Molecular and Genomic Epidemiology of Pathogens

Question 1

What is molecular epidemiology?

Answer 1

➝Molecular epidemiology : a resolved measure (diversity) of differences (variables) that determines
➝Disease distribution in time and place
➝Disease transmission
➝Disease manifestation
➝Disease progression

Question 2

What can molecular epidemiology confirm?

Answer 2

➝ outbreaks

Question 3

Where can molecular epidemiology confirm outbreaks from?

Answer 3

➝ Inside institutions
- whether it was the same strain  
➝Inside institutions
-who the index case was and the source 
➝In the past 
- what drives the geographical spread of important strains
➝In the past 
-outbreak or containment

Question 4

What risks can molecular epidemiology identify?

Answer 4

➝ disease risks

Question 5

What are functional targets?

Answer 5

➝ biochemistry
➝ serology
➝ virulence

Question 6

How many functional targets do you need to look at?

Answer 6

➝ single functional target

Question 7

What are the genomic targets?

Answer 7

➝ DNA - gene, amino acid sequence, base sequence

➝ RNA - ribosome, miRNA

Question 8

How many genomic targets do you need to look at?

Answer 8

➝ multiple

Question 9

What is a single weighting?

Answer 9

➝ presence or absence of a target

Question 10

What is an additive weighting?

Answer 10

➝ a combination of single tests

Question 11

What are the 4 ways of investigating E.coli?

Answer 11

➝ culture on selective media
➝ O157 serotyping using antibody on blue latex beads
➝ PCR of DNA verotoxin genes
➝ phage typing

Question 12

For multiple weighting what genomic factors do you look at?

Answer 12

➝ factoral : presence or absence of a gene/base/change in a genome/gene relative to the location in the genome
➝ functional : type of substitution (synonymous-non synoymous)
➝ temporal : mutation rate (time since last alteration)

Question 13

How does spoligotyping work?

Answer 13

➝PCR with
RE region primers
generates multiple length
amplicons
➝Hybridization of labelled PCR products onto 43 spacer specific oligonucleotides (between RE sequences)
fixed on a membrane then visualise signal with RE probe

Question 14

How do factoral copy numbers work in TB?

Answer 14

➝ there is one part of the genome which is called the DR region
➝ it has the possibility of having upto 43 copies of the same gene
➝ the 43 copies are not in every single organism
➝ the number varies as the organism is transferred from one patient to another

Question 15

What is the strain of TB based on?

Answer 15

➝ the variation in copy number

➝ and the pattern of the copies

Question 16

What does the result of spoligotyping give you?

Answer 16

➝ profile of the presence/absence of specific repeats at one locus

Question 17

What does a spoligotyping dendrogram show?

Answer 17

➝ relatedness of pattern

Question 18

What is another method to find out copy numbers?

Answer 18

➝ PCR

Question 19

What does the result of PCR give you?

Answer 19

➝ the number of specific repeats at multiple genomic loci

Question 20

What is a silent mutation?

Answer 20

➝ Mutations that are Intragenic (between genes)

➝or Synonymous (not altering coding)

Question 21

What is a non synonymous mutation?

Answer 21

➝ Substitutions causing coding to be altered

Question 22

What are 4 corruptive mutations?

Answer 22

➝Deletions or Insertions (disrupting coding frame)
➝ Creation of STOP codons (truncation)
➝Corruption of STOP codons (elongation)
➝Corruption of CONTROL sequences (eg. promoters)

Question 23

What is gradual alteration in sequence called?

Answer 23

➝ DRIFT

Question 24

What does herd immunity do to viruses?

Answer 24

➝ Herd immunity (after large vaccination program) kills most but also selects for escape mutants that maintain the drift

Question 25

What is antigenic drift?

Answer 25

➝ the same antigen changing its sequence base by base

Question 26

What is the assumption that allows us to make accurate predictions ?

Answer 26

➝ constant molecular clock

Question 27

Why does diversity progress?

Answer 27

➝ Random mutations occur at a regular rate

Question 28

What are the 5 things that can affect the speed of the molecular clock?

Answer 28

➝ Bacterial replication rate
➝ DNA or RNA polymerase proof reading fidelity
➝ selection pressure from the host or environment
➝ degree of redundancy in the genome
➝ transmission rate

Question 29

What does a higher bacterial replication rate provide?

Answer 29

➝ A high division rate provides a higher mutation rate

Question 30

What does having low proof reading fidelity mean?

Answer 30

➝ Some species (eg HIV) have low fidelity promoting high mutation rate

Question 31

What does having high and low selection pressure mean?

Answer 31

➝ High selection pressure removes ‘weak’ mutants and emphasises clusters
➝Loss of selection pressure allows deletions

Question 32

What does having redundancy in the genome mean?

Answer 32

➝ 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 affect phenotype

Question 33

What does a high transmission rate result in?

Answer 33

➝ High transmission rates relative to the mutation rate

results in dissemination and single strain outbreaks

Question 34

Which genes change the most?

Answer 34

➝ Hyper-variable genes change more rapidly than conserved genes

Question 35

Which genes are more likely to be associated with phenotype and virulence?

Answer 35

➝ Conserved genes are more likely to be associated with phenotype and virulence

Question 36

What is convergent evolution?

Answer 36

➝ Not all changes are new

Some may revert BACK to an older profile (convergent evolution)

Question 37

What do large and rapid changes lead to?

Answer 37

➝ escape from existing herd protection

Question 38

What is antigenic shift?

Answer 38

➝ a sudden replacement of an antigen by recombination with another viral type that has evolved separately (either in another animal or another human population)

Question 39

What are the three epidemiological associations?

Answer 39

➝ Transmission
➝ reservoirs of infection - contact tracing or determining introduction events
➝ spread or emergence of resistance

Question 40

What can monitor effectiveness of control measures?

Answer 40

➝ Molecular restriction digest

Question 41

What does choosing the most appropriate system require?

Answer 41

➝ Knowing the most appropriate variable/s
➝Quantitating variations and deriving diversity
➝ Generating identities or clusters
➝ Applying related data