Medical Microbiology

If one cannot purify a microbial agent that causes disease because the bacterium cannot be cultured, would Koch’s postulated be satisfied?
a) no, the bacterium or virus has to be purified and cultured to demonstrate that a given microbe is an agent of a disease
b) no, because the Koch’s postulates only apply to a viral infection
c) yes, Koch’s postulates do not apply to non-culturable organisms
d) yes, Koch’s postulates simply state that one can re-infect animal, so the healthy and diseases animals can be instead kept together for easy transmission of an agent.

What is a causative agent of the bubonic plague?
a) salmonella typhimurium
b) klebsiella pneumoniae
c) iraquibacter
d) yersinia pestis

What was the accomplishment of Antonie van Leewenhoeck?
a) drafted the germ theory postulates
b) improved the fermentation methods
c) designed the first microscopes
d) discovered penicillin

Penicillin was first used in 1943. When were the Penicillin-resistance bacteria identified?
a) 2011
b) 1670
c) 1940
d) 2019

Escherichia coli O157:H7 is a bacterium that causes foodborne infections. What do O and H signify in the nomenclature of this bacterium?
a) O and H are abbreviations of proteins that bind E. coli
b) O is LPS antigen, and H is flagella antigen
c) O and H stand for the resistance to antibiotics, oritavancin and hyrgromycin
d) OH are the initials of the person who first discovered this bacterium

T/F The longer human co-evolved with pathogens, the more likely that bacterium causes a particular disease.

Best way to decrease the incidence of anti-microbial resistance
a) prescribe antibiotics only when absolutely needed
b) add antibiotics to water supply
c) prescribe more antibiotics
d) limit the use of antibiotics to farms and animals and stop using them in humans

what is an extra layer in the cell envelope that Gram-negative have in comparison to Gram-positive bacteria?
a) inner membrane
b) mycolic acid membrane
c) outer membrane
d) Gram-negative bacteria have no membrane

What are PAMPs
a) component of bacteria that are recognized by such receptors like Toll-like receptors
b) antibody that coats a pathogen
c) a type of vasodilating cytokine
d) type of ATPases found on a phagosome that reduce the pH

Select three features which describe the endothelial cell
a) lines the blood vessels inside the vessel
b) layer of cells only inside the body
c) difficult to breach
d) a layer of cells exposed to the environment
e) present on skin
f) easy to breach

What is the function of C3 convertase?
a) it is a protease that activates C3 into C3a and C3b
b) it is a cytokine that coats bacteria
c) it binds mannose on the surface of some bacteria
d) it binds antibody on the surface of bacteria

ciliated epithelium
respiratory tract

stratified squamous epithelium
skin on a hand

simple columnar epithelium
small intestine

simple squamous epithelium

how many epithelia layers does the skin have?

does the skin have a neutral or low pH?
low pH

Does the skin provide a dry or humid environment?

How many layers does the mucosal tissue have?
only one epithelial layer

Does the mucosal tissue have a low or neutral pH?

Does the mucosal layer provide a dry or humid environment?

How is the myeloperoxidase actively regulated
a) it is activated when in contact with a NADPH oxidase
b) it is activated by LPS
c) it is activated upon low pH
d) it is activated upon high pH
e) it is down-regulated by defensins

What is the main function of inflammasome?
a) activation of capsase-1 and secretion of pro-inflammatory IL-1beta cytokine
b) down-regulation of inflammation via decrease in NFkappaB signaling
c) ubiquitination of bacteria
d) secretion of NFkappaB molecule outside of the cell to down-regulate inflammation

Which cell is not phagocytic?
a) neutrophil
b) dendritic cell
c) mast cell
d) NK cell
e) macrophage

These cells are critical in the adaptive immune responses to intracellular pathogens, and they bind MHC I displayed antigens.
a) T helper (effector) cells
b) CD8+ T cells
c) CD4+ T cells
d) Th17 cells

The secondary, but not the primary, immune response is based on which component?
a) mast cell degranulation
b) IgM multivalency
c) memory cells
d) complement activation

Which two immunoglobulins are involved in maternal immunity?
a) IgG1 and IgF
b) IgE and IgM
c) IgG and IgA
d) IgM and IgG1

This protein complex is expressed on professional phagocytic cells such as macrophages and is primarily involved in presenting the epitopes of an antigen to CD4+ cells.
a) TLR5
b) TLR4
c) MHC I

T cell surface receptors for antigen partly recognize
a) MHC
b) cytokine
c) IL-2

These cells are responsible for mediating the production of antigen-specific immunoglobulin (Ig) directed against invasive pathogens (antibodies). These cells differentiate into plasma cells.
a) Th17 cells
b) B cells
c) cytotoxic T cells
d) DCs

Which cell type produces antibodies?
a) macrophages
b) eosinophils
c) NK cells
d) plasma cells

For vaccination against mycobacterial diseases such as tuberculosis, the most important facet of the immune response to be stimulated is:
a) macrophage-activating cell-mediated immunity
b) antibody in the gut lumen
c) cytotoxic T cells and humoral response
d) a high titer of antibody

Which would be the best vaccine to use for an immunocompromised individual who is traveling for a short time to a country where the disease is prevalent?
a) subunit vaccines
b) live attenuated vaccines
c) variolation

Which adjuvant would you use to elicit a strong Th2 response in humans, if you have appropriate filtration strategy? Consider the safety of the adjuvant for humans.
a) aluminum salts
b) triterpenoid-based adjuvant
c) complete Freund’s adjuvant

Which regions of 16S rRNA would you use for the sequencing step during 16S rRNA sequencing to differentiate between the different microbial species?
a) variable regions
b) conserved regions
c) repetitive region
d) shared region

Which gene transcript has a higher copy number based on this graph obtained from the qPCR analysis?
a) gene A
b) gene B
c) both genes are present at the same level since they both reach the threshold cycle
a, gene A has more fluorescence so higher copy number

Which regions of 16S rRNA would you use for the PCR amplification to obtain microbial census by sequencing?
a) conserved regions
b) variable regions
c) species-specific regions
d) any DNA that is specific to a given species

Which omics technique can be used to identify the gene transcripts?
a) RNAseq
b) metabolomics
c) proteomics
d) genomics

What is the term used to describe the impaired microbiota or microbial imbalance?
a) dysbiosis
b) gnotobiosis
c) anabolism
d) opportunistic infection

anaerobic Gram-negative bacterium that lives in the human colon:
a) Bacteroides
b) E. coli
c) Lactobacillus
d) Staphylococcus epidermis

number or microbes in colon
large number

number of microbes in small intestine
small number

transit time of contents in colon

transit time of contents in small intestine

what is absorbed in the small intestine?

what is absorbed by the colon?
short-chain fatty acids

Where are propionibacterium?

Where are Lactobacillus?

Where are Streptococcus salivarius?

Where are Bacteroidetes

Typhoid fever is caused by Salmonella Typhi, which is a Gram-negative facultative intracellular pathogen and it can grow in pure culture. This bacterium sometimes doesn’t cause disease and instead leads to asymptomatic carriers of typhoid fever, where the persons who have the presence of bacteria remain healthy. Which postulate is problematic to meet in case of typhoid fever?


This bacterium stains by acid-fast staining and has been discovered by Robert Koch. Moreover, this bacterium can lead to the infection of the lungs. What is it?
a) Bacillus anthracis
b) Yersina pseudotuberculosis
c) Helicobacter pylori
d) Mycobacterium tuberculosis

Put Koch’s postulates in order.
1) The microbe can be isolated and grown in a pure culture outside of the host
2) The same microorganism must be isolated from the inoculated animal
3) The microbe must be present in every animal with the disease and absent in healthy
4) The cultured microorganism must cause the same disease in inoculated animals

What alternative method other than Koch’s postulates relies on the cure or prevention of disease to show that a specific disease is caused by a specific pathogen?
a) introduction of a pathogenic bacterium into germ-free mice
b) no other methods can be used because 4 postulates are a golden standard
c) sequencing can be used to show that bacterium is present in diseased tissue
d) culture of a pathogen in axenic media
e) vaccination can be used to prevent the disease

Colitis in a specific mice model correlates with the presence of Klebsiella pneumoniae and Proteus mirabilis, which induce the disease in specific pathogen free wild type mice. However, these two bacteria do not by themselves induce colitis when administered to germ-free mice. What type of pathogens are these bacteria?
a) dominant
b) keystone
c) vector

You identified a new pathogen, which is present in the inflamed colon of individuals, and it is not present in any healthy individuals. You are able to culture this bacterium in vitro, unfortunately this pathogen doesn’t infect any animals, and no brave individuals will expose themselves to the infection with this bacterium. Which Koch postulate is not met based on this information?


You are interested in the detection of Salmonella Typhimurium in the diseased tissue of a patient. This bacterium is a facultative intracellular pathogen and it can grow in pure culture. What would be the best technique to use for the detection of this bacterium?
this bacterium can be detected by first enrichment of bacteria in the media followed my qPCR. This bacterium grows in media and host cells are not necessary for its growth.

How is the sandwich ELISA different from the indirect ELISA?
a) sandwich ELISA uses two types of antibodies that recognize the antigen- capture antibody and primary antibody
b) sandwich ELISA cannot e used to capture and the detect the antigen
c) sandwich ELISA is used with two pathogen-specific PCR primers

In which years was there a golden age of microbiology?
a) 1800-1830
b) 1850-1915
c) 2000-2010
d) 1950-1990

Did John Needham’s experimental results support/agree with Francesco Redi’s conclusions?
No, they disagreed on a matter of spontaneous generation

Which group of bacteria has LPS?
Gram-negative bacteria

This bacterium was discovered after an outbreak in 1976, it causes pneumonia and is a waterborne infection, increasingly present in the USA.
Legionella pneumophilia

What is the part of LPS that contains endotoxin and secures LPS to the outer membrane?
Lipid A

The function of these structures on cells can enhance the cell’s surface area and facilitate the absorption of nutrients. What is the name of the structure?

What is the name of the structure of the cell on the side of the cell that is marked with a green square? (refer to slide 20 in lecture 2.1)
Apical surface

You are a microbe trying to establish an infection in a host. You are trying to evade the immune system as best as you can. Explain how you would avoid the immune response in the following scenarios.

  1. You are a bacteria trying to avoid macrophage killing.
  2. You are trying to block cells from reaching you.
  3. You prevent phagolysosome fusion
  4. You destroy chemokines

What is the fate of Salmonella that is within the Salmonella containing vacuole?
Salmonella can survive within the vacuole

Which of the following statements does NOT apply to IgG?
appears early in the primary immune response

Which cells are described below? These cells are responsible for mediating the production of antigen specific immunoglobulin (Ig) directed against invasive pathogens (typically known as antibodies). These cells differentiate into plasma cells
B cells

Please match an adaptive immune cells with its function: Th1 cells
Recognition of MHC II- epitope by these cells stimulates the production and release of IL-2 and IFN-y

Please match an adaptive immune cell with its function: Th2 cells
MHC II epitope stimulation of these cells stimulate naïve B cells to proliferate into B cells

Please match an adaptive immune cell with its function: Memory T cells
these cells are easily stimulated to proliferate and produce cytokine response upon encounter with specific epitopes of APCs

Please match an adaptive immune cell with its function: CD8+ T cells
these cells release cytotoxic granules to kill bacteria and/or infected cells

Protection against microorganisms inside cells is provided by:
T cells

A Fab fragment in the antibody
Binds antigen

What is the minimum percentage of children which needs to be vaccinated successfully in order to achieve herd immunity to diphtheria:

Look at this phylogenetic tree and answer which species of bacteria below are most closely related
B & C

What is the name of the DNA that is the product of amplification or replication events, for instance during rRNA sequence analysis process?

The idea that diseases, such as cholera are spread by pollutants or unpleasant odors is known as:
Miasma theory

Which of the following is NOT a step in Koch’s postulates?
Bacteria photomicrograph of the causative agent must be taken

Koch’s Postulates establish:
a cause-effect relationship between a specific microorganism and an infectious disease

Which one(s) is an example of Microbiota Shift Disease?
All of the answers are correct

Which claims are refuted by Redi’s experiment in 1668?
Animals cannot arise spontaneously from nonliving matter

Which bacterium is described below? This bacterium is also called Iraqibacter, it is a soil bacterium that was first identified in wounds but now present in hospitals. This bacterium is characterized by high incidence of antimicrobial resistance.
Acinetobacter baumannii

Why did tuberculosis come back in the 1990’s
Dismantled infrastructure could not contain the spread, presence of susceptible individuals

Match agents with a disease:
Typhoid fever
Gastric ulcer
Bacillus anthrax
salmonella typhi
halobacter pylori
salmonella typhimurium

This cell type has a short half-life and produces NETs to entrap bacteria it is a phagocytic cell that often undergoes a process of apoptosis

This cell is a non phagocytic cell and is present in close proximity to blood vessels; one of the functions of the cell is to increase vascular permeability
Mast cell

Please select which belongs in the innate immune system
Macrophage, Dendritic cell , eosinophil, neutrophil

Which type of B Cell Activation is absent children under the age of 2?
B cell activation independent of T cells

You plan an experiment and you would like to obtain a profile of bacterial microorganisms from a colon of a person infected with Clostriudium difficile, but you’re not interested in gene pathways or quantification of these microorganisms. Which technique could you use for this experiment.
16s rRNA sequencing

A family member went through antibiotic treatment and asked you to bring him or her probiotics to improve digestion. what would you bring?
Lactobacillus containing kefir

The woman is presenting with gray or white vaginal discharge, strong, fish like odor, and burning sensation when urinating. Which types of bacteria do you think are now predominantly present in the vagina of this woman .
Gram-negative bacteria

What is an example of anabolic function of the gut microbiota?
Production of vitamin B12

Which of the following choices lists the steps of pathogenesis in the correct order
survival outside the host,
adherence, invasion,
evasion of host defenses

How can you detect the presence of pathogen in diseased tissue?
Immunohistochemistry, enzyme-linked immunosorbent assay, pcr-based test

Which disease does not meet postulate #2 as formulated by Koch and for what reason?
Syphilis caused by Trypanema pallidum because this bacterium is not culturable in vitro

Bacteria grow and metabolize by oxidizing sulfides, reducing sulfate, oxidizing ammonia or reducing nitrate. T/F

What are the examples of PAMPs>
Flagellin, CpG, DNA, LPS

What do goblet cells produce?

In humans, skin epithelium is…

A feature of a salmonella-based vaccine expressing antigens from other infectious agents is that:
It elicits secretory IgA as well as cellular immune response

What is true about IgM?
Is involved in the primary response to antigen and activates complement via classical pathway.

Specific antibodies are readily detectable in serum following primary contact with antigen after:
5-7 days

What was one of the very first bacteria diseases to be identified and linked to a specific disease, and by who?
Bacillus anthracis was shown to cause Anthrax by Robert Koch

What is the name of a chemical that is used only on inanimate objects and cannot be safely ingested as antimicrobial?

Describe the innate immune system
Is less specific towards particular pathogen
Is always on and rapid
It is short in duration

The circulation of a two-month old breastfed baby will contain maternal _ due to the breastfeeding.

This omics technique utilizes specific proteolytic cleavage by trypsin, followed by mass spectrometry-based analysis using peptide fragmentation. What type of molecules can you analyze using this workflow?

Match the bacterium with the appropriate term:
Salmonella sp
Chlamydia trachomatis
Mycobacterium leprae
Listeria monocytogenes
-facultative intracellular pathogen
-obligate intracellular pathogen
-obligate intracellular pathogen
-facultative intracellular pathogen

This specific detection method relies on an antibody-based detection of a bacterial pathogen, and it can provide quantitative information about the concentration of an antigen in a sample. This method will not provide information about the co-localization of the bacteria with cellular compartments nor other types of visualization. Which method is it?

Which cells are keratinized to protect the tissue?
epithelial cells of the skin

You are a microbe trying to establish an infection in a host. You are trying to evade the immune system as best as you can. Explain what you would do to avoid being killed by a macrophage?
You decrease autophagy
You produce a virulence factor that prevents phagolysosomal fusion
You hide in your own vacuole inside a macrophage

Which cell is described in this paragraph? This cell is a non-phagocytic cell that can lyse tumor cells. One of the functions of this cell is to kill cells infected with the virus. This cell is also a primary source of IFN gamma.
NK cell

Which cell is described in this paragraph? It is a phagocytic cell of the innate immune system, whose primary functions in the activation of T cells. This cell presents antigens and migrates via the lymphatic system to lymph nodes upon activation with PAMPs.
dendritic cells

Which one of the following diseases has been completely eradicated world-wide?

Which of the following is a product of microbiota metabolism?
Smelly fart, vitamin K, and sweat

Which of the following was a goal of the Human Microbiome Project?
Create a repository of reference microbial genome sequences from 5 different body sites

To detect the presence of a single species of bacteria in a patient sample using real-time PCR, primers that anneal to conserved regions of the 16S rRNA gene of this species must be used. T/F

_ refers to the capacity of an organism to cause disease.

_ refers to the process by which microbes cause disease in a host.

What are the specific-pathogen-free mice?
Mice that are not infected with a specific pathogen

Pathogen A has an ID50 of 50 particles, pathogen B has an ID50 of 1,000 particles, and pathogen C has an ID50 of 1 x 10^6 particles. Which pathogen is most virulent?
Pathogen A

You are interested in the detection of Chlamydia trachomatis in diseased tissue of a patient. The bacterium is an obligate intracellular pathogen and it cannot grow in a pure culture. What would be the best technique to use for the detection of this bacterium?
Fluorescent microscopy using anti-chlamydia antibodies

You would like to prove cause and effect for a pathogen that is suspected to cause specific diseases, where you would like to use a method, such as Koch’s postulates, but you cannot cultivate the organism you suspect is causing disease outside of the organism. What could you do to help here?
You can design an antibiotic therapy to eliminate a given pathogen and observe if the disease still affects the animal

Which assay can be used to be used to measure the cell-to-cell spread of intracellular bacteria, but it does not require the use of expensive fluorescence/luminescence microscopy
Plaque assay

How is the severity of the disease determined?
it is determined by both microbial factors as well as host factors

True pathogen or opportunistic:
Yersinia pestis
Burhkholderia cepacia
Acinetobacter baumannii
Pseudomonas aeruginosa

You would like to find the best animal model to study human disease in an animal. There are many important factors to consider while choosing the animal model. Which factor is the least important one/not essential in choosing the animal model
The animal should be close in size to humans

What is the role of IRB?
To ensure that the proposed research study involving human subjects is ethical

Please select features which describe the M1 phenotype of macrophages:
It is differentiated to this phenotype by LPS or TNF-alpha;
It releases such cytokines like IL-1 beta;
It has pro-inflammatory function

Please select the answers the describes the innate immune system
It is short in duration;
Is less specific towards particular pathogen;
Is always on and rapid

Which of the following organs/body surface would normally contain the most bacteria

You would like to find the best animal model to study the function of th1 cells (adaptive immune cells) in the control of bacterial infection. This specific bacterium can infect Caenorhabditis elegans, and you would like to avoid writing an IACUC protocol to perform this research. Based on this information, can you use C. elegans as a model for your study?
False, no

What type of effect do cytokines such as IL-8 have on neutrophils?
Neutrophils are directed from blood vessels to transmigration to the infected tissue.

Match a vaccine type with the description.

  1. Inactivated vaccine
  2. Subunit vaccine
  3. Toxoid vaccine
  4. Live-attenuated vaccine
  5. Use a killed bacteria
  6. Use a specific protein from a bacteria
  7. Use a toxin from a bacteria.
  8. Use an attenuated form of the bacteria

Match Koch’s postulates to Dr. Marshall’s experimental observations/data supporting the postulate with respect to H. pylori as a causative agent of gastric ulcers.
Inoculation of a human with a pure culture of Helicobacter pylori resulted in gastritis symptoms – 3;
Spiral bacteria were present on the Gram stain of the stomach biopsy from human infected with a pure culture of H. pylori – 1

It is 2020 and you would like to conduct a study of 20,000 human patients suffering from bacterial infections in hepatic cirrhosis which were admitted to the clinic between 2018 and 2019. What type of study would it be?
Retrospective study

Which organism is NOT regulated by IACUC protocols?
C. elegans

Under which conditions the human volunteer research is NOT ethical and should not be performed? Select one.
The research is life-threatening yet has to be performed because otherwise postulate #3 will not be fulfilled

Match the animal model with a negative feature of that model:

  1. Caenorhabditis elegans
  2. Galleria mellonella
  3. Drosophila melanogaster (fruit fly)
  4. mouse
  5. it cannot grow at 37 degrees Celsius
  6. It lacks well-established methods for generating mutants
  7. High inoculums of pathogenic bacterium might be needed
  8. Coprophagy behavior can affect microbiota

What are the PAMPs?
pathogen-associated molecular patterns that are components of bacteria and are recognized by host cell receptors


  1. competition assay
  2. ID50
  3. biophotonic imaging
  4. gentamicin protection assay
  5. measures the ratio of mutant to wild-type bacteria
  6. measures the dose of bacteria required to initiate disease in half of animal cohort
  7. measures the infection of luminescent bacteria inside the animal without the need of killing the animals
  8. measures the number of intracellular and adhering bacteria

You plated serial dilutions of Salmonella-infected cell culture from the gentamicin protection assay to establish the number of intracellular bacteria based on the colony-forming units. The next day you obtain colonies on the agar plate and you count them all. Which one(s) of these plates would you use to calculate the number of bacteria? Remember that you have to ensure that the colony numbers are within the appropriate range for meaningful calculation and also for statistical tests.
55 colonies

How does the beneficence principle ensure ethical human volunteer research?
The benefit of the study is maximized while the harm is minimized

You plan an experiment in germ-free mice to identify the function of the complex gram-positive microbiome, which is not culturable in vitro, on the clearance of Salmonella from the gut. Which type of approach would you use?
human microbiota-associated approach

Why do you use gentamicin in gentamicin protection assay?
To kill extracellular bacteria

You would like to find the best animal model to study the function of macrophages (innate immune cells) in the control of bacterial infection. This specific bacterium can infect Caenorhabditis elegans, and you would like to avoid writing an IACUC protocol to perform this research. Based on this information, can you use Caenorhabditis elegans as a model for your study?
Yes, true

Which bacterial molecule is recognized by the TLR4 receptor on human macrophages?

Standard Koch’s postulates can be easily used to study microbial shift diseases

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