Lecture 11 - Molecular Epidemiology

Question 1

What are some problems with standard identification protocols of infectious microbes?

Answer 1

Unable to be cultured.

Closely related strains unable to be distinguished.

Question 2

What is a solution to these aforementioned problems?

Answer 2

Molecular strain typing

Question 3

What make a good molecular technique?

Answer 3

Reliability - same result as other experiments.
Reproducibility - easily reproduce same result when repeated.
Distinction - fine distinction between closely related strains.
Ease of interpretation
Cost effective

Question 4

How are differences identified by restriction enzyme digestion?

Answer 4

Genetic fragments are generated when the genome is digested by restriction enzymes that will cut at specific locations. Generates different number of fragments of different sizes. When run on standard gel electrophoresis will generate different genetic fingerprints.

Question 5

How is Pulse Field Gel Electrophoresis used?

Answer 5

Run on an agarose gel, electric pulse is switched to change direction constantly, creates a genetic fingerprint that can be compared to online database. Used for larger genomes e.g. bacteria.

Question 6

What is fragments based methods using amplification?

Answer 6

Amplify DNA by probes, run on agarose gel. Generate PCR. Similar to restriction fragment length polymorphism.

Question 7

How is target repetitive sequence changes used to identify differences?

Answer 7

Only amplify VNTR region, differences in number of repeats will create different fragment.

Question 8

Outline target single nucleotide sequence method.

Answer 8

Amplify region with SNP then sequence. Can have MultiLocus Sequence Typing or sequence whole genome.