iii. Normal Bacterial Flora and Colonization Resistance

Question 1

Where do microbes exist?

Answer 1

• Microbes exist on body surfaces (skin and mucous membranes are not sterile) and are
  described as normal flora or microbiota.

Comprised mainly of bacteria, but depending on the site may include viruses, fungi and protozoa as well.

Question 2

• Microbes that usually occupy a particular body site are called the ______ flora.
• Microbes that colonize a site only transiently (even for hours to weeks) are called _______
  flora.

Found on the superficial layer of the skin and are more amenable to hand washing

Answer 2

resident
transient

Question 3

• Surgical scrub (cleaning of hands and lower arms) reduces the number of resident flora on
  the surgeon’s _____. Antimicrobial soap is used while scrubbing for __-___ minutes.
  Even though a surgeon may use double gloves, glove _______ may still occur and surgical scrubbing prevents the spread of organisms from the surgeon’s hand to ______ areas on the patient’s body.
  Resident flora reduce in numbers but re-establish themselves with time.

Answer 3

skin
3-5
perforations
sterile

Question 4

Normal Flora-Host Interaction:
- The relationship between the normal flora and the human host may be one of: (3)

Answer 4

o Commensalism
o Mutualism
o Parasitism

Question 5

What is o Commensalism?

Answer 5

o Commensalism: The microbe derives benefit from the host and the host is not harmed.

Question 6

What is o Mutualism?

Answer 6

o Mutualism: Both the host and the microbe benefit from the interaction. Microbe usually benefits by living in a specific niche within the host.

Question 7

Host benefits from bacteria presence in many ways: (5)

Answer 7

Question 8

What is parasitism?

Answer 8

o Parasitism: The microbe benefits at the expense of the host.

Example: Hook-worm infection where the worms attach to the small intestine epithelium using their hooklets. Hooklets result in intestinal blood loss and can lead to anaemia in the host.

Question 9

The gut microbiota influence local and systemic processes: (4)

Answer 9

• Gut-to-brain communication
• Proper functioning of the gut microbiota is dependant on a stable cellular composition.
• Dysbiosis
• Several exogenous and endogenous factors can affect the composition of the gut microbiota

Question 10

What is gut-to-brain communication?

Answer 10

Bidirectional interactions between the CNS, Enteric nervous system (ANS of the gut) and the GIT overall.
Studies in rodents show that changes in their microbiota can exert effects on emotional behaviour and stress modulation systems. This occurs through multiple mechanisms including endocrine and neurocrine pathways. However, it is not clear whether rodent findings can be transferred to human physiology but if so, diseases such as anxiety disorders, Parkinson’s and Autism can potentially be impacted by manipulating gut microbiota.

Question 11

How is the proper functioning of the gut microbiota is dependant on a stable cellular composition?

Answer 11

There is a balance in terms of the types of microbes and the relative numbers of each type of
microbe that need to be maintained for normal functioning of the gut microbiota.

Question 12

What is dysbiosis?

Answer 12

Disturbance in composition and function of microbiota. Alterations can persist for prolonged periods and often the initial state is not completely recovered. Gain or loss of specific microbiota or a change in the relative abundance of specific microbiota.

Question 13

• Several exogenous and endogenous factors can affect the composition of the gut microbiota
  o Use of antibiotics:

Answer 13

Suppression of (components of) the normal flora and changes in metabolism in the gut.

Example: E.coli UTI, prescribed Amoxicillin-clavulanate. Broad-spectrum beta lactam antibiotic, spectrum includes gram-positive organisms, gram-negative organisms and anaerobes. Ideally you would want the drug to specifically target the bladder and eradicate E.coli in the bladder. However, Amoxicillin-clavulanate is taken orally so the gut flora is exposed to it, it is absorbed into the bloodstream and all parts of the body will be exposed to the drug.

This antibiotic as a result is able to supress your normal bacterial flora but will allow for fungi, such as candida in your mouth and urogenital tract, to proliferate (advantage) – Oral or Vaginal thrush.
Antibiotics can also change metabolism in the gut, does this by changing the types of nutrients available and the amount of nutrients available. It is possible that pathogenic organisms from outside the body are able to use these carbohydrates and can colonise the host, while the normal flora cannot utilise the changed nutrients and die.

Question 14

• Several exogenous and endogenous factors can affect the composition of the gut microbiota
  o Diet:

Answer 14

High sugar, high fat and low amounts of fermentable fibre are associated with dysbiosis.

In contrast, high fibre diets with low sugar and aft are able to promote appropriate energy homeostasis and a s a result reduce the chances of obesity and metabolic disorders. Also able to promote appropriate immune responses and decrease the risk of auto-immune conditions.

Question 15

• Impact of dysbiosis can be far reaching: (3)

Answer 15

o Loss of colonization resistance
Pathogenic organisms are easily able to gain access to our bodies.

o Risk/severity of auto-immune conditions

o Neurological disorders and metabolic disorders

Question 16

• The relationship between the host and the normal flora can change from time to time. This may be due to: (3)

Answer 16

o Dysbiosis (change in the function or composition of normal flora)

o Change in host local non-specific defence mechanisms

o Systemic immune-compromise

Question 17

o Change in host local non-specific defence mechanisms

Give a few examples: (2)

Answer 17

Question 18

o Systemic immune-compromise
How does this change the relationship between the host and normal flora?

Answer 18

Question 19

• Resident flora at each body site comprises several different types of microbes.
• Factors such as ….. (7) influence the microbial composition of resident flora.

Answer 19

age, diet, genetic make-up, gender, geographical location, sanitary conditions and hygiene habits

Question 20

• Faecal flora of young children is less ______ than adults. The first bacteria to colonize the gut of new-borns originates from the mother’s birth canal – Organisms such as Escherichia coli, Streptococci, Lactobacillus, _______ organisms such as Clostridium species, Bacteroides and Bifidobacterium.

Around the ages of __-___ years, the normal flora of children starts to resemble that of an adult.

Answer 20

complex
anaerobic
1-3

Question 21

• In the developing world where access to piped water and sanitation is problematic.

______ of protozoa like Entamoeba coli may be more common.
- If disturbed, by hand washing for example, the _____ flora re-establish themselves

Answer 21

colonisation
resident

Question 22

• Antimicrobial use (antibiotics), healthcare exposure and underlying medical conditions are
  important factors that can influence the composition of an individual’s normal flora.

What are 2 examples of this?

Answer 22

• Example 1: Antibiotic like metronidazole which has activity largely against anaerobic organisms only, may result in suppression of large amounts of flora within the colon. With this suppression, there is the potential for more pathogenic organisms to colonize the colon.
• Example 2: If a broad-spectrum antibiotic is used, there may be widespread suppression of all bacterial flora throughout the body which may result in the overgrowth of candida.
  In the healthcare setting there are many organisms that are ‘hardy’ and able to persist on surfaces in the hospital environment (bedrails, bedside tables, doorknobs can all become colonized with hospital-derived organisms). Healthcare worker hands can also become a problem – If not sanitized before and after all patient contact will lead to transmission of organisms from patient to patient.
  Often when patients are admitted into hospital, invasive devices may be needed for survival

Question 23

– ICU ventilation._______ with an endotracheal tube – Tube passes through the mouth, glottis and into the trachea. Therefore, all the oropharyngeal flora will ______ the endotracheal tube and form biofilm which may act as a source of infections.

Another important factor within hospitals is the fact that large amounts of antibiotics are used, this antibiotic burden may result in the selection of multidrug-resistant organisms. Thus, being exposed to the hospital environment increases a patient’s risk of becoming colonized with more resistant organisms, particularly if you have received antibiotics that have ______ your normal flora.

Underlying medical condition example: Patients with Bronchiectasis. Condition where there is abnormal irreversible dilation of bronchi – Patients are unable to clear normal secretions which reach the lower respiratory tract. Patients become colonized with unusual organisms such as _________ (very unusual for a person with normal airways).

Answer 23

Incubation
colonize
suppressed
pseudomonas

Question 24

CONCEPT OF DIFFERENT TYPES OF MICROBES BEING FOUND AT DIFFERENT ANATOMICAL SITES (Don’t need to know the specific organisms at each site – Know that different anatomical sites will have a different spectrum of organisms)

Upper Respiratory Tract Normal Flora: (5)

Answer 24

Question 25

Gastrointestinal Tract Normal Flora: (4)

Answer 25

Question 26

Genitourinary Tract Flora: (2)

Answer 26

• Lower urethra: Enterobacterales, streptococci, enterococci
• Vagina: As above, plus Lactobacillus spp, anaerobes

Question 27

Skin Normal Flora:

Answer 27

• Coagulase negative staphylococci (CNS), Bacillus spp, diphtheroids, Propionebacterium (now renamed Cutibacterium spp, Staphylococcus aureus – Transient or resident carriers (perineum and axilla in some individuals), viridans streptococci, Micrococcus spp

Question 28

What is Colonization Resistance?

Answer 28

• Normal flora play an important role in protecting the host from colonization and invasion by pathogenic microbes (microbes that are able to cause infections).

Question 29

Colonization Resistance
- Direct mechanisms: (3)

Answer 29

Question 30

Colonization Resistance
- Indirect mechanisms: (3)

Answer 30

o Enhancement of epithelial barrier function
Thick impermeable mucus layer found on the inner surface of the colon. Barrier prevents organisms from adhering to the epithelium layer in the colon – Development of this mucus layer is dependent on normal flora which induce goblet cells to produce larger amounts of mucus.

o Stimulation of innate immune system
With exposure to certain pathogens, the normal flora is able to promote immune defences by triggering specific responses that lead to the secretion of proinflammatory and antimicrobial proteins by the host.

o Stimulation of adaptive immune system
Certain parts of normal flora are able to preferentially drive the differentiation of individual T lymphocyte subsets. Thus, able to influence the types of cytokines produced and the immune response to resist infection by pathogens. Normal flora also contribute to the development of B lymphocyte cells in the GALT and result in the production and secretion of IgA (part of the intestinal barrier, preventing adherence to colonic epithelium by invading organisms).

Question 31

What are probiotics?

Answer 31

• “Live microorganisms, which, when consumed in adequate amounts, confer a health benefit on the host” - UN and WHO, 2001

Question 32

Probiotics
- Evaluated as prevention or treatment strategies for multiple gastrointestinal and other diseases: (9)

Answer 32

Question 33

What are the most commonly studied organisms?

Answer 33

• Most commonly studied organisms are of the Bifidobacterium and Lactobacillus genera These organisms are often found in dairy products, but you can also take it in a pill form. Advised to take a probiotic when prescribed an antibiotic – Antibiotics suppress normal flora and cause dysbiosis. Probiotic will prevent this dysbiosis and allow for restoration and balance of normal flora.

Question 34

• Example: Clostridiodes difficile-associated diarrhoea

Most of us have small amounts of no ________ difficile in our gut. But when you are prescribed a broad-spectrum antibiotic, normal flora are suppressed and allows small amounts of Clostridiodes difficile to proliferate OR in the hospital become exposed and you become colonized with it.

Clostridiodes ______ is allowed to multiple and produces large amounts of a toxin which causes severe diarrhoea.

One effective treatment option for this diarrhoea is a _____ ______ _____ - Stool transplant to patient from someone who doesn’t have Clostridiodes difficile-associated diarrhoea. Stool is administered through a nasogastric tube or through a colonoscopy. Resolves the ______ and restores the balance of the normal colon flora. If the balance is restored the Clostridiodes difficile will be suppressed, and the diarrhoea will improve.

Answer 34

Clostridiodes
difficile
faecal microbiota transplant
dysbiosis

Question 35

• Mechanisms of probiotic action include: (4)

Answer 35

Question 36

• Future research on probiotics: (2)

Answer 36

o Characterize probiotics and their mode of actions against specific pathogens.

o Identification of vulnerabilities within target pathogens to aid probiotic design.