Learning Objectives and Study Guide
Fundamentals II Bacteriology
The overall goals of the Bacteriology Component of the Fundamentals II Course are to acquaint
students with major bacterial agents of human diseases, their general characteristics,
physiology, genetics, classification, virulence mechanisms, disease spectrum, epidemiology,
transmissibility, clinical manifestations, methods for laboratory diagnosis, and how antimicrobial
resistance develops. Achievement of the stated goals will occur through dissemination of
information in lecture format, through assigned readings in the textbook, and in the 2 hands-on
laboratory sessions. This course is limited to the study of selected major bacterial agents that
cause human disease in the United States and those which may be of concern because of
bioterrorism.This is not a comprehensive course encompassing all human bacterial pathogens.
Study should be focused only on the microorganisms that are emphasized in the lectures,
power point presentations, laboratory sessions, as outlined in the written learning objectives.
Specific Bacteriology Learning Objectives
(referenced to Murray’s textbook, 6th edition where relevant)
1. Bacterial Structure, Physiology, Classification, & Genetics
Chapters 2, 3; Lab Manual
A. Compare and contrast the properties of eukaryotes vs. prokaryotes.
B. Compare and contrast cell wall components in gram-positive vs. gram-negative bacteria.
C. Understand structure and function of each bacterial major ultrastructural component:
chromosome, plasmid, ribosome, inner (cytoplasmic) membrane, outer membrane,
mesosome, teichoic acid, peptidoglycan, lipopolysaccharide, capsule, pili, flagella,
endospores.
D. Describe the procedure for Gram-stain and explain the purpose of each reagent.
E. Explain the structural differences of the mycobacterial cell wall from other bacteria that
cause it to be “acidfast.
F. Explain the process by which peptidoglycan is synthesized.
G. Explain the process and purpose of spore formation and name the two main genera of
bacterial pathogens that produce spores.
H. Describe how mycoplasmas are unique from other bacteria and how these differences
are responsible for their morphology and life cycle.
I.
Explain how the presence of a capsule is important as a bacterial virulence factor and
provide examples of clinically important bacteria that are encapsulated.
J. Understand the processes of DNA replication, mRNA transcription and translation and
the steps involved in each.
K. Describe the events that occur in each phase of bacterial growth.
L.
Explain the difference between oxidation and fermentation and give examples of
bacteria which are “fermenters”, “oxidizers” or “asaccharolytics”.
M. Explain the importance of determining genetic relatedness of bacteria in epidemiology
and infection control.
N. Explain the differences, advantages, and disadvantages among phenotypic, analytic,
and genotypic classification of bacteria and provide examples of each approach.
O. Explain the specific advantages and reasons that characterization of rRNA is a useful
means for determining genetic relatedness of bacteria.
P. Describe differences between the bacterial and human genomes, including size,
composition, arrangement, presence of extrachromosomal elements, numbers of
chromosomes.
Q. Explain these mechanisms of transfer of genetic information between bacterial cells:
transduction, transformation, transposition, and plasmid conjugation.
2. Bacterial Pathogenesis
Chapters 7, 18, 47
A. Explain the differences between microbial colonization and infection and give examples
of each process.
B. Understand the differences between strict pathogens and opportunistic pathogens; be
able to give specific examples of each and describe host conditions that are favorable
for opportunistic infection
C. Describe which anatomic locations in the human body contain normal flora versus those
locations which are normally sterile and the major types of bacteria that comprise the
normal flora in each of these sites.
D. Describe the beneficial roles of normal flora in the host-microorganism ecological
relationship.
E. Explain how prolonged hospitalization or antibiotic therapy can affect the composition of
normal flora.
F. Describe the clinical manifestations of endotoxin shock and mechanisms responsible for
these manifestations.
G. Describe the similarities and differences between exotoxins and endotoxins, including
structure, mechanism of action, targets, and sources.
H. Describe 3 mechanisms by which exotoxins work and provide examples of bacterial
diseases that are caused by each of them.
I.
Explain how bacteria can circumvent destruction by the host immune system in order to
effectively colonize humans and produce disease.
J. Describe 3 mechanisms by which certain bacteria can circumvent phagocytic killing after
ingestion by host phagocytes and provide an example of a bacterial species that utilizes
each mechanism.
K. Explain the differences between active and passive immunization.
L. Explain why a polyvalent polysaccharide-conjugate vaccine is used to immunize infants
against invasive pneumococcal disease whereas a polyvalent vaccine alone is used in
adults at risk for invasive pneumococcal disease.
M. Describe the different mechanisms by which host resistance to infection by extracellular
bacteria versus intracellular bacteria occurs.
3. Anaerobic Bacteria
Chapters 39, 40, 41
A. Describe 2 enzyme systems that are lacking in strict anaerobes and why the lack of
these enzymes renders oxygen toxic to them
B. Describe the anatomic sites where anaerobes are normal flora.
C. Learn clinical characteristics, responsible organism(s), and mechanisms of disease for
these conditions caused as described in the lecture and assigned reading:
 Periodontitis
 Brain and lung abscess
 Vincent’s Angina
 Gas gangrene
 Lumpy Jaw
 Tetanus
 Botulism
 Pseudomembranous colitis
D. Understand how laboratory diagnosis of the above anaerobic infections is achieved.
E. Explain differences between gaseous requirements for bacterial growth, including
microaerophiles, capnophiles, obligate anaerobes, obligate aerobes, facultative
anaerobes, aerotolerant anaerobe.
4. Important concepts related to specific groups of bacteria
Chapters: 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43,
44, 45, 46
Listed below are specific examples of important concepts related to major bacterial groups
and species and their diseases that should be learned in addition to the characteristics of
individual bacteria.
A. Gram-positive cocci and bacilli
1. How do Protein A and the P-V leucocidin aid Staphyloccoccus aureus in causing disease?
2. What advantage does the presence of coagulase confer on Staphylococcus aureus?
3. Explain the concept of a “superantigen” and how the staphylococcal toxic shock toxin
initiates tissue damage in the Toxic Shock Syndrome.
4. How does catalase assist organisms such as staphylococci resist destruction by the host
immune response?
5. Compare and contrast the virulence factors and diseases caused by Staphylococcus
aureus versus the coagulase-negative staphylococci.
6.
Acute glomerulonephritis and rheumatic heart disease are both autoimmune sequelae of
Group A streptococcal infections. Explain their similarities and differences with respect to
immune mechanisms involved and clinical manifestations.
7. How can a recent Group A streptococcal infection be diagnosed in someone who has
already taken antibiotics?
8.
9.
Explain the role of bacteriophage lysogeny in pathogenesis of some streptococcal
infections.
Describe the pathogenesis of streptococcal necrotizing fasciitis.
10. Explain the basis for the Lancefield groups and how they are used to classify the
streptococci?
11. Explain why the Enterococcus is especially well-suited to be a nosocomial pathogen.
12. What unique features of Bacillus anthracis help to differentiate from other Bacillus species in
the clinical laboratory?
13. Discuss the features of Bacillus anthracis that make it such a logical organism for
bioterrorism attacks.
14. Describe the epidemiology and pathogenesis of meningitis due to Listeria monocytogenes,
Escherichia coli, Streptococcus agalactiae, Neisseria meningitidis, and Haemophilus
influenzae and emphasize the differences and similarities among them.
B. Gram-negative bacilli
1. Compare and contrast diarrheal diseases caused by Salmonella, Shigella, Campylobacter,
Staphylococcus aureus, Bacillus cereus, Escherichia coli, Yersinia, and Vibrio species with
respect to epidemiology, modes of transmission, mechanism (infection vs. intoxication), and
invasiveness.
2. Describe 4 characteristics that can be used to define the family Enterobacteriaceae.
3. Which property of Helicobacter pylori enables it to reside in the stomach at pH of 2 and how
does this related to the ability of the organism induce an inflammatory reaction?
4. Which virulence factor of Pseudomonas aeruginosa contributes to its pathogenesis in burn
patients?
5. Discuss the relative organism load needed to cause diarrheal disease due to Escherichia
coli, Shigella spp., Salmonella spp. and VIbrio cholera.
6. Explain the difference between osmotic and secretory diarrhea. (lecture outline
7. What is the hemolytic-Uremic Syndrome and how is it related to bacterial infection?
C. Fastidious bacteria
1. Describe the process by which Mycoplasma pneumoniae attaches to the
respiratory epithelium and produces pneumonia.
2. Explain the differences in clinical manifestations, epidemiology, natural
history, and pathogenesis of pneumonia caused by Streptococcus
pneumoniae, Staphylococcus aureus, Klebsiella pneumoniae,
Mycoplasma pneumoniae, Chlamydophila pneumoniae, Haemophilus
influenzae, and Legionella pneumophila.
3. Discuss the impact of the Hib vaccine on epidemiology and spectrum of
disease caused by Haemophilus influenzae in adults and children.
4. Explain why Haemophilus influenzae must be supplied with X and V factors
in order to grow on trypticase soy agar.
5. Explain why Bordetella pertussis infections have increased in adolescents
and adults in the United States over recent years.
6. Compare and contrast the diseases of diphtheria and pertussis, including
their epidemiology, pathogenesis, and prevention.
7. Explain why the initial outbreak of legionellosis in 1976 was so difficult to
characterize initially.
8. Describe 5 methods for laboratory diagnosis of legionellosis and discuss
the advantages and disadvantages of each.
9. What are the consequences of having the smallest genome of any known
free-living human pathogen on laboratory diagnosis of Mycoplasma
genitalium infections?
D. Spirochetes and Rickettsiae
1. Explain the differences between obligate intracellular bacteria and
facultative intracellular bacteria and give examples of each.
2. Describe the life cycle of Borrelia burgdorferi, the agent of Lyme disease.
3. Does Lyme Disease occur endemically in Alabama? Explain the reason
for your answer.
4. Explain why laboratory diagnosis of Lyme Disease is complex and difficult.
5. What is the difference between a “non-treponemal test” and a “treponemal
test” and how can each be used most effectively in diagnosis of syphilis?
6. Explain how the life cycle of Rickettsia rickettsii is responsible for clinical
manifestations of Rocky Mountain Spotted Fever.
7. Describe the procedures that are necessary in order to cultivate rickettsiae
in vitro and explain whether or not this is a worthwhile method for
diagnosis of rickettsial diseases.
8. Describe 3 different human diseases for which ticks are a vector.
F. Neisseriae and Chlamydiae
1. Describe the unique life cycle of chlamydiae and the roles of the
elementary body and reticulate body in infectivity.
2. Give an explanation for the failure to develop an effective vaccine against
Neisseria gonorrhoeae.
3. Describe the diagnostic method of choice for chlamydial urogenital
infections and explain why it is preferred over other methods.
G. Mycobacteria
1. How do the methods of laboratory diagnosis for mycobacteria differ from
those used for the common gram-positive cocci?
2. Give a logical argument why the BCG vaccine is not used routinely in the
United States.
3. Is tuberculosis increasing or decreasing in the United States? Explain
your answer.
4. Explain why persons with HIV/AIDS are especially prone to develop
disease due to mycobacteria.
5. A 30 year-old dentist in apparent good health who is exposed to a patient
with tuberculosis develops a positive PPD skin test. Explain the most
appropriate course of action that should be taken.
6. Compare and contrast the pathogenesis and clinical manifestations of
tuberculoid and lepromatous leprosy.
Important Bacteria
 Chapter 48 (p. 473-484) provides and excellent summary of selected
bacteria, their clinical features, epidemiologic features, and virulence factors
in an easy to read tabular form. Additional material pertinent to each specific
organism or group can be found in the assigned readings in these Chapters:
22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45,
46, 47. Refer also to individual lectures outlines from Drs. Waites, Moser,
and Benjamin.
 For each bacterial group & species below, understand the following
characteristics (a-i).
a.
b.
c.
d.
e.
f.
g.
h.
i.
Gram stain reaction
Cell morphology (rod, coccus, etc.)
Natural habitat or reservoir (humans, animals, water, soil, etc.)
Major virulence factors (how it causes disease)
Epidemiology (life cycle, how infection is contracted, transmissibility, etc.)
Disease type & spectrum (relate virulence factors to manifestations)
Means of detection or diagnosis (culture, serology, biopsy, PCR, etc.)
Unique features to distinguish from others (structure, biochemicals, etc.)
Prevention (public health measures, vaccines, antibiotics, etc.)
Gram-positive cocci
Staphylococcus
Staphylococcus aureus
Staphylococcus epidermidis
Staphylococcus saprophyticus
Streptococcus
Streptococcus pyogenes
Streptococcus agalactiae
Streptococcus pneumoniae
Viridans Streptococcus species
Enterococcus species
Gram-positive bacilli
Corynebacterium diphtheriae
Bacillus anthracis
Bacillus cereus
Listeria monocytogenes
Nocardia spp.
Gram-negative bacilli
Enterobacteriaceae
Escherichia coli
Klebsiella pneumoniae
Proteus mirabilis
Salmonella enterica
Shilgella spp.
Yersinia enterocolitica
Yersinia pestis
Other Gram-negative bacilli
Pseudomonas aeruginosa
Acinetobacter spp.
Vibrio cholera
Campylobacter spp.
Helicobacter pylori
Haemophilus influenzae
Bordetella pertussis
Legionella pneumophila
Gram-negative cocci
Neisseria gonorrhoeae
Neisseria meningitidis
Moraxella catarrhalis
Chlamydiae
Chlamydia trachomatis
Chlamydophila pneumoniae
Chlamydophila psittaci
Mycoplasmas
Mycoplasma pneumoniae
Mycoplasma hominis
Mycoplasma genitalium
Ureaplasma spp.
Spirochetes
Treponema pallidum
Borrelia burgorderi
Leptospira spp.
Rickettsiae
Rickettsia rickettsii
Rickettsia prowazekii
Rickettsia typhi
Ehrlichia spp.
Mycobacteria
Mycobacterium tuberculosis
Mycobacterium leprae
Mycobacterium avium-intracellulare
Anaerobes
Bacteroides fragilis
Clostridium tetani
Clostridium perfringens
Clostridium botulinum
Clostridium difficile
Actinomyces spp.
Fusobacterium spp.
Diagnostic Laboratory Tests
Students should be familiar with the following diagnostic laboratory tests, media,
and procedures that were discussed in lecture and/or demonstrated in the
laboratory and how they are used in the identification of bacteria. Consult the
Laboratory Manual and textbook for further information
Gram stain
Kinyoun acidfast stain
Auramine-Rhodamine Stain
Alpha, beta, gamma hemolysis
Catalase test
Coagulase test
Optochin test
Bacitracin test
Novobiocin test
Nitrocefin (Cefinase) test
Oxidase test
PYR test
Indole test
Bile esculin test
6.5% NaCl test
CAMP test
Motility test
Sheep blood agar
MacConkey agar
Xylose-lysine-desoxycholate agar
Chocolate agar
Mannitol salt agar
Mueller-Hinton agar
Thayer Martin agar
Sabouraud dextrose agar
Lowenstein-Jensen agar
Selective media
Differential media
Enriched media
Nutritive media
Oxidation reaction
Fermentation reaction
API Biochemical strip
Agar disk diffusion test
Agar gradient diffusion test
Agar dilution test
Microbroth dilution test
Minimum inhibitory concentration
Satellitism
X and V Factor test
Sterility test with biological indicator
Enzyme immunoassay
Complement fixation
Latex agglutination
Darkfield microscopy
TERMINOLOGY
Abscess
Active immunization
Adaptive immunity
Antibiotic
Antibiotic synergy
Antibiotic antagonism
Antiseptic
Autoclave
Bactericidal
Bacteriostatic
Bacteriophage
Beta lactamase
Beta lactamase inhibitor
Biotype
Capsule
Carbuncle
Cell wall
Cell membrane
Cellular immunity
Cellulitis
Cistron
Codon
Conjugation
Colonization
Commensal
Complement
Cytokine
Disinfectant
DNA hybridization
Empyema
Endotoxin
Enterobactin
Enterotoxin
Exotoxin
Extended Spectrum Beta Lactamase
Frameshift mutation
Furuncle
Gene
Generalized transduction
Genetic code
Flagella
H antigen
Herd immunity
Homologous recombination
Humoral immunity
Innate immunity
Interferon
Interleukin
K antigen
Lipid A
Lipopolysaccharide
Lysogeny
Lysozyme
Macrophage
Minimal inhibitory concentration (MIC)
Minimal cidal concentration (MCC)
Missense mutation
Nonhomologous recombination
Acquired drug resistance
Nonsense mutation
Normal flora
Nosocomial infection
Null mutation
O antigen
Operon
Opportunistic pathogen
Opsonization
Osmotic diarrhea
Passive immunization
Peptidoglycan
Phagocytosis
Plasmid
Pili
Primary drug resistance
Promoter
Restriction enzyme
Secretory diarrhea
Serotype
Shiga Toxin
Siderophore
Silent mutation
Specialized transduction
Superantigen
Superoxide dismutase
Teichoic acid
Transcription
Transformation
Translation
Transition mutation
Transposition
Transposon
Transversion mutation
Vaccine
Virulence factor