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