System for detection of pathogens

Question 1

What is a commensal pathogen?

Answer 1

present but not capable of causing disease in the host

Question 2

What is a zoonotic pathogen?

Answer 2

present but only capable of causing disease in another host

Question 3

What is a commensal opportunist?

Answer 3

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

Question 4

What is a pathogen?

Answer 4

= microbe capable of causing a specific degree of host damage

Question 5

When detecting for pathogens, what must the sample require?

Answer 5

• Sterile sites free from contamination
• Non-sterile sites require decontamination of normal flora
• Samples with high volume or low load of pathogens requires concentration

Question 6

What are the 3 basic ways of identifing different types of pathogens?

Answer 6

1. Direct light microscopy of big samples is useful
2. Direct electron microscopy of small samples
3. Direct bacterial staining of samples - gram negative (orange), gram positive (pink)

Question 7

What are the basics of using classical culture to identify pathogens?

Answer 7

Bacteriology relies on the ability of the test system to be able to grow the pathogen

Different types of media:

• Non-selective media - no limit on what to grow
• Semi-selective media - what you want to grow
• Selective growth temperatures - different organisms like cows and humans have different body temperatures
• Selective atmosphere - eg. Different levels of oxygen, CO2 etc. (top of lungs like oxygen, bottom like CO2)
• Specific haemolysis of blood

Question 8

What is molecular gene targeting?

Answer 8

= aims to detect a gene or gene products that are pathogen specific

NAAT

• PCR- amplfication cycle
  
  • quantitative PCR - measures the speed at which a PCR amplicion product accumulates by the amount of florescence released
• Strand displacement amplificiation SDA

Mass spectromtetry - MALDI-TOF

• length of time it takes to get to the detector, depending on charge and size
• it makes a peak once it hits the detector, which can then be interpreted and compared against the control profile to see what is present
• advantages - rapid and sepcific identification
• disavantages - requires pure culture, will only identify known profiles

Question 9

What are the checklists for molecular testing?

Answer 9

• Specificity
• Reliability
• Sensitivity - how many organisms can it detect
• Accuracy - live or dead organism
• Rapidity - beneficial to patient, bed side/same day

Question 10

What are biomarkers of virulence?

Answer 10

= looking for selected genes or gene products that drive the disease process

• serotyping = looks for antibodies present from the virus/disease
  
  • specific cell wall antigens are predictive of invasiveness and virulence
  • using an ELISA to detect
• advantages = good specificity and sensitivity and easily automated
• disadvantages = response isnt rapid, some antibodies are cross-reactive and not useful in acute infections - you are relying on the body to make antibodies to find presence of the pathogen

Question 11

What is rapid sequencing?

Answer 11

= Next generation sequencing

• Sequencing can show differences between single bases in strains or resistance mutations to antibodies
• **not all of the possible mutations are involved in virulence

Advantages - rapid, allows appropriate therapy

Disadvantages - expensive, requires expertise, labour intensive