T3: Normal Microbiota

Question 1

Define normal flora.

Answer 1

Organisms found in a given location in a state of health.

Question 2

Define colonisation.

Answer 2

Establishment at a site in the body.

Question 3

Define microbiota.

Answer 3

All the organisms in a given community.

Question 4

Define microbiome.

Answer 4

All the genes present within the microbiota .

Question 5

Define symbiosis.

Answer 5

Two or more organisms co-exist in close physical association.

Question 6

Give the different forms of symbiosis.

Answer 6

There is different types of symbiosis:

• Mutualism: Both organisms benefit from symbiosis
• Neutralism: Neither organism derives benefit or harm
• Commensalism: One organism benefits, the other derives neither benefit nor harm
• Parasitism: One organism (parasite) benefits at the expense of the other (host)

Question 7

What is the impact of non-sterile sites on clinical samples from sterile sites?

Answer 7

The non-sterile site vary with the amount of normal flora. The genital tract in females in a non-sterile site along with the GI, nasopharynx, conjunctiva and the skin. Non-sterile sites therefore may have an influence on clinical samples from sterile sites.

• Blood culture/CSF/pleural fluid - are all obtained by passing a needle through the skin. There is therefore the potential for contamination with skin organisms
• Sputum sample - obtained by expectoration of lower airway secretions through the upper airway. There is the risk for contamination.
• Urine sample – obtained by passing urine from the bladder/upper urinary tract (‘sterile site’) via the terminal urethra (‘non-sterile site’). Risk of contamination reduced by collecting Mid Stream Urine (MSU) sample - the first part of the stream is discarded and the next part is collected into the sample pot.

Question 8

How are sterile sites maintained?

Answer 8

• Sterility maintained by surface cleaning
• e.g. lower respiratory tract - uses cilia to clear secretions from the surface
• Sterility maintained by barriers (allow uni-directional flow) - anatomical distances involved my help to protect higher parts with an prefix
• These are Adjacent to non-sterile sites
• e.g. upper genital tract protected by the cervix
• e.g. urinary tract protected by the urethra
• Sterility maintained by physical separation from non-sterile sites
• Closed cavities - many parts have no immediate opening to the outside world
• e.g. pleural cavity, peritoneal cavity, spinal cord and meninges

Question 9

What is tissue tropism?

Answer 9

This is a propensity for a particular organism to grow in a particular habitat.

Question 10

What is the difference in the microbiota that can colonise the skin compared to the teeth?

Answer 10

The skin Has a very variable temperature, it is dry (some have more moisture than others) and subject to abrasion. It is an aerobic environment, nutrient-poor and there are skin-surface components e.g. secretions by hair follicles which may influence how and wear organisms survive. Huge variation between microbe composition of different areas. Most bacteria sequestered in sweat glands.

The gingival crevice (between the skin) - has a constant body temperature that reflects the bodies temperature. It is more moist and few physical challenges (toothbrush, food etc.). It is mostly an anaerobic environment and bathed in nutrients (saliva, food etc.) Mucosal surface excretions are different from those in the skin. It therefore holds more anaerobes and oral streptoccocci.

Question 11

What flora are common to the skin?

Answer 11

Skin flora include:

• Gram positive organism such as Coagulase-negative staphylococci (Staphylococcus epidermis) survive and prosper in this area.
• Staphylococcus aureus (esp. in nasal carriers) especially in areas of broken skin.
• Propionibacterium species (Propionibacterium acnes) - found in areas that produce large amounts of sweat

Question 12

What flora are common to the vagina?

Answer 12

The flora here will change depending on the age.

Pre-puberty the flora is similar to the skin flora and lower GI flora i.e. mainly E. coli.

Post-puberty there is glycogen produced due to circulating oestrogens affecting the mucosal surface. This facilitates colonisation of different organisms such as:

• Lactobacillus spp. Lactobacillus acidophilus. These bacteria ferment glycogen, maintaining a pH ≈3, preventing overgrowth of other species.
• Skin flora
• A few C. albicans

In the menopause and the hormonal balance changes back again it goes back to an environment similar to that of the skin and lower GI tract. There is a low pH beneficial in preventing infection by opportunistic pathogens e.g. overgrowth of C. albicans – causing Thrush.

Question 13

What flora are common to the nasopharynx?

Answer 13

Find here skin flora - Staphylococcus aureus is a very common organism found here (found in 25% of people at any one time). The pharynx may support the growth of other respiratory flora:

• Streptococcus pyogenes (group A) - causes strep.
• Haemophilus influenzae
• Streptococcus pneumoniae
• Neisseria meningitidis 7-34% in UK university students - in most people causes no harm.
• S. aureus

Question 14

What flora are common to the GI tract?

Answer 14

Low pH inhibits bacterial growth. Tends to be predominantly aerobic bacteria e.g.

• Acid-tolerant Lactobacilli
• Helicobacter pylori (associated with duodenal and gastric ulceration)

As you move down the GI tract, the count increase away from the acidic environment. Much larger and greater density of microbes. The greater bulk are anaerobes:
- 95-99% Anaerobes
such as Bacteroides spp., Clostridium spp. Bifidobacteria spp
- Aerobic bacteria
include Enteric Gram-negative bacilli such as Escherichia coli (most common), Klebsiella spp., Enterobacter spp., Proteus spp., Citrobacter spp. etc.

Question 15

What are the benefits of microbiota in health?

Answer 15

• Metabolism - Synthesis secondary metabolites/vitamins. Enteric bacteria helps to produce vitamins which are then absorbed e.g. vitamins K and B12 secreted by enteric bacteria. The bacteria also work in fermenting unused energy substrates (SCFA).
• Colonisation resistance - a defence of pathogenic organisms. They do this by environmental manipulation e.g. changing the pH to inhibit the growth. It is also done through the production of antibacterial agents e.g. colicins, bacteriocins, fatty acids, metabolic waste products.
• Induction of cross-reactive antibodies. May have a protective effect for example carrying N. meningitis reduces the chance of you getting meningitis.
• Oral microbiota helps in the production of nitric oxide - this may help maintaining healthy blood pressure. Mouth wash which contains antiseptics, may cause damage microflora and cause a raise in blood pressure in the long term.
• Normal healthy flora may be linked to gut health and hormone levels.
• Maintaining diversity may be associated with obesity. Athletes tend to have a greater range.

Question 16

What are the features of a C. diff infection?

Answer 16

• Often a Hospital acquired infection. (can be acquired in community.
• Usually found in over 60s.
• Main risk factor ANTIBIOTIC TREATMENT - this is due to a disturbance in normal microflora and so there is overgrowth of C. difficle so it can produce a toxin that interacts with the mucosal surface in the large bowel and leads to diarrhoea and pseudomembranous colitis. In extreme examples it can be life threatening.
• Perturbation of normal colonic microflora allows C. difficile overgrowth

Question 17

How can faecal transplants be used in treatment?

Answer 17

Recently this has made a comeback in the treatment of C.diff. It helps to restore the previously lost healthy microflora.

Question 18

How can we get pathology of normal flora? Give examples of each case.

Answer 18

• Translocation of microflora. This is the presence of flora at the wrong site. It may have spread from one surface to another or inoculation into a normally sterile site. An example of this is in chemotherapy for cancer such as leukaemia, and you become neutropenic, you can get gut translocation. Bacteria from the gut can leak into the blood stream and you can get sepsis.
• Over-growth of microflora - an example of this is vaginal thrush. A case could include a 26 year old female treated with broad spectrum antibiotic for sinusitis. You therefore may kill off the normal flora. This leads to a development vaginal itch with creamy vaginal discharge.
• Cross-infection - can be exogenous or endogenous. An example of the is MRSA.

Question 19

How can clinical conditions be caused by normal flora?

Answer 19

Depending on the particular situation.

• Pneumonia may be caused by micro aspiration of organisms form the upper areas from the organisms that live there in the nasopharynx such as streptococcus pneumonae and haemophillius influenzae.
• Endocarditis - may be cause by oropharyngeal streptococci that get into the blood stream which happens normally when we brush our teeth or we bite our gums. If you have an underlying valvular disease, the organisms can lodge on this can cause endocarditis.
• Urogenital infections - there is E.coli at the end of the urethra and these can extend or climb, adhere to the uroepithelia and ascend to the bladder and cause urinary tract infections such as cystitis, and even further to cause pyonephritis.
• Gastroenteritis - C.diff etc. and gut translocation in neutropenia. In a perforation, ion malignancy, diverticular disease, then you can get peritonitis as you release large gut flora into a sterile site.