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
What is antigenic drift?
β the same antigen changing its sequence base by base
What is the assumption that allows us to make accurate predictions ?
β constant molecular clock
Why does diversity progress?
β Random mutations occur at a regular rate
What are the 5 things that can affect the speed of the molecular clock?
β Bacterial replication rate
β DNA or RNA polymerase proof reading fidelity
β selection pressure from the host or environment
β degree of redundancy in the genome
β transmission rate
What does a higher bacterial replication rate provide?
β A high division rate provides a higher mutation rate
What does having low proof reading fidelity mean?
β Some species (eg HIV) have low fidelity promoting high mutation rate
What does having high and low selection pressure mean?
β High selection pressure removes βweakβ mutants and emphasises clusters
βLoss of selection pressure allows deletions
What does having redundancy in the genome mean?
β multiple copies of a single gene in the genome allow for
mutations in one copy without compromising overall functionality
βMovement or recombination within genome may not affect phenotype
What does a high transmission rate result in?
β High transmission rates relative to the mutation rate
results in dissemination and single strain outbreaks
Which genes change the most?
β Hyper-variable genes change more rapidly than conserved genes
Which genes are more likely to be associated with phenotype and virulence?
β Conserved genes are more likely to be associated with phenotype and virulence
What is convergent evolution?
β Not all changes are new
Some may revert BACK to an older profile (convergent evolution)
What do large and rapid changes lead to?
β escape from existing herd protection
What is antigenic shift?
β a sudden replacement of an antigen by recombination with another viral type that has evolved separately (either in another animal or another human population)
What are the three epidemiological associations?
β Transmission
β reservoirs of infection - contact tracing or determining introduction events
β spread or emergence of resistance
What can monitor effectiveness of control measures?
β Molecular restriction digest
What does choosing the most appropriate system require?
β Knowing the most appropriate variable/s
βQuantitating variations and deriving diversity
β Generating identities or clusters
β Applying related data
