L13, 14 Antibiotics and microbiome

Question 1

13

What is an antibiotic?

Answer 1

A compound that inhibits the growth of or kills bacteria, either derived from natural sources or synthesised.

Question 2

13

What is the difference between an antibiotic and an antimicrobial?

Answer 2

• Antibiotic: Specifically targets bacteria.
• Antimicrobial: Targets a broader range of microbes, including viruses, fungi, and protozoa.

Question 3

13

What is selective toxicity in antibiotics?

Answer 3

The ability of an antibiotic to target bacteria specifically without harming the host.

Question 4

13

What are the two main uses of antibiotics?

Answer 4

• Treatment of bacterial infections.
• Prophylaxis to prevent bacterial infections (e.g., surgery or outbreaks).

Question 5

13

How do antibiotics benefit society?

Answer 5

They reduce mortality, prevent disease spread, and enable complex medical procedures like organ transplants and chemotherapy.

Question 6

13

Name five bacterial targets of antibiotics.

Answer 6

• Cell wall biosynthesis.
• Cell membrane integrity.
• DNA and RNA synthesis.
• Protein synthesis.
• Metabolic pathways.

Question 7

13

What is the Minimum Inhibitory Concentration (MIC)?

Answer 7

The lowest concentration of an antibiotic that inhibits bacterial growth.

Question 8

13

What is a breakpoint concentration?

Answer 8

The antibiotic concentration below which bacteria are considered susceptible to the drug.

Question 9

13

What are the two main ways bacteria develop resistance?

Answer 9

• Mutations in chromosomal genes.
• Acquisition of foreign DNA (e.g., plasmids).

Question 10

13

What is the Mutant Prevention Concentration (MPC)?

Answer 10

The antibiotic concentration that prevents the growth of resistant mutants.

Question 11

13

What are beta-lactams, and how do they work?

Answer 11

A class of antibiotics that inhibit bacterial cell wall synthesis (e.g., penicillins, cephalosporins).

Question 12

13

Name an example of a fluoroquinolone and its target.

Answer 12

Ciprofloxacin, which targets DNA synthesis.

Question 13

13

What is the main use of aminoglycosides like gentamicin?

Answer 13

Treating severe infections caused by gram-negative bacteria.

Question 14

13

What does pharmacokinetics (PK) study in antibiotics?

Answer 14

How the body absorbs, distributes, metabolises, and eliminates the drug.

Question 15

13

What does pharmacodynamics (PD) study?

Answer 15

The effects of the drug on the bacteria, including potency and time-dependent or concentration-dependent killing.

Question 16

13

How do quinolones differ in their distribution compared to beta-lactams?

Answer 16

Quinolones penetrate more effectively into tissues like sputum and alveolar macrophages.

Question 17

13

How do gram-positive bacteria differ from gram-negative bacteria structurally?

Answer 17

• Gram-positive: Thick peptidoglycan layer, no outer membrane.
• Gram-negative: Thin peptidoglycan layer, outer membrane present.

Question 18

13

Name two gram-positive and two gram-negative pathogens.

Answer 18

• Gram-positive: Staphylococcus aureus, Streptococcus pneumoniae.
• Gram-negative: Escherichia coli, Pseudomonas aeruginosa.

Question 19

13

What strategies are being pursued to combat resistance?

Answer 19

• Modifications to existing antibiotic classes.
• Development of combination therapies.
• Targeting gram-positive pathogens.

Question 20

13

What is synergy in antibiotic combinations?

Answer 20

When the combined effect of two antibiotics is greater than their effects individually.

Question 21

13

Why is combination therapy sometimes necessary?

Answer 21

To prevent resistance, broaden spectrum, or enhance efficacy.

Question 22

13

What colour do gram-positive bacteria stain, and why?

Answer 22

Purple, because the thick peptidoglycan layer retains the crystal violet stain during the Gram-staining process.

Question 23

13

What colour do gram-negative bacteria stain, and why?

Answer 23

Pink or red, because the thin peptidoglycan layer does not retain the crystal violet stain and takes up the counterstain (safranin).

Question 24

13

What is the role of the outer membrane in gram-negative bacteria?

Answer 24

• Acts as a barrier to many antibiotics.
• Contains lipopolysaccharides (LPS) which can trigger strong immune responses in humans.

Question 25

# 13 Why are gram-negative bacteria often more resistant to antibiotics?

Answer 25

* The outer membrane acts as an additional barrier to antibiotic entry. * Many produce beta-lactamases, which degrade beta-lactam antibiotics.

Question 26

# 13 Which antibiotics are most effective against gram-positive bacteria?

Answer 26

* Penicillin. * Vancomycin. * Clindamycin. * Macrolides (e.g., erythromycin, azithromycin).

Question 27

# 13 Which antibiotics are most effective against gram-negative bacteria?

Answer 27

* Aminoglycosides (e.g., gentamicin). * Fluoroquinolones (e.g., ciprofloxacin). * Carbapenems (e.g., meropenem). * Third-generation cephalosporins (e.g., ceftriaxone).

Question 28

# 13 Why are beta-lactam antibiotics sometimes combined with beta-lactamase inhibitors?

Answer 28

To overcome resistance in beta-lactamase-producing bacteria (e.g., augmentin = amoxicillin + clavulanic acid).

Question 29

# 13 What are the steps of the Gram-staining process?

Answer 29

1. Crystal violet stain: Both gram-positive and gram-negative bacteria are stained purple. Iodine treatment: Forms a complex with the crystal violet. 2. Alcohol/acetone wash: - Gram-positive: Retains the purple stain. - Gram-negative: Loses the stain. 3. Counterstain (safranin): - Gram-positive: Remains purple. - Gram-negative: Stains pink/red.

Question 30

# 13 What is the purpose of iodine in Gram staining?

Answer 30

It binds to the crystal violet, forming a complex that is harder to wash out.

Question 31

# 13 Why do gram-negative bacteria lose the crystal violet stain during alcohol washing?

Answer 31

The thinner peptidoglycan layer and the presence of an outer membrane allow the crystal violet-iodine complex to be washed out.

Question 32

# 13 Which types of infections are commonly caused by gram-positive bacteria?

Answer 32

Skin infections (e.g., cellulitis by Staphylococcus aureus). Respiratory infections (e.g., pneumonia by Streptococcus pneumoniae). Endocarditis (infection of the inner lining of the heart)

Question 33

# 13 How do gram-positive bacteria develop resistance to antibiotics?

Answer 33

* Modification of penicillin-binding proteins (e.g., MRSA). * Efflux pumps to expel antibiotics. * Enzymatic inactivation (e.g., beta-lactamase production).

Question 34

# 13 How do gram-negative bacteria develop resistance to antibiotics?

Answer 34

* Outer membrane prevents drug entry. * Production of extended-spectrum beta-lactamases (ESBLs). * Efflux pumps and porin mutations reduce antibiotic uptake.

Question 35

# 13 What is the primary definition of an antibiotic today? A. A substance that kills viruses B. A compound that enhances bacterial growth C. A compound that inhibits or kills bacteria D. A synthetic chemical used to treat fungal infections

Answer 35

Answer: C. A compound that inhibits or kills bacteria Explanation: Antibiotics are compounds—either natural or synthetic—that inhibit the growth of or kill bacteria, making them essential in treating bacterial infections.

Question 36

# 13 Which of the following is NOT an antimicrobial? A. Antiviral B. Antibacterial C. Antifungal D. Antiseptic

Answer 36

Answer: D. Antiseptic Explanation: Antiseptics act on surfaces to kill microbes but are not classified as antimicrobials, which are agents used internally to treat infections caused by microbes.

Question 37

# 13 Who was responsible for the development of the sulphonamide class of drugs? A. Alexander Fleming B. Gerhard Domagk C. Paul Ehrlich D. Louis Pasteur

Answer 37

Answer: B. Gerhard Domagk Explanation: Gerhard Domagk, working for I.G. Farbenindustrie, played a key role in the discovery and development of sulphonamide antibiotics.

Question 38

# 13 What percentage of people with pneumococcal pneumonia died before penicillin was introduced? A. 10% B. 50% C. 70% D. 90%

Answer 38

Answer: D. 90% Explanation: Before penicillin, 90% of people with pneumococcal pneumonia died. After its introduction, survival rates reversed dramatically.

Question 39

# 13 Which of the following is NOT a correct use of antibiotics? A. Treatment of bacterial infections B. Prophylaxis before surgery C. Prevention of viral infections D. Treatment of neonatal bacterial infections

Answer 39

Answer: C. Prevention of viral infections Explanation: Antibiotics are ineffective against viruses and should not be used to treat or prevent viral infections.

Question 40

# 13 Which structural feature do Gram-positive bacteria lack compared to Gram-negative bacteria? A. Cell wall B. Cytoplasmic membrane C. Outer membrane D. Ribosomes

Answer 40

Answer: C. Outer membrane Explanation: Gram-positive bacteria lack the outer membrane that is characteristic of Gram-negative bacteria.

Question 41

# 13 Which of the following antibiotic targets is unique to bacteria and contributes to selective toxicity? A. DNA B. Mitochondrial enzymes C. Cell wall biosynthesis D. Plasma membrane

Answer 41

Answer: C. Cell wall biosynthesis Explanation: Humans do not have cell walls, so targeting bacterial cell wall synthesis ensures selective toxicity.

Question 42

# 13 What does MIC stand for in antimicrobial testing? A. Maximum Inhibitory Capacity B. Minimum Inhibitory Concentration C. Minimum Isolated Contaminant D. Most Infected Culture

Answer 42

Answer: B. Minimum Inhibitory Concentration Explanation: MIC is the lowest concentration of an antimicrobial that prevents visible bacterial growth.

Question 43

# 13 Which statement about bacteriostatic drugs is correct? A. They kill bacteria instantly B. They inhibit bacterial growth C. They are effective only against viruses D. They always cause hypersensitivity reactions

Answer 43

Answer: B. They inhibit bacterial growth Explanation: Bacteriostatic antibiotics stop bacteria from multiplying, allowing the immune system to eliminate the infection.

Question 44

# 13 Which combination is most appropriate for prophylaxis in dental surgery for a penicillin-allergic patient? A. Gentamicin B. Metronidazole C. Erythromycin D. Cefoxitin

Answer 44

Answer: C. Erythromycin Explanation: Erythromycin is used as an alternative in penicillin-allergic patients to prevent endocarditis during dental procedures.

Question 45

# 13 Which of the following antibiotics has the highest alveolar macrophage penetration? A. Quinolones B. Azithromycin C. β-lactams D. Cephalosporins

Answer 45

Answer: B. Azithromycin Explanation: Azithromycin reaches extremely high concentrations in alveolar macrophages, enhancing its effect on respiratory infections.

Question 46

# 13 What is the main concern with ESBL-producing organisms? A. Resistance to aminoglycosides B. Resistance to carbapenems C. Resistance to beta-lactam antibiotics D. Susceptibility to tetracyclines

Answer 46

Answer: C. Resistance to beta-lactam antibiotics Explanation: ESBLs (Extended-Spectrum Beta-Lactamases) break down most beta-lactam antibiotics, rendering them ineffective.

Question 47

# 13 Which is an example of synergistic antibiotic interaction? A. Penicillin alone B. Chloramphenicol and penicillin together C. Penicillin and gentamicin D. Azithromycin and ciprofloxacin

Answer 47

Answer: C. Penicillin and gentamicin Explanation: These antibiotics have a synergistic effect, often used together in endocarditis to enhance bacterial killing.

Question 48

# 13 What does the term "antimicrobial resistance" (AMR) describe? A. Natural immunity to infection B. Bacteria surviving antibiotics they were previously susceptible to C. The ability of humans to resist infection D. Reduction of infection via vaccines Answer: B. Bacteria surviving antibiotics they were previously susceptible to

Answer 48

Answer: B. Bacteria surviving antibiotics they were previously susceptible to Explanation: AMR refers to bacteria acquiring mechanisms to evade the effects of antibiotics.

Question 49

# 13 Which of the following mechanisms contributes to the spread of antibiotic resistance? A. Inhibition of cell wall synthesis B. Increased susceptibility of bacteria C. Acquisition of plasmids D. Activation of lysosomes

Answer 49

Answer: C. Acquisition of plasmids Explanation: Plasmids often carry resistance genes and can be transferred between bacteria, spreading resistance.

Question 50

# 14 What is the difference between 'microbiota' and 'microbiome'?

Answer 50

Microbiota refers to all micro-organisms in an environment, whereas microbiome includes the microorganisms, their genomes, and environmental conditions.

Question 51

# 14 What is metagenomics?

Answer 51

The genomic study of genetic material recovered directly from environmental samples.

Question 52

# 14 What are the two main types of DNA sequencing technologies used in microbiome research?

Answer 52

Illumina sequencers (short-read, low error) and long-read platforms like Oxford Nanopore and Pacific Biosciences (long-read, higher error, more expensive).

Question 53

# 14 What are the main differences between 16S rRNA gene profiling and shotgun metagenomic sequencing?

Answer 53

16S rRNA: Targets bacteria only, provides taxonomic data, cheaper, easier. Shotgun: Covers all DNA (bacteria, viruses, fungi), reveals gene function, more expensive, complex analysis.

Question 54

# 14 Where in the human body is the highest concentration of bacteria found?

Answer 54

In the colon—about 60% of faeces consist of bacteria.

Question 55

# 14 How stable is the gut microbiome over time?

Answer 55

It is generally stable but can change due to events like illness or travel; it often returns to its original state.

Question 56

# 14 How does geography and diet affect the gut microbiome?

Answer 56

Populations from different regions (e.g. Malawi, USA, Venezuela) have markedly different microbiomes, likely due to dietary and environmental factors.

Question 57

# 14 How does the gut microbiome differ between infants and adults?

Answer 57

Adults have a more diverse microbiome (~1500 species), while infants' microbiomes are still developing.

Question 58

# 14 What factors can disrupt the development of the infant microbiome?

Answer 58

Caesarean section, formula feeding, and antibiotic use can all disrupt microbiome development and increase risks of allergies, asthma, infections, and possibly obesity.

Question 59

# 14 What are the effects of antibiotics on the gut microbiome?

Answer 59

They reduce diversity, select for resistant bacteria, and may cause long-term changes; can lead to C. difficile infections in hospital settings.

Question 60

# 14 What is Clostridioides difficile and why is it significant?

Answer 60

A spore-forming bacterium that causes severe colon inflammation, often after antibiotic use; resistant to treatment due to spore formation.

Question 61

# 14 How can C. difficile infections be treated when antibiotics fail?

Answer 61

Faecal microbiota transplantation (FMT) can restore the gut microbiome and cure the infection.

Question 62

# 14 How does the gut microbiome affect cancer treatment?

Answer 62

It can influence both the efficacy and side effects of cancer therapies, especially immunotherapies like PD-1 checkpoint blockade.

Question 63

# 14 What is PD-1 checkpoint blockade?

Answer 63

A cancer therapy using antibodies to block immune checkpoints (e.g. PD-1/PD-L1), enhancing T-cell response against tumours.

Question 64

# 14 Which bacterium was associated with better response to PD-1 therapy in cancer patients?

Answer 64

Akkermansia muciniphila.

Question 65

# 14 What evidence suggests the microbiome affects PD-1 blockade response?

Answer 65

Mice with transplanted responder microbiomes showed better outcomes, and FMT improved therapy in some refractory melanoma patients.

Question 66

# 14 How does microbial metabolism affect irinotecan chemotherapy?

Answer 66

Bacterial β-glucuronidases reactivate SN-38 (toxic form), leading to diarrhoea in about 30% of patients.

Question 67

# 14 What increases the risk of irinotecan-induced toxicity?

Answer 67

High levels of bacterial transporters and β-glucuronidases in the gut.

Question 68

# 14 What increases the risk of irinotecan-induced toxicity?

Answer 68

High levels of bacterial transporters and β-glucuronidases in the gut.

Question 69

# 14 Why are culture-independent methods crucial for studying the microbiome?

Answer 69

Many gut microbes cannot be cultured due to sensitivity to oxygen or lack of appropriate growth media.

Question 70

# 14 Summarise the overall role of the gut microbiome.

Answer 70

It is a complex ecosystem influencing immune function, disease risk, treatment outcomes, and general health; shaped by numerous factors including antibiotics and geography.

Question 71

# 14 Why are most gut bacteria non-culturable using standard methods?

Answer 71

Many gut bacteria are highly sensitive to oxygen, and no appropriate growth media exist for some species. This limits the utility of culture-based methods and necessitates the use of DNA-based, culture-independent approaches.

Question 72

# 14 What functional insights can be gained from shotgun metagenomic sequencing?

Answer 72

Shotgun sequencing allows detection of genes involved in virulence, antibiotic resistance, and metabolic functions across the entire microbial community, including bacteria, viruses, and fungi.

Question 73

# 14 What happens to the gut microbiome after a disruption like travel or illness?

Answer 73

Although travel (e.g. from the USA to Thailand) and infections (e.g. Salmonella enteritis) can disrupt the gut microbiome, it usually reverts to its pre-disruption state, indicating a form of microbial resilience and equilibrium.

Question 74

# 14 Aside from Akkermansia muciniphila, are there other microbial patterns associated with immunotherapy outcomes?

Answer 74

While Akkermansia is a top hit, studies also associate different microbial profiles with responders (R) vs non-responders (NR) to PD-1 blockade. The relationship is correlational, and causality is often tested in mouse models using FMT (faecal microbiota transplantation).

Question 75

# 14 What are the limitations of the evidence linking the microbiome to cancer immunotherapy outcomes?

Answer 75

Much of the data comes from mouse models, not direct human trials. Effect sizes are modest, meaning microbiome modulation may support but not replace cancer therapy. Responses vary between individuals, and the microbiome is only one of several influencing factors.

Question 76

# 14 What is the biochemical process by which the microbiome causes irinotecan toxicity?

Answer 76

1. SN-38G, a glucuronidated detoxified form of SN-38, is excreted into the gut. 2. Bacterial β-glucuronidases hydrolyse SN-38G back to SN-38, the active and toxic compound. 3. SN-38 causes local gut epithelial damage, resulting in severe diarrhoea. 4. The process involves both transport into microbial cells and enzyme activation.

Question 77

# 14 How has FMT been used in patients with refractory melanoma?

Answer 77

In patients who had become non-responsive to PD-1 therapy, FMT from PD-1 responders, when combined with renewed anti-PD-1 treatment, restored responsiveness in a subset of cases (Davar et al., 2021), suggesting therapeutic potential of microbiome manipulation.

Question 78

# 14 A 58-year-old man is hospitalised with severe pseudomembranous colitis after a prolonged course of broad-spectrum antibiotics. Despite antibiotic therapy, his symptoms persist. Which of the following best explains the failure of conventional antibiotics to resolve this infection? A) Resistance due to β-lactamase production by C. difficile B) Mutation of ribosomal RNA targets in C. difficile C) Formation of bacterial spores resistant to antibiotics and disinfectants D) Horizontal gene transfer from other gut bacteria E) Impaired host T-cell mediated immunity

Answer 78

Answer: C Explanation: C. difficile forms spores that are resistant to antibiotics and disinfectants, making infections difficult to treat conventionally.

Question 79

# 14 Which of the following most accurately explains why faecal microbiota transplantation (FMT) is effective in treating recurrent Clostridioides difficile infection? A) FMT eradicates all remaining C. difficile spores through bacteriophages B) FMT restores microbial diversity, outcompeting C. difficile and reversing dysbiosis C) FMT provides exogenous anti-toxin antibodies D) FMT stimulates T-regulatory cells to suppress colonic inflammation E) FMT enhances bile acid synthesis which inhibits C. difficile toxin production

Answer 79

Answer: B Explanation: FMT works by restoring microbial diversity and ecological balance in the gut, reducing conditions favourable to C. difficile overgrowth.

Question 80

# 14 A patient undergoing irinotecan chemotherapy develops severe diarrhoea. Microbial reactivation of SN-38G in the gut is suspected. Which of the following bacterial enzymes and processes are most directly involved in this toxicity? A) DNA topoisomerase IV and bacterial efflux pumps B) β-glucuronidases and microbial transporters C) Aminoglycoside-modifying enzymes and porin channels D) Sulfatases and hydrogen sulphide production E) β-lactamases and oxidative stress

Answer 80

Answer: B Explanation: Gut bacteria express β-glucuronidases that convert SN-38G (inactive) back to SN-38 (active), causing toxicity; this process also involves transporter-mediated uptake.

Question 81

# 14 Which of the following is the most plausible reason why Akkermansia muciniphila has been associated with improved response to PD-1 checkpoint blockade therapy in cancer? A) It produces short-chain fatty acids that directly kill tumour cells B) It suppresses T-regulatory cells in the tumour microenvironment C) It enhances antigen presentation and T-cell activation in the host D) It secretes IL-2 to support cytotoxic lymphocyte proliferation E) It inhibits hepatic metabolism of immune checkpoint inhibitors

Answer 81

Answer: C Explanation: Certain bacteria like Akkermansia are thought to support anti-tumour immunity by improving antigen presentation and promoting T-cell responses.

Question 82

# 14 A 1-month-old infant born via Caesarean section is formula-fed and recently treated with oral antibiotics for otitis media. Which of the following is the greatest concern regarding the infant’s long-term health? A) Permanent colonisation with C. difficile B) Increased risk of coeliac disease C) Failure of hepatic immune tolerance D) Dysregulated immune development and increased allergy risk E) Persistent vitamin K deficiency

Answer 82

Answer: D Explanation: Disruption of early microbiome development (due to birth mode, formula feeding, and antibiotics) increases the risk of immune dysregulation, including allergies and asthma.

Question 83

# 14 Which of the following statements best differentiates 16S rRNA gene profiling from shotgun metagenomic sequencing in gut microbiome analysis? A) 16S rRNA sequencing can detect viruses, while shotgun sequencing cannot B) Shotgun sequencing provides taxonomic classification, 16S gives functional gene profiles C) 16S sequencing offers high accuracy for fungal pathogens D) Shotgun sequencing identifies gene functions and microbial interactions; 16S does not E) 16S sequencing requires longer read lengths than shotgun sequencing

Answer 83

Answer: D Explanation: Shotgun sequencing provides information on the functional gene content (e.g. antibiotic resistance, virulence), while 16S focuses on bacterial taxonomy and lacks functional detail.

Question 84

# 14 In a study involving faecal transplants from immunotherapy responders and non-responders into germ-free mice with tumours, which outcome most directly supports a causal role of the microbiome in therapy response? A) Tumour regression in all transplanted mice B) Improved survival only in mice that received responder FMT C) Activation of hepatic drug-metabolising enzymes D) Increase in circulating neutrophil counts E) Reversion of tumour cells to normal phenotype

Answer 84

Answer: B Explanation: Mice with responder microbiomes showed improved responses to PD-1 therapy, providing experimental evidence for a causal relationship.