Bacterial Evolution Flashcards

1
Q

Bacterial classification levels

A

over 90 phylum
Under species there is strain
Under strain there is isolates
- obtained from pure cultures

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2
Q

Biochemical profiling

A

Species have set of specific enzymes
Use API strips to test which enzymes present in culture
If species infectious can use antibiotic susceptibility test

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3
Q

Different phenotypic species ID methods

A
  • MALDI-TOF mass spectrometry
  • Chemotaxonomic markers
  • Expressed features
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4
Q

MALDI-TOF mass spectrometry

A

Samples are ionised into changed molecules
Measure their ratio mass to charge
= each species unique ratio

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5
Q

Chemo taxonomic markers

A

Variation between species in:
Fatty acids
Cell wall compounds
Exopolysaccharide

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6
Q

Expressed features in bacteria

A

Physiology
Morphology
Serology
Antibiotic resistance

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7
Q

Genotypic methods of bacterial species ID

A
DNA. 
- need >70% to be similar 
DNA segments 
- sequence discriminatory/housekeeping genes to see variation 
- e.g. recA, gryB
rRNA 
- bac = 16s rRNA (eukarya = 18s rRNA) 
- need >97% similarity 
Whole genome sequencing 
- look at average nucleotide identity (ANI)
- want >95% ANI between genomes
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8
Q

Species

A

Large number of strain with similar phenotypic/genetic properties
- >70% DNA-DNA hybridisation, >97% 16s rRNA gene sequencing similarity, >95% ANI whole genome sequencing

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9
Q

Strain

A

When there is knowledge of clonality or genetic identity

Using strain typing techniques to identify

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10
Q

Isolate

A

Cultures from an infection or elsewhere

When you have no genetic knowledge but its a single pure colony

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11
Q

Phenotypic strain typing techniques

A

Serotyping
Resistotyping
Biotyping
MALDI-TOF mass spec

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12
Q

Serotyping

A

Serotype = distinct variation within bacteria species
- classified via cell surface antigens = epidemiological classification
- take sample and mix with blood containing antibodies = antiserum
- blood will agglutinate (clump)
Resulting combination of antigens defines serotype

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13
Q

Resistotyping

A
  • testing bacterial strains against arbitrarily chosen chemicals
  • show the selective toxicity at a critical concentration
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14
Q

Biotyping

A

Identifying bacteria based on a series of bios chemical tests
The same as biochemical profiling ?

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15
Q

Genotypic strain typing techniques

A
DNA finger printing 
- Restriction analysis 
- PCR based methods 
Sequence based ID
- gene sequencing 
- multi locus sequence typing (housekeeping genes)
- whole genome sequencing
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16
Q

Restriction analysis

A

Using restriction enzymes to digest DNA
Will cleave DNA at restriction sites
Look at sizes using gel electrophoresis

17
Q

Desirable trains when strain typing

A
  • typeability: how many isolates an you type?
  • reproducibility: consistent results?
  • accuracy
  • discrimination: diff strains from same species?

= TRAD criteria

18
Q

Phenotypic or genotypic better at ID?

A

Genotypic more likely to meet TRAD criteria
- discriminatory
- more stable
Phenotypic relies on growth and can be variable

19
Q

Describe the bacterial genome

A

Highly variable in size from 100-10 mil bases
G + C content = 20-75%
One double circular DNA chromosome
Almost all coding material

20
Q

Accessory genome elements

A
  • Non essential genes
  • foreign DNA
  • drives diversity between species = rapid evolutionary change e.g. plasmids
  • multiple genetic applications
  • contains bacteriophages, genomic islands, ICEs
21
Q

Core genome elements

A
  • essential genes
  • stable GC content
  • shared within species but also suggests diversity
  • slow evolution
  • stable basis for genotype growth: wont change often but therefore good at showing diversity between species
22
Q

The bacterial pan genome

A
  • entire collection of genes found in a species
  • overlay strains and there will be a core section of shared genes
  • the moe strains you compare the smaller the core genomes
23
Q

What drives bacterial genome evolution?

A
  • horizontal gene transfer
  • recombination
  • gene duplication
  • mutation
  • additive evolution
  • reductive evolution
24
Q

Additive evolution

A

Gene acquisition e.g. plasmids, transposons, genomic islands
Gene duplication and rearrangement

25
Q

Reductive evolution

A

Deletion: loss of 1+ genes

Inactivation and pseudogene formation

26
Q

Horizontal gene transfer

A

Transformation
Transduction or transfection
Conjugation
Other mobile genetic elements

Low freq but causes rapid evolution

Caused by plasmids, bacteriophages, transposable elements genomic islands

27
Q

Genomic horizontal transfer and genomic islands

A
  • large regions of DNA integrated into the genome
  • not present in all strains of a species
  • can cause selective advantage
28
Q

Transformation

A

Foreign DNA incorporated into genome

29
Q

Transduction

A

Bacteriophage mediated transfer

30
Q

Conjugation

A

DNA transferred by cell-cell contact

E.g. plasmids

31
Q

Gene cloning vectors

A

Plasmids
Phases
Cosmics (phage and plasmid hybrid)

32
Q

Transposon mutagenesis

A
  • deliver transposon into host cell
  • transposon integrates into host genome
  • disrupts gene function
  • one copy per cell. Integration is in a random location
  • if a gene is disrupted you can see where its location by identifying transposons location

Good for finding genes of interest