Bacterial Evolution Flashcards
Bacterial classification levels
over 90 phylum
Under species there is strain
Under strain there is isolates
- obtained from pure cultures
Biochemical profiling
Species have set of specific enzymes
Use API strips to test which enzymes present in culture
If species infectious can use antibiotic susceptibility test
Different phenotypic species ID methods
- MALDI-TOF mass spectrometry
- Chemotaxonomic markers
- Expressed features
MALDI-TOF mass spectrometry
Samples are ionised into changed molecules
Measure their ratio mass to charge
= each species unique ratio
Chemo taxonomic markers
Variation between species in:
Fatty acids
Cell wall compounds
Exopolysaccharide
Expressed features in bacteria
Physiology
Morphology
Serology
Antibiotic resistance
Genotypic methods of bacterial species ID
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
Species
Large number of strain with similar phenotypic/genetic properties
- >70% DNA-DNA hybridisation, >97% 16s rRNA gene sequencing similarity, >95% ANI whole genome sequencing
Strain
When there is knowledge of clonality or genetic identity
Using strain typing techniques to identify
Isolate
Cultures from an infection or elsewhere
When you have no genetic knowledge but its a single pure colony
Phenotypic strain typing techniques
Serotyping
Resistotyping
Biotyping
MALDI-TOF mass spec
Serotyping
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
Resistotyping
- testing bacterial strains against arbitrarily chosen chemicals
- show the selective toxicity at a critical concentration
Biotyping
Identifying bacteria based on a series of bios chemical tests
The same as biochemical profiling ?
Genotypic strain typing techniques
DNA finger printing - Restriction analysis - PCR based methods Sequence based ID - gene sequencing - multi locus sequence typing (housekeeping genes) - whole genome sequencing
Restriction analysis
Using restriction enzymes to digest DNA
Will cleave DNA at restriction sites
Look at sizes using gel electrophoresis
Desirable trains when strain typing
- typeability: how many isolates an you type?
- reproducibility: consistent results?
- accuracy
- discrimination: diff strains from same species?
= TRAD criteria
Phenotypic or genotypic better at ID?
Genotypic more likely to meet TRAD criteria
- discriminatory
- more stable
Phenotypic relies on growth and can be variable
Describe the bacterial genome
Highly variable in size from 100-10 mil bases
G + C content = 20-75%
One double circular DNA chromosome
Almost all coding material
Accessory genome elements
- Non essential genes
- foreign DNA
- drives diversity between species = rapid evolutionary change e.g. plasmids
- multiple genetic applications
- contains bacteriophages, genomic islands, ICEs
Core genome elements
- 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
The bacterial pan genome
- 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
What drives bacterial genome evolution?
- horizontal gene transfer
- recombination
- gene duplication
- mutation
- additive evolution
- reductive evolution
Additive evolution
Gene acquisition e.g. plasmids, transposons, genomic islands
Gene duplication and rearrangement
Reductive evolution
Deletion: loss of 1+ genes
Inactivation and pseudogene formation
Horizontal gene transfer
Transformation
Transduction or transfection
Conjugation
Other mobile genetic elements
Low freq but causes rapid evolution
Caused by plasmids, bacteriophages, transposable elements genomic islands
Genomic horizontal transfer and genomic islands
- large regions of DNA integrated into the genome
- not present in all strains of a species
- can cause selective advantage
Transformation
Foreign DNA incorporated into genome
Transduction
Bacteriophage mediated transfer
Conjugation
DNA transferred by cell-cell contact
E.g. plasmids
Gene cloning vectors
Plasmids
Phases
Cosmics (phage and plasmid hybrid)
Transposon mutagenesis
- 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
