Molecular Markers II & III Flashcards
A cluster is…
In the context of an outbreak, a subset of the collected genotyped data from individuals that share the same transmission event. Cases are linked by the same transmission chain. Strains that have been recently transmission should have minimal differences.
This can be because of strain, phenotype or genotype differences between isolates.
On a phylogenetic tree, clusters would normally have short branch lengths.
Why is sampling important in cluster analysis?
The conclusions you draw from a population in terms of an oubtreak can depend on the sample selection.
Too few representatives in the subset and you could miss capturing particular strains/ individuals.
If there are non-clustered strains within your subset, this may be due to sampling bias (the isolate really should be clustered but you’re missing like individuals in the subset) or due to an importation event.
What are the steps of WGS?
Clinical sample (blood, urine, etc)
->
Pathogen isolation
->
Protein/ nucleic acid extraction from isolates
->
Purify DNA
->
fragment DNA
->
Sequence
->
Align/ assemble reads where fragments overlap
->
Genome
Short (Illumina) AND long (nanopore) reads can be sequenced depending on the sequencing technology used.
Long reads are easier to cope with repetitive regions (generally discarded), inversions and translocations.
Difference between cladogram and phylogenetic tree?
Cladogram purely a representation of the number of differences between the isolates involved. can be a measure of relatedness but no measure of HOW related or when the differences arose.
Phylogenetic trees represent genetic differences (substitutions or time) as a scale for the branch lengths.
branch length = quantitative measure of genetic distance.
Unit = substitutions per site
Compute the genetic distance between two isolates on a tree.
On a tree with units for genetic distance (substitutions per site), only add the branch lengths (horizontal) not vertical lines.
What is the difference between acquired and primary resistance?
Acquired - convergent evolution (could be result of HGT). Resistance mutation appears multiple times across isolate in tree, even in those without a common ancestor.
Primary - suggest one acquisition of resistance. This was passed down to next generations. Those with the resistance mutation can be grouped together in the tree.
Are phylogenetic trees representative of transmission events?
No, transmission trees are and they are distinct from phylogenetic trees.
Additional to phylogeny, they take into account how the pathogen evolves, transmits, how the pathogen sampled as well as considering patients who weren’t sampled.
Can indicate who gave pathogen to who.
