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Clinical Microbiology explores the fundamental principles and advanced techniques involved in the identification, characterization, and management of microorganisms that cause human disease. The course covers the biology of bacteria, viruses, fungi, and parasites, emphasizing their roles in human health and disease. Students will learn diagnostic laboratory methods, antimicrobial susceptibility testing, infection control practices, and the interpretation of clinical laboratory data. Special attention is given to emerging infectious diseases, antimicrobial resistance, and the clinical significance of various pathogens. By integrating case studies and laboratory exercises, the course prepares students to understand and address microbial threats in clinical settings.
Recommended Textbook
Microbiology The Human Experience 1st Edition by John W. Foster
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Q1) Which of the following organisms would you NOT be able to see using Robert Hooke's microscope?
A) vinegar eels
B) dust mites
C) mold filaments
D) Mycobacterium tuberculosis
Answer: D
Q2) In 1884,the Gram stain was devised to distinguish bacteria from ________ cells.
Answer: human
Q3) Which of the following was an unexpected benefit of the bubonic plague?
A) There was no benefit to the bubonic plague.
B) The population of Europe experienced a baby boom.
C) It resulted in a better understanding of aseptic practices and how to prevent the spread of infection.
D) The population decline enabled the cultural advancement of the Renaissance.
Answer: D
Q4) Why did agar offer an improvement over gelatin for the growth of microorganisms?
Answer: Agar remains more solid at higher temperatures than does gelatin.
Q5) Bacteria and archaea are classified as ________.
Answer: prokaryotes

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Q1) Describe how a pathogen could use an exit portal different from the portal it used to enter the host.
Answer: Possible answers include the following: diarrhea-causing bacteria and viruses can enter via the oral route but leave via defecation;HIV can enter via the urogenital route and leave via the parental route in a needle (or vice versa-enter via a needle and exit via urogenital).
Q2) Infectious dose is measured by determining how many microbes are required to cause
A) disease symptoms in half of an experimental group of hosts.
B) death in half of an experimental group of hosts.
C) disease symptoms in all of an experimental group of hosts.
D) death in all of an experimental group of hosts.
Answer: A
Q3) What is the difference between a sign and a symptom?
Answer: Signs (such as rashes)can be observed by others.Symptoms (body aches)cannot be directly observed by others but are felt by the patient.
Q4) A disease that can spread to humans from nonhuman animals is known as a ________ disease.
Answer: zoonotic
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Q1) You are performing a Gram stain on Gram-positive bacteria and you stop after the addition of the mordant.What is the appearance of the bacteria at this point?
A) purple
B) colorless
C) pink
D) blue
Answer: A
Q2) In an acid-fast stain,carbolfuchsin specifically stains ________ of Mycobaterium tuberculosis.
Answer: mycolic acid
Q3) The bending of light as it enters a substance that slows its speed is known as A) reflection.
B) refraction.
C) absorption.
D) scattering.
Answer: B
Q4) Electron microscopy uses beams of ________ to generate high-resolution images. Answer: electrons
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Q1) Endosomes and phagosomes are both types of
A) catalysts.
B) oxidizing agents.
C) pseudopods.
D) vesicles.
Q2) The bacterial cell wall offers protection against what type of environment?
A) isotonic
B) hypertonic
C) hypotonic
D) endergonic
Q3) What is osmosis and why is it important for cells to maintain osmotic balance?
Q4) Which of the following is true of glucose?
A) It is a component of DNA and RNA.
B) It can form a ring structure.
C) It contains numerous amino groups.
D) It is a five-carbon sugar.
Q5) The molecular formula of the amino acid glycine is C H NO .What is the molecular formula of a glycine pentapeptide?
Q6) What is a condensation reaction?
Q7) What are some structural differences between cellular DNA and RNA?
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Q1) The bacterial cell wall is an attractive target for antibiotics because
A) bacterial cells cannot develop resistance to antibiotics that target the cell wall.
B) animal cells lack a cell wall.
C) the cell wall is unimportant for bacterial survival.
D) the cell wall is the only structure bacteria require for survival.
Q2) Which of the following structures is obligatory for all bacterial cells?
A) nucleoid
B) flagella
C) pili
D) magnetosomes
Q3) Explain how bacterial cells can divide so rapidly,some in as little as ten minutes between generations.
Q4) Pili and stalks enable bacterial
A) adherence.
B) chemotaxis.
C) photosynthesis.
D) symport.
Q5) The bacterial nucleoid contains loops of DNA that emanate from a central point called the ________.
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Q1) Production of urease by Helicobacter pylori allows it to do which of the following?
A) sense when it has entered the intracellular environment of its host
B) survive in basic conditions
C) increase production of ion pumps
D) neutralize stomach pH to survive in acidic conditions
Q2) How is it possible for a strict anaerobic bacteria to cause a disease in humans?
Q3) What classification is also given to barophilic organisms that grow at the ocean floor?
A) mesophilic
B) psychrophilic
C) halophilic
D) acidophilic
Q4) Direct counting of bacterial cells under the microscope can be accomplished using a ________.
Q5) Mesophilic proteins are ________ flexible than psychrophilic proteins.
Q6) If you were trying to isolate a pure culture of Staphylococcus aureus from the skin lesion of an infected individual,you would use appropriate sampling techniques and would specifically have to culture the microorganism onto ________.
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Q1) Lithotrophs donate electrons from inorganic reduced molecules directly to an ETS to generate a proton motive force.Why might these lithotrophs still possess the tricarboxylic acid cycle?
Q2) Why does sugar production from CO require NADPH in addition to ATP? In other words,why is ATP not sufficient?
Q3) If in the ETS electrons are passed from a to b and finally accepted by c, then
A) a is a stronger electron acceptor than b.
B) a is a stronger electron acceptor than c.
C) a is a stronger electron donor than b.
D) c is a stronger electron donor than b.
Q4) If Fe³ is the final electron acceptor at the end of an electron transport system,the waste product is ________.
Q5) Compare and contrast ATP production in chloroplasts and mitochondria.How are they similar and how do they differ?
Q6) Which of the following is true of energy and living cells?
A) Organisms can create their own energy.
B) Organisms do not require inputs of energy from the environment.
C) Organisms require inputs of energy from the environment to survive.
D) Only heterotrophic organisms require environmental energy inputs to survive.
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Q1) PrfA protein is a global regulator of virulence genes in Listeria,a bacterium that can cause severe food poisoning.Below host body temperatures PrfA mRNA exists in a conformation that hides the ribosome binding site.Upon entry into a host and a rise in temperature,hydrogen bonds in the mRNA break,exposing the ribosome binding site.What level of gene regulation is seen here?
A) changing the DNA sequence
B) transcription control
C) translation control
D) posttranslational control
Q2) EF-G is involved in
A) transcription initiation.
B) transcription elongation.
C) translation initiation.
D) translation elongation.
Q3) If DNA polymerase misincorporates a base,leading to a mismatch,how do repair enzymes distinguish the parental and daughter DNA strands to specifically fix the daughter strand?
Q4) Proteins that assist the folding of newly formed proteins are known as ________.
Q5) Transcription of genes starts at regions of the genome called ________.
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Q1) Create an example that shows how random mutations lead to natural selection and divergence of organisms.
Q2) Griffith's observations from his experiments infecting mice with smooth and rough strain Streptococcus pneumoniae were later found to be due to A) conjugation.
B) transposition.
C) transduction.
D) transformation.
Q3) Why might an organism transform DNA that is homologous to its own?
A) as a food source
B) to obtain new DNA
C) to repair its own damaged genome
D) Organisms are not capable of transforming homologous DNA.
Q4) A ________ relationship develops between endosymbionts and their hosts.
Q5) Genes for transfer RNA can be predicted through A) amino acid sequence similarity.
B) protein function prediction.
C) gene function prediction.
D) conservation over vast phylogenetic distances.
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Q1) The major group of bacteria that causes sexually transmitted infections and the eye disease trachoma and are obligate intracellular pathogens is ________.
Q2) How is it possible for humans to use some Proteobacteria,such as Geobacter species,to generate electricity?
A) Geobacter species use lipopolysaccharide, or LPS, within their outer membrane to store energy that can be harnessed.
B) Geobacter species transfer electrons to electrodes in fuel cells because they transfer electrons to iron or magnesium.
C) Geobacter species are heavily flagellated and display swarming behavior that generates electricity.
D) Geobacter species produce gases during fermentation of carbohydrates, and these gases are used in fuel cells.
Q3) Autoclaves use high temperatures and steam to sterilize surgical instruments.When instruments are sterilized they do not contain any bacteria.Explain how Bacillus stearothermophilus,a bacterium within the phylum Firmicutes,can be used to test sterilization within autoclaves.
Q4) Describe the two developmental stages of the Chlamydias.
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Q1) The group of organisms that includes ciliates,dinoflagellates,and apicomplexans is known as
A) fungi.
B) amebas.
C) trypanosomes.
D) alveolates.
Q2) Why is perianal itching significant in the life cycle of pinworms?
A) When a host scratches the anus, pinworm larvae enter the bloodstream.
B) Eggs are trapped under fingernails and transferred to new hosts.
C) Scratching allows mature worms to break through the surface of the skin.
D) Transmission of pinworms ends when the host scratches the anus.
Q3) A free-living soil ameba may contaminate contact lens solutions and cause amebic keratitis.What is the genus name of one common causative agent of amebic keratitis?
A) Acanthamoeba
B) Entamoeba
C) Babesia
D) Toxoplasma
Q4) Describe how the parasites that cause malaria are able to evade an immune response during an infection.
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Q1) A phage genome integrated into the DNA of the bacterial host cell is known as a
Q2) Why would a virus have evolved to cause cancer in a host cell?
A) to kill the host cell
B) to produce more cells for the virus to infect
C) to allow for increased mutagenesis of the virus
D) Viruses are not capable of causing cancer in a host cell.
Q3) Why must influenza have highly efficient host-to-host transmission?
A) because of its rapid infection
B) because of its slow infection
C) because of genetic reassortment
D) because of latent infection
Q4) Where are HPV virions assembled?
A) in the nucleus
B) in the cytoplasm
C) in the ribosome
D) outside the cell
Q5) ________ is an example of a virus with a large double-stranded DNA viral genome.
Q6) A retrovirus that causes infections progressing slowly over many years is a
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Q1) In which of the following mechanisms of microbial control might some pathogens still survive?
A) sanitization
B) antisepsis
C) disinfection
D) sterilization
Q2) Explain why norovirus and the prion that causes bovine spongiform encephalopathy are not susceptible to irradiation of food.
Q3) Explain how organisms can develop resistance to chemical disinfectants.
Q4) A drug is classified as bactericidal if its minimum bactericidal concentration is no more than ________ its minimum inhibitory concentration.
Q5) ________ is when infecting bacteria "play dead" when an antibiotic is present,only to grow again when the antibiotic is gone.
Q6) How is griseofulvin selectively toxic?
A) it inhibits DNA synthesis of fungal DNA only
B) it disrupts the mitotic spindle of fungi but not humans
C) it blocks synthesis of a fungal cell wall
D) it inhibits synthesis of fungal-specific ergosterol
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Q1) Which of the following would NOT be a good organism choice for a vaccine delivery system?
A) Streptococcus salivarius
B) Lactobacillus acidophilus
C) Staphylococcus epidermidis
D) Staphylococcus aureus
Q2) Describe the positive and negative side of enterotoxins.
Q3) Give an example of how our cells communicate with the microbiome.
Q4) ________ are organisms that cause disease in an immunocompromised host only.
Q5) Explain two potential negative effects of using phage therapy to treat bacterial infections.
Q6) When do anaerobes begin to colonize the human oral cavity?
A) when teeth emerge
B) in the womb
C) during birth
D) during the first feeding
Q7) Sequestered body sites tend to be ________.
Q8) What is wrong with the situation described below?
After vaginal delivery,a gnotobiotic mouse was moved to an axenic environment. Page 16
Q9) The presence of a core ________ is most important for a healthy microbiome.
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Q1) Macrophages arise from which of the following?
A) neutrophils
B) monocytes
C) eosinophils
D) basophils
Q2) A chill is a sign that
A) body temperature is falling.
B) body temperature is rising.
C) body temperature is not changing.
D) blood vessels are dilating.
Q3) Innate immunity includes all of the following EXCEPT
A) phagocytosis.
B) inflammation.
C) activation of complement.
D) production of antibody.
Q4) A clinical that counts the total number of white blood cells and identifies their various cell types is called a ________.
Q5) Compare and contrast the innate and adaptive immune responses.
Q6) Substances that cause fever are known as ________.
Q7) Cytokines that have chemotactic properties are called ________. Page 18
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Q1) One health risk associated with excessive cytokine release is the chance of A) severe tissue damage.
B) cytokines destroying antibodies.
C) damage to virally infected cells.
D) inactivating mitosis.
Q2) Proteins that do not require antigen processing and presentation are referred to as ________.
Q3) If you had a box of 200 beads that were different shapes and you randomly chose and linked together 3 beads,you would be performing a process analogous to the way
A) T cells are able to use 200 genes to produce 3 receptor types.
B) 200 B cells are able to produce 3 different antibodies.
C) antigens are processed by antigen-presenting cells.
D) antibody diversity is created within our bodies.
Q4) MHC molecules are required for
A) B cell activation.
B) phagocytosis of microbes.
C) T cell activation.
D) proteasome degradation of viruses.
Q5) Describe the process of affinity maturation.
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Q1) Patients with primary immunodeficiencies and who are immunosuppressed are prone to developing cancers.Which is the most commonly developed cancer for these patients?
A) Epstein-Barr
B) B-cell lymphomas
C) myelomas
D) mononucleosis
Q2) All of the following pertain to serology EXCEPT that they
A) can detect antibodies.
B) cannot detect antigens.
C) can be used to diagnose various diseases.
D) can reveal the contents of serum.
Q3) Which item is from the patient in a direct ELISA test?
A) antigen
B) substrate for the enzyme
C) antibodies against the antigen
D) antihuman immune serum
Q4) The process that detects and eliminates cancer cells as they arise is called a(n)________.
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Q1) Explain the difference between antigenic drift and antigenic shift.How might antigenic shift relate to the generation of a new flu pandemic?
Q2) Endotoxins are
A) associated with Gram-positive bacteria.
B) molecules that bind nerve cells.
C) part of the Gram-negative cell wall.
D) excreted from the cell.
Q3) The fimbriae of E.coli is an example of a(n)
A) adhesion.
B) receptor.
C) endotoxin.
D) exotoxin.
Q4) Which statement about horizontal gene transfer is correct?
A) Few pathogenicity islands are generated by horizontal transmission.
B) Horizontal gene transfers move whole blocks of DNA from one organism to another.
C) Horizontal gene transfer helps pathogens evolve.
D) All genes code for toxins.
Q5) Draw and label an AB toxin.List two diseases that are caused by AB toxins.
Q6) Most pathogenicity island genes were acquired by ________ transmission.
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Q1) Fungal skin diseases are diagnosed based on A) PCR.
B) KOH preparation of skin scrapes.
C) Gram-positive stain.
D) Gram-negative stain.
Q2) Which of the following lists the layers of the skin in the correct order from deepest to superficial?
A) stratum basale, stratum spinosum, stratum granulosum, stratum corneum
B) stratum corneum, stratum granulosum, stratum spinosum, stratum basale
C) stratum granulosum, stratum corneum, stratum basale, stratum spinosum
D) stratum spinosum, stratum basale, stratum corneum, stratum granulosum
Q3) Fungi that love human skin are called ________.
Q4) Necrotizing fasciitis is often caused by ________.
Q5) Staphylococcus aureus is responsible for all of the following EXCEPT
A) boils.
B) carbuncles.
C) acne.
D) pimples.
Q6) Explain the cycle of acne.What is the causative agent and why are some individuals more prone to acne than others?
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Q1) A day-care worker reports that two young children have been coughing all day.She first noticed that both children had runny noses a few days ago,but is not sure if they had fevers.She states that they both sound like barking seals.Most likely these children have
A) the common cold.
B) croup.
C) influenza.
D) respiratory syncytial disease.
Q2) Explain how the M proteins associated with some strains of Streptococcus pyogenes lead to streptococcal sequelae.
Q3) The most likely mutation to cause an influenza pandemic would be a mutation in A) the head of hemagglutinin.
B) the stalk of hemagglutinin.
C) M2 protein inside the virion envelope.
D) influenza nucleoprotein.
Q4) The two bacterial diseases of the respiratory system that are prevented by the DTaP vaccine are ________.
Q5) Coccidioidomycosis is endemic in the ________ United States.
Q6) Moraxella catarrhalis may cause bacterial ________.
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Q1) The herpes virus that initially infects the oropharyngeal epithelium,tonsils,and salivary glands,and is associated with endemic Burkitt's lymphoma,is known as
Q2) Borrelia burgdorferi produces an enzyme that cleaves proteoglycans.This enzyme mainly affects ________ tissue.
A) epithelial
B) connective
C) muscle
D) nervous
Q3) The cells infected by cytomegalovirus (CMV)include
A) fibroblasts.
B) osteocytes.
C) lymphocytes.
D) neurons.
Q4) What causes lymphadenitis in a patient with an Epstein-Barr virus infection?
A) proliferation of B and T cells
B) removal of abnormal blood cells from circulation
C) infection of epithelial cells within lymph nodes
D) production of heterophile antibodies
Q5) The blood vessels returning oxygenated blood to the heart are the ________.
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Q1) Infection with ________ could mimic symptoms of hepatitis.
A) Entamoeba histolytica
B) Cryptosporidium hominis
C) Cyclospora cayetanensis
D) Giardia intestinalis
Q2) The part of a tooth protruding outward from the gum is called the ________.
Q3) How would you distinguish between gingivitis,periodontal disease,and trench mouth?
Q4) Which part of the human digestive tract cannot be colonized by microorganisms?
A) mouth
B) All parts of the digestive tract can be colonized.
C) liver
D) small intestine
Q5) When does breakdown of food begin?
A) in the esophagus
B) when saliva is secreted by the salivary glands
C) in the gastric acids of the stomach
D) in the large intestine
Q6) Jack presents at the clinic with mild nausea,vomiting,abdominal pain,and jaundice.The most likely cause of Jack's condition is ________.
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Q1) The vaginal pH is maintained by the species Lactobacillus,which produces
Q2) Which of the following is true about urine production?
A) The wall of the ureters is made of skeletal muscle that is voluntary.
B) Filtrate is collected in the bladder.
C) The urinary bladder is made up of squamous epithelial cells.
D) Extra water is removed and returned to the vascular system in the collecting duct.
Q3) A patient presents with fever and extensive lesions of the labia minora.Her VDRL test was negative.What is the most likely treatment?
A) metronidazole
B) acyclovir
C) cephalosporins
D) No treatment is available.
Q4) There are two types of urinary tract infections: bladder infections,or ________,and kidney infections,or ________.
Q5) Nearly 70% of patients seen in STI clinics are men.Offer a reason why men are more likely to seek treatment than women.Why is it important that women seek treatment for STIs?
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Q1) Which of the following pairs is mismatched?
A) tetanus - releases potent neurotoxin
B) botulism - stimulates transmission of nerve impulse
C) poliomyelitis - multiplication of virus occurs in throat and small intestine
D) rabies - destroys cells of the CNS
Q2) What is the prescribed treatment for Naegleria?
A) ketoconazole
B) eflornithine
C) penicillin
D) vaccine
Q3) The symptoms of tetanus are due to A) tetanospasmin.
B) endospore formation.
C) inflammation.
D) the relaxation of muscles.
Q4) Discuss the advantages and disadvantages of the Salk and Sabin vaccines.
Q5) List and describe the defensive mechanisms that are in place to protect the central nervous system.
Q6) Fungal infections of the central nervous system are also known as ________.
Q7) A small proteinaceous infectious particle is known as a ________.
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Q1) Which of the following would typically be the initial indicator of bacteria growing within a blood culture tube?
A) An automated incubator will detect fluorescence.
B) Bacterial colonies will appear on blood agar.
C) Bacterial colonies will appear on MacConkey agar.
D) Centrifugation will cause sediment to appear at the end of the tube.
Q2) Eosin methylene blue (EMB)agar contains dyes that inhibit the growth of Gram-positive organisms and bile salts that prevent the growth of Gram-negative bacteria other than fecal coliforms.Also included in EMB are stains that show a color change when an organism ferments lactose.This media is best described as A) selective.
B) differential.
C) selective and differential.
D) nonselective.
Q3) Which of the following samples would be expected to contain normal microbiota?
A) peritoneal fluid
B) cerebrospinal fluid
C) blood
D) fecal stool sample
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Q1) CASE HISTORY
Stephanie was a bright seven-year-old girl who came to her rural Manitoba hospital for a tonsillectomy.She was a little scared,but her mother was with her and she liked the surgeon,Dr.Ryan,and his funny Winnie-the-Pooh ties.Sometimes she would even grab his tie while Dr.Ryan was examining her.However,she did not much like the IV catheter Dr.Ryan had to insert in her arm.It hurt a little,but she was brave and did not cry much.The surgery went well and Stephanie was recovering in her hospital room a few hours later.However,that night the nurse noted her temperature had risen to 102°F.By the next day,Stephanie's heart was racing and her breathing was labored.She was rushed to the pediatric intensive care unit and empiric antibiotic therapy was initiated.Despite this treatment,her blood pressure began to fall.Stephanie was diagnosed with postsurgical septic shock.To everyone's horror,Stephanie died two days later of MRSA sepsis.The organism recovered from her blood was a MRSA strain identical to one causing a wound infection in a 57-year-old man two floors down.
Discuss at least three key measures implemented in health care settings that are designed to prevent transmission of infectious diseases in health care environments,and offer a scenario that reveals how a breach in these procedures could have led to Stephanie's tragic death.
Q2) Explain the relationship between the terms endemic,epidemic,and pandemic.
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Q1) An obligate association exists between a gut microbe and an insect.A new mutation in the microbe allows the microbe to utilize nutrients that were previously accessible to the insect.This change benefits the microbe,but causes some harm to the insect.The change in the relationship is best described as a change from
A) mutualism to parasitism.
B) synergism to parasitism.
C) commensalism to amensalism.
D) parasitism to synergism.
Q2) A microbe's contribution to an ecosystem's health depends on the A) microbe's genome and the physical and chemical characteristics of the environment. B) microbe's age and number of primary producers in the environment.
C) microbe's ability to cycle carbon and the number of decomposers in the ecosystem. D) bioremediation capacity of the microbe and the number of predators in the ecosystem.
Q3) Using organisms such as bacteria to neutralize pollutants from a contaminated site is referred to as ________.
Q4) What are the three factors that control the ways in which food spoils?
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