System for Detection of Pathogens 1 and 2

Question 1

Recap the way that we classify all organisms - taxonomy

Answer 1

Question 2

How many mycobacteria (a genus) are obligate human pathogens?

Answer 2

3

Question 3

Name the mycobacteria that are obligate human pathogens

Answer 3

• M. tuberculosis
• M. leprae
• M. ulcerans

Question 4

Explain what a commensal non pathogen is

Answer 4

Present but not capable of causing disease in the host

Question 5

Explain what a Zoonotic non pathogen is

Answer 5

Present but only capable of causing disease in another host

Question 6

Explain what a commensal opportunist is

Answer 6

Present and capable of causing disease in the host but only in certain circumstances

Question 7

How can we define a pathogen?

Answer 7

A microbe capable of causing a specific degree of host damage

• does not HAVE to cause damage

Question 8

Why might samples not come back as positive for a pathogen when they should be?

Answer 8

• sterile sites (like blood) need to be free from contamination
• non-sterile sites require decontamination of normal flora
• samples with high volume or low pathogen load require concentration by centrifugation or filtering

Question 9

Do all pathogen samples need to be cultured?

Answer 9

No

Question 10

Apart from gram staining, what might we look for in a bacterium?

Answer 10

• capsule
• spores formation (anthrax) - also where they are on the bacterium
• immunofluorescence and other tests

Question 11

What is meant by non-selective vs semi-selective media on an agar plate?

Answer 11

These are mediums that only grow specific organisms

• Non Selective Media
  
  • e.g. Blood agar
• Semi selective media
  
  • e.g. MacConkey Agar, DCA, CLED

Question 12

What is an aerobic culture?

Answer 12

A culture in oxygen - you can also do an anearobic culture which does not have any oxygen (or CO2?) at all

Question 13

What type of bacteria tend to grow in anaerobic cultures?

Answer 13

Gut bacteria

e.g Clostridium tetani, Clostrium botulinum, Clostridium difficile, Bacteroides fragilis

Question 14

What is a microaerophillic culture - what kind of bacteria can grow?

Answer 14

This is growing in CO₂ - so respiratory pathogens will grow, including gonorrhoeah and meningitis

Question 15

Give an example of a bacteria type that we can identify by growing it at the specific temperature of 42 degrees

Answer 15

Campylobacter

Question 16

Aside from selectiveness of media on agar plate, name other ways that we can identify bacteria by culturing it from a swab (not genotyping)

Answer 16

• we can also use selective growth temperatures to do this
• we can also do this by the environment (so, like, oxygen content)
• specific haemolysis of blood for strep
• metabolic testing (how it uses sugars)

Question 17

What is phage testing?

Answer 17

bacteriphages are very specific to certain bacteria and only lyse certain bacteria - so we can test if the bacterium lyses in the presence of a specific phage

• this will not identify it but will phage type

Question 18

What is serotyping?

Answer 18

Serotyping is a subtyping test based on differences in microbial (e.g. viral or bacterial) surfaces Serology refers to the antibodies that form because of a viral or bacterial infection.

• is testing the outer surface!

Question 19

What is meant by molecular gene targeting in this context of detection of pathogens?

Answer 19

Where we aim to detect a gene or gene product that is specific to the pathogen

Question 20

Name a way that we can do molecular gene targeting in this context (detection of pathogens)

Answer 20

• PCR (polymerase chain reaction)

NAAT (nucleic acid amplification techniques) - PCR is a type of NAAT

Question 21

What is strand displacement amplification?

Answer 21

This is another type of amplification that is slightly different to PCR - this is also a type of NAAT

Question 22

What is MALDI-TOF?

Answer 22

• Matrix Assisted Laser Desorption Ionization-Time-of-Flight

Question 23

How does MALDI-TOF work?

Answer 23

Breaks up the bacterium with lasers and other means and measures the ‘time of flight’ of the different components and produces a signature specific to the bacterium species

Question 24

How can we use MALDI-TOF?

Answer 24

We can compare the signatures of an unknown bacterium to known profiles

Question 25

Name some advantages and disadvantages of MALDI TOF profiling

Answer 25

Advantages

• Rapid
• Specific Identification

Disadvantages

• Requires pure culture
• Requires rigorous calibration and protocol standardisation
• Will only identify known profiles

Question 26

What is metabolic profiling?

Answer 26