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Genetics > Lecture 6 _ Molecular Epidemiology > Flashcards

Lecture 6 _ Molecular Epidemiology Flashcards

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1
Q

What are phylogenetic trees

A

A graphical representation of the evolutionary relationships among a set of species or taxa. Can also be applies to populations, individuals, and even genes

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2
Q

Phylogenetic trees are also called

A

Phylogenies or evolutionary trees & this field of study is known as phylogenetics

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3
Q

Phylogenetic trees - nodes

A

Hypothetical ancestors of the children taxa

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4
Q

Phylogenetic trees - root

A

Common ancestor of all species/individuals on chart. Sometimes you know the root, other times you don’t

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5
Q

Phylogenetic trees - branches

A

Show who is related to who

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6
Q

Phylogenetic trees - leaves/tips

A

Represent species, taxa, populations, individuals, or genes

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7
Q

In an unrooted tree, what do you not know

A

Where the tree starts, who is common ancestor, and passage of time

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8
Q

What is a cladogram vs phylogram?

A

Cladogram - length of branches is arbitrary & shows you clades (groups or species)
Phylogram - length of branches does mean something

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9
Q

Phylogenetic trees - does axis that root is on have a meaning

A

No meaning

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10
Q

Phylogenetic trees - does axis from root to branches have a meaning

A

Yes - shows passage of time

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11
Q

QUESTION ON FINAL!!!! Look at slide 9 & 10 and figure out who shares a common ancestor

A
  1. A, B, C, & D -
  2. C&D also have a common ancestor
  3. A & B have a common ancestor
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12
Q

Haplotype network

A

A graphical representation of evolutionary relationships among haplotypes (sequence of a specific stretch of DNA/RNA) within a population or species
- could be a small stretch of DNA, big stretch of DNA, or could also be genome

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13
Q

If you have a stretch of DNA/phenotypes you can build the

A

Haplotype

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14
Q

In a Haplotype, the size of the circle shows

A

How abundant that sequence is

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15
Q

Dashes in Haplotype represent

A

of differences between those 2 sequences (2 circles)

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16
Q

With a Haplotype network, you can track

A

How sequences change over time in a population

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17
Q

What is epidemiology

A

The study of the distribution (who, when, where) patterns, and determinants of disease in a defined population

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18
Q

Examples of epi uses

A

Outbreak investigation, identifying cause of disease, disease transmission, identify risk factors, improve public health, and preventative health care

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19
Q

Epidemiologic triangle

A

Agent
Host
Environment

With disease in the middle of the triangle

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20
Q

Epidemiologic triangle - agent

A

Actual cause of the disease

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21
Q

Epidemiologic triangle - host

A

Organisms that harbour the disease

22
Q

Epidemiologic triangle - environment

A

External factors that affect disease transmission (sanitation, temperature, etc)

23
Q

What is BRD

A

Bovine Respiratory Disease - A multifactorial disease caused by the interaction of pathogenic bacteria and viruses & causes a variety of clinical signs

24
Q

What’s a leading cause of death in dairy heifers

A

BRD

25
Q

Risk of BRD is reduced by

A

-Feeding calves with milk rather than milk replacers
- feeding over 3.8L of milk per day to calves under 21d of age
-frequent changing of maternity pen bedding
-housing calves in all wood or plastic hutches rather than metal roofed hutches (very hot, leads to heat stress)
-administration of BRD vaccines to dams before calving

26
Q

Molecular epidemiology can tell us

A

Cause of disease (agent)
Source of infection (where did outbreak start - DNA)
Routes of transmission
Virulence - molecular tools used to find strain
Host susceptibility - GWAS

27
Q

Molecular epidemiology tools for pathogen/species detection

A

PCR/qPCR
DNA metabarcoding

28
Q

Molecular epidemiology tools - Within-species variation

A

Cutting up genome with restriction enzymes (looks for strain of different bacteria)
Sequencing

29
Q

Criteria for selecting the most appropriate approach

A

Measure the construct of interest (PCR enough to test for presence/absence) - (need to sequence if want diff variants)
Level of discrimination - sufficiently discriminatory in the population of interest
Reliable, reproducible
Requirements for specimen collection, storage, and handling
Cost effective

30
Q

Cutting up of DNA uses

A

Restriction enzymes

31
Q

Restriction enzymes do what

A

Characterize differences between bacterial strains
Variety is below species level

32
Q

What is difference between restriction enzymes vs restriction endonuclease

A

Restriction enzymes are one class of restriction endonucleases

33
Q

Restriction enzymes recognize a sequence motif then

A

Cut DNA at those points & cut the bacteria into pieces

34
Q

If restriction site is GAATTC, what is restriction enzyme cutting site

A

G - CUT - AATTC

35
Q

What is Pulses-Field Gel Electrophoresis (PFGE)?

A

Used in microbiology for typing bacteria (identifying bacteria strains)
Grow bacteria colonies, then put restriction enzymes in, put through a gel, and bands show up where cuts are made (so where sequences were recognized)

36
Q

In PFGE, will bacteria that is genetically similar get cut at same spots?

A

Yes

37
Q

What is standard approach at CFIA and Public Health Agency of Canada (PHAC) for food borne and waterborne disease

A

PFGE

38
Q

E. coli are a diverse group of bacteria that normally live in

A

The intestines of humans and animals

39
Q

Most E Coli strains are harmless but

A

Some produce toxins that can cause disease such as severe and bloody diarrhea, and life-threatening kidney failure

40
Q

PFGE major drawbacks

A

Time consuming - 3:5 days
Genome not always cuttable
Identical bands do NOT equal identical genomes - only looking at few cut sites, not looking at all DNA (sequencing DNA is more accurate)

41
Q

For outbreak at goat farm, what were the methods for source tracing

A

Molecular sub typing to determine outbreak strains
PFGE pattern = unique DNA fingerprint
Isolates with same PFGE patterns = more likely to share common source
Joint farm visit with Connecticut department of agriculture and local health director - conducted environmental and animal sampling

42
Q

Read case study in lecture slides on source tracing on goat farm !

A

Do it !

43
Q

In case study, they sampled for E. coli where

A

Kid barn, goats themselves, doe barn, & food samples stored
Fecal samples & rectal swabs
Cheeses & unpasteurized milk

44
Q

Conclusions of case study on goat farm outbreak

A

Epi & laboratory evidence for outbreak of E. coli
Exposure to goats & widespread contamination in environment
- farm had a lack of awareness of risks - no hand washing facilities
- availability of hand sanitizer an ineffective measure

45
Q

What is Foot and Mouth Disease

A

A highly infection viral disease that causes fever, blister like sores on tongue, lips, mouth, teats, and between hooves. can also cause weight loss, lameness, and occasional abortions

46
Q

Which animals does foot and mouth disease affect

A

Cloven hoof animals (cattle, sheep, swine)

47
Q

FMD virus

A

Single strand, positive sense RNA with high mutation rate (lots of genetic variation)

48
Q

FMD virus - conventional molecular epidemiology

A

Sequencing of VP1 (8% of genome, which is not enough to resolve a single outbreak) - not enough detail

49
Q

Look at FMD case study slides 37-42

A

Do it <3

50
Q

How was FMD transmitted from farm to farm

A

No animal move,ent
Animals form premises 1 & 2 were disinfected prior to infection of premise 5
-movement of person, object, and aerosols?

Genetics (10 decks)

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