Flashcards in Lecture 25 - Molecular Epidemiology of HCAI Deck (20):
What are we detecting when we do PFGE?
SNPs within the bacterial population
Create a phylogeny
Can determine relatedness and thus common source
How do we differentiate bacterial in the population?
- compare whole genomes
Describe E. faecium resistance
- glycopeptide antibiotics
How does E. faecium get resistance to vancomycin?
with the VanB locus
Changes the peptidoglycan so that vancomycin can no longer bind
Describe the transmission models of VRE
- VRE spread from patient to patient in hospital
- people have gut anaerobe commensals with vanB locus, as well as VSE
- in hospital, treatment with vancomycin selects for VRE
What were the surprising findings about our gut commensal?
50% of gut commensals have vanB
What was the French experiment with the mice?
- Mice with gut commensals with vanB and VSE
- Mice treated with vancomycin
- Tn1549 transferred to VSE
- VRE now selected for
Is VSE commonly found in the gut microflora?
Describe the process of genome sequencing
1. Bacteria grown up
2. DNA extracted
Describe the sequencing stage
- ion torrent
'Reads' read against reference genomes
In the study, there were 61 ...
invasive E. faecium isolated studied
What is the phylogeny on slide 26?
Relatedness of the 61 isolates
- core genomes of 61 were sequenced
- many SNPs analysed
- relatedness gave us the tree
What is the phylogeny on slide 28?
What does it tell us?
Analysis of the sequence of the Tn1549
- two different types of the transposon
- some other bacterial species have this transposon
What are the different parameters to do with the transposon that can be analysed?
- sequence of transposon
- orientation of transposon
- position of insertion
- coupling sequence
What would be observed when all the information about the transposon is overlayed on the core genome phylogeny if model A were correct?
Closely related bacteria have similar transposon features
The transposon has been passed on from a common ancestor
What would be observed when all the information about the transposon is overlayed on the core genome phylogeny if the alternative model were correct?
De Novo formation
Closely related bacteria have differe transposon features
Because the transposon has arisen de novo, not been passed on from common ancestors
What conclusions have been made from this new study?
VRE arises by de novo evolution
Gut anaerobes are potential sources of Tn1549
What is the transposon that conferrs vancomycin resistance?
What is vanB?
This is a single locus (gene) on the Tn1549 transposon