Molecular and Genomic Epidemiology of Infections

Question 1

Molecular Epidemiology - define and describe what it determines

Answer 1

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

Question 2

What kind of questions can molecular epidemiology answer in confirming outbreaks - inside institutions

Answer 2

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?

Question 3

What kind of questions can molecular epidemiology answer in confirming outbreaks - in the community

Answer 3

in the community

Who was the index case and what is the likely source?

Question 4

What kind of questions can molecular epidemiology answer in confirming outbreaks - in the past

Answer 4

in the past

What has driven the geographical spread of important strains?

Question 5

What kind of questions can molecular epidemiology answer in confirming outbreaks - in the lab

Answer 5

in the lab

Is this an outbreak or a contaminant?

Question 6

What kind of questions can molecular epidemiology answer in identifying disease risks

Answer 6

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?

Question 7

How to determine targets in epidemiology

Answer 7

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

Question 8

How to determine diversity in epidemiology - single/additive weighting

Answer 8

Single Weighting

Presence or absence =

Biochemical test
Presence of O157 antigen
Presence of Verotoxin

Additive Weighting
Combination of single tests

Question 9

How to determine diversity in epidemiology - multiple weighting

Answer 9

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)

Question 10

Factoral multiple copy number systems – (eg. Spoligotyping) - method

Answer 10

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

Question 11

Factoral multiple copy number systems – (eg. Spoligotyping) - result

Answer 11

Result is a profile of the presence/absence of specific repeats at ONE locus

Question 12

Silent mutation - define

Answer 12

Silent : Mutations that are Intragenic (between genes)
or Synonymous (not altering coding)

Question 13

Non-Synonymous mutation - define

Answer 13

Non-Synonymous: Substitutions causing coding to be altered

Question 14

Corruptive mutation - define

Answer 14

Corruptive:

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

Question 15

Describe role of herd immunity in genetic drift

Answer 15

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

Question 16

Antigentic drift in genetic drift

Answer 16

Antigenic drift is the same antigen changing its sequence base by base

Question 17

Assumption in molecular epidemiology

Answer 17

Accurate predictions in molecular epidemiology thus requires
an assumption that evolution is driven by a
‘Constant Molecular Clock’

Question 18

Diversity progresses because

Answer 18

Mutations are the raw materials of evolution

Diversity progresses because random mutations occurring at a regular rate

Question 19

Bacterial replication rate effect on mutation

Answer 19

Bacterial replication rate:

A high division rate provides a higher mutation rate

Question 20

DNA or RNA polymerase proof reading fidelity effect on mutation

Answer 20

DNA or RNA polymerase proof reading fidelity:

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

Question 21

Selection pressure from the host or environment effect on mutation

Answer 21

Selection pressure from the host or environment:

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

Question 22

Degree of redundancy in the genome effect on mutation

Answer 22

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

Question 23

Transmission rate effect on mutation

Answer 23

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)

Question 24

Sequence mutation relate effect on pathogenicity

Answer 24

High sequence mutation rate may not affect pathogenicity (Antigenic drift)

Question 25

Which genes change the most?

Answer 25

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

Question 26

Antigenic shift - define and its effect

Answer 26

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.

Question 27

Molecular Restriction Digest typing - define and brief method

Answer 27

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

Question 28

Molecular epidemiology offers what

Answer 28

Molecular epidemiology offers a variety of methods to test questions
Involving disease transmission, strain virulence, pathogen evolution

Question 29

Choosing the most appropriate system for molecular epidemiology requires what

Answer 29

1. Knowing the most appropriate variable/s
2. Quantitating variations and deriving diversity
3. Generating identities or clusters
4. Applying related data
   - geographic location
   - time of isolation
   - incidence
   - prevalence
   - transmission rate
   - severity of disease

Question 30

Epidemiological associations - list

Answer 30

a) Transmission:
Hospital acquired infection

b) Reservoirs of infection :
- Contact tracing
- Determining introduction
events

c) Spread or emergence of resistance