King Stinear of Mind Maps

Question 1

Staph Aureus

Answer 1

GP cocci
Facultative anaerobe
Non motile
Normal inhabitants of URT, skin, VAGINA, intestine
Multiplies and spreads rapidly
MANY VIRULENCE FACTORS - exfoliative toxins, haemolysins, lipases, proteases, protein A (binds Fc component of IgG), beta-lactamase

Question 2

S.aureus antibiotic resistance

Answer 2

Ability to rapidly acquire resistance to new antibiotics
Penicillin resistance (1-2 years resistance)
Methicillin resistance (<1 year resistance)
Resistance to macrolides, tetracyclines, quinolones by acquiring a plasmid

Question 3

MRSA

Answer 3

Hospital pathogen mainly
More difficult to treat - resistance, more persistent phenotype
Acquires SCC Mec locus (MecA) , encodes penicillin-binding protein - replaces methicillin binding site
Less virulent in the lab - adapted to hospital

Question 4

S.aureus genomics

Answer 4

2.8MB
Core genome (75%) - essential genes
Accessory genome (25%) - vary between different strains
e.g. genomic islands, bacteriophage, plasmids/transposons, pathogenicity island
Very conserved

Question 5

Vancomycin

Answer 5

High level resistance (VRSA) very rare (MIC>16)
Acquires gene from enterococci (vanA from VRE) - Encodes ligase which modifies peptidoglycan residue from D-ala-D-ala to Dala-D-lac

Question 6

Vancomycin action

Answer 6

Binds dipeptide while cell is dividing

Question 7

Lower level resistance

Answer 7

Vancomycin intermediate S.aureus (VISA), MIC 4-8mg/L

Question 8

vancomycin case study

Answer 8

Patient presents to hospital
Develop staph bloodstream infection
VSSA (vancomycin…… + Rif & FA —> VISA –> linezolid used –> cure

Question 9

Population analysis profile

Answer 9

Grow patient sample s.aureus
Plate culture onto growth media containing increasing concentrations of vancomycin
Incubator
Count colonies at concentration of vancomycin
Calculate area under curve to detect differences between isolates

Question 10

VISA

Answer 10

Upregulation of capsule, cell wall
Charge repulsion
Thickened cell wall
Reduced protein A
CHANGES IN REGULATORY GENES

Question 11

T/F:

BLAST is used during the process of genome annotation

Answer 11

TRUE

Question 12

T/F: Comparative genomics relies on the function of all CDS within a genome to be known.

Answer 12

FALSE: relies on having 2 or more genomes to compare, not necessary to know the function of every CDS

Question 13

T/F:Phylogeography combines phylogenetics with geographical mapping

Answer 13

TRUE

Question 14

T/F: Genomics can be used to reconstruct metabolic pathways for a bacterium

Answer 14

TRUE - possible to reconstruct metabolic pathways

Question 15

Read mapping

Answer 15

Sequence reads are aligned with a reference and differences identified

Question 16

BLAST is an algorithm used to

Answer 16

Compare a DNA or protein sequence against a database of sequences

Question 17

T/F:Most cases of tuberculosis in Australia come from reactivation of latent infection rather than recent transmission

Answer 17

TRUE:

10% of TB cases are related to recent transmission in Aus

Question 18

T/F: “Multi drug resistant” tuberculosis is defined as strains which are resistant to either isoniazid or rifampicin

Answer 18

FALSE: MDR-TB resistant to AT LEAST isoniazid AND rifampicin

Question 19

Proportion of TB cases in Victoria which are MDR

Answer 19

1-3%

Question 20

ILLUMINA -SEQUENCE BY SYNTHESIS

Answer 20

1. DNA broken up into random pieces and ligate adaptors to both ends
2. Attach DNA to surface
3. Bridge amplification
4. Fragments become double stranded
5. denature the ds molecules –> ss
6. Complete amplification
7. Determine 1st base
8. Image 1st base with fluorescence
9. determine 2nd base
10. Image second chemistry cycle
11. sequence reads over multiple chemistry cycles
12. Align data - compare to reference, identify sequence differences

Question 21

Sanger sequencing

Answer 21

Sequence by synthesis

Fluorescent dideoxy nucleotides

Question 22

Pac Bio

Answer 22

Single molecule, real-time sequencing
DNA synthesis by immobilised DNA pol
Phospholinked nucleotides release light when incorporated
No amplification

Question 23

Phylogenetics

Answer 23

Process of inferring phylogeny from a set of taxa

Estimates evolutionary relationships among a set of taxa

Question 24

Phylogeography

Answer 24

Combines phylogenetics with geographical mapping to infer how bacteria spread

Question 25

Mycobacterium

Answer 25

``` Acid-fast bacilli, non-motile, aerobic Cell wall has mycolic acid lipids 3 weeks to form colonies Zihel-Neilson stain Disinfectant resistant, heat susceptible ```

Question 26

M.fortuitum

Answer 26

Footspa | Obligate pathogens

Question 27

M. leprae

Answer 27

``` Multidrug therapy BCG vaccine Th1 immunity tropism: macrophage, schwann cells Pathology: leprosy, paralysis ```

Question 28

M.tuberculosis

Answer 28

DOTS treatment Th1 immunity Tropism: macrophages, monocytes Pathology: pulmonary TB (90%), disseminated 10%

Question 29

TB pathogenesis

Answer 29

90-95% control initial infection by mounting a robust cell mediated immune (CMI) response - Ghon's complex calcification lesion (--> latent infection) 5-10% Primary TB: miliary TB, meningitis 2nd TB: Reactivation, pulmonary, cell death, liquefaction of granuloma ESAT-6 and CFP10: required for escape from phagolysosome

Question 30

M.ulcerans

Answer 30

SR8 (strep and rifampicin) treatment Th1 tropism: subcutaneous tissue, extracellular Pathology: Buruli ulcer, necrosis

Question 31

Leprae vs TB

Answer 31

Leprae undergone massive reductive evolution Smaller genome lower GC content Pseudogenes

Question 32

Marinum vs TB

Answer 32

``` Minor skin disease Granuloma like TB in fish Pathogenesis: survive and replicates in host macrophage phagosomes Prevent lysosome fusion T7SS cellcell spread ```

Question 33

M.ulcerans

Answer 33

Subcutaneous necrosis Granulomas absent or poorly formed Extracellular infection

Question 34

Mycolactone

Answer 34

``` Lipid toxin Mutants are avirulent Comparison of 16SrRNA gene show M.ulcerans Niche adaptation Mosquito --> possum --> faeces ```