40 – Outbreaks and Molecular Epidemiology

Question 1

Molecular epidemiology

Answer 1

• Focuses on potential genetic and environmental risk factors
• ID at the molecular level
• Etiology
• Distribution and prevention of disease

Question 2

E. coli and the mite infestation

Answer 2

• Pulsed field gel electrophoresis: to compare the DNA
• *E. coli septicemia secondary to parasitism
  o Infestation led to immune suppression
  o Hematogenous spread of E. coli following invasion through mite BITES

Question 3

John Snow: importance

Answer 3

• Importance of understanding the SOURCE of the infection

Question 4

Epidemiological data is invaluable: why

Answer 4

• Etiology
• Temporal relationships
• Avoid temptation to draw conclusions about bacterial relatedness form susceptibility profiles

Question 5

What are the advantages of susceptibility data?

Answer 5

• Info you have already
• Info you are comfortable/familiar with
• Quick, cheap

Question 6

What is the disadvantage of susceptibility data?

Answer 6

• Resistance phenotype VERY POORLY predicts relatedness

Question 7

Phenotypic prediction problems

Answer 7

• Homogenizing effect of local antimicrobial use
• Horizontal gene transfer
  o Bacteria can share plasmid with unrelated organisms=TRASNFER OF RESISTANCE
• Common things are common!
  o Regionally, unrelated organisms often have similar susceptibility

Question 8

What do molecular epidemiological techniques allow us to do?

Answer 8

• Compare relatedness of isolates
• Based on detecting polymorphisms (differences) in the genome
• *look at DNA sequence directly OR indirectly

Question 9

Molecular epidemiological technique: based on DNA sequence directly

Answer 9

• Specific gene
• Whole genomes

Question 10

Molecular epidemiological technique: based on DNA sequence indirectly

Answer 10

• Restriction digestion patterns
• PCR
• Combination techniques

Question 11

What method is best?

Answer 11

• Talk to diagnostic lab if an outbreak occurs
  o Can likely help you perform tests and know which one will help you understand the scenario that is happening

Question 12

Whole genome sequencing

Answer 12

• Rapid developments
• Posing a question that your tool can address is KEY
• Replacing all previous ‘classical’ techniques
• Cost going down rapidly
• Increasingly adopted by major organizations

Question 13

Next-generation sequencing (NGS)

Answer 13

• Already into 3 generation
• ‘massively’ parallel sequencing
• *allows 10^4-10^9 fragments to be sequenced simultaneously
  o Started at 384 at a time

Question 14

Where are molecular epidemiological techniques used?

Answer 14

• *trying to find the source
  o Outbreak investigation
  o Rack movement of strains within community/animals/people
  o Studies of bacterial evolution
  o Monitor the dissemination of mobile genetic elements
• *many countries have national level organizations which utilize them for ongoing disease surveillance