L3: Molecular Markers I

Question 1

What can Mol. Epi. be used for?

Answer 1

On the one hand you can apply it to classical problems such as outbreak investigations and surveillance, on the other hand you have more derived applications such as learning about the origin and evolution of pathogens or the study of host-parasite coevolution.

Question 2

Design of a Mol. Epi. study

Answer 2

1. Study objective
2. Study sample
3. Obtaining isolates
4. Choosing markers
5. Choosing typing method
6. Analysis

Question 3

What type of sample can you obtain?

Answer 3

• Patient isolates form hospitals
• Clinical specimens from an outbreak
• Food items (outbreak investigations)
• Environmental samples

Question 4

What is commonly used as molecular marker?

Answer 4

• SNPs (single nucleotide polymorphism)
• Insertions
• Deletions
• Transposons
• VNTRs (variable number of tandem repeats)
• CRISPR regions

Question 5

How do you select the correct technique to answer your research question?

Answer 5

1. Identify the research question
2. Decide at which level you want to type
3. Choose appropriate markers

For 2. Local, regional, global?
For 3. Performance and convenience is an importent criterium, but also the discriminatory power and stability of the marker.

Question 6

What is discriminatory power?

Answer 6

For a marker, the discriminatory power is essential. It is the ability to distinguish units of information from a given set of isolates i.e. distinguish what is different. The higher the numbers of discrete units of typing generated the higher the discriminatory power the more “resolution” you can get, not just on the species level but on the level of isolates.

Question 7

Stability of a marker

Answer 7

Different molecular markers have different rates of changing. This depends on the molecular clock. When choosing a marker the rate of change must be high enough to distinguish unrelated strains but low enough to link related cases.

For outbreak investigations: stability around 6 months.
For long term surveillance: 2 years

Question 8

Definition

What is an outbreak?

Answer 8

The appearance of a cluster of an illness that occurs in numbers higher than expected for that time/place.

Question 9

Definition

What is cluster analysis?

Answer 9

Cluster analysis is a comparative analysis of (typing) data collected for a multitude of isolates in order to group the isolates according to their similarities. It can lead to the identification of common traits shared within the cluster.

Question 10

You wish to elucidate the origin of a pathogen and its derived species. You choose SNPs as markers. Is this appropriate?

Answer 10

No. In order to answer the question “who was first” you always need to do whole genome analysis.