Molecular and Genomic Epidemiology of Infections Flashcards
Molecular Epidemiology - define and describe what it determines
A resolved measure (diversity) of differences (variables)
that determines
a) Disease distribution in time and place
b) Disease transmission
c) Disease manifestation
d) Disease progression
What kind of questions can molecular epidemiology answer in confirming outbreaks - inside institutions
inside institutions
Did patient A catch this pathogen from patient B?
Do patients A, B & C from the same hospital ward have the same strain?
What kind of questions can molecular epidemiology answer in confirming outbreaks - in the community
in the community
Who was the index case and what is the likely source?
What kind of questions can molecular epidemiology answer in confirming outbreaks - in the past
in the past
What has driven the geographical spread of important strains?
What kind of questions can molecular epidemiology answer in confirming outbreaks - in the lab
in the lab
Is this an outbreak or a contaminant?
What kind of questions can molecular epidemiology answer in identifying disease risks
Identifying disease risks:
Shifts in virulence:
- Has the incidence of annual infections increased from …last year?
- Are drug resistant strains on the rise? From where?
Reservoirs of infection:
- New infection or recrudescence?
How to determine targets in epidemiology
Functional characteristic
Classical Biochemistry
Serology O157 antigen
Virulence Verotoxin
Genomic characteristic
DNA = Gene (rpo gene [rifampicin resistance] MDR TB)
Amino acid sequence
Base sequence
RNA = Ribosome
miRNA
How to determine diversity in epidemiology - single/additive weighting
Single Weighting
Presence or absence =
Biochemical test
Presence of O157 antigen
Presence of Verotoxin
Additive Weighting
Combination of single tests
How to determine diversity in epidemiology - multiple weighting
Multiple Weighting
Genomic factors:
Factoral
Presence or absence of a gene/base/s change
in genome/gene relative to location in the genome
Functional
Type of substitution (synonymous/non synonymous )
Temporal Mutation rate (time since the last alteration)
Factoral multiple copy number systems – (eg. Spoligotyping) - method
STEP 1 PCR with RE region primers generates multiple length amplicons
STEP 2
Hybridization of labelled PCR products onto
43 spacer specific oligonucleotides (between RE sequences)
fixed on a membrane then visualise signal with RE probe
Factoral multiple copy number systems – (eg. Spoligotyping) - result
Result is a profile of the presence/absence of specific repeats at ONE locus
Silent mutation - define
Silent : Mutations that are Intragenic (between genes) or Synonymous (not altering coding)
Non-Synonymous mutation - define
Non-Synonymous: Substitutions causing coding to be altered
Corruptive mutation - define
Corruptive:
Deletions or Insertions (disrupting coding frame)
` Creation of STOP codons (truncation)
Corruption of STOP codons (elongation)
Corruption of CONTROL sequences (eg. promoters)
Describe role of herd immunity in genetic drift
Herd immunity (after large vaccination program) kills most but also selects for escape mutants that maintain the drift
Antigentic drift in genetic drift
Antigenic drift is the same antigen changing its sequence base by base
Assumption in molecular epidemiology
Accurate predictions in molecular epidemiology thus requires
an assumption that evolution is driven by a
‘Constant Molecular Clock’
Diversity progresses because
Mutations are the raw materials of evolution
Diversity progresses because random mutations occurring at a regular rate
Bacterial replication rate effect on mutation
Bacterial replication rate:
A high division rate provides a higher mutation rate
DNA or RNA polymerase proof reading fidelity effect on mutation
DNA or RNA polymerase proof reading fidelity:
Some species (eg HIV) have low fidelity promoting high mutation rate
Selection pressure from the host or environment effect on mutation
Selection pressure from the host or environment:
High selection pressure removes ‘weak’ mutants and emphasises clusters
Loss of selection pressure allows deletions
Degree of redundancy in the genome effect on mutation
Degree of redundancy in the genome:
multiple copies of a single gene in the genome allow for
mutations in one copy without compromising overall functionality
Movement or recombination within genome may not effect phenotype
Transmission rate effect on mutation
Transmission rate:
High transmission rates relative to the mutation rate
results in dissemination and single strain outbreaks
(Flu A = 2-3 bases per year and 1.5 transmissions per infection)
Sequence mutation relate effect on pathogenicity
High sequence mutation rate may not affect pathogenicity (Antigenic drift)
Which genes change the most?
Hyper-variable genes change more rapidly than conserved genes
but
Conserved genes are more likely to be associated with phenotype and virulence
—————–
Not all changes are new
Some may revert BACK to an older profile (convergent evolution)
—————-
Large and rapid changes are rare
but often lead to escape from existing herd protection
Antigenic shift - define and its effect
Antigenic shift is a sudden replacement of an antigen by recombination with
another viral type that has evolved separately (either in another animal or another
human population).
New types will not be protected against by previous infection or
vaccination - leading to new epidemics.
Molecular Restriction Digest typing - define and brief method
Molecular Restriction Digest typing can monitor effectiveness of control measures
DNA extracted and cut with the same restriction enzymes then pieces
separated on a gel then visualised
Molecular epidemiology offers what
Molecular epidemiology offers a variety of methods to test questions
Involving disease transmission, strain virulence, pathogen evolution
Choosing the most appropriate system for molecular epidemiology requires what
- Knowing the most appropriate variable/s
- Quantitating variations and deriving diversity
- Generating identities or clusters
- Applying related data
- geographic location
- time of isolation
- incidence
- prevalence
- transmission rate
- severity of disease
Epidemiological associations - list
a) Transmission:
Hospital acquired infection
b) Reservoirs of infection :
- Contact tracing
- Determining introduction
events
c) Spread or emergence of resistance
