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Clinical Microbiology Objectives
Specimen Processing
1. Describe selective and differential media.
2. Discuss the purpose of the following media and indicate whether it is nutritive,
selective, differential, or a combination:
a. Sheep blood agar
b. MacConkey agar
c. Chocolate agar
d. Hektoen agar
e. CDC anaerobic blood agar
f. Columbia colistin-nalidixic acid (CNA) agar
g. Phenyl-ethyl alcohol (PEA) agar
h. Eosin methylene blue (EMB) agar
i. Thayer-Martin agar
j. Campy blood agar
k. Gram-negative (GN) broth
l. Thioglycolate broth
m. Cefsulodin-irgasan-novobiocin (CIN) agar
n. Cycloserine-cefoxitin-fructose-egg yolk (CCFA) agar
o. LKV
p. Bismuth sulfite
3. Name the medium (or media) and growth conditions recommended for recovery of
the following organisms:
a. Corynebacterium diphtheriae
b. Francisella tularensis
c. Brucella species
d. Bordetella pertussis
e. Legionella species
f. Vibrio species
g. Leptospira interrogans
h. Campylobacter jejuni
4. Discuss the rationale for screening sputum specimens and describe the procedure for doing
the screen.
5. Explain why stool specimens for routine culture and ova & parasite examination
from patients who have been hospitalized for >3 days are rejected.
6. Discuss the sensitivity and specificity of the antigen tests for direct detection of
group A streptococcus in throat swab specimens.
Bacteriology
1. Describe the principles of the commercial automated blood culture systems.
a. Discuss advantages and disadvantages.
2. Describe disk diffusion, Etest and microdilution methods for susceptibility
testing of aerobic and facultative bacteria. Discuss the advantages and limitations of
each. Describe the -lactamase test and indicate when it should be performed.
3. Discuss the special circumstances (i.e., media, incubation period) recommended for
susceptibility testing of:
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a. Haemophilus influenzae
b. Streptococcus pneumoniae
c. Neisseria gonorrhoeae
d. Anaerobes
e. Enterococci
f. Staphylococci
Describe the conditions recommended for detection of oxacillin-resistant staphylococci
when using disk diffusion and broth microdilution.
Name the gene responsible to oxacillin resistance in staphylococci.
Describe how the D test is performed, how it is interpreted, and when it should be done.
List the antimicrobials that CLSI (formerly NCCLS) recommends for routine testing and
reporting for:
a. Enterobacteriaceae
b. Pseudomonas & Acinetobacter
c. Staphylococci
d. Enterococci
e. Viridans streptococci
f. Haemophilus
g. Stenotrophomonas maltophilia
h. Streptococcus pneumoniae
i. Salmonella
Explain extended-spectrum -lactamases (ESBLs). Indicate when testing for ESBLs
should be performed. Describe CLSI recommendations for ESBL testing.
For Mycoplasma pneumoniae:
a. Describe the usual clinical presentation of disease.
b. Discuss available methods for laboratory diagnosis, including the advantages &
disadvantages of each.
List the medically important genera of Gram-positive cocci.
Name the test that will differentiate staphylococci from streptococci; give the
expected reaction for each genus.
Name the conventional (enzymatic) test that will differentiate Staphylococcus aureus from
almost all other staphylococci that infect humans. Describe 2 ways in which that test
can be performed.
Describe the clinical manifestations and pathogenesis of the following diseases
caused by S. aureus:
a. Scalded skin syndrome
b. Gastroenteritis
c. Toxic shock syndrome
Describe the usual clinical manifestations of infection with Staphylococcus
epidermidis and Staphylococcus saprophyticus.
Describe colonies of S. aureus and coagulase negative staphylococci on blood agar.
Name the test that commonly is used to differentiate S. saprophyticus from other
coagulase negative staphylococci. Give the expected reaction for S. saprophyticus.
Discuss the need to identify coagulase negative staphylococci to the species level.
Discuss the limitations of the commercially available methods by which this can be
done.
Describe colonies of the following organisms on sheep blood agar and name the
presumptive (if appropriate) and definitive tests that will provide an identification of:
a. Groups A, B, C, G strep
b. S. pneumoniae
c. Enterococci
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d. Viridans strep
e. S. bovis
Discuss the epidemiology, clinical manifestations, pathogenesis, and laboratory
diagnosis of the following diseases caused by group A strep:
a. Pharyngitis
b. Impetigo
c. Scarlet fever
d. Acute rheumatic fever
e. Acute glomerulonephritis
Discuss the most common diseases caused by groups B, C, and G strep.
Describe the clinical importance of isolation of Streptococcus bovis from blood (i.e..
what disease should the clinician suspect and evaluate the patient for?).
List the Gram-positive cocci that are intrinsically vancomycin-resistant.
Discuss methods for prevention of acute rheumatic fever and invasive
pneumococcal disease.
Describe colonies of Bacillus species on sheep blood agar. Describe how to differentiate
B. anthracis from other Bacillus spp.
Discuss the epidemiology, clinical manifestations, and laboratory diagnosis of
listeriosis.
Explain why identification of Corynebacterium jeikeium is important.
Discuss the laboratory diagnosis of diphtheria.
Discuss the epidemiology, clinical manifestations, laboratory diagnosis, and
susceptibility testing of nocardiosis.
Describe the clinical manifestations of disease caused by Neisseria gonorrhoeae,
Neisseria meningitidis and Moraxella catarrhalis. Discuss the laboratory diagnosis of
these infections.
Describe the appearance of the following organisms on the named medium:
a. Pseudomonas aeruginosa - sheep blood, MacConkey, Mueller Hinton
b. Proteus - sheep blood agar
c. Escherichia coli - MacConkey
d. Klebsiella pneumoniae - MacConkey
e. Serratia marcescens - sheep blood agar
List the characteristics of the Enterobacteriaceae that differentiate them from other
families of bacteria.
Name the reaction for lactose, H 2 S, and indole for each of the following:
a. Escherichia coli
b. Proteus mirabilis
c. Proteus vulgaris
d. Salmonella species
e. Shigella species
f. Klebsiella pneumoniae
g. Klebsiella oxytoca
h. Citrobacter freundii
Explain the reactions that occur in Kligler's iron agar (KIA). Describe the KIA
reactions expected with organisms a, d, e, and f listed in # 32 above and with P.
aeruginosa.
Name the 2 genera of Enterobacteriaceae that are nonmotile.
Name the genus that is motile & VP positive at 25°C but nonmotile & VP negative at
37°C.
Describe the epidemiology, pathogenesis, and laboratory diagnosis of
Shiga-like-toxin producing E. coli.
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37. Discuss the epidemiology and treatment of gastroenteritis caused by Salmonella,
Shigella, Campylobacter jejuni, and Yersinia enterocolitica.
38. Discuss the clinical manifestations of the most common infections caused by
Proteus, Klebsiella pneumoniae, Enterobacter species, and Serratia marcescens.
39. Discuss the epidemiology and clinical manifestations of the most common
infections caused by Pseudomonas aeruginosa and Burkholderia cepacia.
40. Define "nonfermenter." Name the most common nonfermenters encountered in the
clinical microbiology laboratory.
41. Name the etiologic agent(s) and discuss the epidemiology, clinical manifestations,
and laboratory diagnosis of:
a. Tularemia
b. Brucellosis
c. Pertussis
d. Legionnaires' disease
42. Describe cells of Campylobacter in a Gram-stained smear.
43. Name the tests used (and the reactions expected) to identify Campylobacter
jejuni/coli.
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44. Discuss the epidemiology, pathogenesis, and clinical manifestations of cholera.
45. For Vibrio cholerae, describe:
a. Gram stain appearance of cells
b. Appearance of colonies on sheep blood agar
c. Oxidase reaction
d. Glucose fermentation (+ or-)
46. Describe the epidemiology and clinical manifestations or disease caused by Vibrio
vulnificus.
47. Discuss the epidemiology, clinical manifestations, and laboratory diagnosis of
infections caused by Aeromonas species.
48. Discuss the epidemiology, pathogenesis, and clinical manifestations of infections caused by
Haemophilus influenzae.
49. Name the growth requirements for H. influenzae.
50. Describe the typical appearance of cells of H. influenzae in a Gram-stained smear.
51. Explain the -aminolevulinic acid (ALA)-porphyrin test. What is the expected
reaction for H. influenzae?
52. Discuss the epidemiology, clinical manifestations, laboratory diagnosis, and
treatment of infections caused by Pasteurella multocida.
53. Describe the clinical manifestations and laboratory diagnosis of infections caused
by Helicobacter pylori.
54. Discuss the epidemiology, pathogenesis, clinical manifestations, and laboratory
diagnosis of botulism, tetanus, and Clostridium difficile-associated disease.
55. Describe colonies of C. perfringens on blood agar.
56. Describe what you would expect to see in a Gram-stained smear of exudate from a
case of myonecrosis caused by C. perfringens.
57. Colonies grow on media incubated anaerobically. Describe how you would
determine if the isolate is a true anaerobe.
58. Describe different ways in which an anaerobic atmosphere for culture of clinical
specimens can be created.
59. Discuss the epidemiology, pathology, clinical manifestations, laboratory diagnosis,
and treatment of actinomycosis.
60. Describe the typical appearance in Gram-stained smears of cells of Bacteroides
species, Porphyromonas species, Prevotella species, and Fusobacterium species.
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61. Name the types of specimens in which anaerobes should be suspected and those
that are unacceptable for anaerobic culture. Describe the most optimal specimens
and transport methods.
62. If you were the microbiology laboratory director, what tests would you institute for
identification of anaerobes?
63. Describe colonies of Porphyromonas and some Prevotella on blood agar, especially
laked blood agar.
64. Name the antimicrobial agents that are effective against virtually all Bacteroides
species. Explain why penicillin G is no longer the agent of choice for treatment of
aspiration pneumonia.
65. List the bacteria that usually are considered contaminants when recovered from
blood cultures. These organisms, however, may be true pathogens in some
patients. Name the criteria that are used to suggest that one of these organisms is
likely to be a pathogen rather than a contaminant.
66. Discuss the epidemiology, clinical manifestations, and laboratory diagnosis of:
a. Syphilis
b. Lyme disease
c. Leptospirosis
67. Discuss the epidemiology, clinical manifestations, and laboratory diagnosis of:
a. Rocky Mountain spotted fever
b. Q fever
c. Human ehrlichiosis in the US
d. Infection caused by Bartonella henselae
68. Describe the clinical manifestations, usual etiologic agents, and laboratory diagnosis
of bacterial vaginosis.
Mycobacteria
1. Discuss the epidemiology of tuberculosis in the US, including:
a. Transmission
b. Incidence
c. Risk groups
2. Describe the pathogenesis, pathology, and clinical manifestations of infection with
M. tuberculosis.
3. List the human pathogens in the M. tuberculosis complex (MTBC).
4. Explain why the term "atypical mycobacteria" is not recommended for
mycobacteria other than MTBC. What names are preferred?
5. Indicate what specimens should be collected for diagnosis of tuberculosis.
Describe how those specimens should be handled in the clinical laboratory.
6. Describe how mycobacteria often appear in Gram-stain smears.
7. List the stains used to detect mycobacteria in smears from clinical specimens. Name the one
that is currently recommended by the CDC and indicate why.
8. Describe the methods currently available for culture of mycobacteria and the
advantages and disadvantages of each. Indicate the culture method currently
recommended by the CDC and the time period in which growth of AFB should be
recognized.
9. Describe the methods currently available for identification of mycobacteria and the
advantages and disadvantages (or limitations) of each. Indicate the methods
currently recommended by the CDC and the time period in which detection and
identification of MTBC should be reported (from specimen receipt).
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10. Describe the methods currently available for susceptibility testing of MTBC and the
advantages and disadvantages of each. Indicate which method is recommended by
the CDC and the time period in which results should be reported (from specimen
receipt).
11. Discuss the epidemiology, pathology, and clinical manifestations of the following
nontuberculous mycobacteria:
a. Mycobacterium avium complex
b. Mycobacterium kansasii
c. Mycobacterium fortuitum group
d. Mycobacterium chelonae
e. Mycobacterium abscessus
f. Mycobacterium marinum
g. Mycobacterium haemophilum
h. Mycobacterium genavense
i. Mycobacterium gordonae
12. Describe the growth requirements of M. haemophilum.
13. Define each of the following terms as described by Runyoun:
a. Photochromogen
b. Nonphotochromogen
c. Scotochromogen
d. Rapid grower
14. Classify each of the mycobacteria listed in #11 above in one of the Runyoun groups.
15. Name the most common mycobacterial "contaminant" and the Runyoun group in
which it belongs.
16. Give the niacin, nitrate, and catalase reactions expected for MTBC.
17. Name the tests that will best differentiate M. tuberculosis from M. bovis.
Fungi
1. Describe "stains" used for direct detection of fungi in clinical specimens.
2. Describe the media recommended for culture of fungi from clinical specimens and
the blood culture system recommended for optimal detection of fungemia
(especially with moulds such as Histoplasma capsulatum).
3. Discuss the culture conditions (temperature, duration) recommended for recovery of
fungi from clinical specimens.
4. Name 2 methods for rapid diagnosis of cryptococcal meningitis. Indicate the
sensitivity & specificity of each.
5. Describe the germ tube test and indicate its purpose.
6. Discuss the epidemiology and clinical manifestations of candidiasis, and describe
the pathology of invasive disease.
7. Describe the appearance of the following Candida species on Chrom agar: C. albicans, C.
dubliniensis, C. krusei, C. tropicalis
8. Discuss the epidemiology, pathogenesis, pathology, and clinical manifestations of
cryptococcosis.
9. Name the stain often used to differentiate Cryptococcus neoformans from other
yeasts and the expected results. Name the yeast other than C. neoformans that also
will stain positively.
10. Discuss methods for identification of yeasts used in the clinical laboratory.
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11. Define thermal dimorphic fungus and list them. For each of these, indicate the
areas of endemicity in the US and the mechanism in which humans acquire
infection.
12. Describe the tissue pathology, colony morphology, and microscopic appearance
(scotch tape preparation or slide culture) of colonies on agar media for:
a. Histoplasma capsulatum
b. Blastomyces dermatitidis
c. Coccidioides immitis
d. Sprorthrix schenckii
e. Aspergillus fumigatus
f. Aspergillus niger
g. Aspergillus flavus
h. Fusarium species
i. Pseudalleschena boydii
13. Indicate how the above organisms are identified in the laboratory.
14. Name the serologic test useful for rapid diagnosis of invasive aspergillosis. Name the
antimicrobial agent most commonly responsible for a false-positive result.
15. List the zygomycetes commonly encountered in the clinical laboratory.
16. Discuss the epidemiology, clinical manifestations, pathology, and laboratory
diagnosis (colony morphology and microscopic appearance) of infection caused by
the zygomycetes.
17. Name the 3 sites of dermatophyte infection.
18. List the 3 genera of dermatophytes. Indicate the sites (hair, skin, nails) that each of
the genera infect.
19. Discuss the clinical manifestations of the dermatophytoses.
20. Describe the colony morphology and microscopic appearance of cultures of:
a. Microsporum canis
b. Trichophyton mentagrophytes
c. Trichophyton rubrum
21. Name the drugs commonly used to treat fungal infections. Indicate when
susceptibility testing of fungi might be useful.
22. Discuss the etiology, epidemiology, clinical manifestations, and tissue pathology of
chromoblastomycosis and phaeohyphomycosis.
Parasitology
1. Discuss the epidemiology, clinical manifestations, pathology (tissue), and laboratory
diagnosis (in the microbiology laboratory) of infection caused by:
a. Giardia lamblia
b. Entamoeba histolytica
c. Cryptosporidium
d. Microsporidia
2. Describe the life cycle and laboratory diagnosis of:
a. Trichuris trichiura
b. Hookworms
c. Ascaris lumbricoides
d. Strongyloides stercoralis
e. Fasciolopsis buski
f. Taenia saginata (Taeniarhynchus saginatus)
g. Taenia solium (including cysticercosis)
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h. Diphyllobothrium
i. Enterobius vermicularis
j. Dirofilaria immitis
Discuss the epidemiology (including geography, transmission [vector], life cycle of
the etiologic agent, etc), clinical manifestations, pathology, and laboratory diagnosis
of:
a. Cutaneous leishmaniasis
b. Visceral leishmaniasis
c. Chagas' disease
Describe the epidemiology, pathology, clinical manifestations, and laboratory
diagnosis of infection with the free-living amebae (Naegleria fowleri &
Acanthamoeba).
Discuss the life cycle, epidemiology, pathology, clinical manifestations (in
congenital disease and immune competent and immunocompromised hosts),
laboratory diagnosis, treatment, and prevention of infection with Toxoplasma
gondii.
Name the species of Plasmodium and recognize each in a peripheral blood smear.
Describe the epidemiology (including life cycle, transmission, geography, etc),
clinical manifestations, laboratory diagnosis, and treatment of malaria.
Describe the clinical manifestations and laboratory diagnosis (name the appropriate
specimens and stains and be able to interpret the latter) of Pneumocyctis jirovecii infection.
Discuss the epidemiology (including life cycle of the etiologic agent, transmission,
geography, etc), clinical manifestations, and laboratory diagnosis of infection caused
by schistosomes.
Chlamydia
1. Describe the 2 morphologically distinct forms of chlamydiae.
2. Name the 3 species of Chlamydia and discuss the epidemiology, clinical
manifestations, and laboratory diagnosis of infection with each of the agents.
3. For C. trachomatis, discuss specimen collection and transport, and explain the
advantages and disadvantages of the different laboratory tests for its detection.
4. Explain how the chlamydiae differ from other bacteria such as E. coli.
Virology
1. Discuss the epidemiology (including transmission, seasonality [if applicable], typical
age group affected, etc), clinical manifestations, and laboratory diagnosis (includ ing
specimen collection, tests commercially available, and the advantages &
disadvantages of those tests) of infection with the following viruses:
a. Herpes simplex virus (HSV)
b. Varicella zoster virus (VZV)
c. Cytomegalovirus (CMV)
d. Epstein-Barr virus (EBV)
e. Human herpesvirus 6 (HHV 6)
f. Adenovirus
g. JC virus
h. Parvovirus B19
i. Hepatitis A, B, C, D, E, & G viruses
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Parainfluenza viruses
Mumps virus
Measles virus
Respiratory syncytial virus (RSV)
Human metapneumovirus
Influenza viruses
Enteroviruses
Rotavirus
Rubella virus
Encephalitis viruses (West Nile virus, St. Louis, California, La Crosse, eastern &
western equine)
t. Human immunodeficiency virus (HIV)
u. Human T-cell leukemia virus types I & II
v. Norwalk virus
w. Hantavirus (in the US)
x. SARS-associated coronavirus
For each of the viruses listed above (a-x), indicate whether it is a DNA or an RNA
virus.
Describe the cellular changes (cytopathic effect observed in tissues or stained
smears of cells) associated with HSV, VZV, CMV, adenovirus, papillomaviruses, JC
virus, measles virus, rabies virus.
Name the antiviral agent(s) effective against:
a. HSV
b. VZV
c. CMV
d. RSV
e. Influenza viruses
f. HIV
Discuss recommendations for prevention of infection with the following viruses:
a. Influenza viruses
b. CMV (in seronegative immunocompromised patients, such as organ transplant
recipients or neonates)
c. Measles
d. Mumps
e. Rubella
f. HIV
Describe isolation precautions necessary for hospitalized patients infected with:
a. RSV
b. Influenza
c. HIV
d. VZV
e. Parvovirus B19
Explain latency and list viruses that can become latent.
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