Epidemiology

Question 1

Epidemiology

Answer 1

How often disease occurs + why

Question 2

molecular epidemiology

- what is it?

Answer 2

molecular biology techniques in epidemiological studies

Question 3

molecular epidemiology

- applications

Answer 3

confirm epidemiological linkage

understand linkages

study pathogen population

Question 4

studying pathogen population

Answer 4

> structure

> factors affecting distribution
e.g. virulence factors, AMR

> pathogen microevolution

> emergence of new pathogen

Question 5

confirm epidemiological linkage

Answer 5

outbreak investigations
- new outbreak or strain re-emerging from dormant state

transmission between cases

source of infection
e.g. water source

Question 6

understand linkages

= generating hypotheses on epidemiological relationships

Answer 6

surveillance

chains of transmission

distinguish relapse + reinfection

mixed infections

Question 7

why do we need typing?

Answer 7

to identify epidemiologically-linked isolates

Question 8

what does typing show?

Answer 8

related chases share same strain

unrelated cases have a different strain

BUT unrelated isolates may appear the same
depending on ability of typing method to discriminate isolates

Question 9

Typing methods

- examples

Answer 9

serotyping
phage typing
AB susceptibility 
MLEE
RFLP
spoligotyping + MIRUS-VNTR

Question 10

MLST

• means
• what is it?

Answer 10

multi-locus sequence for strain differentiation

DNA-based typing approach

Question 11

MLST

Answer 11

sequence multiple housekeeping genes distributed in genome

-> look at variations in gene sequence compared with others for that gene

Question 12

MLST

- graph

Answer 12

make list of all sequence types in allele profile

compare across different strains

same no. at that locus = share same allele

Question 13

whole genome sequencing

Answer 13

gives single base resolution
- good for low genetic diversity bacteria

can trace transmission in real time
- diversity will be low

Question 14

MRSA

- facts

Answer 14

S. aureus

nosocomial
AMR

2 strains analysed
- 43 global isolates over 20yrs

Question 15

Harris et. al

Thailand study

Answer 15

20 isolates from Thai hospital over 7months

ST239 isolates
created phylogenetic tree

shows intercontinental spread
= same/ closely related isolates found in different parts of the world

all samples from hospital v similar
SO got ST239 when they arrived

Question 16

Campylobacter

- facts

Answer 16

Gram -ve
motile

microaerophilic

2.4M cases/yr in US

sporadic events, not part of outbreaks

Question 17

Campylobacter

- transmission

Answer 17

commensal in birds + animals

contaminated food, water + unpasteurised milk

contact w/ infected animals

between people via faecal-oral route

Question 18

Campylobacter

• symptoms
• complications

Answer 18

diarrhoea
fever
vomiting

UTIs
meningitis

Question 19

Campylobacter

- analytical epidemiology

Answer 19

case-control studies

outbreak investigation

natural experiments

Question 20

Campylobacter

- case control studies

Answer 20

identify cohort of people same in every way except 1 group had campylobacter

• then do risk assessment

Question 21

Campylobacter

- outbreak investigation

Answer 21

see what infected people had in common

e.g. people going to same wedding etc?

Question 22

Campylobacter

- identify source of infection using genotyping

Answer 22

different hosts have different Campylobacter types

look at relatedness between different clusters of isolates
- cluster based on host they’re from

Question 23

Campylobacter

- quantitative probabilistic assignment of human disease

Answer 23

assign probability to source
e.g. X% sure that Y% of isolates came from…?

1.genotype isolate in human

2.genotype isolates from different sources e.g. cow + pig
(may contain different types of isolates but probablity have a majority of one)

3. if genotype is similar to those from one host e.g. cow
   - probably from cow but COULD be from pig

Question 24

Campylobacter

- MLST

Answer 24

sampled all cases in Scotland for 1 yr
+ food, rivers etc

sequenced isolates

developed probabilistic model for identifying source

Question 25

Campylobacter

- Bayesian clustering algorithm of clinical isolates

Answer 25

60% of samples
from chicken reservoir
- meat contaminated in slaughter process
(via faeces from gut)

80% chicken in supermarkets has campylobacter

Question 26

MLST limitation

Answer 26

7 loci give limited resolution

ignores informative variation elsewhere in genome

Question 27

Campylobacter

- host switching

Answer 27

can switch hosts + niches

= adapt to new enviros

Question 28

high resolution allows..

Answer 28

great discrimination power