Epidemiology Flashcards
Epidemiology
How often disease occurs + why
molecular epidemiology
- what is it?
molecular biology techniques in epidemiological studies
molecular epidemiology
- applications
confirm epidemiological linkage
understand linkages
study pathogen population
studying pathogen population
> structure
> factors affecting distribution
e.g. virulence factors, AMR
> pathogen microevolution
> emergence of new pathogen
confirm epidemiological linkage
outbreak investigations
- new outbreak or strain re-emerging from dormant state
transmission between cases
source of infection
e.g. water source
understand linkages
= generating hypotheses on epidemiological relationships
surveillance
chains of transmission
distinguish relapse + reinfection
mixed infections
why do we need typing?
to identify epidemiologically-linked isolates
what does typing show?
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
Typing methods
- examples
serotyping phage typing AB susceptibility MLEE RFLP spoligotyping + MIRUS-VNTR
MLST
- means
- what is it?
multi-locus sequence for strain differentiation
DNA-based typing approach
MLST
sequence multiple housekeeping genes distributed in genome
-> look at variations in gene sequence compared with others for that gene
MLST
- graph
make list of all sequence types in allele profile
compare across different strains
same no. at that locus = share same allele
whole genome sequencing
gives single base resolution
- good for low genetic diversity bacteria
can trace transmission in real time
- diversity will be low
MRSA
- facts
S. aureus
nosocomial
AMR
2 strains analysed
- 43 global isolates over 20yrs
Harris et. al
Thailand study
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
Campylobacter
- facts
Gram -ve
motile
microaerophilic
2.4M cases/yr in US
sporadic events, not part of outbreaks
Campylobacter
- transmission
commensal in birds + animals
contaminated food, water + unpasteurised milk
contact w/ infected animals
between people via faecal-oral route
Campylobacter
- symptoms
- complications
diarrhoea
fever
vomiting
UTIs
meningitis
Campylobacter
- analytical epidemiology
case-control studies
outbreak investigation
natural experiments
Campylobacter
- case control studies
identify cohort of people same in every way except 1 group had campylobacter
- then do risk assessment
Campylobacter
- outbreak investigation
see what infected people had in common
e.g. people going to same wedding etc?
Campylobacter
- identify source of infection using genotyping
different hosts have different Campylobacter types
look at relatedness between different clusters of isolates
- cluster based on host they’re from
Campylobacter
- quantitative probabilistic assignment of human disease
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)
- if genotype is similar to those from one host e.g. cow
- probably from cow but COULD be from pig
Campylobacter
- MLST
sampled all cases in Scotland for 1 yr
+ food, rivers etc
sequenced isolates
developed probabilistic model for identifying source
Campylobacter
- Bayesian clustering algorithm of clinical isolates
60% of samples
from chicken reservoir
- meat contaminated in slaughter process
(via faeces from gut)
80% chicken in supermarkets has campylobacter
MLST limitation
7 loci give limited resolution
ignores informative variation elsewhere in genome
Campylobacter
- host switching
can switch hosts + niches
= adapt to new enviros
high resolution allows..
great discrimination power
