SECTION II
Microbiology
“What lies behind us and what lies ahead of us are tiny matters
compared to what lives within us.”
––Oliver Wendell Holmes
This high-yield material covers the basic concepts of microbiology
and immunology. The emphasis in previous examinations has been High-Yield Clinical
Vignettes
approximately 40% bacteriology (20% basic, 20% quasi-clinical),
High-Yield Glossy
25% immunology, 25% virology (10% basic, 15% quasi-clinical), Material
5% parasitology, and 5% mycology. Learning the distinguishing High-Yield Topics
characteristics, target organs, and method of spread of—as well as Clinical Bacteriology
relevant laboratory tests for—major pathogens can improve your Bacteriology
score substantially. Mycology
Parasitology
Many students preparing for this part of the boards make the mistake Virology
of studying bacteriology very well without devoting sufficient time to Systems
the other topics. For this reason, learning immunology and virology Immunology
well is high yield. Learn the components and mechanistic details of
the immune response, including T cells, B cells, and the structure
and function of immunoglobulins. Also learn the major immunodefi-
ciency diseases (e.g., AIDS, agammaglobulinemia, DiGeorge’s syn-
drome). Knowledge of viral structures and genomes remains impor-
tant as well.
167
,MICROBIOLOGY—HIGH-YIELD CLINICAL VIGNETTES
These abstracted case vignettes are designed to demonstrate the thought processes necessary to
answer multistep clinical reasoning questions.
■ An alcoholic vomits gastric contents and develops foul-smelling sputum → what organisms are
most likely? → anaerobes.
■ Middle-age male presents with acute-onset monoarticular joint pain and bilateral Bell’s palsy →
what is the likely disease and how did he get it? → Lyme disease, Ixodes tick vector.
■ Patient with Mycoplasma pneumoniae exhibits cryoagglutinins during recovery phase → what
types of immunoglobulins are reacting? → IgM.
■ Urinalysis of patient shows WBC casts → what is the diagnosis? → pyelonephritis.
■ Young child presents with tetany and candidiasis. Hypocalcemia and immunosuppression are
found → what cell is deficient? → T-cell (DiGeorge’s).
■ Patient presents with rose gardener’s scenario (thorn prick with ulcers along lymphatic
drainage) → what is the infectious bug? → Sporothrix schenckii.
■ 25-year-old medical student from the Midwest has a burning feeling in his gut after meals.
Biopsy of gastric mucosa shows gram-negative rods → what is the likely organism? → H. pylori.
■ 32-year-old male has cauliflower lesions. Tissue biopsy shows broad-based budding yeasts
→ what is the likely organism? → Blastomyces.
■ Breast-feeding woman suddenly develops redness and swelling of her right breast. On examina-
tion, it is found to be a fluctuant mass → what is the diagnosis? → mastitis caused by S. aureus.
■ Young child has recurrent lung infections and granulomatous lesions → what is the defect in
neutrophils? → NADPH oxidase.
■ 20-year-old college student presents with lymphadenopathy, fever, and hepatosplenomegaly. His
serum agglutinates sheep red blood cells → what cell is infected? → B cell (EBV; infectious
mononucleosis).
■ One hour after eating custard at a picnic, a whole family began to vomit. After 10 hours, they
were all right → what is the organism? → S. aureus.
■ Infant becomes flaccid after eating honey → what gram-positive rod is implicated? → Clostrid-
ium botulinum → what is the mechanism of action? → inhibited release of acetylcholine.
■ Man with squamous cell carcinoma of penis had exposure to what virus? → HPV.
■ Patient develops endocarditis three weeks after receiving prosthetic heart valve → what organ-
ism is suspected? → S. aureus or S. epidermidis.
M I C R O B I O L O G Y — H I G H - Y I E L D G L O S S Y M AT E R I A L
1. Patient who visited Mexico presents with bloody diarrhea → what infectious form is found in
the stool? → erythrocyte-ingesting trophozoite → Entamoeba histolytica.
2. Glossy photograph of cardiac valve with cauliflower growth → diagnosis? → bacterial endo-
carditis.
3. Adolescent with cough and rusty sputum → what does Gram stain of sputum show? → gram-
positive diplococci (Streptococcus pneumoniae/pneumococci).
4. HIV-positive patient with CSF showing 75/mm3 lymphocytes suddenly dies. Picture of yeast
in meninges → diagnosis? → cryptococcal meningitis.
168
, MICROBIOLOGY—HIGH-YIELD TOPICS
Microbiology
1. Principles and interpretation of bacteriologic lab tests (culture, drug sensitivity, specific
growth requirements).
2. Dermatologic manifestations of bacterial and viral infections (e.g., syphilis, Rocky Mountain
spotted fever, meningococcemia, herpes zoster, coxsackievirus infection).
3. Common sexually transmitted diseases (e.g., syphilis, AIDS, HSV, gonorrhea, chlamydia).
4. Viral gastroenteritis in the pediatric and adult populations.
5. Common causes of community-acquired and nosocomial pneumonia.
6. Protozoa that frequently cause disease in the U.S. (e.g., Entamoeba histolytica, Giardia).
7. Parasites (protozoa, helminths) that cause disease more commonly outside the U.S. (e.g.,
malaria, Chagas’ disease, elephantiasis).
8. Herpes simplex encephalitis (temporal lobe lesion, mental status changes, treat with acy-
clovir).
9. Tests available for diagnosis of viral infections (e.g., plaque assay, PCR).
10. Microscopic appearance of organisms.
Immunology
1. Principles and interpretation of immunologic tests (e.g., ELISA, complement-fixation tests,
direct and indirect Coombs’ test).
2. Immune complex diseases (e.g., post strep glomerulonephritis, systemic lupus erythematosus,
serum sickness).
3. Genetics of immunoglobulin variety and specificity (class switching, VDJ recombination,
affinity maturation).
4. Mechanisms of antigenic variation and immune system evasion employed by bacteria, fungi,
protozoa, and viruses.
5. How different types of immune deficiencies lead to different susceptibilities to infection (e.g.,
T-cell defects and viral/fungal infection; splenectomy and encapsulated organisms).
6. MHC/HLA serotypes: transplant compatibility, disease associations, familial inheritance.
7. Allergies: common antigens, antigen-IgE-mast cell complex, presumed mechanism of
immunotherapy (blocking antibodies).
8. Granulomas: role of macrophages, foreign body versus immune granulomas, caseating (TB)
versus noncaseating (sarcoid) granulomas, common causes (e.g., TB, sarcoid, fungi).
9. Components of vaccines and how they produce immunity.
10. Characteristics and functions of macrophages and NK (natural killer) cells.
169
, MICROBIOLOGY—CLINICAL BACTERIOLOGY
Bacterial structures
Structure Function Chemical composition
Peptidoglycan Gives rigid support, protects against osmotic pressure Sugar backbone with cross-
linked peptide side chains
Cell wall/cell mem- Major surface antigen Teichoic acid induces TNF
brane (gram and IL-1
positives)
Outer membrane Site of endotoxin (lipopolysaccharide); Lipid A induces TNF and IL-1;
(gram negatives) major surface antigen polysaccharide is the antigen
Plasma membrane Site of oxidative and transport enzymes Lipoprotein bilayer
Ribosome Protein synthesis RNA and protein in 50S and
30S subunits
Periplasm Space between the cytoplasmic membrane and outer Contains many hydrolytic
membrane in gram-negative bacteria enzymes, including
β-lactamases
Capsule Protects against phagocytosis Polysaccharide (except
Bacillus anthracis, which
contains D-glutamate)
Pilus/fimbria Mediates adherence of bacteria to cell surface; sex pilus Glycoprotein
forms attachment between 2 bacteria during
conjugation
Flagellum Motility Protein
Spore Provides resistance to dehydration, heat, and Keratin-like coat;
chemicals dipicolinic acid
Plasmid Contains a variety of genes for antibiotic resistance, DNA
enzymes, and toxins
Glycocalyx Mediates adherence to surfaces, especially foreign Polysaccharide
surfaces (e.g., indwelling catheters)
Cell walls
Unique to Common to both Unique to
gram-positive gram-negative
organisms organisms
Flagellum
;;;; ;;;
Pilus
;;;; ;;;
Teichoic
acid
Capsule
Endotoxin/LPS
Peptidoglycan
;;;;;;;;;;;;;;;;;;
;;;;;;;;;;;;;;;;;; Cytoplasmic ;;;;;;;;;;;;;;;;;;
;;;;;;;;;;;;;;;;;;
;;;;;;;;;;;;;;;;;;
;;;;;;;;;;;;;;;;;; membrane ;;;;;;;;;;;;;;;;;;
;;;;;;;;;;;;;;;;;;
Gram positive Gram negative
170
Microbiology
“What lies behind us and what lies ahead of us are tiny matters
compared to what lives within us.”
––Oliver Wendell Holmes
This high-yield material covers the basic concepts of microbiology
and immunology. The emphasis in previous examinations has been High-Yield Clinical
Vignettes
approximately 40% bacteriology (20% basic, 20% quasi-clinical),
High-Yield Glossy
25% immunology, 25% virology (10% basic, 15% quasi-clinical), Material
5% parasitology, and 5% mycology. Learning the distinguishing High-Yield Topics
characteristics, target organs, and method of spread of—as well as Clinical Bacteriology
relevant laboratory tests for—major pathogens can improve your Bacteriology
score substantially. Mycology
Parasitology
Many students preparing for this part of the boards make the mistake Virology
of studying bacteriology very well without devoting sufficient time to Systems
the other topics. For this reason, learning immunology and virology Immunology
well is high yield. Learn the components and mechanistic details of
the immune response, including T cells, B cells, and the structure
and function of immunoglobulins. Also learn the major immunodefi-
ciency diseases (e.g., AIDS, agammaglobulinemia, DiGeorge’s syn-
drome). Knowledge of viral structures and genomes remains impor-
tant as well.
167
,MICROBIOLOGY—HIGH-YIELD CLINICAL VIGNETTES
These abstracted case vignettes are designed to demonstrate the thought processes necessary to
answer multistep clinical reasoning questions.
■ An alcoholic vomits gastric contents and develops foul-smelling sputum → what organisms are
most likely? → anaerobes.
■ Middle-age male presents with acute-onset monoarticular joint pain and bilateral Bell’s palsy →
what is the likely disease and how did he get it? → Lyme disease, Ixodes tick vector.
■ Patient with Mycoplasma pneumoniae exhibits cryoagglutinins during recovery phase → what
types of immunoglobulins are reacting? → IgM.
■ Urinalysis of patient shows WBC casts → what is the diagnosis? → pyelonephritis.
■ Young child presents with tetany and candidiasis. Hypocalcemia and immunosuppression are
found → what cell is deficient? → T-cell (DiGeorge’s).
■ Patient presents with rose gardener’s scenario (thorn prick with ulcers along lymphatic
drainage) → what is the infectious bug? → Sporothrix schenckii.
■ 25-year-old medical student from the Midwest has a burning feeling in his gut after meals.
Biopsy of gastric mucosa shows gram-negative rods → what is the likely organism? → H. pylori.
■ 32-year-old male has cauliflower lesions. Tissue biopsy shows broad-based budding yeasts
→ what is the likely organism? → Blastomyces.
■ Breast-feeding woman suddenly develops redness and swelling of her right breast. On examina-
tion, it is found to be a fluctuant mass → what is the diagnosis? → mastitis caused by S. aureus.
■ Young child has recurrent lung infections and granulomatous lesions → what is the defect in
neutrophils? → NADPH oxidase.
■ 20-year-old college student presents with lymphadenopathy, fever, and hepatosplenomegaly. His
serum agglutinates sheep red blood cells → what cell is infected? → B cell (EBV; infectious
mononucleosis).
■ One hour after eating custard at a picnic, a whole family began to vomit. After 10 hours, they
were all right → what is the organism? → S. aureus.
■ Infant becomes flaccid after eating honey → what gram-positive rod is implicated? → Clostrid-
ium botulinum → what is the mechanism of action? → inhibited release of acetylcholine.
■ Man with squamous cell carcinoma of penis had exposure to what virus? → HPV.
■ Patient develops endocarditis three weeks after receiving prosthetic heart valve → what organ-
ism is suspected? → S. aureus or S. epidermidis.
M I C R O B I O L O G Y — H I G H - Y I E L D G L O S S Y M AT E R I A L
1. Patient who visited Mexico presents with bloody diarrhea → what infectious form is found in
the stool? → erythrocyte-ingesting trophozoite → Entamoeba histolytica.
2. Glossy photograph of cardiac valve with cauliflower growth → diagnosis? → bacterial endo-
carditis.
3. Adolescent with cough and rusty sputum → what does Gram stain of sputum show? → gram-
positive diplococci (Streptococcus pneumoniae/pneumococci).
4. HIV-positive patient with CSF showing 75/mm3 lymphocytes suddenly dies. Picture of yeast
in meninges → diagnosis? → cryptococcal meningitis.
168
, MICROBIOLOGY—HIGH-YIELD TOPICS
Microbiology
1. Principles and interpretation of bacteriologic lab tests (culture, drug sensitivity, specific
growth requirements).
2. Dermatologic manifestations of bacterial and viral infections (e.g., syphilis, Rocky Mountain
spotted fever, meningococcemia, herpes zoster, coxsackievirus infection).
3. Common sexually transmitted diseases (e.g., syphilis, AIDS, HSV, gonorrhea, chlamydia).
4. Viral gastroenteritis in the pediatric and adult populations.
5. Common causes of community-acquired and nosocomial pneumonia.
6. Protozoa that frequently cause disease in the U.S. (e.g., Entamoeba histolytica, Giardia).
7. Parasites (protozoa, helminths) that cause disease more commonly outside the U.S. (e.g.,
malaria, Chagas’ disease, elephantiasis).
8. Herpes simplex encephalitis (temporal lobe lesion, mental status changes, treat with acy-
clovir).
9. Tests available for diagnosis of viral infections (e.g., plaque assay, PCR).
10. Microscopic appearance of organisms.
Immunology
1. Principles and interpretation of immunologic tests (e.g., ELISA, complement-fixation tests,
direct and indirect Coombs’ test).
2. Immune complex diseases (e.g., post strep glomerulonephritis, systemic lupus erythematosus,
serum sickness).
3. Genetics of immunoglobulin variety and specificity (class switching, VDJ recombination,
affinity maturation).
4. Mechanisms of antigenic variation and immune system evasion employed by bacteria, fungi,
protozoa, and viruses.
5. How different types of immune deficiencies lead to different susceptibilities to infection (e.g.,
T-cell defects and viral/fungal infection; splenectomy and encapsulated organisms).
6. MHC/HLA serotypes: transplant compatibility, disease associations, familial inheritance.
7. Allergies: common antigens, antigen-IgE-mast cell complex, presumed mechanism of
immunotherapy (blocking antibodies).
8. Granulomas: role of macrophages, foreign body versus immune granulomas, caseating (TB)
versus noncaseating (sarcoid) granulomas, common causes (e.g., TB, sarcoid, fungi).
9. Components of vaccines and how they produce immunity.
10. Characteristics and functions of macrophages and NK (natural killer) cells.
169
, MICROBIOLOGY—CLINICAL BACTERIOLOGY
Bacterial structures
Structure Function Chemical composition
Peptidoglycan Gives rigid support, protects against osmotic pressure Sugar backbone with cross-
linked peptide side chains
Cell wall/cell mem- Major surface antigen Teichoic acid induces TNF
brane (gram and IL-1
positives)
Outer membrane Site of endotoxin (lipopolysaccharide); Lipid A induces TNF and IL-1;
(gram negatives) major surface antigen polysaccharide is the antigen
Plasma membrane Site of oxidative and transport enzymes Lipoprotein bilayer
Ribosome Protein synthesis RNA and protein in 50S and
30S subunits
Periplasm Space between the cytoplasmic membrane and outer Contains many hydrolytic
membrane in gram-negative bacteria enzymes, including
β-lactamases
Capsule Protects against phagocytosis Polysaccharide (except
Bacillus anthracis, which
contains D-glutamate)
Pilus/fimbria Mediates adherence of bacteria to cell surface; sex pilus Glycoprotein
forms attachment between 2 bacteria during
conjugation
Flagellum Motility Protein
Spore Provides resistance to dehydration, heat, and Keratin-like coat;
chemicals dipicolinic acid
Plasmid Contains a variety of genes for antibiotic resistance, DNA
enzymes, and toxins
Glycocalyx Mediates adherence to surfaces, especially foreign Polysaccharide
surfaces (e.g., indwelling catheters)
Cell walls
Unique to Common to both Unique to
gram-positive gram-negative
organisms organisms
Flagellum
;;;; ;;;
Pilus
;;;; ;;;
Teichoic
acid
Capsule
Endotoxin/LPS
Peptidoglycan
;;;;;;;;;;;;;;;;;;
;;;;;;;;;;;;;;;;;; Cytoplasmic ;;;;;;;;;;;;;;;;;;
;;;;;;;;;;;;;;;;;;
;;;;;;;;;;;;;;;;;;
;;;;;;;;;;;;;;;;;; membrane ;;;;;;;;;;;;;;;;;;
;;;;;;;;;;;;;;;;;;
Gram positive Gram negative
170
