ex23 Flashcards
Most clinical isolates of GBS evade the innate immune system but not the adaptive immune system. How does the capsule enable evasion?
The capsule blocks complement deposition and phagocytosis but is targeted by adaptive immune antibodies.
Principles of Illumina sequencing
Illumina uses short reads, sequencing-by-synthesis, and fluorescence detection for high accuracy.
Principles of Oxford Nanopore sequencing
Nanopore uses electrical current changes as long DNA passes through nanopores, producing long but error-prone reads.
Method for accurate bacterial typing in outbreak investigations
Illumina is preferred for its high accuracy in detecting SNPs.
Determinants of symptomatic disease in Staphylococcus aureus
Host immunity, bacterial virulence factors (adhesins, toxins), and environmental factors affect disease outcome.
Monomorphic vs polymorphic bacteria
Monomorphic bacteria have low genetic diversity (e.g., M. tuberculosis), while polymorphic bacteria have high diversity (e.g., E. coli).
Distribution of sequence types in monomorphic bacteria
Monomorphic bacteria have limited sequence type variation due to clonal evolution.
Factors included in clinical breakpoint assessments
PK/PD parameters, MIC distributions, clinical outcomes, resistance mechanisms, and drug exposure levels.
Typability
Typability is a method’s ability to produce results for all tested strains (e.g., MLST).
Discriminatory power
Discriminatory power is a method’s ability to distinguish unrelated strains (e.g., WGS).
Why is the 16S rRNA gene a good barcode molecule?
The 16S rRNA gene is universal, has conserved regions for primers, and variable regions for species differentiation.
Limitations of the 16S rRNA gene
Limited strain resolution, horizontal gene transfer confusion, and PCR bias reduce its accuracy.
Analyses for diagnosing M. tuberculosis
Microscopy (low sensitivity), culture (gold standard), molecular PCR (high sensitivity), and DST (drug resistance testing).
Principle of Lancefield grouping
Agglutination with latex beads recognizing group-specific polysaccharides.
Why is Lancefield grouping not PCR-based?
Lancefield uses antibodies against polysaccharides, not genetic detection.
How does HylB enable GBS immune evasion?
Cleaved HA binds the GBS surface, hiding it from phagocytes.
Why can’t HylB inhibit TLR activation?
HylB masks bacteria but does not inhibit TLR signaling directly.
What makes a GBS strain more virulent?
Presence of adhesins with high binding affinity to host extracellular matrix.
Why doesn’t antibiotic resistance directly increase virulence?
Resistance helps survival but does not enhance tissue adhesion or toxins.
Principle of Sanger sequencing
Use of ddNTPs for chain termination to stop DNA elongation.
Why is sequencing-by-synthesis not Oxford Nanopore’s principle?
Nanopore detects electrical current changes, not nucleotide synthesis.
Cause of different antibiotic susceptibility in identical E. coli genotypes
Uptake of a resistance plasmid via conjugation.
Why is plasmid uptake the most likely cause?
Conjugation rapidly transfers resistance genes, altering susceptibility profiles.
Significance of the rpoB gene in TB management
Mutations in rpoB cause rifampicin resistance, guiding treatment.
Main advantage of molecular TB diagnosis
Produces faster results and detects resistance markers early.
Factor influencing bacterial pangenome size
Number of genes in the accessory genome.
Specific bacterial defense against mobile genetic elements
CRISPR-Cas systems recognize and degrade foreign DNA.
What causes DNA loss in bacterial genomes?
Transposase excision removes unnecessary or mobile elements.
Main mechanisms of bacterial evolution
Mutation and horizontal gene transfer enable rapid adaptation.
What does a GFF/GTF file provide?
Annotated genes within a DNA sequence.
Tool for bacterial species identification
Kraken identifies species using k-mer algorithms.
How does SNP distance indicate bacterial relatedness?
High SNP distances suggest the strains are not closely related.
