology 151
—Henry S. Haskins Glycocalyx Loose network of polysaccharides. Mediates adherence to surfaces, especially Salmonella Periodic acid–Schiff Stains glycogen, mucopolysaccharides; used PaSs the sugar.
` Parasitology 155 foreign surfaces (eg, indwelling catheters). Serratia stain to diagnose Whipple disease (Tropheryma
“Infectious disease is merely a disagreeable instance of a widely prevalent Shigella whipplei B )
Outer membrane Outer leaflet: contains endotoxin (LPS/LOS). Gram ⊝ only.
tendency of all living creatures to save themselves the bother of building, ` Virology 162 Vibrio Ziehl-Neelsen stain Acid-fast bacteria (eg, Mycobacteria C , Auramine-rhodamine stain is more often used
Embedded proteins: porins and other outer Endotoxin: lipid A induces TNF and IL-1;
by their own efforts, the things they require.” Yersinia (carbol fuchsin) Nocardia; stains mycolic acid in cell wall); for screening (inexpensive, more sensitive).
membrane proteins (OMPs) antigenic O polysaccharide component.
—Hans Zinsser ` Systems 178 Respiratory: protozoa (eg, Cryptosporidium oocysts)
Inner leaflet: phospholipids. Most OMPs are antigenic. Acinetobacter baumannii
Porins: transport across outer membrane. India ink stain Cryptococcus neoformans D ; mucicarmine
` Antimicrobials 187 Bordetella
Periplasm Space between cytoplasmic membrane Accumulates components exiting gram can also be used to stain thick polysaccharide
Burkholderia cepacia
Microbiology questions on the Step 1 exam often require two (or more) and outer membrane in gram ⊝ bacteria. ⊝ cells, including hydrolytic enzymes capsule red
Haemophilus (pleomorphic)
steps: Given a certain clinical presentation, you will first need to identify (Peptidoglycan in middle.) (eg, β-lactamases). Legionella (silver stain) Silver stain Fungi (eg, Coccidioides E , Pneumocystis
the most likely causative organism, and you will then need to provide Cell wall Peptidoglycan is a sugar backbone with peptide Net-like structure gives rigid support, protects Zoonotic: jirovecii), Legionella, Helicobacter pylori
an answer regarding some feature of that organism. For example, a side chains cross-linked by transpeptidase. against osmotic pressure damage. Bartonella Fluorescent antibody Used to identify many bacteria and viruses. Example is FTA-ABS for syphilis.
description of a child with fever and a petechial rash will be followed Brucella stain
Cytoplasmic Phospholipid bilayer sac with embedded Site of oxidative and transport enzymes; PBPs
by a question that reads, “From what site does the responsible organism Francisella A B C D E
membrane proteins (eg, penicillin-binding proteins involved in cell wall synthesis.
usually enter the blood?” Pasteurella
[PBPs]) and other enzymes. Lipoteichoic acids induce TNF-α and IL-1.
Lipoteichoic acids (gram ⊕ only) extend from Branching filamentous Actinomyces
This section therefore presents organisms in two major ways: in membrane to exterior. Nocardia (weakly acid fast)
individual microbial “profiles” and in the context of the systems Pleomorphic (no cell Anaplasma, Ehrlichia
they infect and the clinical presentations they produce. You should wall) Chlamydiae (Giemsa)
become familiar with both formats. When reviewing the systems Cell envelope
Rickettsiae (Giemsa)
approach, remind yourself of the features of each microbe by returning Unique to Common to both Unique to Mycoplasma (contains sterols, which do not
gram ⊕ gram ⊝
to the individual profiles. Also be sure to memorize the laboratory Gram stain), Ureaplasma
Flagellum
characteristics that allow you to identify microbes. Lipoteichoic acid Spiral Spirochetes: Properties of growth The same type of media can possess both (or neither) of these properties.
Pilus
Borrelia (Giemsa) media
Capsule
Leptospira Selective media Favors the growth of particular organism while preventing growth of other organisms, eg, Thayer-
Endotoxin/LPS Treponema Martin agar contains antibiotics that allow the selective growth of Neisseria by inhibiting the
Outer
Porin membrane growth of other sensitive organisms.
Cell wall Indicator (differential) Yields a color change in response to the metabolism of certain organisms, eg, MacConkey agar
Peptidoglycan Periplasmic space
(β-lactamase location) media contains a pH indicator; a lactose fermenter like E coli will convert lactose to acidic metabolites
Cytoplasmic
membrane color change.
Gram ⊕ Gram ⊝
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Special culture requirements Intracellular bugs Pigment-producing Actinomyces israelii—yellow “sulfur” granules, Israel has yellow sand. Bacterial genetics
BUG MEDIA USED FOR ISOLATION MEDIA CONTENTS/OTHER Obligate intracellular Rickettsia, CHlamydia, COxiella. Rely on host Stay inside (cells) when it is Really CHilly and bacteria which are composed of filaments of bacteria. Transformation Competent bacteria can bind and import short Degraded
uncombined Recipient DNA
H influenzae Chocolate agar Factors V (NAD+) and X (hematin) ATP. COld. S aureus—yellow pigment. Aureus (Latin) = gold. pieces of environmental naked bacterial DNA Donor DNA
N gonorrhoeae, Thayer-Martin agar Selectively favors growth of Neisseria by Facultative Salmonella, Neisseria, Brucella, Mycobacterium, Some Nasty Bugs May Live FacultativeLY. P aeruginosa—blue-green pigment (pyocyanin Aerugula is green. chromosomal DNA (from bacterial cell
N meningitidis inhibiting growth of gram ⊕ organisms intracellular Listeria, Francisella, Legionella, Yersinia pestis. and pyoverdin). lysis). The transfer and expression of newly
Naked DNA Recipient cell Transformed cell
with Vancomycin, gram ⊝ organisms except transferred genes is called transformation.
Serratia marcescens—red pigment. Think red Sriracha hot sauce.
Neisseria with Trimethoprim and Colistin, A feature of many bacteria, especially
and fungi with Nystatin Encapsulated bacteria Examples are Pseudomonas aeruginosa, Please SHiNE my SKiS. S pneumoniae, H influenzae type b, and
Very Typically Cultures Neisseria Streptococcus pneumoniae A , Haemophilus Are opsonized, and then cleared by spleen. Neisseria (SHiN).
A In vivo biofilm- S epidermidis Catheter and prosthetic device infections
influenzae type b, Neisseria meningitidis, Asplenics (No Spleen Here) have opsonizing Adding deoxyribonuclease degrades naked
B pertussis Bordet-Gengou agar (Bordet for Bordetella) Potato extract producing bacteria Viridans streptococci (S mutans, S sanguinis) Dental plaques, infective endocarditis
Escherichia coli, Salmonella, Klebsiella ability and thus risk for severe infections; DNA, preventing transformation.
Regan-Lowe medium Charcoal, blood, and antibiotic
pneumoniae, and group B Strep. Their need vaccines to protect against: P aeruginosa Respiratory tree colonization in patients with Conjugation
C diphtheriae Tellurite agar, Löffler medium cystic fibrosis, ventilator-associated pneumonia
capsules serve as an antiphagocytic virulence N meningitidis F+ × F– F+ plasmid contains genes required for sex pilus Single strand
M tuberculosis Löwenstein-Jensen agar factor. S pneumoniae Contact lens–associated keratitis Sex pilus transferred
and conjugation. Bacteria without this plasmid
M pneumoniae Eaton agar Requires cholesterol Capsular polysaccharide + protein conjugate H influenzae Nontypeable (unencapsulated) H influenzae Otitis media are termed F–. Sex pilus on F+ bacterium Plasmid
Lactose-fermenting MacConkey agar Fermentation produces acid, causing colonies to serves as an antigen in vaccines. contacts F− bacterium. A single strand
enterics turn pink of plasmid DNA is transferred across the F+ cell F– cell F+ cell F– cell F+ cell F+ cell
Bacterial virulence These promote evasion of host immune response. conjugal bridge (“mating bridge”). No transfer
E coli Eosin–methylene blue (EMB) agar Colonies with green metallic sheen
Encapsulated bacteria Some vaccines containing polysaccharide Pneumococcal vaccines: PCV13 (pneumococcal factors of chromosomal DNA.
Legionella Charcoal yeast extract agar buffered with vaccines capsule antigens are conjugated to a carrier conjugate vaccine), PPSV23 (pneumococcal Protein A Binds Fc region of IgG. Prevents opsonization and phagocytosis. Expressed by S aureus. Hfr × F– F+ plasmid can become incorporated into Plasmid incorporates Transfer and replication
cysteine and iron protein, enhancing immunogenicity by polysaccharide vaccine with no conjugated into bacterial DNA of part of the chromosome
IgA protease Enzyme that cleaves IgA, allowing bacteria to adhere to and colonize mucous membranes. Secreted bacterial chromosomal DNA, termed high-
Fungi Sabouraud agar “Sab’s a fun guy!” promoting T-cell activation and subsequent protein)
by S pneumoniae, H influenzae type b, and Neisseria (SHiN). frequency recombination (Hfr) cell. Transfer Plasmid
class switching. A polysaccharide antigen H influenzae type b (conjugate vaccine)
M protein Helps prevent phagocytosis. Expressed by group A streptococci. Shares similar epitopes to human of leading part of plasmid and a few flanking F+ cell F– cell Hfr cell F– cell Hfr cell F– cell Hfr cell Recombinant
alone cannot be presented to T cells. Meningococcal vaccine (conjugate vaccine) F– cell
cellular proteins (molecular mimicry); possibly underlies the autoimmune response seen in acute chromosomal genes. High-frequency
Aerobes Use an O2-dependent system to generate ATP. Nagging Pests Must Breathe.
rheumatic fever. recombination may integrate some of those
Examples include Nocardia, Pseudomonas
bacterial genes. Recipient cell remains F– but
aeruginosa, and MycoBacterium tuberculosis. Urease-positive Proteus, Cryptococcus, H pylori, Ureaplasma, Pee CHUNKSS.
now may have new bacterial genes.
Reactivation of M tuberculosis (eg, after organisms Nocardia, Klebsiella, S epidermidis,
immunocompromise or TNF-α inhibitor use) S saprophyticus. Urease hydrolyzes urea Type III secretion Also known as “injectisome.” Needle-like protein appendage facilitating direct delivery of toxins Transduction
has a predilection for the apices of the lung. to release ammonia and CO2 pH. system from certain gram ⊝ bacteria (eg, Pseudomonas, Salmonella, Shigella, E coli) to eukaryotic host Generalized A packaging “error.” Lytic phage infects Cleavage of Bacterial DNA package
Lytic
Predisposes to struvite (ammonium cell. bacterium, leading to cleavage of bacterial phage
Bacteria bacterial DNA in phage capsid
magnesium phosphate) stones, particularly DNA. Parts of bacterial chromosomal DNA

Anaerobes Examples include Clostridium, Bacteroides, Anaerobes Can’t Breathe Fresh Air. Proteus. may become packaged in phage capsid. Phage
Fusobacterium, and Actinomyces israelii. They Anaerobes are normal flora in GI tract, typically infects another bacterium, transferring these
lack catalase and/or superoxide dismutase pathogenic elsewhere. AminO2glycosides are genes.
and are thus susceptible to oxidative damage. ineffective against anaerobes because these Catalase-positive Catalase degrades H2O2 into H2O and Cats Need PLACESS to Belch their Hairballs.
Generally foul smelling (short-chain fatty antibiotics require O2 to enter into bacterial organisms bubbles of O2 A before it can be converted
acids), are difficult to culture, and produce gas cell. A
to microbicidal products by the enzyme
Release of new phage Infects other Phage’s genes
in tissue (CO2 and H2). myeloperoxidase. People with chronic from lysed cell bacteria transferred
granulomatous disease (NADPH oxidase
Facultative anaerobes May use O2 as a terminal electron acceptor to Streptococci, staphylococci, and enteric gram ⊝ Specialized An “excision” event. Lysogenic phage infects Viral DNA Viral DNA
generate ATP, but can also use fermentation deficiency) have recurrent infections with Lysogenic incorporates in Phage particles
bacteria. bacterium; viral DNA incorporates into phage Bacteria bacterial DNA carry bacterial DNA
and other O2-independent pathways. certain catalase ⊕ organisms.
bacterial chromosome. When phage DNA
Examples: Nocardia, Pseudomonas, Listeria,
is excised, flanking bacterial genes may be
Aspergillus, Candida, E coli, Staphylococci,
excised with it. DNA is packaged into phage
Serratia, B cepacia, H pylori.
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
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Bacterial genetics (continued) Bugs with exotoxins Bugs with exotoxins (continued) MICROBIOLOGY—CLINICAL BACTERIOLOGY
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Transposition Segment of DNA (eg, transposon) that can BACTERIA TOXIN MECHANISM MANIFESTATION BACTERIA TOXIN MECHANISM MANIFESTATION
Plasmid
“jump” (copy/excise and reinsert) from one Inhibit protein synthesis Lyse cell membranes Gram-positive lab algorithm
location to another, can transfer genes from Corynebacterium Diphtheria toxina Pharyngitis with pseudomembranes in throat Clostridium Alpha toxin Phospholipase (lecithinase) Degradation of phospholipids myonecrosis Gram (purple/blue)
plasmid to chromosome and vice versa. This Integration of genes diphtheriae Inactivate elongation factor and severe lymphadenopathy (bull neck) perfringens that degrades tissue and (“gas gangrene”) and hemolysis (“double zone”
Transposons
is a critical process in creating plasmids with (EF-2) cell membranes of hemolysis on blood agar)
Bacterial Pseudomonas Exotoxin A a Host cell death
multiple antibiotic resistance which can be DNA Branching
aeruginosa Streptococcus Streptolysin O Protein that degrades cell Lyses RBCs; contributes to β-hemolysis; Bacilli Cocci
transferred across species lines (eg, Tn1546 filaments
Target site
Shigella spp. Shiga toxin (ST)a GI mucosal damage dysentery; ST also pyogenes membrane host antibodies against toxin (ASO) used to
carrying vanA gene from vancomycin-resistant
Inactivate 60S ribosome by enhances cytokine release, causing hemolytic- diagnose rheumatic fever (do not confuse
Enterococcus to S aureus).
removing adenine from uremic syndrome (HUS) with immune complexes of poststreptococcal Aerobic Anaerobic Anaerobic/facultative Aerobic Anaerobic
rRNA glomerulonephritis)
Spore-forming Some bacteria can form spores A when Bacillus anthracis Anthrax Enterohemorrhagic Shiga-like toxin SLT enhances cytokine release, causing HUS Listeria Clostridium Nocardia Actinomyces
bacteria nutrients are limited. Bacillus cereus Food poisoning E coli (SLT)a (prototypically in EHEC serotype O157:H7). Superantigens causing shock Bacillus Cutibacterium (weakly acid fast) (not acid fast)
Corynebacterium
Unlike Shigella, EHEC does not invade host Staphylococcus Toxic shock Cross-links β region of Toxic shock syndrome: fever, rash, shock; other (formerly
A
Spores lack metabolic activity. Clostridium botulinum Botulism
Propionibacterium)
Spores are highly resistant to heat and Clostridium difficile Pseudomembranous cells aureus syndrome toxin TCR to MHC class II toxins cause scalded skin syndrome (exfoliative Catalase
chemicals. Core contains dipicolinic acid. colitis Increase fluid secretion (TSST-1) on APCs outside of the toxin) and food poisoning (heat-stable
Must autoclave to kill spores (as is done to Clostridium perfringens Gas gangrene antigen binding site enterotoxin)
Enterotoxigenic Heat-labile Overactivates adenylate Watery diarrhea: “labile in the Air (Adenylate Streptococcus Staphylococcus
surgical equipment) by steaming at 121°C for Clostridium tetani Tetanus Streptococcus Erythrogenic overwhelming release Toxic shock–like syndrome: fever, rash, shock;
E coli toxin (LT)a cyclase ( cAMP) Cl− cyclase), stable on the Ground (Guanylate
15 minutes. pyogenes exotoxin A of IL-1, IL-2, IFN-γ, and scarlet fever Hemolysis Coagulase
secretion in gut and H2O cyclase)”
TNF-α shock
efflux
α γ
(Partial (Complete
Heat-stable
toxin (ST)
Overactivates guanylate
cyclase ( cGMP)
hemolysis,
green)
β hemolysis,
clear)
(No hemolysis,
grows in bile)
S aureus
Endotoxin LPS found in outer membrane of gram ⊝ ENDOTOXINS: Novobiocin
Main features of exotoxins and endotoxins resorption of NaCl
bacteria (both cocci and rods). Composed of Edema Optochin sensitivity Bacitracin sensitivity Growth in 6.5% NaCl sensitivity
and H2O in gut
Exotoxins Endotoxin O antigen + core polysaccharide + lipid A (the Nitric oxide and bile solubility
Bacillus anthracis Edema toxina Mimics adenylate cyclase Likely responsible for characteristic edematous toxic component). DIC/Death
SOURCE Certain species of gram ⊕ and gram ⊝ bacteria Outer cell membrane of most gram ⊝ bacteria
( cAMP) borders of black eschar in cutaneous anthrax Released upon cell lysis or by living cells by Outer membrane
SECRETED FROM CELL Yes No Group B Group A S saprophyticus S epidermidis
Vibrio cholerae Cholera toxina Overactivates adenylate Voluminous “rice-water” diarrhea blebs detaching from outer surface membrane TNF-α S agalactiae S pyogenes
CHEMISTRY Polypeptide Lipid A component of LPS (structural part of cyclase ( cAMP) by (vs exotoxin, which is actively secreted). O-antigen + core polysaccharide + lipid A
bacteria; released when lysed) permanently activating Gs Three main effects: macrophage activation eXtremely heat stable
LOCATION OF GENES Plasmid or bacteriophage Bacterial chromosome Cl− secretion in gut (TLR4/CD14), complement activation, and IL-1 and IL-6 Viridans streptococci
Enterococcus
and H2O efflux tissue factor activation. Neutrophil chemotaxis (no capsule) S pneumoniae Nonenterococcus E faecium
ADVERSE EFFECTS High (fatal dose on the order of 1 µg) Low (fatal dose on the order of hundreds of S mutans (encapsulated) S bovis
Inhibit phagocytic ability Shock S mitis E faecalis
micrograms)
CLINICAL EFFECTS Various effects (see following pages) Fever, shock (hypotension), DIC Bordetella pertussis Pertussis toxina Overactivates adenylate Whooping cough—child coughs on expiration Important tests are in bold. Important pathogens are in bold italics.
Note: Enterococcus is either α- or γ-hemolytic.
MODE OF ACTION Various modes (see following pages) Induces TNF, IL-1, and IL-6 cyclase ( cAMP) by and “whoops” on inspiration (toxin may IL-1, IL-6 Fever
disabling Gi, impairing not actually be a cause of cough; can cause
ANTIGENICITY Induces high-titer antibodies called antitoxins Poorly antigenic phagocytosis to permit “100-day cough” in adults) Macrophage activation TNF-α Fever and hypotension
VACCINES Toxoids used as vaccines No toxoids formed and no vaccine available survival of microbe (TLR4/CD14) Gram-positive cocci antibiotic tests
HEAT STABILITY Destroyed rapidly at 60°C (except Stable at 100°C for 1 hr Inhibit release of neurotransmitter Nitric oxide Hypotension Staphylococci NOvobiocin—Saprophyticus is Resistant; On the office’s “staph” retreat, there was
staphylococcal enterotoxin and E coli heat- Epidermidis is Sensitive. NO StRESs.
Clostridium tetani Tetanospasmina Both are proteases that Toxin prevents release of inhibitory (GABA
stable toxin) and glycine) neurotransmitters from Renshaw C3a
Histamine release: Streptococci Optochin—Viridans is Resistant; Pneumoniae is OVRPS (overpass).
cleave SNARE (soluble Endotoxin Hypotension and edema
TYPICAL DISEASES Tetanus, botulism, diphtheria Meningococcemia; sepsis by gram ⊝ rods NSF attachment cells in spinal cord spastic paralysis, risus Complement activation Sensitive.
(lipid A component)
protein receptor), a set sardonicus, trismus (lockjaw) C5a Neutrophil chemotaxis Bacitracin—group B strep are Resistant; group B-BRAS.
Clostridium Botulinum toxina of proteins required for Toxin prevents release of stimulatory (ACh) A strep are Sensitive.
botulinum neurotransmitter release signals at neuromuscular junction flaccid Tissue factor activation Coagulation DIC
cascade
via vesicular fusion paralysis (floppy baby)
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.
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α-hemolytic bacteria Gram ⊕ cocci. Partial reduction of hemoglobin causes greenish or brownish color without clearing Staphylococcus Gram ⊕, catalase ⊕, coagulase ⊝, urease ⊕ cocci in clusters. Novobiocin resistant. Streptococcus Gram ⊕ cocci, bacitracin resistant, β-hemolytic, Group B for Babies! Bacillus cereus Gram ⊕ rod. Causes food poisoning. Spores survive cooking rice (also known as reheated rice
A around growth on blood agar A . Include the following organisms: saprophyticus Normal flora of female genital tract and perineum. agalactiae (group B colonizes vagina; causes pneumonia, syndrome). Keeping rice warm results in germination of spores and enterotoxin formation.
Streptococcus pneumoniae (catalase ⊝ and optochin sensitive) Second most common cause of uncomplicated UTI in young women (most common is E coli). streptococci) meningitis, and sepsis, mainly in babies. Emetic type usually seen with rice and pasta. Nausea and vomiting within 1–5 hr. Caused by
Viridans streptococci (catalase ⊝ and optochin resistant) Produces CAMP factor, which enlarges the cereulide, a preformed toxin.
area of hemolysis formed by S aureus. (Note: Diarrheal type causes watery, nonbloody diarrhea and GI pain within 8–18 hr.
Streptococcus Gram ⊕, lancet-shaped diplococci A . Pneumococcus is associated with “rusty” CAMP stands for the authors of the test, not
pneumoniae Encapsulated. IgA protease. Optochin sputum, sepsis in patients with sickle cell cyclic AMP.) Hippurate test ⊕. PYR ⊝.
A sensitive. Most common cause of: disease, and asplenic patients. Screen pregnant women at 35–37 weeks of Clostridia (with Gram ⊕, spore-forming, obligate anaerobic rods.
Meningitis No virulence without capsule. gestation with rectal and vaginal swabs. exotoxins)
Otitis media (in children) MOPS commonly spread pneumonia. Patients with ⊕ culture receive intrapartum C tetani Produces tetanospasmin, an exotoxin causing Tetanus is tetanic paralysis.
Pneumonia penicillin prophylaxis. tetanus. Tetanus toxin (and botulinum toxin)
β-hemolytic bacteria Gram ⊕ cocci. Complete lysis of RBCs clear area surrounding colony on blood agar A . Include Sinusitis are proteases that cleave SNARE proteins for
A the following organisms:
neurotransmitters. Blocks release of inhibitory
Staphylococcus aureus (catalase and coagulase ⊕) Streptococcus bovis Gram ⊕ cocci, colonizes the gut. S gallolyticus Bovis in the blood = cancer in the colon. neurotransmitters, GABA and glycine, from
Streptococcus pyogenes—group A strep (catalase ⊝ and bacitracin sensitive) (S bovis biotype 1) can cause bacteremia and Renshaw cells in spinal cord.
Streptococcus agalactiae—group B strep (catalase ⊝ and bacitracin resistant) subacute endocarditis and is associated with Causes spastic paralysis, trismus (lockjaw), risus
colon cancer. sardonicus (raised eyebrows and open grin),
Viridans group Gram ⊕, α-hemolytic cocci. Resistant Viridans group strep live in the mouth, because
opisthotonos (spasms of spinal extensors).
streptococci to optochin, differentiating them from they are not afraid of-the-chin (op-to-chin
Prevent with tetanus vaccine. Treat with
S pneumoniae which is α-hemolytic but resistant). Enterococci Enterococci are more resilient than
Gram ⊕ cocci. Enterococci (E faecalis and antitoxin +/− vaccine booster, antibiotics,
optochin sensitive. Normal flora of the Sanguinis = blood. Think, “there is lots of streptococci, can grow in 6.5% NaCl and bile
E faecium) are normal colonic flora that are diazepam (for muscle spasms), and wound
oropharynx. blood in the heart” (endocarditis). (lab test).
Staphylococcus aureus Gram ⊕, β-hemolytic, catalase ⊕, coagulase TSST-1 is a superantigen that binds to MHC penicillin G resistant and cause UTI, biliary debridement.
Streptococcus mutans and S mitis cause dental tract infections, and subacute endocarditis Entero = intestine, faecalis = feces, strepto =
⊕ cocci in clusters A . Protein A (virulence II and T-cell receptor, resulting in polyclonal C botulinum Produces a heat-labile toxin that inhibits Symptoms of botulism (the 4 D’s): Diplopia,
A caries.
factor) binds Fc-IgG, inhibiting complement T-cell activation. (following GI/GU procedures). Catalase ⊝, twisted (chains), coccus = berry.
S sanguinis makes dextrans that bind to fibrin- ACh release at the neuromuscular junction, Dysarthria, Dysphagia, Dyspnea.
activation and phagocytosis. Commonly Staphylococcal toxic shock syndrome (TSS)— PYR ⊕, variable hemolysis.
platelet aggregates on damaged heart valves, causing botulism. In adults, disease is caused Botulinum is from bad bottles of food, juice, and
colonizes the nares, ears, axilla, and groin. fever, vomiting, rash, desquamation, shock, VRE (vancomycin-resistant enterococci) are an
causing subacute bacterial endocarditis. by ingestion of preformed toxin. In babies, honey (causes a descending flaccid paralysis).
Causes: end-organ failure. TSS results in AST, ALT, important cause of nosocomial infection.
ingestion of spores (eg, in honey) leads to Local botox injections used to treat focal
Inflammatory disease—skin infections, bilirubin. Associated with prolonged use of disease (floppy baby syndrome). Treat with dystonia, achalasia, and muscle spasms. Also
organ abscesses, pneumonia (often after vaginal tampons or nasal packing. human botulinum immunoglobulin. used for cosmetic reduction of facial wrinkles.
Streptococcus Gram ⊕ cocci in chains A . Group A strep Pharyngitis can result in rheumatic “phever” Bacillus anthracis
influenza virus infection), endocarditis, Compare with Streptococcus pyogenes TSS (a Gram ⊕, spore-forming rod that produces anthrax toxin. The only bacterium with a polypeptide
pyogenes (group A cause: and glomerulonephritis. C perfringens Produces α toxin (lecithinase, a phospholipase) Perfringens perforates a gangrenous leg.
septic arthritis, and osteomyelitis. toxic shock–like syndrome associated with capsule (contains d-glutamate). Colonies show a halo of projections, sometimes referred to as
streptococci) Pyogenic—pharyngitis, cellulitis, impetigo Strains causing impetigo can induce that can cause myonecrosis (gas gangrene A ;
Toxin-mediated disease—toxic shock painful skin infection). “medusa head” appearance. A
A (“honey-crusted” lesions), erysipelas glomerulonephritis. presents as soft tissue crepitus) and hemolysis.
syndrome (TSST-1), scalded skin syndrome S aureus food poisoning due to ingestion of Cutaneous anthrax Painless papule surrounded by vesicles ulcer with black eschar ( A ) (painless, necrotic)
Toxigenic—scarlet fever, toxic shock–like Scarlet fever—blanching, sandpaper-like body Spores can survive in undercooked food;
(exfoliative toxin), rapid-onset food preformed toxin short incubation period uncommonly progresses to bacteremia and death.
syndrome, necrotizing fasciitis rash, strawberry tongue, and circumoral A when ingested, bacteria release heat-labile
poisoning (enterotoxins). (2–6 hr) followed by nonbloody diarrhea
Immunologic—rheumatic fever, pallor in the setting of group A streptococcal enterotoxin food poisoning.
MRSA (methicillin-resistant S aureus)— and emesis. Enterotoxin is heat stable not
glomerulonephritis pharyngitis (erythrogenic toxin ⊕).
important cause of serious nosocomial and destroyed by cooking.
Bacitracin sensitive, β-hemolytic, pyrrolidonyl
community-acquired infections; resistant to Bad staph (aureus) make coagulase and toxins.
arylamidase (PYR) ⊕. Hyaluronic acid capsule
methicillin and nafcillin because of altered Forms fibrin clot around self abscess.
and M protein inhibit phagocytosis. Antibodies C difficile Produces 2 toxins. Toxin A, an enterotoxin, Difficile causes diarrhea. Treatment:
penicillin-binding protein.
to M protein enhance host defenses against S B
binds to brush border of gut and alters fluid metronidazole or oral vancomycin. For
pyogenes but can give rise to rheumatic fever. secretion. Toxin B, a cytotoxin, disrupts recurrent cases, consider repeating prior
Pulmonary anthrax Inhalation of spores flu-like symptoms that rapidly progress to fever, pulmonary hemorrhage, cytoskeleton via actin depolymerization. Both regimen, fidaxomicin, or fecal microbiota
ASO titer or anti-DNase B antibodies indicate
Staphylococcus Gram ⊕, catalase ⊕, coagulase ⊝, urease ⊕ cocci in clusters. Novobiocin sensitive. Does not mediastinitis, and shock. Also known as woolsorter’s disease. CXR may show widened
recent S pyogenes infection. toxins lead to diarrhea pseudomembranous transplant.
epidermidis ferment mannitol (vs S aureus). mediastinum. colitis B . Often 2° to antibiotic use, especially
Normal flora of skin; contaminates blood cultures.
clindamycin or ampicillin; associated with PPIs.
Infects prosthetic devices (eg, hip implant, heart valve) and IV catheters by producing adherent
Diagnosed by PCR or antigen detection of one
biofilms.
or both toxins in stool.
MICROBIOLOGY
`M̀ICROBIOLOGY—CLINICAL MICROBIOLOGY `M̀ICROBIOLOGY—CLINICAL BACTERIOLOGY SEC TION II 141 142 SEC TION II MICROBIOLOGY `M̀ICROBIOLOGY—CLINICAL BACTERIOLOGY
Corynebacterium Gram ⊕ rod; transmitted via respiratory Coryne = club shaped. Mycobacteria Mycobacterium tuberculosis (TB, often TB symptoms include fever, night sweats, Leprosy (Hansen Caused by Mycobacterium leprae, an acid-fast bacillus that likes cool temperatures (infects skin Neisseria Gram ⊝ diplococci. Metabolize glucose MeninGococci ferment Maltose and Glucose.
diphtheriae droplets. Causes diphtheria via exotoxin Black colonies on cystine-tellurite agar. A
resistant to multiple drugs). weight loss, cough (nonproductive or disease) and superficial nerves—“glove and stocking” loss of sensation A ) and cannot be grown in vitro. A and produce IgA proteases. Contain Gonococci ferment Glucose.
A encoded by β-prophage. Potent exotoxin ABCDEFG: M avium–intracellulare (causes disseminated, productive), hemoptysis. A
Diagnosed via skin biopsy or tissue PCR. Reservoir in United States: armadillos. lipooligosaccharides (LOS) with strong
inhibits protein synthesis via ADP-ribosylation ADP-ribosylation non-TB disease in AIDS; often resistant Cord factor creates a “serpentine cord” Hansen disease has 2 forms (many cases fall temporarily between two extremes): endotoxin activity. N gonorrhoeae is often
of EF-2. β-prophage to multiple drugs). Prophylaxis with appearance in virulent M tuberculosis strains; Lepromatous—presents diffusely over the skin, with leonine (lion-like) facies B , and is intracellular (within neutrophils) A .
Symptoms include pseudomembranous Corynebacterium azithromycin when CD4+ count < 50 cells/ activates macrophages (promoting granuloma communicable (high bacterial load); characterized by low cell-mediated immunity with a
Diphtheriae mm3. formation) and induces release of TNF-α. humoral Th2 response. Lepromatous form can be lethal. Gonococci Meningococci
pharyngitis (grayish-white membrane A )
with lymphadenopathy, myocarditis, and Elongation Factor 2 M scrofulaceum (cervical lymphadenitis in Sulfatides (surface glycolipids) inhibit Tuberculoid—limited to a few hypoesthetic, hairless skin plaques; characterized by high cell- No polysaccharide capsule Polysaccharide capsule
arrhythmias. Granules children). phagolysosomal fusion. mediated immunity with a largely Th1-type immune response and low bacterial load. Maltose not fermented Maltose fermentation
B
Lab diagnosis based on gram ⊕ rods with M marinum (hand infection in aquarium Treatment: dapsone and rifampin for tuberculoid form; clofazimine is added for lepromatous form. B
No vaccine due to antigenic variation of pilus Vaccine (type B vaccine not widely available)
metachromatic (blue and red) granules and handlers).
proteins
⊕ Elek test for toxin. All mycobacteria are acid-fast organisms (pink
Toxoid vaccine prevents diphtheria. rods; arrows in A ). Sexually or perinatally transmitted Transmitted via respiratory and oral secretions
Causes gonorrhea, septic arthritis, neonatal Causes meningococcemia with petechial
conjunctivitis (2–5 days after birth), pelvic hemorrhages and gangrene of toes B ,
Listeria Gram ⊕, facultative intracellular rod; acquired by ingestion of unpasteurized dairy products and Tuberculosis inflammatory disease (PID), and Fitz-Hugh– meningitis, Waterhouse-Friderichsen
monocytogenes cold deli meats, via transplacental transmission, or by vaginal transmission during birth. Grows Curtis syndrome syndrome (adrenal insufficiency, fever, DIC,
Mycobacterium PPD ⊕ if current infection or past exposure.
well at refrigeration temperatures (4°–10°C; “cold enrichment”). tuberculosis shock)
A Hilar nodes PPD ⊝ if no infection and in sarcoidosis or
Forms “rocket tails” (red in A ) via actin polymerization that allow intracellular movement and cell- Gram-negative lab algorithm Rifampin, ciprofloxacin, or ceftriaxone
+ HIV infection (especially with low CD4+ cell Condoms sexual transmission, erythromycin
Ghon
to-cell spread across cell membranes, thereby avoiding antibody. Characteristic tumbling motility Ghon focus count). Gram (pink) eye ointment prevents neonatal blindness prophylaxis in close contacts
complex
in broth. (usually mid/ Interferon-γ release assay (IGRA) has fewer
lower lobes)
Treatment: ceftriaxone (+ azithromycin Treatment: ceftriaxone or penicillin G
Can cause amnionitis, septicemia, and spontaneous abortion in pregnant women; granulomatosis Primary tuberculosis false positives from BCG vaccination. or doxycycline, for possible chlamydial
infantiseptica; neonatal meningitis; meningitis in immunocompromised patients; mild, self- Caseating granulomas with central necrosis Coccobacilli
> 90% < 10% Diplococci Comma-shaped rods coinfection)
limited gastroenteritis in healthy individuals. Healing by fibrosis Progressive primary tuberculosis and Langhans giant cell (single example
Treatment: ampicillin. Calcification (AIDS, malnutrition)
in A ) are characteristic of 2° tuberculosis.
(PPD )
Aerobic Haemophilus influenzae Oxidase Haemophilus Small gram ⊝ (coccobacillary) rod. Aerosol Vaccine contains type b capsular polysaccharide
Reactivation Progressive A Bordetella pertussis
lung disease
Pasteurella influenzae transmission. Nontypeable (unencapsulated) (polyribosylribitol phosphate) conjugated
Nocardia vs Both are gram ⊕ and form long, branching filaments resembling fungi. 2° tuberculosis
Bacteremia Maltose fermentation
Fibrocaseous
Brucella
A strains are the most common cause of mucosal to diphtheria toxoid or other protein. Given
Actinomyces Nocardia Actinomyces Francisella tularensis Grows in 42°C Grows in alkaline media Produces urease
cavitary lesion infections (otitis media, conjunctivitis, between 2 and 18 months of age.
(usually upper
A Aerobe Anaerobe Miliary
Meninges
N gonorrhoeae Campylobacter jejuni Vibrio cholerae Helicobacter pylori bronchitis) as well as invasive infections since Does not cause the flu (influenza virus does).
lobes)
tuberculosis N meningitidis
Acid fast (weak) A Not acid fast B
Moraxella the vaccine for capsular type b was introduced.
Vertebrae
(Pott disease) Produces IgA protease.
Found in soil Normal oral, reproductive, and GI flora Culture on chocolate agar, which contains
Localized destructive disease Lymph nodes
Causes pulmonary infections in Causes oral/facial abscesses that drain through Cavity factors V (NAD+) and X (hematin) for growth;
Caseation
immunocompromised (can mimic TB but sinus tracts; often associated with dental caries/ Caseation Lungs
Spleen
Bacilli can also be grown with S aureus, which
with ⊝ PPD); cutaneous infections after extraction and other maxillofacial trauma; Scar
Liver Adrenal B provides factor V via RBC hemolysis.
trauma in immunocompetent; can spread to forms yellow “sulfur granules”; can also cause Lactose fermentation
gland HaEMOPhilus causes Epiglottitis (endoscopic
B
CNS PID with IUDs Joints and appearance in A , can be “cherry red” in
long bones
Treat with sulfonamides (TMP-SMX) Treat with penicillin children; “thumb sign” on lateral neck
Oxidase Fast Slow
x-ray B ), Meningitis, Otitis media, and
Treatment is a SNAP: Sulfonamides—Nocardia; Actinomyces—Penicillin
E coli Pneumonia.
Citrobacter
Pseudomonas
Klebsiella
Serratia
Treatment: amoxicillin +/− clavulanate for
H2S production Enterobacter
mucosal infections; ceftriaxone for meningitis;
on TSI agar
rifampin prophylaxis for close contacts.
Shigella Salmonella
Yersinia Proteus
Important tests are in bold. Important pathogens are in bold italics.
MICROBIOLOGY
MICROBIOLOGY
Bordetella pertussis Gram ⊝, aerobic coccobacillus. Virulence factors include pertussis toxin (disables Gi), adenylate Salmonella vs Shigella Both Salmonella and Shigella are gram ⊝ rods, non-lactose fermenters, oxidase ⊝, and can invade Escherichia coli Gram ⊝ rod. E coli virulence factors: fimbriae—cystitis and pyelonephritis (P-pili); K capsule— Vibrio cholerae Gram ⊝, flagellated, comma shaped A , oxidase ⊕, grows in alkaline media. Endemic to
cyclase toxin ( cAMP), and tracheal cytotoxin. Three clinical stages: the GI tract via M cells of Peyer patches. pneumonia, neonatal meningitis; LPS endotoxin—septic shock. A developing countries. Produces profuse rice-water diarrhea via enterotoxin that permanently
Catarrhal—low-grade fevers, Coryza. Salmonella typhi Salmonella spp. Shigella STRAIN TOXIN AND MECHANISM PRESENTATION
activates Gs, cAMP. Sensitive to stomach acid (acid labile); requires large inoculum (high ID50)
Paroxysmal—paroxysms of intense cough followed by inspiratory “whooP” (“whooping cough”), (except S typhi) unless host has gastric acidity. Transmitted via ingestion of contaminated water or uncooked
Enteroinvasive E coli Microbe invades intestinal mucosa and causes EIEC is Invasive; dysentery. Clinical
posttussive vomiting. RESERVOIRS Humans only Humans and animals Humans only food (eg, raw shellfish). Treat promptly with oral rehydration solution.
necrosis and inflammation. manifestations similar to Shigella.
Convalescent—gradual recovery of chronic cough.
SPREAD Can disseminate Can disseminate Cell to cell; no hematogenous spread Enterotoxigenic E coli Produces heat-labile and heat-stable ETEC; Traveler’s diarrhea (watery).
Prevented by Tdap, DTaP vaccines. May be mistaken as viral infection due to lymphocytic
hematogenously hematogenously enteroToxins. No inflammation or invasion.
infiltrate resulting from immune response.
H2S PRODUCTION Yes Yes No Enteropathogenic No toxin produced. Adheres to apical surface, Diarrhea, usually in children (think EPEC and
FLAGELLA Yes (salmon swim) Yes (salmon swim) No E coli flattens villi, prevents absorption. Pediatrics).
Legionella Gram ⊝ rod. Gram stains poorly—use silver Think of a French legionnaire (soldier) with Enterohemorrhagic O157:H7 is most common serotype in US. Often Dysentery (toxin alone causes necrosis and
VIRULENCE FACTORS Endotoxin; Vi capsule Endotoxin Endotoxin; Shiga toxin (enterotoxin) Helicobacter pylori Curved, flagellated (motile), gram ⊝ rod A that is triple ⊕: catalase ⊕, oxidase ⊕, and urease ⊕
pneumophila stain. Grow on charcoal yeast extract his silver helmet, sitting around a campfire E coli transmitted via undercooked meat, raw leafy inflammation).
(charcoal) with his iron dagger—he is no sissy
INFECTIOUS DOSE (ID50) High—large inoculum High Low—very small inoculum required; A (can use urea breath test or fecal antigen test for diagnosis). Urease produces ammonia, creating
A medium with iron and cysteine. Detected by vegetables. Does not ferment sorbitol (vs other E coli).
(cysteine). required; acid-labile acid stable (resistant to gastric acids) an alkaline environment, which helps H pylori survive in acidic mucosa. Colonizes mainly
presence of antigen in urine. Labs may show Shiga-like toxin causes hemolytic-uremic Hemorrhagic, Hamburgers, Hemolytic-uremic
(inactivated by gastric acids) antrum of stomach; causes gastritis and peptic ulcers (especially duodenal). Risk factor for peptic
hyponatremia. syndrome: triad of anemia, thrombocytopenia, syndrome.
Aerosol transmission from environmental EFFECT OF ANTIBIOTICS ON FECAL Prolongs duration Prolongs duration Shortens duration ulcer disease, gastric adenocarcinoma, and MALT lymphoma.
EXCRETION and acute renal failure due to microthrombi Most common initial treatment is triple therapy: Amoxicillin (metronidazole if penicillin allergy)
water source habitat (eg, air conditioning forming on damaged endothelium
systems, hot water tanks). No person-to-person IMMUNE RESPONSE Primarily monocytes PMNs in disseminated Primarily PMN infiltration + Clarithromycin + Proton pump inhibitor; Antibiotics Cure Pylori.
mechanical hemolysis (with schistocytes on
transmission. disease
peripheral blood smear), platelet consumption,
Treatment: macrolide or quinolone. GI MANIFESTATIONS Constipation, followed by Diarrhea (possibly bloody) Bloody diarrhea (bacillary dysentery) and renal blood flow.
Legionnaires’ disease—severe pneumonia diarrhea
(often unilateral and lobar A ), fever, GI and Spirochetes Spiral-shaped bacteria A with axial filaments. BLT.
VACCINE Oral vaccine contains live No vaccine No vaccine
CNS symptoms. Common in smokers and in Klebsiella Gram ⊝ rod; intestinal flora that causes lobar 5 A’s of KlebsiellA: Includes Borrelia (big size), Leptospira, and Borrelia is Big.
attenuated S typhi A
chronic lung disease. pneumonia in alcoholics and diabetics when Aspiration pneumonia Treponema. Only Borrelia can be visualized
IM vaccine contains Vi A
Pontiac fever—mild flu-like syndrome. aspirated. Very mucoid colonies A caused by Abscess in lungs and liver using aniline dyes (Wright or Giemsa stain)
capsular polysaccharide
abundant polysaccharide capsules. Dark red Alcoholics in light microscopy due to size. Treponema is
UNIQUE PROPERTIES Causes typhoid fever Poultry, eggs, pets, and Four F’s: Fingers, Flies, Food, Feces
“currant jelly” sputum (blood/mucus). DiAbetics visualized by dark-field microscopy or direct
Pseudomonas Corneal ulcers/keratitis in contact lens wearers/ (rose spots on abdomen, turtles are common In order of decreasing severity (less
Aeruginosa—aerobic; motile, gram ⊝ rod. Non- Also cause of nosocomial UTIs. Associated with “CurrAnt jelly” sputum fluorescent antibody (DFA) microscopy.
aeruginosa minor eye trauma. constipation, abdominal sources toxin produced): S dysenteriae,
lactose fermenting. Oxidase ⊕. Frequently evolution of multidrug resistance (MDR).
Ecthyma gangrenosum—rapidly progressive, pain, fever); treat Antibiotics not S flexneri, S boydii, S sonnei
A found in water. Has a grape-like odor.
necrotic cutaneous lesion B caused by with ceftriaxone or indicated Invasion of M cells is key to
PSEUDOMONAS is associated with:
Pseudomonas bacteremia. Typically seen in fluoroquinolone Gastroenteritis is pathogenicity: organisms that
Pneumonia, Sepsis, Ecthyma gangrenosum,
immunocompromised patients. Carrier state with usually caused by non- produce little toxin can cause disease Lyme disease Caused by Borrelia burgdorferi, which is A Key Lyme pie to the FACE:
UTIs, Diabetes, Osteomyelitis, Mucoid
Treatments include “CAMPFIRE” drugs: gallbladder colonization typhoidal Salmonella Campylobacter jejuni Gram ⊝, comma or S shaped (with polar flagella) A , oxidase ⊕, grows at 42°C (“Campylobacter transmitted by the Ixodes deer tick A (also Facial nerve palsy (typically bilateral)
polysaccharide capsule, Otitis externa A
(swimmer’s ear), Nosocomial infections (eg, Carbapenems likes the hot campfire”). vector for Anaplasma spp. and protozoa Arthritis
A
catheters, equipment), Addicts (drug abusers), Aminoglycosides Major cause of bloody diarrhea, especially in children. Fecal-oral transmission through person- Babesia). Natural reservoir is the mouse (and Cardiac block
Yersinia enterocolitica Gram ⊝ rod. Usually transmitted from pet feces (eg, puppies), contaminated milk, or pork. Causes
Skin infections (eg, hot tub folliculitis, wound Monobactams to-person contact or via ingestion of undercooked contaminated poultry or meat, unpasteurized important to tick life cycle). Erythema migrans
acute diarrhea or pseudoappendicitis (right lower abdominal pain due to mesenteric adenitis and/
B infection in burn victims). Polymyxins (eg, polymyxin B, colistin) milk. Contact with infected animals (dogs, cats, pigs) is also a risk factor. Common in northeastern United States. Treatment: doxycycline (1st line); amoxicillin
or terminal ileitis).
Mucoid polysaccharide capsule may contribute Fluoroquinolones (eg, ciprofloxacin, Common antecedent to Guillain-Barré syndrome and reactive arthritis. Stage 1—early localized: erythema migrans and cefuroxime in pregnant women and
to chronic pneumonia in cystic fibrosis levofloxacin) (typical “bulls-eye” configuration B is children.
patients due to biofilm formation. ThIRd- and fourth-generation pathognomonic but not always present),
Lactose-fermenting Fermentation of lactose pink colonies Lactose is key.
Produces PEEP: Phospholipase C (degrades cephalosporins (eg, ceftazidime, cefepime) B flu-like symptoms.
enteric bacteria on MacConkey agar. Examples include Test with MacConKEE’S agar.
cell membranes); Endotoxin (fever, shock); Extended-spectrum penicillins (eg, Stage 2—early disseminated: secondary lesions,
Citrobacter, Klebsiella, E coli, Enterobacter, EMB agar—lactose fermenters grow as purple/
Exotoxin A (inactivates EF-2); Pigments: piperacillin, ticarcillin) carditis, AV block, facial nerve (Bell) palsy,
and Serratia (weak fermenter). E coli produces black colonies. E coli grows colonies with a
pyoverdine and pyocyanin (blue-green migratory myalgias/transient arthritis.
β-galactosidase, which breaks down lactose green sheen.
pigment A ; also generates reactive oxygen Stage 3—late disseminated: encephalopathy,
into glucose and galactose.
species). chronic arthritis.
MICROBIOLOGY
MICROBIOLOGY
Leptospira interrogans Spirochete with hook-shaped ends found in water contaminated with animal urine. VDRL false positives VDRL detects nonspecific antibody that False-Positive results on VDRL with: Chlamydia trachomatis serotypes Rickettsial diseases Treatment: doxycycline (caution during pregnancy; alternative is chloramphenicol).
reacts with beef cardiolipin. Quantitative, Pregnancy Types A, B, and C Chronic infection, cause blindness due to ABC = Africa, Blindness, Chronic infection. and vector-borne
Leptospirosis—flu-like symptoms, myalgias (classically of calves), jaundice, photophobia with
inexpensive, and widely available test for Viral infection (eg, EBV, hepatitis) follicular conjunctivitis in Africa. illnesses
conjunctival suffusion (erythema without exudate). Prevalent among surfers and in tropics (eg,
syphilis (sensitive but not specific). Drugs RASH COMMON
Hawaii). Types D–K Urethritis/PID, ectopic pregnancy, neonatal D–K = everything else.
Rheumatic fever Rocky Mountain Rickettsia rickettsii, vector is tick. Despite its Classic triad—headache, fever, rash (vasculitis).
pneumonia (staccato cough) with eosinophilia, Neonatal disease can be acquired during
Weil disease (icterohemorrhagic leptospirosis)—severe form with jaundice and azotemia from liver Lupus and leprosy spotted fever name, disease occurs primarily in the South Palms and soles rash is seen in Coxsackievirus
neonatal conjunctivitis (1–2 weeks after birth). passage through infected birth canal.
and kidney dysfunction, fever, hemorrhage, and anemia. Atlantic states, especially North Carolina. A infection (hand, foot, and mouth disease),
Types L1, L2, and L3 Lymphogranuloma venereum—small, painless
Rash typically starts at wrists A and ankles and Rocky Mountain spotted fever, and 2° Syphilis
Jarisch-Herxheimer Flu-like syndrome (fever, chills, headache, myalgia) after antibiotics are started; due to killed ulcers on genitals swollen, painful inguinal
then spreads to trunk, palms, and soles. (you drive CARS using your palms and soles).
Syphilis Caused by spirochete Treponema pallidum. reaction bacteria (usually spirochetes) releasing toxins. lymph nodes that ulcerate (buboes). Treat with
doxycycline. Typhus Endemic (fleas)—R typhi. Rickettsii on the wRists, Typhus on the Trunk.
Primary syphilis Localized disease presenting with painless chancre A . If available, use dark-field microscopy to Epidemic (human body louse)—R prowazekii.
visualize treponemes in fluid from chancre B . VDRL ⊕ in ~ 80%. Rash starts centrally and spreads out, sparing
Gardnerella vaginalis A pleomorphic, gram-variable rod involved in I don’t have a clue why I smell fish in the vagina
Secondary syphilis Disseminated disease with constitutional symptoms, maculopapular rash C (including Zoonotic bacteria Zoonosis: infectious disease transmitted between animals and humans. palms and soles.
A
bacterial vaginosis. Presents as a gray vaginal garden!
palms D and soles), condylomata lata E (smooth, painless, wart-like white lesions on genitals), RASH RARE
discharge with a fishy smell; nonpainful (vs Amine whiff test—mixing discharge with 10% SPECIES DISEASE TRANSMISSION AND SOURCE
lymphadenopathy, patchy hair loss; also confirmable with dark-field microscopy. Ehrlichiosis Ehrlichia, vector is tick. Monocytes with MEGA berry—
vaginitis). Associated with sexual activity, but KOH enhances fishy odor. Anaplasma spp. Anaplasmosis Ixodes ticks (live on deer and mice)
Serologic testing: VDRL/RPR (nonspecific), confirm diagnosis with specific test (eg, FTA-ABS). morulae B (mulberry-like inclusions) in Monocytes = Ehrlichiosis
not sexually transmitted. Bacterial vaginosis
Secondary syphilis = Systemic. Latent syphilis (⊕ serology without symptoms) may follow. Bartonella spp. Cat scratch disease, bacillary angiomatosis Cat scratch cytoplasm. Granulocytes = Anaplasmosis
is also characterized by overgrowth of
Tertiary syphilis Gummas F (chronic granulomas), aortitis (vasa vasorum destruction), neurosyphilis (tabes dorsalis, certain anaerobic bacteria in vagina. Clue Borrelia burgdorferi Lyme disease Ixodes ticks (live on deer and mice) Anaplasmosis Anaplasma, vector is tick. Granulocytes with
“general paresis”), Argyll Robertson pupil (constricts with accommodation but is not reactive to cells (vaginal epithelial cells covered with Borrelia recurrentis Relapsing fever Louse (recurrent due to variable surface morulae C in cytoplasm.
light; also called “prostitute’s pupil” since it accommodates but does not react). Gardnerella) have stippled appearance along antigens)
Signs: broad-based ataxia, ⊕ Romberg, Charcot joint, stroke without hypertension. Q fever Coxiella burnetii, no arthropod vector. Spores Q fever is Queer because it has no rash or vector
outer margin (arrow in A ).
Brucella spp. Brucellosis/undulant fever Unpasteurized dairy inhaled as aerosols from cattle/sheep amniotic and its causative organism can survive outside
For neurosyphilis: test spinal fluid with VDRL, FTA-ABS, and PCR. Treatment: metronidazole or clindamycin.
Campylobacter Bloody diarrhea Feces from infected pets/animals; contaminated fluid. Presents as pneumonia. Common cause in its endospore form. Not in the Rickettsia
Congenital syphilis Presents with facial abnormalities such as rhagades (linear scars at angle of mouth, black arrow of culture ⊝ endocarditis. genus, but closely related.
meats/foods/hands
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. Chlamydiae Chlamydiae cannot make their own ATP. They Chlamys = cloak (intracellular). Chlamydophila psittaci Psittacosis Parrots, other birds A B C
To prevent, treat mother early in pregnancy, as placental transmission typically occurs after first A
are obligate intracellular organisms that cause C psittaci—has an avian reservoir (parrots), Coxiella burnetii Q fever Aerosols of cattle/sheep amniotic fluid
trimester. mucosal infections. 2 forms: causes atypical pneumonia.
Ehrlichia chaffeensis Ehrlichiosis Amblyomma (Lone Star tick)
Elementary body (small, dense) Lab diagnosis: PCR, nucleic acid amplification
A B C D
is “Enfectious” and Enters cell via test. Cytoplasmic inclusions (reticulate bodies) Francisella tularensis Tularemia Ticks, rabbits, deer flies
Endocytosis; transforms into reticulate body. seen on Giemsa or fluorescent antibody– Leptospira spp. Leptospirosis Animal urine in water; recreational water use
Reticulate body Replicates in cell by fission; stained smear. Mycobacterium leprae Leprosy Humans with lepromatous leprosy; armadillo
Reorganizes into elementary bodies. The chlamydial cell wall lacks classic (rare)
Chlamydia trachomatis causes reactive arthritis peptidoglycan (due to reduced muramic acid),
Pasteurella multocida Cellulitis, osteomyelitis Animal bite, cats, dogs
(Reiter syndrome), neonatal and follicular rendering β-lactam antibiotics ineffective.
adult conjunctivitis A , nongonococcal Rickettsia prowazekii Epidemic typhus Human to human via human body louse
urethritis, and PID. Rickettsia rickettsii Rocky Mountain spotted fever Dermacentor (dog tick)
E F G H Chlamydophila pneumoniae and Chlamydophila
Rickettsia typhi Endemic typhus Fleas Mycoplasma Classic cause of atypical “walking” pneumonia No cell wall. Not seen on Gram stain.
psittaci cause atypical pneumonia; transmitted
Salmonella spp. Diarrhea (which may be bloody), vomiting, Reptiles and poultry pneumoniae (insidious onset, headache, nonproductive Pleomorphic A .
by aerosol.
(except S typhi) fever, abdominal cramps A
cough, patchy or diffuse interstitial infiltrate). Bacterial membrane contains sterols for stability.
Treatment: azithromycin (favored because one-
X-ray looks worse than patient. High titer of Mycoplasmal pneumonia is more common in
time treatment) or doxycycline (+ ceftriaxone Yersinia pestis Plague Fleas (rats and prairie dogs are reservoirs)
cold agglutinins (IgM), which can agglutinate patients < 30 years old.
for possible concomitant gonorrhea).
RBCs. Grown on Eaton agar. Frequent outbreaks in military recruits and
Treatment: macrolides, doxycycline, or prisons.
fluoroquinolone (penicillin ineffective since Mycoplasma gets cold without a coat (cell wall).
Mycoplasma have no cell wall).
MICROBIOLOGY `M̀ICROBIOLOGY—MYCOLOGY SEC TION II 151 152 SEC TION II MICROBIOLOGY

MICROBIOLOGY
`M̀ICROBIOLOGY—MYCOLOGY
`M̀ICROBIOLOGY—MYCOLOGY MICROBIOLOGY
MICROBIOLOGY
`M̀ICROBIOLOGY—MYCOLOGY
`M̀ICROBIOLOGY—MYCOLOGY SEC TION II 153 154 SEC TION II MICROBIOLOGY `M̀ICROBIOLOGY—MYCOLOGY
MICROBIOLOGY—MYCOLOGY
`` Cutaneous mycoses Opportunistic fungal infections Pneumocystis jirovecii Causes Pneumocystis pneumonia (PCP), a diffuse interstitial pneumonia A . Yeast-like fungus
Tinea Clinical name for dermatophyte (cutaneous fungal) infections. Dermatophytes include Candida albicans alba = white. Dimorphic; forms pseudohyphae and budding yeasts at 20°C A , germ tubes at (originally classified as protozoan). Most infections are asymptomatic. Immunosuppression
Systemic mycoses All of the following can cause pneumonia and can disseminate. (dermatophytes) Microsporum, Trichophyton, and Epidermophyton. Branching septate hyphae visible on KOH 37°C B . (eg, AIDS) predisposes to disease. Diffuse, bilateral ground-glass opacities on CXR/CT, with
All are caused by dimorphic fungi: cold (20°C) = mold; heat (37°C) = yeast. Only exception is preparation with blue fungal stain A . Associated with pruritus. Systemic or superficial fungal infection. Causes oral C and esophageal thrush in pneumatoceles B . Diagnosed by lung biopsy or lavage. Disc-shaped yeast seen on methenamine
Coccidioides, which is a spherule (not yeast) in tissue. immunocompromised (neonates, steroids, diabetes, AIDS), vulvovaginitis (diabetes, use of silver stain of lung tissue C .
Tinea capitis Occurs on head, scalp. Associated with lymphadenopathy, alopecia, scaling B .
Systemic mycoses can form granulomas (like TB); cannot be transmitted person-to-person (unlike antibiotics), diaper rash, endocarditis (IV drug users), disseminated candidiasis (especially in Treatment/prophylaxis: TMP-SMX, pentamidine, dapsone (prophylaxis only), atovaquone. Start
TB). Tinea corporis Occurs on torso. Characterized by erythematous scaling rings (“ringworm”) and central prophylaxis when CD4+ count drops to < 200 cells/mm3 in HIV patients.
neutropenic patients), chronic mucocutaneous candidiasis.
Treatment: fluconazole or itraconazole for local infection; amphotericin B for systemic infection. clearing C . Can be acquired from contact with an infected cat or dog.
Treatment: oral fluconazole/topical azole for vaginal; nystatin, fluconazole, or echinocandins for A B C
DISEASE ENDEMIC LOCATION PATHOLOGIC FEATURES UNIQUE SIGNS/SYMPTOMS NOTES
Tinea cruris Occurs in inguinal area D . Often does not show the central clearing seen in tinea corporis. oral/esophageal; fluconazole, echinocandins, or amphotericin B for systemic.
Histoplasmosis Mississippi and Ohio Macrophage filled Palatal/tongue ulcers, Histo hides (within Tinea pedis Three varieties: Aspergillus Monomorphic septate hyphae that branch at 45° Acute Angle D E .
River Valleys with Histoplasma splenomegaly macrophages) Interdigital E ; most common fumigatus Causes invasive aspergillosis in immunocompromised patients, neutrophil dysfunction (eg, chronic
A
(smaller than Bird (eg, starlings) or Moccasin distribution F granulomatous disease).
RBC) A bat droppings Vesicular type Can cause aspergillomas in pre-existing lung cavities, especially after TB infection.
Diagnosis via urine/ Tinea unguium Onychomycosis; occurs on nails. Some species of Aspergillus produce Aflatoxins (associated with hepatocellular carcinoma).
serum antigen Tinea (pityriasis) Caused by Malassezia spp. (Pityrosporum spp.), a yeast-like fungus (not a dermatophyte despite Allergic bronchopulmonary aspergillosis (ABPA) F —hypersensitivity response associated with
versicolor being called tinea). Degradation of lipids produces acids that damage melanocytes and cause asthma and cystic fibrosis; may cause bronchiectasis and eosinophilia.
Blastomycosis Eastern and Broad-based budding Inflammatory Blasto buds broadly hypopigmented G , hyperpigmented, and/or pink patches. Less pruritic than dermatophytes.
Cryptococcus 5–10 μm with narrow budding. Heavily encapsulated yeast. Not dimorphic.
B Central US of Blastomyces (same lung disease, can Can occur any time of year, but more common in summer (hot, humid weather). “Spaghetti and
neoformans Found in soil, pigeon droppings. Acquired through inhalation with hematogenous dissemination
size as RBC) B disseminate to skin/ meatballs” appearance on microscopy H .
to meninges. Culture on Sabouraud agar. Highlighted with India ink (clear halo G ) and
bone Treatment: selenium sulfide, topical and/or oral antifungal medications. Sporothrix schenckii Sporotrichosis. Dimorphic, cigar-shaped budding yeast that grows in branching hyphae with
mucicarmine (red inner capsule H ). Latex agglutination test detects polysaccharide capsular
Verrucous skin lesions A B C D antigen and is more specific. A rosettes of conidia; lives on vegetation. When spores are traumatically introduced into the
can simulate SCC Causes cryptococcosis, cryptococcal meningitis, cryptococcal encephalitis (“soap bubble” lesions skin, typically by a thorn (“rose gardener’s disease”), causes local pustule or ulcer with nodules
Forms granulomatous in brain), primarily in immunocompromised. along draining lymphatics (ascending lymphangitis A ). Disseminated disease possible in
nodules Treatment: amphotericin B + flucytosine followed by fluconazole for cryptococcal meningitis. immunocompromised host.
Coccidioidomycosis Southwestern US, Spherule (much larger Disseminates to skin/ Treatment: itraconazole or potassium iodide.
Mucor and Rhizopus Irregular, broad, nonseptate hyphae branching at wide angles I .
California than RBC) filled bone Think of a rose gardener who smokes a cigar and pot.
C spp. Causes mucormycosis, mostly in ketoacidotic diabetic and/or neutropenic patients (eg, leukemia).
with endospores of Erythema nodosum Inhalation of spores fungi proliferate in blood vessel walls, penetrate cribriform plate, and enter
Coccidioides C (desert bumps) or brain. Rhinocerebral, frontal lobe abscess; cavernous sinus thrombosis. Headache, facial pain,
multiforme E F G H black necrotic eschar on face; may have cranial nerve involvement.
Arthralgias (desert Treatment: surgical debridement, amphotericin B or isavuconazole.
rheumatism)
A B C D E
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
F G H I
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`` Protozoa—CNS infections Protozoa—hematologic infections Protozoa—others
ORGANISM DISEASE TRANSMISSION DIAGNOSIS TREATMENT ORGANISM DISEASE TRANSMISSION DIAGNOSIS TREATMENT ORGANISM DISEASE TRANSMISSION DIAGNOSIS TREATMENT
Protozoa—gastrointestinal infections Toxoplasma Immunocompetent: Cysts in meat (most Serology, biopsy Sulfadiazine + Plasmodium Malaria—fever, headache, anemia, Anopheles mosquito Blood smear: Chloroquine (for Visceral infections
ORGANISM DISEASE TRANSMISSION DIAGNOSIS TREATMENT gondii mononucleosis-like symptoms, common); oocysts (tachyzoite) B pyrimethamine P vivax/ovale splenomegaly trophozoite ring sensitive species), Trypanosoma Chagas disease—dilated Triatomine Trypomastigote in Benznidazole
Giardia lamblia Giardiasis—bloating, flatulence, Cysts in water Multinucleated Metronidazole ⊝ heterophile antibody test. in cat feces; crosses P falciparum P vivax/ovale—48-hr cycle (tertian; form within which blocks cruzi cardiomyopathy with (“kissing”) bug, a blood smear A or nifurtimox;
foul-smelling, fatty diarrhea trophozoites A or Reactivation in AIDS brain placenta (pregnant P malariae includes fever on first day and RBC A , schizont Plasmodium heme apical atrophy, megacolon, type of reduviid cruzing in my
(often seen in campers/hikers)— cysts B in stool, abscesses usually seen as women should A third day, thus fevers are actually containing polymerase; if megaesophagus; predominantly bug, deposits feces Benz, with a fur
think fat-rich Ghirardelli antigen detection multiple ring-enhancing lesions avoid cats) 48 hr apart); dormant form merozoites; red resistant, use in South America in a painless bite coat on
chocolates for fatty stools of on MRI A . (hypnozoite) in liver granules (Schüffner mefloquine or Unilateral periorbital swelling (much like a kiss)
Giardia Congenital toxoplasmosis: P falciparum—severe; irregular stippling) B atovaquone/ (Romaña sign) characteristic of
Entamoeba Amebiasis—bloody diarrhea Cysts in water Serology, antigen Metronidazole; classic triad of chorioretinitis, fever patterns; parasitized RBCs throughout RBC proguanil acute stage
histolytica (dysentery), liver abscess testing, and/or paromomycin or hydrocephalus, and intracranial occlude capillaries in brain cytoplasm seen If life-threatening,
Leishmania Visceral leishmaniasis Sandfly Macrophages Amphotericin B,
(“anchovy paste” exudate), RUQ trophozoites (with iodoquinol for calcifications. (cerebral malaria), kidneys, lungs with P vivax/ovale use intravenous
B donovani (kala-azar)—spiking fevers, containing sodium
pain; histology of colon biopsy engulfed RBCs C asymptomatic cyst Naegleria fowleri Rapidly fatal meningoencephalitis Swimming in warm Amoebas in CSF C Amphotericin B has P malariae—72-hr cycle (quartan) quinidine or
hepatosplenomegaly, amastigotes B stibogluconate
shows flask-shaped ulcers in the cytoplasm) passers freshwater (think been effective for a artesunate (test for
pancytopenia
or cysts with up to Nalgene bottle few survivors G6PD deficiency)
Cutaneous leishmaniasis—skin
4 nuclei in stool D ; filled with fresh For P vivax/ovale,
ulcers C
Entamoeba Eats water containing add primaquine for
hypnozoite (test for Sexually transmitted infections
Erythrocytes Naegleria); enters
via cribriform plate G6PD deficiency) Trichomonas Vaginitis—foul-smelling, greenish Sexual (cannot exist Trophozoites Metronidazole for
Cryptosporidium Severe diarrhea in AIDS Oocysts in water Oocysts on acid-fast Prevention (by
Babesia Babesiosis—fever and hemolytic Ixodes tick (same as Blood smear: ring Atovaquone vaginalis discharge; itching and burning; outside human (motile) D on wet patient and partner
Mild disease (watery diarrhea) in stain E , antigen filtering city
anemia; predominantly in Borrelia burgdorferi form C1 , “Maltese + azithromycin do not confuse with Gardnerella because it cannot mount; “strawberry (prophylaxis)
immunocompetent hosts detection water supplies); Trypanosoma African sleeping sickness— Tsetse fly, a painful Trypomastigote in Suramin for blood- C
northeastern United States; of Lyme disease; cross” C2 ; PCR vaginalis, a gram-variable form cysts) cervix”
nitazoxanide in brucei enlarged lymph nodes, recurring bite blood smear D borne disease or
asplenia risk of severe disease may often coinfect bacterium associated with
immunocompetent fever (due to antigenic variation), melarsoprol for
humans) bacterial vaginosis
hosts somnolence, coma CNS penetration
(“I sure am A B C D
A B C D E
mellow when
I’m sleeping”;
remember
melatonin helps
with sleep)
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
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Nematodes (roundworms) Cestodes (tapeworms) Ectoparasites MICROBIOLOGY—VIROLOGY

``
ORGANISM DISEASE TRANSMISSION TREATMENT ORGANISM DISEASE TRANSMISSION TREATMENT Sarcoptes scabiei Mite burrow into stratum corneum and cause Common in children, crowded populations
Intestinal Taenia solium A Intestinal tapeworm Ingestion of larvae encysted in Praziquantel scabies—pruritus (worse at night) and (jails, nursing homes); transmission through Viral structure—general features
A
Enterobius vermicularis Causes anal pruritus (diagnosed by seeing Fecal-oral Pyrantel pamoate or undercooked pork serpiginous burrows (lines) in webspace of skin-to-skin contact (most common) or via Surface Capsid head
Surface
hands and feet A . fomites. protein
(pinworm) egg A via the tape test) bendazoles (because Cysticercosis, Ingestion of eggs in food Praziquantel; albendazole for protein Nucleic
Treatment: permethrin cream, washing/drying Lipid bilayer Lipid bilayer acid
worms are bendy) neurocysticercosis (cystic contaminated with human neurocysticercosis Capsid
CNS lesions, seizures) B feces all clothing/bedding, treat close contacts. Collar
Ascaris lumbricoides May cause obstruction at ileocecal Fecal-oral; knobby-coated, Bendazoles Capsid
(giant roundworm) valve, biliary obstruction, intestinal oval eggs seen in feces Diphyllobothrium Vitamin B12 deficiency Ingestion of larvae in raw Praziquantel Core Helical sheath
Nucleic
perforation, migrates from nose/mouth under microscope B latum (tapeworm competes for B12 freshwater fish acid
Strongyloides Autoinfection: rarely, some larvae may Larvae in soil penetrate skin; Ivermectin or in intestine) megaloblastic Nucleic
Helical
Pediculus humanus/ Blood-sucking lice that cause intense pruritus Can transmit Rickettsia prowazekii (epidemic capsid with
stercoralis penetrate the intestinal wall to enter the rhabditiform larvae seen in bendazoles anemia acid
Phthirus pubis with associated excoriations, commonly on typhus), Borrelia recurrentis (relapsing fever), viral RNA Base Spikes
(threadworm) bloodstream without leaving the body feces under microscope Echinococcus Hydatid cysts D (“eggshell Ingestion of eggs in food Albendazole plate
B
scalp and neck (head lice) or waistband and Bartonella quintana (trench fever).
Ancylostoma Cause anemia by sucking blood from Larvae penetrate skin Bendazoles or pyrantel granulosus C calcification”) in liver E ; cyst contaminated with dog feces axilla (body lice). Treatment includes pyrethroids, malathion, or Naked virus Enveloped virus Enveloped virus Bacteriophage
duodenale, Necator intestinal wall pamoate rupture can cause anaphylaxis Sheep are an intermediate host ivermectin lotion, and nit B combing. Children with icosahedral capsid with icosahedral capsid with helical capsid
americanus Cutaneous larva migrans—pruritic, with head lice can be treated at home without
(hookworms) serpiginous rash from walking barefoot A B C D E interrupting school attendance.
on contaminated beach Liver Viral genetics
Trichinella spiralis Larvae enter bloodstream, encyst in Undercooked meat (especially Bendazoles St Recombination Exchange of genes between 2 chromosomes by crossing over within regions of significant base
striated muscle muscle inflammation pork); fecal-oral (less likely) sequence homology.
Trichinosis—fever, vomiting, nausea, Reassortment When viruses with segmented genomes (eg, influenza virus) exchange genetic material. For
periorbital edema, myalgia Parasite hints ASSOCIATIONS ORGANISM example, the 2009 novel H1N1 influenza A pandemic emerged via complex viral reassortment of
Trichuris trichiura Often asymptomatic; loose stools, Fecal-oral Bendazoles Biliary tract disease, cholangiocarcinoma Clonorchis sinensis genes from human, swine, and avian viruses. Has potential to cause antigenic shift.
(whipworm) anemia, rectal prolapse in children Complementation When 1 of 2 viruses that infect the cell has a mutation that results in a nonfunctional protein, the
Brain cysts, seizures Taenia solium (neurocysticercosis)
(heavy infection) nonmutated virus “complements” the mutated one by making a functional protein that serves
Trematodes (flukes) Hematuria, squamous cell bladder cancer Schistosoma haematobium
Tissue both viruses. For example, hepatitis D virus requires the presence of replicating hepatitis B virus
ORGANISM DISEASE TRANSMISSION TREATMENT Liver (hydatid) cysts Echinococcus granulosus
Toxocara canis Visceral larva migrans—nematodes Fecal-oral Bendazoles to supply HBsAg, the envelope protein for HDV.
Schistosoma Liver and spleen enlargement Snails are intermediate host; Praziquantel Microcytic anemia Ancylostoma, Necator
migrate to blood through intestinal wall Phenotypic mixing Occurs with simultaneous infection of a cell with 2 viruses. Genome of virus A can be partially or
A
(S mansoni, egg with cercariae penetrate skin of
inflammation and damage. Often Myalgias, periorbital edema Trichinella spiralis completely coated (forming pseudovirion) with the surface proteins of virus B. Type B protein coat
lateral spine A ), fibrosis, humans in contact with
affects heart (myocarditis), liver, eyes Perianal pruritus Enterobius determines the tropism (infectivity) of the hybrid virus. However, the progeny from this infection
inflammation, portal contaminated fresh water (eg,
(visual impairment, blindness), and have a type A coat that is encoded by its type A genetic material.
hypertension swimming or bathing) Portal hypertension Schistosoma mansoni, Schistosoma japonicum
CNS (seizures, coma)
Chronic infection with
Onchocerca volvulus Skin changes, loss of elastic fibers, and Female blackfly Ivermectin (ivermectin Vitamin B12 deficiency Diphyllobothrium latum
B
S haematobium (egg with
river blindness (black flies, black skin for river blindness) DNA viral genomes All DNA viruses have dsDNA genomes except All are dsDNA (like our cells), except “part-of-a-
terminal spine B ) can lead
nodules, “black sight”); allergic reaction Parvoviridae (ssDNA). virus” (parvovirus) is ssDNA.
to squamous cell carcinoma
to microfilaria possible All are linear except papilloma-, polyoma-, and Parvus = small.
of the bladder (painless
hepadnaviruses (circular).
Loa loa Swelling in skin, worm in conjunctiva Deer fly, horse fly, mango fly Diethylcarbamazine hematuria) and pulmonary
Wuchereria bancrofti Lymphatic filariasis (elephantiasis)— Female mosquito Diethylcarbamazine hypertension
worms invade lymph nodes Clonorchis sinensis Biliary tract inflammation Undercooked fish Praziquantel RNA viral genomes All RNA viruses have ssRNA genomes except All are ssRNA, except “repeato-virus” (reovirus)
inflammation lymphedema C ; pigmented gallstones Reoviridae (dsRNA). is dsRNA.
symptom onset after 9 mo–1 yr Associated with ⊕ stranded RNA viruses: I went to a retro
A B
cholangiocarcinoma (retrovirus) toga (togavirus) party, where
C
I drank flavored (flavivirus) Corona
(coronavirus) and ate hippie (hepevirus)
California (calicivirus) pickles (picornavirus).
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Naked viral genome Purified nucleic acids of most dsDNA (except poxviruses and HBV) and ⊕ strand ssRNA DNA viruses All replicate in the nucleus (except poxvirus). “Pox is out of the box (nucleus).” Herpesviruses (continued) HSV identification Viral culture for skin/genitalia.
infectivity (≈ mRNA) viruses are infectious. Naked nucleic acids of ⊝ strand ssRNA and dsRNA viruses are VIRAL FAMILY ENVELOPE DNA STRUCTURE MEDICAL IMPORTANCE VIRUS ROUTE OF TRANSMISSION CLINICAL SIGNIFICANCE NOTES
A
CSF PCR for herpes encephalitis.
not infectious. They require polymerases contained in the complete virion. Herpesviruses Yes DS and linear See Herpesviruses entry Epstein-Barr Respiratory Mononucleosis—fever, hepatosplenomegaly F , Infects B cells through CD21. Tzanck test—a smear of an opened skin vesicle to detect multinucleated giant cells A commonly
virus (HHV-4) secretions, pharyngitis, and lymphadenopathy (especially Atypical lymphocytes on peripheral seen in HSV-1, HSV-2, and VZV infection. PCR of skin lesions is test of choice.
Poxvirus Yes DS and linear Smallpox eradicated world wide by use of the live-
saliva; aka posterior cervical nodes). Avoid contact sports blood smear G —not infected B Tzanck heavens I do not have herpes.
(largest DNA virus) attenuated vaccine
Viral envelopes Generally, enveloped viruses acquire their DNA = PAPP; RNA = CPR and hepevirus. “kissing disease,” until resolution due to risk of splenic rupture. cells but reactive cytotoxic T cells. Intranuclear eosinophilic Cowdry A inclusions also seen with HSV-1, HSV-2, VZV.
Cowpox (“milkmaid blisters”)
envelopes from plasma membrane when Give PAPP smears and CPR to a naked hippie Molluscum contagiosum—flesh-colored papule with (common in Associated with lymphomas (eg, endemic ⊕ Monospot test—heterophile
they exit from cell. Exceptions include (hepevirus). central umbilication teens, young Burkitt lymphoma), nasopharyngeal antibodies detected by agglutination
herpesviruses, which acquire envelopes from adults) carcinoma (especially Asian adults), of sheep or horse RBCs.
nuclear membrane. Hepadnavirus Yes Partially DS and circular HBV:
lymphoproliferative disease in transplant Use of amoxicillin in mononucleosis
Acute or chronic hepatitis
Naked (nonenveloped) viruses include patients. can cause characteristic
Not a retrovirus but has reverse transcriptase Receptors used by VIRUS RECEPTORS
Papillomavirus, Adenovirus, Parvovirus, maculopapular rash.
Polyomavirus, Calicivirus, Picornavirus, Adenovirus No DS and linear Febrile pharyngitis A —sore throat viruses CMV Integrins (heparan sulfate)
Cytomegalo- Congenital Mononucleosis (⊝ Monospot) in Infected cells have characteristic
Reovirus, and Hepevirus. Acute hemorrhagic cystitis EBV CD21
A virus (HHV-5) transfusion, immunocompetent patients; infection in “owl eye” intranuclear
Pneumonia
sexual contact, immunocompromised, especially pneumonia inclusions H . HIV CD4, CXCR4, CCR5
Conjunctivitis—“pink eye”
saliva, urine, in transplant patients; esophagitis; AIDS Latent in mononuclear cells.
DNA virus Some general rules—all DNA viruses: Gastroenteritis Parvovirus B19 P antigen on RBCs
transplant retinitis (“sightomegalovirus”): hemorrhage,
characteristics Myocarditis Rabies Nicotinic AChR
GENERAL RULE COMMENTS cotton-wool exudates, vision loss.
Are HHAPPPPy viruses Hepadna, Herpes, Adeno, Pox, Parvo, Congenital CMV Rhinovirus ICAM-1
Papilloma, Polyoma. Human Saliva Roseola infantum (exanthem subitum): high Roseola: fever first, Rosy (rash) later.
Are double stranded Except parvo (single stranded). Papillomavirus No DS and circular HPV–warts (serotypes 1, 2, 6, 11), CIN, cervical herpes- fevers for several days that can cause seizures, HHV-7—less common cause of
cancer (most commonly 16, 18) viruses 6 followed by diffuse macular rash I . roseola.
Have linear genomes Except papilloma and polyoma (circular, and 7
supercoiled) and hepadna (circular, Polyomavirus No DS and circular JC virus—progressive multifocal leukoencephalopathy
incomplete). (PML) in HIV Human Sexual contact Kaposi sarcoma (neoplasm of endothelial cells). Can also affect GI tract and lungs.
BK virus—transplant patients, commonly targets kidney herpesvirus Seen in HIV/AIDS and transplant patients.
Are icosahedral Except pox (complex). 8 Dark/violaceous plaques or nodules J
JC: Junky Cerebrum; BK: Bad Kidney
Replicate in the nucleus Except pox (carries own DNA-dependent RNA representing vascular proliferations.
polymerase). Parvovirus No SS and linear B19 virus—aplastic crises in sickle cell disease,
(smallest DNA virus) “slapped cheek” rash in children (erythema A B C D E
infectiosum, or fifth disease)
RBC destruction in fetus leads to hydrops fetalis
and death, in adults leads to pure RBC aplasia and
rheumatoid arthritis–like symptoms
F G H I J
Herpesviruses Enveloped, DS, and linear viruses
Liv
VIRUS ROUTE OF TRANSMISSION CLINICAL SIGNIFICANCE NOTES Sp
Herpes Respiratory Gingivostomatitis, keratoconjunctivitis A , Most commonly latent in trigeminal
simplex secretions, saliva herpes labialis B , herpetic whitlow on finger, ganglia. Most common cause of
virus-1 temporal lobe encephalitis, esophagitis, sporadic encephalitis, can present
erythema multiforme. as altered mental status, seizures,
and/or aphasia.
Herpes Sexual contact, Herpes genitalis C , neonatal herpes. Most commonly latent in sacral
simplex perinatal ganglia. Viral meningitis more
virus-2 common with HSV-2 than with
HSV-1.
Varicella- Respiratory Varicella-zoster (chickenpox D , shingles E ), Latent in dorsal root or trigeminal
Zoster virus secretions encephalitis, pneumonia. ganglia; CN V1 branch
(HHV-3) Most common complication of shingles is post- involvement can cause herpes
herpetic neuralgia. zoster ophthalmicus.

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RNA viruses All replicate in the cytoplasm (except retrovirus and influenza virus). “Retro flu is outta cyt (sight).” Negative-stranded Must transcribe ⊝ strand to ⊕. Virion brings Always Bring Polymerase Or Fail Replication. Influenza viruses Orthomyxoviruses. Enveloped, ⊝ ssRNA Reformulated vaccine (“the flu shot”) contains Paramyxoviruses Paramyxoviruses cause disease in children. They include those that cause parainfluenza (croup),
VIRAL FAMILY ENVELOPE RNA STRUCTURE CAPSID SYMMETRY MEDICAL IMPORTANCE viruses its own RNA-dependent RNA polymerase. viruses with 8-segment genome. Contain viral strains most likely to appear during the flu mumps, measles, RSV, and human metapneumovirus, which causes respiratory tract infection
Reoviruses No DS linear Icosahedral Coltivirusa—Colorado tick fever They include Arenaviruses, Bunyaviruses, hemagglutinin (binds sialic acid and promotes season, due to the virus’ rapid genetic change. (bronchiolitis, pneumonia) in infants. All contain surface F (fusion) protein, which causes
10–12 segments (double) Rotavirus—cause of fatal diarrhea in children Paramyxoviruses, Orthomyxoviruses, viral entry) and neuraminidase (promotes Killed viral vaccine is most frequently used. respiratory epithelial cells to fuse and form multinucleated cells. Palivizumab (monoclonal
Filoviruses, and Rhabdoviruses. progeny virion release) antigens. Patients at Live attenuated vaccine contains temperature- antibody against F protein) prevents pneumonia caused by RSV infection in premature infants.
Picornaviruses No SS ⊕ linear Icosahedral Poliovirus—polio-Salk/Sabin vaccines—IPV/OPV
Echovirus—aseptic meningitis risk for fatal bacterial superinfection, most sensitive mutant that replicates in the nose but Palivizumab for Paramyxovirus (RSV) Prophylaxis in Preemies.
Rhinovirus—“common cold” commonly S aureus, S pneumoniae, and not in the lung; administered intranasally.
Segmented viruses All are RNA viruses. They include BOAR. Random H influenzae.
Coxsackievirus—aseptic meningitis; herpangina mutations
(mouth blisters, fever); hand, foot, and mouth Bunyaviruses, Orthomyxoviruses (influenza Genetic/antigenic Causes pandemics. Reassortment of viral Sudden shift is more deadly than gradual drift. Croup (acute laryngo- Caused by parainfluenza viruses, which are paramyxoviruses. Virus membrane contains
disease; myocarditis; pericarditis viruses), Arenaviruses, and Reoviruses. shift genome segments, such as when segments of tracheobronchitis) hemagglutinin (binds sialic acid and promotes viral entry) and neuraminidase (promotes progeny
HAV—acute viral hepatitis human flu A virus reassort with swine flu A A
virion release) antigens. Results in a “seal-like” barking cough and inspiratory stridor. Narrowing
PERCH virus. of upper trachea and subglottis leads to characteristic steeple sign on x-ray A . Severe croup can
Picornavirus Includes Poliovirus, Echovirus, Rhinovirus, PicoRNAvirus = small RNA virus. result in pulsus paradoxus 2° to upper airway obstruction.
Hepevirus No SS ⊕ linear Icosahedral HEV
Coxsackievirus, and HAV. RNA is translated PERCH on a “peak” (pico). Reassortment
Caliciviruses No SS ⊕ linear Icosahedral Norovirus—viral gastroenteritis into 1 large polypeptide that is cleaved by
Flaviviruses Yes SS ⊕ linear Icosahedral HCV proteases into functional viral proteins. T
Yellow fevera Can cause aseptic (viral) meningitis (except Genetic/antigenic Causes epidemics. Minor (antigenic drift)
Denguea rhinovirus and HAV). All are enteroviruses drift changes based on random mutation in
St. Louis encephalitisa except rhinovirus and HAV. hemagglutinin or neuraminidase genes.
West Nile virusa—meningoencephalitis
Zika virusa Random Measles (rubeola) A paramyxovirus that causes measles. Usual 3 C’s of measles:
mutations
Rhinovirus A picornavirus. Nonenveloped RNA virus. Rhino has a runny nose. virus presentation involves prodromal fever with Cough
Togaviruses Yes SS ⊕ linear Icosahedral Rubella
Cause of common cold; > 100 serologic cough, coryza, and conjunctivitis, then Coryza
Western and Eastern equine encephalitisa A
types. Acid labile—destroyed by stomach acid; eventually Koplik spots (bright red spots with Conjunctivitis
Chikungunya virusa
therefore, does not infect the GI tract (unlike blue-white center on buccal mucosa A ), Vitamin A supplementation can reduce
Retroviruses Yes SS ⊕ linear Icosahedral Have reverse transcriptase followed 1–2 days later by a maculopapular morbidity and mortality from measles,
(HTLV), HTLV—T-cell leukemia the other picornaviruses). Rubella virus A togavirus. Causes rubella, once known as German (3-day) measles. Fever, postauricular and
2 copies rash B that starts at the head/neck and spreads particularly in malnourished children.
complex HIV—AIDS Reassortment
A
other lymphadenopathy, arthralgias, and fine, maculopapular rash that starts on face and spreads
centrifugally to involve trunk and extremities A . downward.
and conical
Yellow fever virus A flavivirus (also an arbovirus) transmitted by Flavi = yellow, jaundice. Causes mild disease in children but serious congenital disease (a ToRCHeS infection). Congenital Lymphadenitis with Warthin-Finkeldey giant
(HIV)
Aedes mosquitoes. Virus has a monkey or rubella findings include “blueberry muffin” appearance due to dermal extramedullary cells (fused lymphocytes) in a background of
Coronaviruses Yes SS ⊕ linear Helical “Common cold,” SARS, MERS B paracortical hyperplasia. Possible sequelae:
human reservoir. hematopoiesis.
Orthomyxoviruses Yes SS ⊝ linear Helical Influenza virus Symptoms: high fever, black vomitus, and SSPE (subacute sclerosing panencephalitis,
8 segments jaundice. May see Councilman bodies occurring years later)
(eosinophilic apoptotic globules) on liver Encephalitis (1:2000)
Paramyxoviruses Yes SS ⊝ linear Helical PaRaMyxovirus:
biopsy. Giant cell pneumonia (rare except in
Nonsegmented Parainfluenza—croup
RSV—bronchiolitis in babies immunosuppressed)
Measles, Mumps
Rhabdoviruses Yes SS ⊝ linear Helical Rabies Rotavirus Segmented dsRNA virus (a reovirus) A . ROTAvirus = Right Out The Anus.
A
Most important global cause of infantile CDC recommends routine vaccination of
Filoviruses Yes SS ⊝ linear Helical Ebola/Marburg hemorrhagic fever—often fatal.
gastroenteritis. Major cause of acute diarrhea all infants except those with a history of Mumps virus A paramyxovirus that causes mumps, Mumps makes your parotid glands and testes as
Arenaviruses Yes SS ⊕ and ⊝ Helical LCMV—lymphocytic choriomeningitis virus in the United States during winter, especially intussusception or SCID. uncommon due to effectiveness of MMR big as POM-Poms.
A
circular Lassa fever encephalitis—spread by rodents in day care centers, kindergartens. vaccine.
2 segments Villous destruction with atrophy leads to Symptoms: Parotitis A , Orchitis (inflammation
Bunyaviruses Yes SS ⊝ circular Helical California encephalitisa absorption of Na+ and loss of K+. of testes), aseptic Meningitis, and Pancreatitis.
3 segments Sandfly/Rift Valley feversa Can cause sterility (especially after puberty).
Crimean-Congo hemorrhagic fevera
Hantavirus—hemorrhagic fever, pneumonia
Delta virus Yes SS ⊝ circular Uncertain HDV is a “defective” virus that requires the
presence of HBV to replicate
SS, single-stranded; DS, double-stranded; ⊕, positive sense; ⊝, negative sense; a= arbovirus, arthropod borne (mosquitoes, ticks).
MICROBIOLOGY
MICROBIOLOGY
Rabies virus Bullet-shaped virus A . Negri bodies Infection more commonly from bat, raccoon, and Hepatitis Signs and symptoms of all hepatitis viruses: episodes of fever, jaundice, ALT and AST. Naked viruses (HAV Extrahepatic manifestations of hepatitis B and C Hepatitis serologic markers
A
(cytoplasmic inclusions B ) commonly skunk bites than from dog bites in the United viruses and HEV) lack an envelope and are not destroyed by the gut: the vowels hit your bowels. Hepatitis B Hepatitis C Anti-HAV (IgM) IgM antibody to HAV; best test to detect acute hepatitis A.
found in Purkinje cells of cerebellum and States; aerosol transmission (eg, bat caves) also HBV DNA polymerase has DNA- and RNA-dependent activities. Upon entry into nucleus, the polymerase
HEMATOLOGIC Aplastic anemia Essential mixed cryoglobulinemia, risk B-cell Anti-HAV (IgG) IgG antibody indicates prior HAV infection and/or prior vaccination; protects against reinfection.
in hippocampal neurons. Rabies has long possible. completes the partial dsDNA. Host RNA polymerase transcribes mRNA from viral DNA to make viral
NHL, ITP, autoimmune hemolytic anemia
incubation period (weeks to months) before proteins. The DNA polymerase then reverse transcribes viral RNA to DNA, which is the genome of the HBsAg Antigen found on surface of HBV; indicates hepatitis B infection.
symptom onset. Postexposure prophylaxis progeny virus. RENAL Membranous GN > membranoproliferative GN Membranoproliferative GN > membranous GN
Anti-HBs Antibody to HBsAg; indicates immunity to hepatitis B due to vaccination or recovery from
is wound cleaning plus immunization with HCV lacks 3′-5′ exonuclease activity no proofreading ability variation in antigenic structures of HCV VASCULAR Polyarteritis nodosa Leukocytoclastic vasculitis infection.
killed vaccine and rabies immunoglobulin. envelope proteins. Host antibody production lags behind production of new mutant strains of HCV. DERMATOLOGIC Sporadic porphyria cutanea tarda, lichen planus HBcAg Antigen associated with core of HBV.
Example of passive-active immunity. Virus HAV HBV HCV HDV HEV
Travels to the CNS by migrating in a retrograde ENDOCRINE risk of diabetes mellitus, autoimmune Anti-HBc Antibody to HBcAg; IgM = acute/recent infection; IgG = prior exposure or chronic infection. IgM
B FAMILY RNA picornavirus DNA hepadnavirus RNA flavivirus RNA deltavirus RNA hepevirus
fashion (via dynein motors) up nerve axons hypothyroidism anti-HBc may be the sole ⊕ marker of infection during window period.
TRANSMISSION Fecal-oral (shellfish, Parenteral (Blood), Primarily blood Parenteral, sexual, Fecal-oral,
after binding to ACh receptors. HBeAg Secreted by infected hepatocyte into circulation. Not part of mature HBV virion. Indicates active
travelers, day care) sexual (Baby- (IVDU, post- perinatal especially
Progression of disease: fever, malaise viral replication and therefore high transmissibility and poorer prognosis.
making), perinatal transfusion) waterborne
agitation, photophobia, hydrophobia, Anti-HBe Antibody to HBeAg; indicates low transmissibility.
(Birthing)
hypersalivation paralysis, coma death.
INCUBATION Short (weeks) Long (months) Long Superinfection Short Important Incubation Prodrome, Convalescence
diagnostic period acute disease Early Late
(HDV after tests
HBsAg Anti- Anti-HBs Surface antigen
HBV) = short HBsAg
(anti-HBc) HBc (anti-HBc) HBsAg
DNA
Coinfection (HDV
Ebola virus A filovirus A that targets endothelial cells, Transmission requires direct contact with bodily DNA Anti-HBc polymerase
with HBV) = long Relative polymerase
phagocytes, hepatocytes. Following an fluids, fomites (including dead bodies), infected DNA
A concentration
incubation period of up to 21 days, presents bats or primates (apes/monkeys); high incidence CLINICAL COURSE Asymptomatic Initially like serum May progress to Similar to HBV Fulminant hepatitis of reactants
HBV particles
with abrupt onset of flu-like symptoms, of nosocomial infection. (usually), Acute sickness (fever, Cirrhosis or in Expectant e antigen (+)
HBsAg HBeAg
diarrhea/vomiting, high fever, myalgia. Can Supportive care, no definitive treatment. Strict arthralgias, rash); Carcinoma (pregnant) women (–)
progress to DIC, diffuse hemorrhage, shock. isolation of infected individuals and barrier may progress to Window period Anti-HBs
Diagnosed with RT-PCR within 48 hr of practices for health care workers are key to carcinoma HBeAg Anti-HBe
Core antigen
HBcAg
symptom onset. High mortality rate. preventing transmission. PROGNOSIS Good Adults mostly Majority develop Superinfection High mortality in Level of
detection
full resolution; stable, Chronic worse prognosis pregnant women
Months after 0 1 2 3 4 5 6 7 8
neonates worse hepatitis C exposure Symptoms
prognosis
Zika virus A flavivirus most commonly transmitted by Sexual and vertical transmission possible. SGPT (ALT)
Aedes mosquito bites. Causes conjunctivitis, Outbreaks more common in tropical and
HCC RISK No Yes Yes Yes No
low-grade pyrexia, and itchy rash in 20% of subtropical climates. Supportive care, no LIVER BIOPSY Hepatocyte Granular Lymphoid Similar to HBV Patchy necrosis HBsAg Anti-HBs HBeAg Anti-HBe Anti-HBc
cases. Can lead to congenital microcephaly or definitive treatment. swelling, eosinophilic aggregates with Acute HBV ✓ ✓ IgM
miscarriage if transmitted in utero. Diagnose monocyte “ground glass” focal areas of
infiltration, appearance; macrovesicular Window ✓ IgM
with RT-PCR or serology.
Councilman cytotoxic T cells steatosis Chronic HBV (high infectivity) ✓ ✓ IgG
bodies mediate damage Chronic HBV (low infectivity) ✓ ✓ IgG
NOTES No carrier state Carrier state Carrier state very Defective virus, Enteric, Epidemic, Recovery ✓ ✓ IgG
(“Alone”) common common Depends on no carrier state
Immunized ✓
HBV HBsAg coat
for entry into
hepatocytes

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HIV Time course of untreated HIV infection Common diseases of As CD4+ cell count , risks of reactivation of past infections (eg, TB, HSV, shingles), dissemination Prions Prion diseases are caused by the conversion of a normal (predominantly α-helical) protein termed
Envelope proteins Diploid genome (2 molecules of RNA). Window period +/– Acute HIV infection Skin and mucous Systemic immuno- HIV-positive adults of bacterial infections and fungal infections (eg, coccidioidomycosis), and non-Hodgkin prion protein (PrPc) to a β-pleated form (PrPsc), which is transmissible via CNS-related tissue
acquired through budding from
The 3 structural genes (protein coded for):
Viral dissemination membrane deficiency/AIDS- lymphomas . (iatrogenic CJD) or food contaminated by BSE-infected animal products (variant CJD). PrPsc
host cell plasma membrane Seeding of lymphoid organs Clinical latency infections defining illnesses
env (gp120 and gp41): resists protease degradation and facilitates the conversion of still more PrPc to PrPsc. Resistant to
p17: Matrix protein PATHOGEN PRESENTATION FINDINGS
Formed from cleavage of gp160 to form standard sterilizing procedures, including standard autoclaving. Accumulation of PrPsc results in
gp120: CD4+ cell count < 500/mm3
Docking Lipid envelope envelope glycoproteins. 1200 107 spongiform encephalopathy and dementia, ataxia, and death.
Anti-envelope antibody (gp120)
glycoprotein Candida albicans Oral thrush Scrapable white plaque, pseudohyphae on
gp120—attachment to host CD4+ T cell. Creutzfeldt-Jakob disease—rapidly progressive dementia, typically sporadic (some familial forms).
gp41:
1100 Death microscopy
Transmembrane p24: gp41—fusion and entry.
glycoprotein Capsid protein
gag (p24 and p17)—capsid and matrix EBV Oral hairy leukoplakia Unscrapable white plaque on lateral tongue Bovine spongiform encephalopathy—also known as “mad cow disease.”
1000
RNA
Reverse proteins, respectively. CD8+ T cell HHV-8 Kaposi sarcoma Biopsy with lymphocytic inflammation Kuru—acquired prion disease noted in tribal populations practicing human cannibalism.
transcriptase 900
pol—reverse transcriptase, aspartate protease, HPV Squamous cell carcinoma, commonly of anus
CD4+ or CD8+ cells/mm3
integrase. 800 (men who have sex with men) or cervix
HIV RNA copies/mL

Reverse transcriptase synthesizes dsDNA from (women)
700
genomic RNA; dsDNA integrates into host CD4+ T cell CD4+ cell count < 200/mm3
genome. MICROBIOLOGY—SYSTEMS
``
600 Histoplasma Fever, weight loss, fatigue, cough, dyspnea, Oval yeast cells within macrophages
Virus binds CD4 as well as a coreceptor, either
capsulatum nausea, vomiting, diarrhea
CCR5 on macrophages (early infection) or 500 Normal flora: Neonates delivered by C-section have no flora but are rapidly colonized after birth.
CXCR4 on T cells (late infection). HIV Dementia dominant
HIV RNA 104 LOCATION MICROORGANISM
400
Homozygous CCR5 mutation = immunity. JC virus (reactivation) Progressive multifocal leukoencephalopathy Nonenhancing areas of demyelination on MRI
Skin S epidermidis
Heterozygous CCR5 mutation = slower course. 300 Pneumocystis jirovecii Pneumocystis pneumonia “Ground-glass” opacities on CXR
Nose S epidermidis; colonized by S aureus
200 103 CD4+ cell count < 100/mm3
Oropharynx Viridans group streptococci
Aspergillus fumigatus Hemoptysis, pleuritic pain Cavitation or infiltrates on chest imaging
HIV diagnosis Presumptive diagnosis made with HIV-1/2 Ag/ Western blot tests are no longer recommended 100 Dental plaque S mutans
Primary Bartonella henselae Bacillary angiomatosis Biopsy with neutrophilic inflammation
Ab immunoassays. These immunoassays by the CDC for confirmatory testing. infection Colon B fragilis > E coli
0 102 Candida albicans Esophagitis White plaques on endoscopy; yeast and
detect viral p24 Ag capsid protein and IgG Abs HIV-1/2 Ag/Ab testing is not recommended in 0 1 2 3 1 2 3 4 5 6 7 8 9 10 11
Months Years pseudohyphae on biopsy Vagina Lactobacillus; colonized by E coli and group B
to HIV-1/2. Very high sensitivity/specificity. babies with suspected HIV due to maternally
CMV Retinitis, esophagitis, colitis, pneumonitis, Linear ulcers on endoscopy, cotton-wool spots strep
⊕ tests are confirmed with HIV-1/2 Ab- transferred antibody. Use HIV viral load Dashed lines on CD4+ count axis indicate moderate immunocompromise Four stages of untreated infection:
differentiation immunoassays which instead. (< 400 CD4+ cells/mm3) and when AIDS-defining illnesses emerge (< 200 1. Flu-like (acute) encephalitis on fundoscopy
determine whether patient has HIV-1 or CD4+ cells/mm3). 2. Feeling fine (latent) Biopsy reveals cells with intranuclear (owl eye)
inclusion bodies Bugs causing food- S aureus and B cereus food poisoning starts quickly and ends quickly.
HIV-2. Most patients who do not receive treatment eventually die of complications of 3. Falling count
borne illness
If inconclusive differentiation assay, an HIV-1 HIV infection. 4. Final crisis Cryptococcus Meningitis Encapsulated yeast on India ink stain or MICROORGANISM SOURCE OF INFECTION
nucleic acid amplification test (NAAT) is During clinical latency phase, virus replicates neoformans capsular antigen ⊕ B cereus Reheated rice. “Food poisoning from reheated
performed; if the NAAT is ⊝, patient had false in lymph nodes Cryptosporidium spp. Chronic, watery diarrhea Acid-fast oocysts in stool rice? Be serious!” (B cereus)
positive initial Ag/Ab immunoassay. C botulinum Improperly canned foods (toxins), raw honey
EBV B-cell lymphoma (eg, non-Hodgkin lymphoma, CNS lymphoma—ring enhancing, may be
Viral load tests determine the amount of viral (spores)
CNS lymphoma) solitary (vs Toxoplasma)
RNA in the plasma. High viral load associated
Mycobacterium Nonspecific systemic symptoms (fever, night C perfringens Reheated meat
with poor prognosis. Also use viral load to
monitor effect of drug therapy. Use HIV avium–intracellulare, sweats, weight loss) or focal lymphadenitis E coli O157:H7 Undercooked meat
genotyping to determine appropriate therapy. Mycobacterium avium
L monocytogenes Deli meats, soft cheeses
AIDS diagnosis ≤ 200 CD4+ cells/mm3 complex
Salmonella Poultry, meat, and eggs
(normal: 500–1500 cells/mm3). HIV ⊕ with Toxoplasma gondii Brain abscesses Multiple ring-enhancing lesions on MRI
AIDS-defining condition (eg, Pneumocystis S aureus Meats, mayonnaise, custard; preformed toxin
pneumonia) or CD4+ percentage < 14%. V parahaemolyticus and V vulnificusa Contaminated seafood
aV vulnificus can also cause wound infections from contact with contaminated water or shellfish.
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Bugs causing diarrhea Common causes of meningitis Urinary tract Cystitis presents with dysuria, frequency, urgency, suprapubic pain, and WBCs (but not WBC ToRCHeS infections Microbes that may pass from mother to fetus. Transmission is transplacental in most cases, or via
Bloody diarrhea NEWBORN (0–6 MO) CHILDREN (6 MO–6 YR) 6–60 YR 60 YR + infections casts) in urine. Primarily caused by ascension of microbes from urethra to bladder. Ascension to delivery (especially HSV-2). Nonspecific signs common to many ToRCHeS infections include
Group B streptococci S pneumoniae S pneumoniae S pneumoniae kidney results in pyelonephritis, which presents with fever, chills, flank pain, costovertebral angle hepatosplenomegaly, jaundice, thrombocytopenia, and growth retardation.
Campylobacter Comma- or S-shaped organisms; growth at 42°C
E coli N meningitidis N meningitidis (#1 in teens) Gram ⊝ rods tenderness, hematuria, and WBC casts. Other important infectious agents include Streptococcus agalactiae (group B streptococci), E coli,
E histolytica Protozoan; amebic dysentery; liver abscess Listeria H influenzae type b Enteroviruses Listeria Ten times more common in women (shorter urethras colonized by fecal flora). Other predisposing and Listeria monocytogenes—all causes of meningitis in neonates. Parvovirus B19 causes hydrops
Enterohemorrhagic O157:H7; can cause HUS; makes Shiga-like toxin Enteroviruses HSV factors: obstruction, kidney surgery, catheterization, GU malformation, diabetes, pregnancy. fetalis.
E coli Males—infants with congenital defects, vesicoureteral reflux. Elderly—enlarged prostate.
Give ceftriaxone and vancomycin empirically (add ampicillin if Listeria is suspected). AGENT MODES OF MATERNAL TRANSMISSION MATERNAL MANIFESTATIONS NEONATAL MANIFESTATIONS
SPECIES FEATURES COMMENTS
Enteroinvasive E coli Invades colonic mucosa Viral causes of meningitis: enteroviruses (especially coxsackievirus), HSV-2 (HSV-1 = encephalitis), HIV, West Nile virus (also Toxoplasma gondii Cat feces or ingestion of Usually asymptomatic; Classic triad: chorioretinitis,
causes encephalitis), VZV. Escherichia coli Leading cause of UTI. Colonies show strong Diagnostic markers: undercooked meat lymphadenopathy (rarely) hydrocephalus, and
Salmonella (non- Lactose ⊝; flagellar motility; has animal reservoir, especially poultry and eggs A
In HIV: Cryptococcus spp. pink lactose-fermentation on MacConkey ⊕ Leukocyte esterase = evidence of WBC
intracranial calcifications,
typhoidal)
Note: Incidence of H influenzae meningitis has greatly due to conjugate H influenzae vaccinations. Today, cases are usually agar. activity. +/− “blueberry muffin” rash A .
Shigella Lactose ⊝; very low ID50; produces Shiga toxin (human reservoir only); bacillary dysentery ⊕ Nitrite test = reduction of urinary nitrates
seen in unimmunized children. Staphylococcus 2nd leading cause of UTI in sexually active
Y enterocolitica Day care outbreaks; pseudoappendicitis saprophyticus women. by bacterial species (eg, E coli).
⊕ Urease test = urease-producing bugs (eg,
Watery diarrhea Klebsiella pneumoniae 3rd leading cause of UTI. Large mucoid capsule
Cerebrospinal fluid findings in meningitis S saprophyticus, Proteus, Klebsiella).
C difficile Pseudomembranous colitis; associated with antibiotics and PPIs; occasionally bloody diarrhea and viscous colonies.
OPENING PRESSURE CELL TYPE PROTEIN GLUCOSE
C perfringens Also causes gas gangrene Bacterial PMNs Serratia marcescens Some strains produce a red pigment; often
Rubella Respiratory droplets Rash, lymphadenopathy, Classic triad: abnormalities
Enterotoxigenic E coli Travelers’ diarrhea; produces heat-labile (LT) and heat-stable (ST) toxins nosocomial and drug resistant.
Fungal/TB lymphocytes polyarthritis, polyarthralgia of eye (cataract) and ear
Protozoa Giardia, Cryptosporidium Enterococcus Often nosocomial and drug resistant. (deafness) and congenital heart
Viral Normal/ lymphocytes Normal/ Normal
V cholerae Comma-shaped organisms; rice-water diarrhea; often from infected seafood Proteus mirabilis Motility causes “swarming” on agar; associated disease (PDA); ± “blueberry
with struvite stones. muffin” rash. “I (eye) ♥ ruby
Viruses Rotavirus, norovirus, enteric adenovirus
Pseudomonas Blue-green pigment and fruity odor; usually (rubella) earrings.”
Infections causing Most commonly viridans streptococci and Staphylococcus aureus. If dental infection or extraction
aeruginosa nosocomial and drug resistant. Cytomegalovirus Sexual contact, organ Usually asymptomatic; Hearing loss, seizures, petechial
brain abscess precedes abscess, oral anaerobes commonly involved.
Common causes of pneumonia B
transplants mononucleosis-like illness rash, “blueberry muffin” rash,
Multiple abscesses are usually from bacteremia; single lesions from contiguous sites: otitis media
chorioretinitis, periventricular
NEONATES (< 4 WK) CHILDREN (4 WK–18 YR) ADULTS (18–40 YR) ADULTS (40–65 YR) ELDERLY and mastoiditis temporal lobe and cerebellum; sinusitis or dental infection frontal lobe.
Common vaginal infections calcifications B
Group B streptococci Viruses (RSV) Mycoplasma S pneumoniae S pneumoniae Toxoplasma reactivation in AIDS.
E coli Mycoplasma C pneumoniae H influenzae Influenza virus Bacterial vaginosis Trichomonas vaginitis Candida vulvovaginitis
C trachomatis S pneumoniae Anaerobes Anaerobes SIGNS AND SYMPTOMS No inflammation Inflammation (“strawberry Inflammation
(infants–3 yr) Viruses (eg, influenza) Viruses H influenzae Osteomyelitis RISK FACTOR ASSOCIATED INFECTION Thin, white discharge A with cervix”) Thick, white, “cottage cheese”
C pneumoniae Mycoplasma Gram ⊝ rods A Assume if no other information is available S aureus (most common overall) fishy odor Frothy, yellow-green, foul- discharge C
(school-aged Sexually active Neisseria gonorrhoeae (rare), septic arthritis more smelling discharge
HIV Sexual contact, needlestick Variable presentation depending Recurrent infections, chronic
children) common Clue cells Motile trichomonads B Pseudohyphae
LAB FINDINGS on CD4+ cell count diarrhea
S pneumoniae pH > 4.5 pH > 4.5 pH normal (4.0–4.5)
Runts May Cough Sickle cell disease Salmonella and S aureus Herpes simplex virus-2 Skin or mucous membrane Usually asymptomatic; herpetic Meningoencephalitis, herpetic
Prosthetic joint replacement S aureus and S epidermidis TREATMENT Metronidazole or clindamycin Metronidazole Azoles contact (vesicular) lesions (vesicular) lesions
Chunky Sputum
Treat sexual partner(s)
Special groups Vertebral involvement S aureus, Mycobacterium tuberculosis (Pott Syphilis Sexual contact Chancre (1°) and disseminated Often results in stillbirth,
disease) A B C rash (2°) are the two stages hydrops fetalis; if child
Alcoholic Klebsiella, anaerobes usually due to aspiration (eg, Peptostreptococcus, Fusobacterium, Prevotella,
Bacteroides) likely to result in fetal infection survives, presents with facial
Cat and dog bites Pasteurella multocida
abnormalities (eg, notched
IV drug users S pneumoniae, S aureus IV drug abuse S aureus; also Pseudomonas, Candida teeth, saddle nose, short
Aspiration Anaerobes Elevated C-reactive protein (CRP) and erythrocyte sedimentation rate common but nonspecific. maxilla), saber shins, CN VIII
Atypical Mycoplasma, Chlamydophila, Legionella, viruses (RSV, CMV, influenza, adenovirus) Radiographs are insensitive early but can be useful in chronic osteomyelitis ( A , left). MRI is best deafness
for detecting acute infection and detailing anatomic involvement ( A , right).
Cystic fibrosis Pseudomonas, S aureus, S pneumoniae, Burkholderia cepacia
Immunocompromised S aureus, enteric gram ⊝ rods, fungi, viruses, P jirovecii (with HIV)
Nosocomial (hospital S aureus, Pseudomonas, other enteric gram ⊝ rods
acquired)
Postviral S pneumoniae, S aureus, H influenzae
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Red rashes of childhood Sexually transmitted infections Pelvic inflammatory Top bugs—Chlamydia trachomatis (subacute, Salpingitis is a risk factor for ectopic pregnancy, Bugs affecting unvaccinated children
AGENT ASSOCIATED SYNDROME/DISEASE CLINICAL PRESENTATION DISEASE CLINICAL FEATURES ORGANISM disease often undiagnosed), Neisseria gonorrhoeae infertility, chronic pelvic pain, and adhesions. CLINICAL PRESENTATION FINDINGS/LABS PATHOGEN
Coxsackievirus type A Hand-foot-mouth disease Oval-shaped vesicles on palms and soles A ; AIDS Opportunistic infections, Kaposi sarcoma, HIV A
(acute). Can lead to perihepatitis (Fitz-Hugh–Curtis Dermatologic
vesicles and ulcers in oral mucosa lymphoma C trachomatis—most common bacterial STI in syndrome)—infection and inflammation of
Rash Beginning at head and moving down with Rubella virus
the United States. liver capsule and “violin string” adhesions of
Human herpesvirus 6 Roseola (exanthem subitum) Asymptomatic rose-colored macules appear Chancroid Painful genital ulcer with exudate, inguinal Haemophilus ducreyi (it’s so painful, you “do postauricular lymphadenopathy
Signs include cervical motion tenderness, peritoneum to liver B .
on body after several days of high fever; can adenopathy cry”) Beginning at head and moving down; rash Measles virus
adnexal tenderness, purulent cervical
present with febrile seizures; usually affects Chlamydia Urethritis, cervicitis, epididymitis, Chlamydia trachomatis (D–K) preceded by cough, coryza, conjunctivitis, and
discharge A .
infants conjunctivitis, reactive arthritis, PID blue-white (Koplik) spots on buccal mucosa
PID may include salpingitis, endometritis,
Measles virus Measles (rubeola) Confluent rash beginning at head and Condylomata Genital warts, koilocytes HPV-6 and -11 hydrosalpinx, and tubo-ovarian abscess. Neurologic
moving down; preceded by cough, coryza, acuminata B Meningitis Microbe colonizes nasopharynx H influenzae type b
conjunctivitis, and blue-white (Koplik) spots
Genital herpes Painful penile, vulvar, or cervical vesicles and HSV-2, less commonly HSV-1 Can also lead to myalgia and paralysis Poliovirus
on buccal mucosa
ulcers; can cause systemic symptoms such as
Parvovirus B19 Erythema infectiosum (fifth disease) “Slapped cheek” rash on face B (can cause Respiratory
fever, headache, myalgia
hydrops fetalis in pregnant women) Epiglottitis Fever with dysphagia, drooling, and difficulty H influenzae type b (also capable of causing
Gonorrhea Urethritis, cervicitis, PID, prostatitis, Neisseria gonorrhoeae
Rubella virus Rubella Pink macules and papules begin at head breathing due to edematous “cherry red” epiglottitis in fully immunized children)
epididymitis, arthritis, creamy purulent
and move down, remain discrete fine epiglottis; “thumbprint sign” on x-ray
discharge
desquamating truncal rash; postauricular Pharyngitis Grayish oropharyngeal exudate Corynebacterium diphtheriae (elaborates toxin
Granuloma inguinale Painless, beefy red ulcer that bleeds readily on Klebsiella (Calymmatobacterium) granulomatis;
lymphadenopathy (“pseudomembranes” may obstruct airway); that causes necrosis in pharynx, cardiac, and
(Donovanosis) contact A cytoplasmic Donovan bodies (bipolar staining)
Streptococcus pyogenes Scarlet fever Flushed cheeks and circumoral pallor C on the Nosocomial infections E coli (UTI) and S aureus (wound infection) are the two most common causes. painful throat CNS tissue)
A
Uncommon in US seen on microscopy
face; erythematous, sandpaper-like rash from RISK FACTOR PATHOGEN UNIQUE SIGNS/SYMPTOMS
neck to trunk and extremities; fever and sore Antibiotic use Clostridium difficile Watery diarrhea, leukocytosis
throat Bug hints CHARACTERISTIC ORGANISM
Aspiration (2° to Polymicrobial, gram ⊝ bacteria, often Right lower lobe infiltrate or right upper/
Varicella-Zoster virus Chickenpox Vesicular rash begins on trunk; spreads to face altered mental status, middle lobe (patient recumbent); purulent Asplenic patient (due to surgical splenectomy Encapsulated microbes, especially SHiN
anaerobes
D and extremities with lesions of different old age) malodorous sputum or autosplenectomy, eg, chronic sickle cell (S pneumoniae >> H influenzae type b >
stages disease) N meningitidis)
Decubitus ulcers, S aureus (including MRSA), gram ⊝ anaerobes Erythema, tenderness, induration, drainage
surgical wounds, from surgical wound sites Branching rods in oral infection, sulfur granules Actinomyces israelii
A B C D (Bacteroides, Prevotella, Fusobacterium)
Hepatitis B Jaundice HBV drains Chronic granulomatous disease Catalase ⊕ microbes, especially S aureus
Lymphogranuloma Infection of lymphatics; painless genital ulcers, C trachomatis (L1–L3) Intravascular catheters S aureus (including MRSA), S epidermidis (long Erythema, induration, tenderness, drainage “Currant jelly” sputum Klebsiella
venereum painful lymphadenopathy (ie, buboes) term), Enterobacter from access sites Dog or cat bite Pasteurella multocida
Primary syphilis Painless chancre Treponema pallidum Mechanical ventilation, Late onset: P aeruginosa, Klebsiella, New infiltrate on CXR, sputum production; Facial nerve palsy (typically bilateral) Borrelia burgdorferi (Lyme disease)
Secondary syphilis Fever, lymphadenopathy, skin rashes, endotracheal Acinetobacter, S aureus sweet odor (Pseudomonas)
Fungal infection in diabetic or Mucor or Rhizopus spp.
condylomata lata intubation
immunocompromised patient
Tertiary syphilis Gummas, tabes dorsalis, general paresis, aortitis, Renal dialysis unit, HBV, HCV
Health care provider HBV, HCV (from needlestick)
Argyll Robertson pupil needlestick
Neutropenic patients Candida albicans (systemic), Aspergillus
Trichomoniasis Vaginitis, strawberry cervix, motile in wet prep Trichomonas vaginalis Urinary catheterization Proteus spp, E coli, Klebsiella (infections in your Dysuria, leukocytosis, flank pain or
PEcKer) costovertebral angle tenderness Organ transplant recipient CMV
Water aerosols Legionella Signs of pneumonia, GI symptoms (diarrhea, PAS ⊕ Tropheryma whipplei (Whipple disease)
nausea, vomiting), neurologic abnormalities Pediatric infection Haemophilus influenzae (including epiglottitis)
Pneumonia in cystic fibrosis, burn infection Pseudomonas aeruginosa
Pus, empyema, abscess S aureus
Rash on hands and feet Coxsackie A virus, Treponema pallidum,
Rickettsia rickettsii
Sepsis/meningitis in newborn Group B strep
Surgical wound S aureus
Traumatic open wound Clostridium perfringens
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MICROBIOLOGY
`M̀ICROBIOLOGY—ANTIMICROBIALS
`M̀ICROBIOLOGY—ANTIMICROBIALS MICROBIOLOGY
MICROBIOLOGY
`M̀ICROBIOLOGY—ANTIMICROBIALS SEC TION II 189 190 SEC TION II MICROBIOLOGY `M̀ICROBIOLOGY—ANTIMICROBIALS
MICROBIOLOGY—ANTIMICROBIALS
`` Penicillinase-sensitive Amoxicillin, ampicillin; aminopenicillins. Cephalosporins Carbapenems Doripenem, Imipenem, Meropenem, Ertapenem (DIME antibiotics are given when there is a
penicillins MECHANISM β-lactam drugs that inhibit cell wall synthesis Organisms typically not covered by 1st–4th 10/10 [life-threatening] infection).
Antimicrobial therapy MECHANISM Same as penicillin. Wider spectrum; AMinoPenicillins are AMPed-up penicillin. but are less susceptible to penicillinases. generation cephalosporins are LAME: MECHANISM Imipenem is a broad-spectrum, β-lactamase– With imipenem, “the kill is lastin’ with
mRNA SYNTHESIS
penicillinase sensitive. Also combine with AmOxicillin has greater Oral bioavailability Bactericidal. Listeria, Atypicals (Chlamydia, Mycoplasma), resistant carbapenem. Always administered cilastatin.”
DNA INTEGRITY
FOLIC ACID SYNTHESIS (via free radicals) (RNA polymerase) GYRASE clavulanic acid to protect against destruction than ampicillin. MRSA, and Enterococci. with cilastatin (inhibitor of renal Newer carbapenems include ertapenem (limited
AND REDUCTION by β-lactamase. CLINICAL USE 1st generation (cefazolin, cephalexin)—gram ⊕ 1st generation—PEcK. dehydropeptidase I) to inactivation of drug Pseudomonas coverage) and doripenem.
(DNA methylation) Fluoroquinolones
Metronidazole Rifampin
Ciprofloxacin CLINICAL USE Extended-spectrum penicillin—H influenzae, Coverage: ampicillin/amoxicillin HHELPSS cocci, Proteus mirabilis, E coli, Klebsiella in renal tubules.
Levofloxacin, etc
Sulfonamides
– –
H pylori, E coli, Listeria monocytogenes, kill enterococci. pneumoniae. Cefazolin used prior to surgery to CLINICAL USE Gram ⊕ cocci, gram ⊝ rods, and anaerobes.
Sulfamethoxazole BACTERIAL CELL Quinolone
Proteus mirabilis, Salmonella, Shigella, prevent S aureus wound infections. Wide spectrum and significant side effects
Sulfisoxazole PABA Nalidixic acid
– enterococci.
Sulfadiazine 2nd generation (cefaclor, cefoxitin, cefuroxime, 2nd graders wear fake fox fur to tea parties. limit use to life-threatening infections or
– after other drugs have failed. Meropenem
ADVERSE EFFECTS Hypersensitivity reactions, rash, cefotetan)—gram ⊕ cocci, H influenzae, 2nd generation—HENS PEcK.
Trimethoprim DNA gyrase Enterobacter aerogenes, Neisseria spp., Serratia has a risk of seizures and is stable to
– DNA
pseudomembranous colitis.
RNA marcescens, Proteus mirabilis, E coli, Klebsiella dehydropeptidase I.
MECHANISM OF RESISTANCE Penicillinase (a type of β-lactamase) cleaves
polymerase pneumoniae. ADVERSE EFFECTS GI distress, rash, and CNS toxicity (seizures) at
MEMBRANE INTEGRITY
DHF PROTEIN SYNTHESIS β-lactam ring.
3rd generation (ceftriaxone, cefotaxime, Can cross blood-brain barrier. high plasma levels.
Daptomycin – 50S SUBUNIT cefpodoxime, ceftazidime)—serious gram ⊝ Ceftriaxone—meningitis, gonorrhea,
mRNA
Chloramphenicol infections resistant to other β-lactams. disseminated Lyme disease.
Penicillinase-resistant Dicloxacillin, nafcillin, oxacillin.
Ribosomes Clindamycin Ceftazidime—Pseudomonas. Monobactams Aztreonam
CELL WALL SYNTHESIS
Linezolid penicillins
THF 50S 50S 50S 4th generation (cefepime)—gram ⊝ organisms, MECHANISM Less susceptible to β-lactamases. Prevents peptidoglycan cross-linking by binding to penicillin-
PEPTIDOGLYCAN SYNTHESIS Macrolides MECHANISM Same as penicillin. Narrow spectrum;
Cell m
30S
30S 30S
– Azithromycin with activity against Pseudomonas and gram binding protein 3. Synergistic with aminoglycosides. No cross-allergenicity with penicillins.
Glycopeptides embrane Clarithromycin penicillinase resistant because bulky R group ⊕ organisms.
Vancomycin – Erythromycin blocks access of β-lactamase to β-lactam ring. CLINICAL USE Gram ⊝ rods only—no activity against gram ⊕ rods or anaerobes. For penicillin-allergic patients
Bacitracin Cell wal Streptogramins 5th generation (ceftaroline)—broad gram ⊕ and
l and those with renal insufficiency who cannot tolerate aminoglycosides.
– Quinupristin CLINICAL USE S aureus (except MRSA). “Use naf (nafcillin) for staph.” gram ⊝ organism coverage; unlike 1st–4th
Dalfopristin
PEPTIDOGLYCAN CROSS-LINKING ADVERSE EFFECTS Hypersensitivity reactions, interstitial nephritis. generation cephalosporins, ceftaroline covers ADVERSE EFFECTS Usually nontoxic; occasional GI upset.
30S SUBUNIT
Penicillinase-sensitive penicillins Antipseudomonal Carbapenems MECHANISM OF RESISTANCE MRSA has altered penicillin-binding protein Listeria, MRSA, and Enterococcus faecalis—
Penicillin G, V Ticarcillin Imipenem
Ampicillin Piperacillin Meropenem
Aminoglycosides Glycylcycline
target site. does not cover Pseudomonas.
– Gentamicin Tigecycline Vancomycin
Amoxicillin Ertapenem
Cephalosporins (I-V)
Doripenem
Neomycin Tetracyclines ADVERSE EFFECTS Hypersensitivity reactions, autoimmune
Penicillinase-resistant penicillins 1st—Cefazolin, etc Amikacin Tetracycline hemolytic anemia, disulfiram-like reaction, MECHANISM Inhibits cell wall peptidoglycan formation by binding D-Ala-D-Ala portion of cell wall precursors.
Oxacillin 2nd—Cefoxitin, etc Monobactams Tobramycin Doxycycline
Nafcillin 3rd—Ceftriaxone, etc Aztreonam Streptomycin Minocycline Antipseudomonal Piperacillin, ticarcillin. vitamin K deficiency. Low rate of cross- Bactericidal against most bacteria (bacteriostatic against C difficile). Not susceptible to
Dicloxacillin 4th—Cefepime
penicillins reactivity even in penicillin-allergic patients. β-lactamases.
5th—Ceftaroline
MECHANISM Same as penicillin. Extended spectrum. Penicillinase sensitive; use with β-lactamase inhibitors. nephrotoxicity of aminoglycosides. CLINICAL USE Gram ⊕ bugs only—serious, multidrug-resistant organisms, including MRSA, S epidermidis,
MECHANISM OF RESISTANCE Inactivated by cephalosporinases (a type of sensitive Enterococcus species, and Clostridium difficile (oral dose for pseudomembranous colitis).
CLINICAL USE Pseudomonas spp. and gram ⊝ rods.
Penicillin G, V Penicillin G (IV and IM form), penicillin V (oral). Prototype β-lactam antibiotics. β-lactamase). Structural change in penicillin- ADVERSE EFFECTS Well tolerated in general—but NOT trouble free. Nephrotoxicity, Ototoxicity, Thrombophlebitis,
ADVERSE EFFECTS Hypersensitivity reactions.
binding proteins (transpeptidases). diffuse flushing—red man syndrome A (largely preventable by pretreatment with antihistamines
MECHANISM D-Ala-D-Ala structural analog. Bind penicillin-binding proteins (transpeptidases). A
and slow infusion rate), drug reaction with eosinophilia and systemic symptoms (DRESS
Block transpeptidase cross-linking of peptidoglycan in cell wall.
syndrome).
Activate autolytic enzymes. β-lactamase inhibitors Include Clavulanic acid, Avibactam, CAST.
CLINICAL USE Mostly used for gram ⊕ organisms (S pneumoniae, S pyogenes, Actinomyces). Also used for gram ⊝ Sulbactam, Tazobactam. Often added
cocci (mainly N meningitidis) and spirochetes (namely T pallidum). Bactericidal for gram ⊕ cocci, to penicillin antibiotics to protect the
gram ⊕ rods, gram ⊝ cocci, and spirochetes. β-lactamase sensitive. antibiotic from destruction by β-lactamase
(penicillinase).
ADVERSE EFFECTS Hypersensitivity reactions, direct Coombs ⊕ hemolytic anemia, drug-induced interstitial nephritis.
MECHANISM OF RESISTANCE Occurs in bacteria (eg, Enterococcus) via amino acid modification of D-Ala-D-Ala to D-Ala-D-Lac.
RESISTANCE β-lactamase cleaves the β-lactam ring. Mutations in penicillin-binding proteins.
“If you Lack a D-Ala (dollar), you can’t ride the van (vancomycin).”

MICROBIOLOGY
MICROBIOLOGY
Protein synthesis inhibitors Specifically target smaller bacterial ribosome Tetracyclines Tetracycline, doxycycline, minocycline. Oxazolidinones Linezolid. Sulfonamides Sulfamethoxazole (SMX), sulfisoxazole,
Linezolid Ribosomal A&P site (70S, made of 30S and 50S subunits), leaving MECHANISM Bacteriostatic; bind to 30S and prevent attachment of aminoacyl-tRNA. Limited CNS penetration. MECHANISM Inhibit protein synthesis by binding to 50S subunit and preventing formation of the initiation sulfadiazine.
(50S) human ribosome (80S) unaffected. Doxycycline is fecally eliminated and can be used in patients with renal failure. Do not take complex. MECHANISM Inhibit dihydropteroate synthase, thus inhibiting
PA
50S
– All are bacteriostatic, except aminoglycosides tetracyclines with milk (Ca2+), antacids (Ca2+ or Mg2+), or iron-containing preparations because folate synthesis. Bacteriostatic (bactericidal
30S CLINICAL USE Gram ⊕ species including MRSA and VRE. PABA + Pteridine
mRNA (bactericidal) and linezolid (variable). divalent cations inhibit drugs’ absorption in the gut. when combined with trimethoprim).
ADVERSE EFFECTS Bone marrow suppression (especially thrombocytopenia), peripheral neuropathy, serotonin Dihydropteroate Sulfonamides,
CLINICAL USE Borrelia burgdorferi, M pneumoniae. Drugs’ ability to accumulate intracellularly makes them very syndrome. CLINICAL USE Gram ⊕, gram ⊝, Nocardia. TMP-SMX for synthase dapsone
Initiator tRNA
Initiation
– Aminoglycosides (30S) 30S inhibitors effective against Rickettsia and Chlamydia. Also used to treat acne. Doxycycline effective against simple UTI.
complex (also cause misreading MECHANISM OF RESISTANCE Point mutation of ribosomal RNA. Dihydropteroic acid
formation of mRNA) Aminoglycosides MRSA. ADVERSE EFFECTS Hypersensitivity reactions, hemolysis if G6PD
Tetracyclines PA Tetracyclines ADVERSE EFFECTS GI distress, discoloration of teeth and inhibition of bone growth in children, photosensitivity. deficient, nephrotoxicity (tubulointerstitial
(30S) Chloramphenicol
(50S) 50S inhibitors Contraindicated in pregnancy. Macrolides Azithromycin, clarithromycin, erythromycin. nephritis), photosensitivity, Stevens-Johnson
– –
Chloramphenicol, Clindamycin MECHANISM OF RESISTANCE uptake or efflux out of bacterial cells by plasmid-encoded transport pumps. syndrome, kernicterus in infants, displace
A-site Peptidyl MECHANISM Inhibit protein synthesis by blocking translocation (“macroslides”); bind to the 23S rRNA of the
tRNA transferase Erythromycin (macrolides) other drugs from albumin (eg, warfarin).
binding
50S ribosomal subunit. Bacteriostatic.
Linezolid MECHANISM OF RESISTANCE Altered enzyme (bacterial dihydropteroate Dihydrofolic acid
Glycylcyclines Tigecycline.
CLINICAL USE Atypical pneumonias (Mycoplasma, Chlamydia, Legionella), STIs (Chlamydia), gram ⊕ cocci
synthase), uptake, or PABA synthesis.
“Buy AT 30, CCEL (sell) at 50.” (streptococcal infections in patients allergic to penicillin), and B pertussis. Dihydrofolate Trimethoprim,
MECHANISM Tetracycline derivative. Binds to 30S, inhibiting protein synthesis. Generally bacteriostatic. reductase pyrimethamine
ADVERSE EFFECTS MACRO: Gastrointestinal Motility issues, Arrhythmia caused by prolonged QT interval, acute
CLINICAL USE Broad-spectrum anaerobic, gram ⊝, and gram ⊕ coverage. Multidrug-resistant organisms (MRSA, Cholestatic hepatitis, Rash, eOsinophilia. Increases serum concentration of theophylline, oral
Tetrahydrofolic acid
Dapsone
VRE) or infections requiring deep tissue penetration. anticoagulants. Clarithromycin and erythromycin inhibit cytochrome P-450.
Translocation MECHANISM Similar to sulfonamides, but structurally distinct Purines Thymidine Methionine
ADVERSE EFFECTS GI symptoms: nausea, vomiting. Methylation of 23S rRNA-binding site prevents binding of drug.
MECHANISM OF RESISTANCE agent.
– CLINICAL USE Leprosy (lepromatous and tuberculoid), DNA, RNA DNA Protein
Chloramphenicol Pneumocystis jirovecii prophylaxis.

Macrolides (eg, erythromycin) (50S) Polymyxins Colistin (polymyxin E), polymyxin B.
Clindamycin (50S)
MECHANISM Blocks peptidyltransferase at 50S ribosomal subunit. Bacteriostatic. ADVERSE EFFECTS Hemolysis if G6PD deficient,
MECHANISM Cation polypeptides that bind to phospholipids on cell membrane of gram ⊝ bacteria. Disrupt cell methemoglobinemia.
CLINICAL USE Meningitis (Haemophilus influenzae, Neisseria meningitidis, Streptococcus pneumoniae) and membrane integrity leakage of cellular components cell death.
rickettsial diseases (eg, Rocky Mountain spotted fever [Rickettsia rickettsii]).
Aminoglycosides Gentamicin, Neomycin, Amikacin, “Mean” (aminoglycoside) GNATS caNNOT CLINICAL USE Salvage therapy for multidrug-resistant gram ⊝ bacteria (eg, P aeruginosa, E coli, K pneumoniae).
Limited use due to toxicity but often still used in developing countries because of low cost.
Tobramycin, Streptomycin. kill anaerobes. Polymyxin B is a component of a triple antibiotic ointment used for superficial skin infections. Trimethoprim
ADVERSE EFFECTS Anemia (dose dependent), aplastic anemia (dose independent), gray baby syndrome (in premature
MECHANISM Bactericidal; irreversible inhibition of initiation ADVERSE EFFECTS Nephrotoxicity, neurotoxicity (eg, slurred speech, weakness, paresthesias), respiratory failure. MECHANISM Inhibits bacterial dihydrofolate reductase.
infants because they lack liver UDP-glucuronosyltransferase).
complex through binding of the 30S subunit. Bacteriostatic.
Can cause misreading of mRNA. Also block MECHANISM OF RESISTANCE Plasmid-encoded acetyltransferase inactivates the drug.
CLINICAL USE Used in combination with sulfonamides
translocation. Require O2 for uptake; therefore (trimethoprim-sulfamethoxazole [TMP-
ineffective against anaerobes. SMX]), causing sequential block of folate
Clindamycin
CLINICAL USE Severe gram ⊝ rod infections. Synergistic with synthesis. Combination used for UTIs,
β-lactam antibiotics. MECHANISM Blocks peptide transfer (translocation) at 50S Shigella, Salmonella, Pneumocystis jirovecii
Neomycin for bowel surgery. ribosomal subunit. Bacteriostatic. pneumonia treatment and prophylaxis,
ADVERSE EFFECTS Nephrotoxicity, Neuromuscular blockade, CLINICAL USE Anaerobic infections (eg, Bacteroides spp., Treats anaerobic infections above the diaphragm toxoplasmosis prophylaxis.
Ototoxicity (especially when used with loop Clostridium perfringens) in aspiration vs metronidazole (anaerobic infections below ADVERSE EFFECTS Megaloblastic anemia, leukopenia,
diuretics). Teratogen. pneumonia, lung abscesses, and oral diaphragm). granulocytopenia, which may be avoided with
infections. Also effective against invasive coadministration of folinic acid. TMP Treats
MECHANISM OF RESISTANCE Bacterial transferase enzymes inactivate the
group A streptococcal infection. Marrow Poorly.
drug by acetylation, phosphorylation, or
adenylation. ADVERSE EFFECTS Pseudomembranous colitis (C difficile
overgrowth), fever, diarrhea.

MICROBIOLOGY
`M̀ICROBIOLOGY—ANTIMICROBIALS MICROBIOLOGY `M̀ICROBIOLOGY—ANTIMICROBIALS SEC TION II 197 198 SEC TION II MICROBIOLOGY `M̀ICROBIOLOGY—ANTIMICROBIALS
Fluoroquinolones Ciprofloxacin, enoxacin, norfloxacin, ofloxacin; respiratory fluoroquinolones—gemifloxacin, Antimycobacterial drugs Isoniazid Antimicrobial CLINICAL SCENARIO MEDICATION
levofloxacin, moxifloxacin. BACTERIUM PROPHYLAXIS TREATMENT MECHANISM synthesis of mycolic acids. Bacterial catalase- prophylaxis High risk for endocarditis and undergoing Amoxicillin
MECHANISM Inhibit prokaryotic enzymes topoisomerase M tuberculosis Isoniazid Rifampin, Isoniazid, Pyrazinamide, peroxidase (encoded by KatG) needed to surgical or dental procedures
II (DNA gyrase) and topoisomerase IV. Ethambutol (RIPE for treatment) convert INH to active metabolite. Exposure to gonorrhea Ceftriaxone
Bactericidal. Must not be taken with antacids. M avium–intracellulare Azithromycin, rifabutin More drug resistant than M tuberculosis. Mycobacterium tuberculosis. The only agent Different INH half-lives in fast vs slow
CLINICAL USE History of recurrent UTIs TMP-SMX
CLINICAL USE Gram ⊝ rods of urinary and GI tracts (including Azithromycin or clarithromycin + ethambutol. used as solo prophylaxis against TB. Also used acetylators.
Exposure to meningococcal infection Ceftriaxone, ciprofloxacin, or rifampin
Pseudomonas), some gram ⊕ organisms, otitis Can add rifabutin or ciprofloxacin. as monotherapy for latent TB.
externa. Pregnant woman carrying group B strep Intrapartum penicillin G or ampicillin
M leprae N/A Long-term treatment with dapsone and rifampin ADVERSE EFFECTS Hepatotoxicity, P-450 inhibition, drug-induced INH Injures Neurons and Hepatocytes.
ADVERSE EFFECTS GI upset, superinfections, skin rashes, Fluoroquinolones hurt attachments to your for tuberculoid form. Add clofazimine for SLE, anion gap metabolic acidosis, vitamin Prevention of gonococcal conjunctivitis in Erythromycin ointment on eyes
headache, dizziness. Less commonly, can bones. lepromatous form. B6 deficiency (peripheral neuropathy, newborn
cause leg cramps and myalgias. sideroblastic anemia). Administer with Prevention of postsurgical infection due to Cefazolin
MYCOBACTERIAL CELL Plasma
Contraindicated in pregnant women, nursing Cell wall membrane Interior of cell pyridoxine (B6). S aureus
mothers, and children < 18 years old due MECHANISM OF RESISTANCE Mutations leading to underexpression of KatG. Prophylaxis of strep pharyngitis in child with Benzathine penicillin G or oral penicillin V
lliippiids,,
to possible damage to cartilage. Some may

dss
s
caann
PPeeppt laaccttaann
prior rheumatic fever

iidd
exx ffr yll lliippiidd
c aacc
ggllyyc
prolong QT interval.
coolliic
mRNA mRNA SYNTHESIS

ggaal
Exposure to syphilis Benzathine penicillin G

reeee
tiiddoo
Accy
(DNA-dependent
Myyc
biinnoo
May cause tendonitis or tendon rupture in

mpplle A
MYCOLIC ACID Pyrazinamide

M
RNA polymerase)
Arraab
people > 60 years old and in patients taking SYNTHESIS

Mechanism uncertain. Pyrazinamide is a prodrug that is converted to the active compound
A
ccoom
MECHANISM
prednisone. Ciprofloxacin inhibits cytochrome
Isoniazid – –
Rifabutin pyrazinoic acid. Works best at acidic pH (eg, in host phagolysosomes). Prophylaxis in HIV patients
P-450. RNA
Rifampin
polymerase
CLINICAL USE Mycobacterium tuberculosis. CELL COUNT PROPHYLAXIS INFECTION
MECHANISM OF RESISTANCE Chromosome-encoded mutation in DNA CD4 < 200 cells/mm3 TMP-SMX Pneumocystis pneumonia
gyrase, plasmid-mediated resistance, efflux ARABINOGALACTAN ADVERSE EFFECTS Hyperuricemia, hepatotoxicity.
SYNTHESIS INTRACELLULAR CD4 < 100 cells/mm3 TMP-SMX Pneumocystis pneumonia and toxoplasmosis
pumps. (arabinosyl transferase) DNA
(unclear mechanism)
CD4 < 50 cells/mm3 Azithromycin or clarithromycin Mycobacterium avium complex
Ethambutol
Ethambutol – – Pyrazinamide
Daptomycin MECHANISM carbohydrate polymerization of mycobacterium cell wall by blocking arabinosyltransferase.
Lipopeptide that disrupts cell membranes of Treatment of highly MRSA: vancomycin, daptomycin, linezolid, tigecycline, ceftaroline, doxycycline.
MECHANISM CLINICAL USE Mycobacterium tuberculosis.
gram ⊕ cocci by creating transmembrane resistant bacteria VRE: linezolid and streptogramins (quinupristin, dalfopristin).
ADVERSE EFFECTS Optic neuropathy (red-green color blindness). Pronounce “eyethambutol.” Multidrug-resistant P aeruginosa, multidrug-resistant Acinetobacter baumannii: polymyxins B and
channels.
Rifamycins Rifampin, rifabutin. E (colistin).
CLINICAL USE S aureus skin infections (especially MRSA), Not used for pneumonia (avidly binds to and is
MECHANISM Inhibit DNA-dependent RNA polymerase. Rifampin’s 4 R’s:
bacteremia, endocarditis, VRE. inactivated by surfactant). Streptomycin
CLINICAL USE Mycobacterium tuberculosis; delay resistance RNA polymerase inhibitor
ADVERSE EFFECTS Myopathy, rhabdomyolysis. Ramps up microsomal cytochrome P-450 MECHANISM Interferes with 30S component of ribosome. Antifungal therapy
to dapsone when used for leprosy. Used
for meningococcal prophylaxis and Red/orange body fluids CLINICAL USE Mycobacterium tuberculosis (2nd line). FUNGAL CELL
LANOSTEROL SYNTHESIS CELL WALL SYNTHESIS
chemoprophylaxis in contacts of children with Rapid resistance if used alone ADVERSE EFFECTS Tinnitus, vertigo, ataxia, nephrotoxicity. Cell
Metronidazole Rifampin ramps up cytochrome P-450, but wa
ll
H influenzae type b. Terbinafine Echinocandins
MECHANISM Forms toxic free radical metabolites in the rifabutin does not. –
– Anidulafungin
ADVERSE EFFECTS Minor hepatotoxicity and drug interactions Squalene Caspofungin
bacterial cell that damage DNA. Bactericidal,
( cytochrome P-450); orange body fluids Squalene epoxidase Micafungin
antiprotozoal.
(nonhazardous side effect). Rifabutin favored Squalene epoxide
CLINICAL USE Treats Giardia, Entamoeba, Trichomonas, GET GAP on the Metro with metronidazole! over rifampin in patients with HIV infection CELL MEMBRANE INTEGRITY
Gardnerella vaginalis, Anaerobes (Bacteroides, Treats anaerobic infection below the diaphragm due to less cytochrome P-450 stimulation. Nucleus
C difficile). Can be used in place of amoxicillin vs clindamycin (anaerobic infections above ERGOSTEROL SYNTHESIS Lanosterol Polyenes
MECHANISM OF RESISTANCE Mutations reduce drug binding to RNA Amphotericin B
in H pylori “triple therapy” in case of penicillin diaphragm). 14–α–demethylase
polymerase. Monotherapy rapidly leads to Azoles Ergosterol Nystatin
allergy.
resistance. Clotrimazole
ADVERSE EFFECTS Disulfiram-like reaction (severe flushing, Fluconazole Ergosterol
Itraconazole e
tachycardia, hypotension) with alcohol; – ra n NUCLEIC ACID SYNTHESIS
Ketoconazole emb
Cell m
headache, metallic taste. Miconazole –
Voriconazole Flucytosine

MICROBIOLOGY
MICROBIOLOGY
Amphotericin B Echinocandins Anidulafungin, caspofungin, micafungin. Antiviral therapy Ganciclovir

MECHANISM Binds ergosterol (unique to fungi); forms Amphotericin “tears” holes in the fungal MECHANISM Inhibit cell wall synthesis by inhibiting synthesis of β-glucan. MECHANISM 5′-monophosphate formed by a CMV viral kinase. Guanosine analog. Triphosphate formed by
HIV ANTIVIRAL OTHER ANTIVIRAL
membrane pores that allow leakage of membrane by forming pores. FUSION cellular kinases. Preferentially inhibits viral DNA polymerase.
CLINICAL USE Invasive aspergillosis, Candida. THERAPY THERAPY
electrolytes. ATTACHMENT CLINICAL USE CMV, especially in immunocompromised patients. Valganciclovir, a prodrug of ganciclovir, has
ADVERSE EFFECTS GI upset, flushing (by histamine release).
CLINICAL USE Serious, systemic mycoses. Cryptococcus Maraviroc – REVERSE PROTEIN Receptor better oral bioavailability.
SYNTHESIS binding
(amphotericin B with/without flucytosine TRANSCRIPTASE
BI
ND ADVERSE EFFECTS Bone marrow suppression (leukopenia, neutropenia, thrombocytopenia), renal toxicity. More toxic
PENETRATION via PKR
for cryptococcal meningitis), Blastomyces, Griseofulvin to host enzymes than acyclovir.
Enfuvirtide – Interferon-α
Coccidioides, Histoplasma, Candida, Uncoating
g
(HBV, HCV)
MECHANISM Interferes with microtubule function; disrupts mitosis. Deposits in keratin-containing tissues (eg, NRTIs Endo- MECHANISM OF RESISTANCE Mutated viral kinase.
Mucor. Intrathecally for fungal meningitis. Abacavir (ABC) cytosis
nails).
Supplement K+ and Mg2+ because of altered Didanosine (ddI)
Emtricitabine (FTC)
renal tubule permeability. CLINICAL USE Oral treatment of superficial infections; inhibits growth of dermatophytes (tinea, ringworm). Reverse – Lamivudine (3TC)
transcription UNCOATING Foscarnet
Stavudine (d4T)
ADVERSE EFFECTS Fever/chills (“shake and bake”), hypotension, ADVERSE EFFECTS Teratogenic, carcinogenic, confusion, headaches, disulfiram-like reaction, cytochrome P-450 and DNA
Tenofovir (TDF) NUCLEIC ACID
warfarin metabolism. integration
Amantadine no longer used – SYNTHESIS MECHANISM Viral DNA/RNA polymerase inhibitor and Foscarnet = pyrofosphate analog.
nephrotoxicity, arrhythmias, anemia, IV INTEGRASE
Zidovudine (ZDV, for Influenza due
formerly AZT) Rimantadine to ! resistance HIV reverse transcriptase inhibitor. Binds to
phlebitis (“amphoterrible”). Hydration
NNRTIs Guanosine analogs pyrophosphate-binding site of enzyme. Does
nephrotoxicity. Liposomal amphotericin Replic
p cation
Acyclovir, etc (HSV, VZV)
Antiprotozoal therapy Pyrimethamine (toxoplasmosis), suramin and melarsoprol (Trypanosoma brucei), nifurtimox Dolutegravir –
ranscription Delavirdine – not require any kinase activation.
toxicity. Elvitegravir Efavirenz Prottein Ganciclovir (CMV)
synthesis
t CMV retinitis in immunocompromised patients
(T cruzi), sodium stibogluconate (leishmaniasis). Raltegravir Nevirapine Viral DNA polymerase CLINICAL USE
inhibitors
Virion Cidofovir HSV*,
when ganciclovir fails; acyclovir-resistant HSV.
Nystatin assembly Foscarnet CMV ADVERSE EFFECTS Nephrotoxicity, electrolyte abnormalities
Anti-mite/louse Permethrin (inhibits Na+ channel deactivation Treat PML (Pesty Mites and Lice) with PML Translation Guanine nucleotide (hypo- or hypercalcemia, hypo- or
MECHANISM Same as amphotericin B. Topical use only as too toxic for systemic use. PROTEASE synthesis
therapy neuronal membrane depolarization), (Permethrin, Malathion, Lindane), because HUMAN Ribavirin (RSV, HCV) hyperphosphatemia, hypokalemia,
CLINICAL USE “Swish and swallow” for oral candidiasis (thrush); topical for diaper rash or vaginal candidiasis. malathion (acetylcholinesterase inhibitor), they NAG you (Na, AChE, GABA blockade).
Proteolytic
CD4+ T CELL CELL
processing hypomagnesemia) can lead to seizures.
lindane (blocks GABA channels Atazanavir *Acyclovir-resistant
Darunavir MECHANISM OF RESISTANCE Mutated DNA polymerase.
neurotoxicity). Used to treat scabies Fosamprenavir
Flucytosine (Sarcoptes scabiei) and lice (Pediculus and Indinavir –
RELEASE OF PROGENY VIRUS
Lopinavir Packaging
MECHANISM Inhibits DNA and RNA biosynthesis by conversion to 5-fluorouracil by cytosine deaminase. Pthirus). Ritonavir and assembly Cidofovir
Saquinavir Neuraminidase inhibitors
CLINICAL USE Systemic fungal infections (especially meningitis caused by Cryptococcus) in combination with Budding
– Oseltamivir
Influenza A, B MECHANISM Preferentially inhibits viral DNA polymerase. Does not require phosphorylation by viral kinase.
amphotericin B. Rele
eas
asee Zanamivir
Chloroquine CLINICAL USE CMV retinitis in immunocompromised patients; acyclovir-resistant HSV. Long half-life.
ADVERSE EFFECTS Bone marrow suppression.
MECHANISM Blocks detoxification of heme into hemozoin. Heme accumulates and is toxic to plasmodia. ADVERSE EFFECTS Nephrotoxicity (coadminister with probenecid and IV saline to toxicity).
CLINICAL USE Treatment of plasmodial species other than P falciparum (frequency of resistance in P falciparum
Azoles Clotrimazole, fluconazole, isavuconazole, itraconazole, ketoconazole, miconazole, voriconazole. is too high). Resistance due to membrane pump that intracellular concentration of drug. Treat Oseltamivir, zanamivir
MECHANISM Inhibit fungal sterol (ergosterol) synthesis by inhibiting the cytochrome P-450 enzyme that converts P falciparum with artemether/lumefantrine or atovaquone/proguanil. For life-threatening malaria, MECHANISM Inhibit influenza neuraminidase release of progeny virus.
lanosterol to ergosterol. use quinidine in US (quinine elsewhere) or artesunate. Treatment and prevention of both influenza A and B. Beginning therapy within 48 hours of
CLINICAL USE
CLINICAL USE Local and less serious systemic mycoses. Fluconazole for chronic suppression of cryptococcal ADVERSE EFFECTS Retinopathy; pruritus (especially in dark-skinned individuals). symptom onset may shorten duration of illness.
meningitis in AIDS patients and candidal infections of all types. Itraconazole for Blastomyces,
Coccidioides, Histoplasma. Clotrimazole and miconazole for topical fungal infections.
Voriconazole for Aspergillus and some Candida. Isavuconazole for serious Aspergillus and Mucor Antihelminthic Pyrantel pamoate, Ivermectin, Mebendazole (microtubule inhibitor), Praziquantel, Acyclovir, famciclovir, valacyclovir
infections. therapy Diethylcarbamazine. Helminths get PIMP’D.
Guanosine analogs. Monophosphorylated by HSV/VZV thymidine kinase and not phosphorylated
MECHANISM
ADVERSE EFFECTS Testosterone synthesis inhibition (gynecomastia, especially with ketoconazole), liver dysfunction in uninfected cells few adverse effects. Triphosphate formed by cellular enzymes. Preferentially
(inhibits cytochrome P-450). inhibit viral DNA polymerase by chain termination.
CLINICAL USE HSV and VZV. Weak activity against EBV. No activity against CMV. Used for HSV-
induced mucocutaneous and genital lesions as well as for encephalitis. Prophylaxis in
Terbinafine immunocompromised patients. No effect on latent forms of HSV and VZV. Valacyclovir, a
MECHANISM Inhibits the fungal enzyme squalene epoxidase. prodrug of acyclovir, has better oral bioavailability.
CLINICAL USE Dermatophytoses (especially onychomycosis—fungal infection of finger or toe nails). For herpes zoster, use famciclovir.
ADVERSE EFFECTS GI upset, headaches, hepatotoxicity, taste disturbance. ADVERSE EFFECTS Obstructive crystalline nephropathy and acute renal failure if not adequately hydrated.
MECHANISM OF RESISTANCE Mutated viral thymidine kinase.
MICROBIOLOGY `M̀ICROBIOLOGY—ANTIMICROBIALS SEC TION II 203 204 SEC TION II MICROBIOLOGY `M̀ICROBIOLOGY—ANTIMICROBIALS
HIV therapy Highly active antiretroviral therapy (HAART): often initiated at the time of HIV diagnosis. Interferons
Strongest indication for patients presenting with AIDS-defining illness, low CD4+ cell counts MECHANISM Glycoproteins normally synthesized by virus-infected cells, exhibiting a wide range of antiviral and
(< 500 cells/mm3), or high viral load. Regimen consists of 3 drugs to prevent resistance: antitumoral properties.
2 NRTIs and preferably an integrase inhibitor.
CLINICAL USE Chronic HBV and HVC, Kaposi sarcoma, hairy cell leukemia, condyloma acuminatum, renal cell
DRUG MECHANISM TOXICITY carcinoma, malignant melanoma, multiple sclerosis, chronic granulomatous disease.
NRTIs ADVERSE EFFECTS Flu-like symptoms, depression, neutropenia, myopathy.
Abacavir (ABC) Competitively inhibit nucleotide binding to Bone marrow suppression (can be reversed with
Didanosine (ddI) reverse transcriptase and terminate the DNA granulocyte colony-stimulating factor [G-CSF]
Emtricitabine (FTC) chain (lack a 3′ OH group). Tenofovir is a and erythropoietin), peripheral neuropathy, Hepatitis C therapy Chronic HCV infection is treated with different combinations of the following drugs; none is
Lamivudine (3TC) nucleoTide; the others are nucleosides. All lactic acidosis (nucleosides), anemia (ZDV), approved as monotherapy. Ribavirin also used to treat RSV (palivizumab preferred in children).
Stavudine (d4T) need to be phosphorylated to be active. pancreatitis (didanosine). DRUG MECHANISM ADVERSE EFFECTS
Tenofovir (TDF) ZDV can be used for general prophylaxis Abacavir contraindicated if patient has Ledipasvir Viral phosphoprotein (NS5A) inhibitor; NS5A
Zidovudine (ZDV, and during pregnancy to risk of fetal HLA-B*5701 mutation due to risk of plays important role in replication.
formerly AZT) transmission. hypersensitivity.
Ribavirin Inhibits synthesis of guanine nucleotides Hemolytic anemia, severe teratogen.
Have you dined (vudine) with my nuclear
by competitively inhibiting inosine
(nucleosides) family?
monophosphate dehydrogenase.
NNRTIs
Simeprevir HCV protease (NS3/4A); prevents viral Photosensitivity reactions, rash.
Delavirdine Bind to reverse transcriptase at site different Rash and hepatotoxicity are common to all replication.
Efavirenz from NRTIs. Do not require phosphorylation NNRTIs. Vivid dreams and CNS symptoms
Sofosbuvir Inhibits HCV RNA-dependent RNA polymerase Fatigue, headache, nausea.
Nevirapine to be active or compete with nucleotides. are common with efavirenz. Delavirdine and
(NS5B) acting as a chain terminator.
efavirenz are contraindicated in pregnancy.
Protease inhibitors
Atazanavir Assembly of virions depends on HIV-1 protease Hyperglycemia, GI intolerance (nausea, Disinfection and Goals include the reduction of pathogenic organism counts to safe levels (disinfection) and the
Darunavir (pol gene), which cleaves the polypeptide diarrhea), lipodystrophy (Cushing-like sterilization inactivation of all microbes including spores (sterilization).
Fosamprenavir products of HIV mRNA into their functional syndrome). Autoclave Pressurized steam at > 120°C. Sporicidal. May not reliably inactivate prions.
Indinavir parts. Thus, protease inhibitors prevent Nephropathy, hematuria, thrombocytopenia
Alcohols Denature proteins and disrupt cell membranes. Not sporicidal.
Lopinavir maturation of new viruses. (indinavir).
Ritonavir Ritonavir can “boost” other drug concentrations Rifampin (potent CYP/UGT inducer) reduces Chlorhexidine Denatures proteins and disrupts cell membranes. Not sporicidal.
Saquinavir by inhibiting cytochrome P-450. protease inhibitor concentrations; use rifabutin Chlorine Oxidizes and denatures proteins. Sporicidal.
Navir (never) tease a protease. instead. Hydrogen peroxide Free radical oxidation. Sporicidal.
Integrase inhibitors Iodine and iodophors Halogenation of DNA, RNA, and proteins. May be sporicidal.
Dolutegravir Inhibits HIV genome integration into host cell creatine kinase. Quaternary amines Impair permeability of cell membranes. Not sporicidal.
Elvitegravir chromosome by reversibly inhibiting HIV
Raltegravir integrase.
Fusion inhibitors Antimicrobials to ANTIMICROBIAL ADVERSE EFFECT
Enfuvirtide Binds gp41, inhibiting viral entry. Skin reaction at injection sites. avoid in pregnancy Sulfonamides Kernicterus
Enfuvirtide inhibits fusion. Aminoglycosides Ototoxicity
Maraviroc Binds CCR-5 on surface of T cells/monocytes, Maraviroc inhibits docking. Fluoroquinolones Cartilage damage
inhibiting interaction with gp120.
Clarithromycin Embryotoxic
Tetracyclines Discolored teeth, inhibition of bone growth
Ribavirin Teratogenic
Griseofulvin Teratogenic
Chloramphenicol Gray baby syndrome
SAFe Children Take Really Good Care.
FAS1_2018_03-Microbiology_indexed_121-204.indd 203 10/10/17 10:51 AM FAS1_2018_03-Microbiology_indexed_121-204.indd 204 10/10/17 10:51 AM

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124 SEC TION II MICROBIOLOGY

HIGH-YIELD PRINCIPLES IN MICROBIOLOGY—BASIC BACTERIOLOGY

magnesium phosphate) stones, particularly DNA. Parts of bacterial chromosomal DNA

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

MICROBIOLOGY `M̀ICROBIOLOGY—MYCOLOGY SEC TION II 151 152 SEC TION II MICROBIOLOGY

MICROBIOLOGY `M̀ICROBIOLOGY—PARASITOLOGY SEC TION II 159 160 SEC TION II MICROBIOLOGY

Nematodes (roundworms) Cestodes (tapeworms) Ectoparasites MICROBIOLOGY—VIROLOGY

MICROBIOLOGY `M̀ICROBIOLOGY—VIROLOGY SEC TION II 163 164 SEC TION II MICROBIOLOGY

MICROBIOLOGY `M̀ICROBIOLOGY—VIROLOGY SEC TION II 167 168 SEC TION II MICROBIOLOGY

MICROBIOLOGY `M̀ICROBIOLOGY—VIROLOGY SEC TION II 175 176 SEC TION II MICROBIOLOGY

integrase. 800 (men who have sex with men) or cervix

HIV RNA copies/mL

MICROBIOLOGY `M̀ICROBIOLOGY—SYSTEMS SEC TION II 179 180 SEC TION II MICROBIOLOGY

MICROBIOLOGY `M̀ICROBIOLOGY—SYSTEMS SEC TION II 183 184 SEC TION II MICROBIOLOGY

MICROBIOLOGY `M̀ICROBIOLOGY—ANTIMICROBIALS SEC TION II 191 192 SEC TION II MICROBIOLOGY

Chloramphenicol Pneumocystis jirovecii prophylaxis.

MICROBIOLOGY `M̀ICROBIOLOGY—ANTIMICROBIALS SEC TION II 195 196 SEC TION II MICROBIOLOGY

to possible damage to cartilage. Some may

prior rheumatic fever

mRNA mRNA SYNTHESIS

Exposure to syphilis Benzathine penicillin G

May cause tendonitis or tendon rupture in

MYCOLIC ACID Pyrazinamide

people > 60 years old and in patients taking SYNTHESIS

MICROBIOLOGY `M̀ICROBIOLOGY—ANTIMICROBIALS SEC TION II 199 200 SEC TION II MICROBIOLOGY

Amphotericin B Echinocandins Anidulafungin, caspofungin, micafungin. Antiviral therapy Ganciclovir

FAS1_2018_03-Microbiology_indexed_121-204.indd 203 10/10/17 10:51 AM FAS1_2018_03-Microbiology_indexed_121-204.indd 204 10/10/17 10:51 AM

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