ex23

Question 1

Most clinical isolates of GBS evade the innate immune system but not the adaptive immune system. How does the capsule enable evasion?

Answer 1

The capsule blocks complement deposition and phagocytosis but is targeted by adaptive immune antibodies.

Question 2

Principles of Illumina sequencing

Answer 2

Illumina uses short reads, sequencing-by-synthesis, and fluorescence detection for high accuracy.

Question 3

Principles of Oxford Nanopore sequencing

Answer 3

Nanopore uses electrical current changes as long DNA passes through nanopores, producing long but error-prone reads.

Question 4

Method for accurate bacterial typing in outbreak investigations

Answer 4

Illumina is preferred for its high accuracy in detecting SNPs.

Question 5

Determinants of symptomatic disease in Staphylococcus aureus

Answer 5

Host immunity, bacterial virulence factors (adhesins, toxins), and environmental factors affect disease outcome.

Question 6

Monomorphic vs polymorphic bacteria

Answer 6

Monomorphic bacteria have low genetic diversity (e.g., M. tuberculosis), while polymorphic bacteria have high diversity (e.g., E. coli).

Question 7

Distribution of sequence types in monomorphic bacteria

Answer 7

Monomorphic bacteria have limited sequence type variation due to clonal evolution.

Question 8

Factors included in clinical breakpoint assessments

Answer 8

PK/PD parameters, MIC distributions, clinical outcomes, resistance mechanisms, and drug exposure levels.

Question 9

Typability

Answer 9

Typability is a method’s ability to produce results for all tested strains (e.g., MLST).

Question 10

Discriminatory power

Answer 10

Discriminatory power is a method’s ability to distinguish unrelated strains (e.g., WGS).

Question 11

Why is the 16S rRNA gene a good barcode molecule?

Answer 11

The 16S rRNA gene is universal, has conserved regions for primers, and variable regions for species differentiation.

Question 12

Limitations of the 16S rRNA gene

Answer 12

Limited strain resolution, horizontal gene transfer confusion, and PCR bias reduce its accuracy.

Question 13

Analyses for diagnosing M. tuberculosis

Answer 13

Microscopy (low sensitivity), culture (gold standard), molecular PCR (high sensitivity), and DST (drug resistance testing).

Question 14

Principle of Lancefield grouping

Answer 14

Agglutination with latex beads recognizing group-specific polysaccharides.

Question 15

Why is Lancefield grouping not PCR-based?

Answer 15

Lancefield uses antibodies against polysaccharides, not genetic detection.

Question 16

How does HylB enable GBS immune evasion?

Answer 16

Cleaved HA binds the GBS surface, hiding it from phagocytes.

Question 17

Why can’t HylB inhibit TLR activation?

Answer 17

HylB masks bacteria but does not inhibit TLR signaling directly.

Question 18

What makes a GBS strain more virulent?

Answer 18

Presence of adhesins with high binding affinity to host extracellular matrix.

Question 19

Why doesn’t antibiotic resistance directly increase virulence?

Answer 19

Resistance helps survival but does not enhance tissue adhesion or toxins.

Question 20

Principle of Sanger sequencing

Answer 20

Use of ddNTPs for chain termination to stop DNA elongation.

Question 21

Why is sequencing-by-synthesis not Oxford Nanopore’s principle?

Answer 21

Nanopore detects electrical current changes, not nucleotide synthesis.

Question 22

Cause of different antibiotic susceptibility in identical E. coli genotypes

Answer 22

Uptake of a resistance plasmid via conjugation.

Question 23

Why is plasmid uptake the most likely cause?

Answer 23

Conjugation rapidly transfers resistance genes, altering susceptibility profiles.

Question 24

Significance of the rpoB gene in TB management

Answer 24

Mutations in rpoB cause rifampicin resistance, guiding treatment.

Question 25

Main advantage of molecular TB diagnosis

Answer 25

Produces faster results and detects resistance markers early.

Question 26

Factor influencing bacterial pangenome size

Answer 26

Number of genes in the accessory genome.

Question 27

Specific bacterial defense against mobile genetic elements

Answer 27

CRISPR-Cas systems recognize and degrade foreign DNA.

Question 28

What causes DNA loss in bacterial genomes?

Answer 28

Transposase excision removes unnecessary or mobile elements.

Question 29

Main mechanisms of bacterial evolution

Answer 29

Mutation and horizontal gene transfer enable rapid adaptation.

Question 30

What does a GFF/GTF file provide?

Answer 30

Annotated genes within a DNA sequence.

Question 31

Tool for bacterial species identification

Answer 31

Kraken identifies species using k-mer algorithms.

Question 32

How does SNP distance indicate bacterial relatedness?

Answer 32

High SNP distances suggest the strains are not closely related.