Molecular and Genomic Epidemiology of Pathogens Flashcards
What is molecular epidemiology?
βMolecular epidemiology : a resolved measure (diversity) of differences (variables) that determines βDisease distribution in time and place βDisease transmission βDisease manifestation βDisease progression
What can molecular epidemiology confirm?
β outbreaks
Where can molecular epidemiology confirm outbreaks from?
β Inside institutions - whether it was the same strain βInside institutions -who the index case was and the source βIn the past - what drives the geographical spread of important strains βIn the past -outbreak or containment
What risks can molecular epidemiology identify?
β disease risks
What are functional targets?
β biochemistry
β serology
β virulence
How many functional targets do you need to look at?
β single functional target
What are the genomic targets?
β DNA - gene, amino acid sequence, base sequence
β RNA - ribosome, miRNA
How many genomic targets do you need to look at?
β multiple
What is a single weighting?
β presence or absence of a target
What is an additive weighting?
β a combination of single tests
What are the 4 ways of investigating E.coli?
β culture on selective media
β O157 serotyping using antibody on blue latex beads
β PCR of DNA verotoxin genes
β phage typing
For multiple weighting what genomic factors do you look at?
β factoral : presence or absence of a gene/base/change in a genome/gene relative to the location in the genome
β functional : type of substitution (synonymous-non synoymous)
β temporal : mutation rate (time since last alteration)
How does spoligotyping work?
βPCR with
RE region primers
generates multiple length
amplicons
βHybridization of labelled PCR products onto 43 spacer specific oligonucleotides (between RE sequences)
fixed on a membrane then visualise signal with RE probe
How do factoral copy numbers work in TB?
β there is one part of the genome which is called the DR region
β it has the possibility of having upto 43 copies of the same gene
β the 43 copies are not in every single organism
β the number varies as the organism is transferred from one patient to another
What is the strain of TB based on?
β the variation in copy number
β and the pattern of the copies
What does the result of spoligotyping give you?
β profile of the presence/absence of specific repeats at one locus
What does a spoligotyping dendrogram show?
β relatedness of pattern
What is another method to find out copy numbers?
β PCR
What does the result of PCR give you?
β the number of specific repeats at multiple genomic loci
What is a silent mutation?
β Mutations that are Intragenic (between genes)
βor Synonymous (not altering coding)
What is a non synonymous mutation?
β Substitutions causing coding to be altered
What are 4 corruptive mutations?
βDeletions or Insertions (disrupting coding frame)
β Creation of STOP codons (truncation)
βCorruption of STOP codons (elongation)
βCorruption of CONTROL sequences (eg. promoters)
What is gradual alteration in sequence called?
β DRIFT
What does herd immunity do to viruses?
β Herd immunity (after large vaccination program) kills most but also selects for escape mutants that maintain the drift
