Methods for studying the microbiome US Medical PG Practice Questions and MCQs
Practice US Medical PG questions for Methods for studying the microbiome. These multiple choice questions (MCQs) cover important concepts and help you prepare for your exams.
Methods for studying the microbiome US Medical PG Question 1: A medical technician is trying to isolate a pathogen from the sputum sample of a patient. The sample is heat fixed to a slide then covered with carbol fuchsin stain and heated again. After washing off the stain with clean water, the slide is covered with 1% sulfuric acid for decolorization. The sample is rinsed again and stained with methylene blue. Microscopic examination shows numerous red, branching filamentous organisms. Which of the following is the most likely isolated pathogen?
- A. Cryptococcus neoformans
- B. Tropheryma whipplei
- C. Nocardia asteroides (Correct Answer)
- D. Rickettsia rickettsii
- E. Staphylococcus aureus
Methods for studying the microbiome Explanation: ***Nocardia asteroides***
- The described staining procedure is a **modified acid-fast stain**, indicated by the use of **carbol fuchsin**, heating, and decolorization with **weak acid (1% sulfuric acid)**, followed by a counterstain with methylene blue.
- **Nocardia species** are **weakly acid-fast bacteria** that resist decolorization with weak acids (1-3% sulfuric acid), appearing as **red, branching filamentous organisms** under this staining method.
- The **modified acid-fast stain** uses weaker decolorizing agents compared to the standard Ziehl-Neelsen stain, making it suitable for detecting weakly acid-fast organisms like Nocardia.
- Nocardia are aerobic actinomycetes commonly found in soil and can cause pulmonary infections, especially in immunocompromised patients.
*Cryptococcus neoformans*
- This is a **yeast** that is typically identified using an **India ink stain** to visualize its polysaccharide capsule, or through fungal stains like Gomori methenamine silver (GMS).
- It would not appear as acid-fast red branching filaments with the described technique.
*Tropheryma whipplei*
- This bacterium is typically identified by **periodic acid-Schiff (PAS) stain** in tissue biopsies, which highlights its cell wall glycoproteins (appears magenta).
- It is not acid-fast and would not retain the carbol fuchsin after acid decolorization.
*Rickettsia rickettsii*
- This is an **obligate intracellular bacterium** that is difficult to culture and is often diagnosed by **serological tests** or **immunohistochemistry** on skin biopsy specimens.
- It is not acid-fast and would not be detected by this staining technique.
*Staphylococcus aureus*
- This is a **Gram-positive coccus** that would be stained **purple** by a Gram stain as it retains crystal violet.
- It is not acid-fast and would be completely decolorized by sulfuric acid in the described procedure, appearing blue (counterstain color) rather than red.
Methods for studying the microbiome US Medical PG Question 2: An investigator is studying the growth of an organism in different media. The organism is inoculated on a petri dish that contains heated sheep blood, vancomycin, nystatin, trimethoprim, and colistin. The resulting growth medium is incubated at 37°C. Numerous small, white colonies are seen after incubation for 48 hours. This organism is most likely to cause which of the following conditions?
- A. Pontiac fever
- B. Pseudomembranous colitis
- C. Hemolytic uremic syndrome
- D. Oral thrush
- E. Gonorrhea (Correct Answer)
Methods for studying the microbiome Explanation: ***Gonorrhea***
- The growth medium described is **Thayer-Martin agar**, a selective medium containing **heated sheep blood** (supplies NAD+), **vancomycin** (inhibits Gram-positives), **colistin** (inhibits Gram-negatives), **nystatin** (inhibits fungi), and **trimethoprim** (inhibits Proteus). This medium is specifically designed for the isolation of *Neisseria gonorrhoeae* from polymicrobial samples.
- *Neisseria gonorrhoeae* typically grows as **small, translucent-to-white colonies** on selective media like Thayer-Martin agar, and incubation at 37°C in CO2 (not explicitly mentioned but often required) for 24-48 hours yields visible growth, causing **gonorrhea**.
*Pontiac fever*
- Pontiac fever is a mild, self-limiting form of **legionellosis**, caused by *Legionella pneumophila*.
- *Legionella* requires a specialized medium such as **buffered charcoal yeast extract (BCYE) agar** for growth, not Thayer-Martin agar.
*Pseudomembranous colitis*
- This condition is caused by **toxin-producing *Clostridioides difficile***, often after antibiotic use.
- *C. difficile* is an obligate anaerobe and requires **anaerobic conditions** and specific selective media (e.g., CCFA agar) for isolation, not Thayer-Martin agar under aerobic conditions.
*Hemolytic uremic syndrome*
- Hemolytic uremic syndrome (HUS) is often caused by **Shiga toxin-producing *Escherichia coli* (STEC)**, particularly O157:H7.
- STEC can be isolated on media like **sorbitol MacConkey agar (SMAC)**, where O157:H7 appears as non-sorbitol fermenting colonies, distinct from the growth seen on Thayer-Martin.
*Oral thrush*
- Oral thrush is caused by *Candida albicans*, a yeast.
- *Candida* would be inhibited by **nystatin** in the Thayer-Martin medium, which is an antifungal agent.
Methods for studying the microbiome US Medical PG Question 3: A 62-year-old woman with type 2 diabetes mellitus is brought to the emergency department by her husband because of fever, chills, and purulent drainage from a foot ulcer for 2 days. Her hemoglobin A1c was 15.4% 16 weeks ago. Physical examination shows a 2-cm ulcer on the plantar surface of the left foot with foul-smelling, purulent drainage and surrounding erythema. Culture of the abscess fluid grows several bacteria species, including gram-negative, anaerobic, non-spore-forming bacilli that are resistant to bile and aminoglycoside antibiotics. Which of the following is the most likely source of this genus of bacteria?
- A. Stomach
- B. Oropharynx
- C. Vagina
- D. Colon (Correct Answer)
- E. Skin
Methods for studying the microbiome Explanation: ***Colon***
- The description of the bacteria—**gram-negative, anaerobic, non-spore-forming bacilli** that are **resistant to bile** and **aminoglycoside antibiotics**—is highly characteristic of the genus *Bacteroides*, especially *Bacteroides fragilis*.
- *Bacteroides fragilis* is a prominent component of the normal **colonic microflora** and is frequently implicated in infections originating from breaches in the gastrointestinal tract, such as a diabetic foot ulcer with a mixed infection.
*Stomach*
- The stomach's highly acidic environment generally limits significant bacterial colonization, and it is not a primary source of mixed anaerobic infections as described.
- While *Helicobacter pylori* can colonize the stomach, it does not fit the described microbiological characteristics.
*Oropharynx*
- The oropharynx contains a diverse microbiota, including anaerobes like **Peptostreptococcus** and **Fusobacterium**, but it is not the typical source for *Bacteroides fragilis* or the specific resistance profile mentioned.
- Oropharyngeal anaerobes are more commonly associated with head and neck infections, aspiration pneumonia, or dental abscesses.
*Vagina*
- The vaginal flora includes various anaerobes such as **Gardnerella vaginalis** and some *Bacteroides* species, but it is not the most common or primary source of widespread mixed anaerobic infections matching this description.
- Infections originating from the vagina would typically be linked to pelvic or genitourinary conditions.
*Skin*
- The skin surface predominantly harbors **aerobic** and **facultative anaerobic bacteria** like **Staphylococcus** and **Streptococcus** species.
- While skin breaches can lead to infections, the described **anaerobic, gram-negative, bile-resistant** profile points away from the typical skin flora as the primary source for the specific bacterial characteristics given.
Methods for studying the microbiome US Medical PG Question 4: A scientist is studying the mechanisms by which bacteria become resistant to antibiotics. She begins by obtaining a culture of vancomycin-resistant Enterococcus faecalis and conducts replicate plating experiments. In these experiments, colonies are inoculated onto a membrane and smeared on 2 separate plates, 1 containing vancomycin and the other with no antibiotics. She finds that all of the bacterial colonies are vancomycin resistant because they grow on both plates. She then maintains the bacteria in liquid culture without vancomycin while she performs her other studies. Fifteen generations of bacteria later, she conducts replicate plating experiments again and finds that 20% of the colonies are now sensitive to vancomycin. Which of the following mechanisms is the most likely explanation for why these colonies have become vancomycin sensitive?
- A. Point mutation
- B. Gain of function mutation
- C. Viral infection
- D. Plasmid loss (Correct Answer)
- E. Loss of function mutation
Methods for studying the microbiome Explanation: ***Plasmid loss***
- The initial **vancomycin resistance** in *Enterococcus faecalis* is often mediated by genes located on **plasmids**, which are extrachromosomal DNA.
- In the absence of selective pressure (vancomycin), bacteria that lose the plasmid (and thus the resistance genes) have a **growth advantage** over those that retain the energetically costly plasmid, leading to an increase in sensitive colonies over generations.
*Point mutation*
- A **point mutation** typically involves a change in a single nucleotide and could lead to loss of resistance if it occurred in a gene conferring resistance.
- However, since there was no selective pressure for loss of resistance, it is less likely that 20% of the population would acquire such a specific point mutation to revert resistance.
*Gain of function mutation*
- A **gain of function mutation** would imply that the bacteria acquired a *new* advantageous trait, not the *loss* of resistance.
- This type of mutation would not explain why some colonies became sensitive to vancomycin after the drug was removed.
*Viral infection*
- **Viral infection** (bacteriophages) can transfer genes through transduction or cause bacterial lysis, but it's not the primary mechanism for a widespread reversion of resistance in the absence of antibiotic pressure.
- It would not explain the observed increase in vancomycin-sensitive colonies due to evolutionary pressure.
*Loss of function mutation*
- While a **loss of function mutation** in a gene conferring resistance could lead to sensitivity, it's generally less likely to explain a 20% shift without selective pressure than **plasmid loss**.
- Plasmids are often unstable and are easily lost in the absence of selection, whereas a specific gene mutation causing loss of function would need to arise and become prevalent in the population.
Methods for studying the microbiome US Medical PG Question 5: A 10-year-old girl is brought to the emergency department because of a 2-day history of bloody diarrhea and abdominal pain. Four days ago, she visited a petting zoo with her family. Her temperature is 39.4°C (102.9°F). Abdominal examination shows tenderness to palpation of the right lower quadrant. Stool cultures at 42°C grow colonies that turn black after adding phenylenediamine. Which of the following best describes the most likely causal organism?
- A. Gram-positive, anaerobic, rod-shaped bacteria that form spores
- B. Gram-positive, aerobic, rod-shaped bacteria that produce catalase
- C. Gram-negative, non-flagellated bacteria that do not ferment lactose
- D. Gram-negative, flagellated bacteria that do not ferment lactose (Correct Answer)
- E. Gram-negative, non-flagellated bacteria that ferment lactose
Methods for studying the microbiome Explanation: ***Gram-negative, flagellated bacteria that do not ferment lactose***
- The clinical presentation of **bloody diarrhea**, **abdominal pain**, and fever, along with a history of **petting zoo exposure**, strongly suggests a *Campylobacter* infection, which is a **gram-negative, flagellated, curved rod** that does not ferment lactose.
- The growth at **42°C (thermophilic)** and a **positive oxidase test** (indicated by colonies turning black after adding phenylenediamine, an oxidase reagent) are characteristic features of *Campylobacter spp*.
*Gram-positive, anaerobic, rod-shaped bacteria that form spores*
- This description typically refers to organisms like *Clostridium difficile* or *Clostridium perfringens*, which can cause diarrhea.
- However, they are **anaerobic** and would not grow well in typical stool culture conditions without specific anaerobic techniques, nor would they produce a positive oxidase test.
*Gram-positive, aerobic, rod-shaped bacteria that produce catalase*
- This describes organisms like *Listeria monocytogenes* or *Bacillus cereus*.
- While *Listeria* can cause gastrointestinal symptoms, it's less commonly associated with the acute, bloody diarrhea and petting zoo exposure seen here, and *Bacillus cereus* typically causes food poisoning with vomiting.
*Gram-negative, non-flagellated bacteria that do not ferment lactose*
- This description commonly applies to *Shigella spp.*
- While *Shigella* causes **bloody diarrhea** and **abdominal pain**, it is typically **non-motile** (non-flagellated), whereas *Campylobacter* is motile due to its flagella.
*Gram-negative, non-flagellated bacteria that ferment lactose*
- This description would fit organisms like enteropathogenic *E. coli* (EPEC) or enterotoxigenic *E. coli* (ETEC).
- However, the specific growth conditions (thermophilic) and positive oxidase test pointed to by phenylenediamine reactivity are not characteristic of these organisms.
Methods for studying the microbiome US Medical PG Question 6: A 31-year-old woman comes to the emergency department because of a 4-day history of fever and diarrhea. She has abdominal cramps and frequent bowel movements of small quantities of stool with blood and mucus. She has had multiple similar episodes over the past 8 months. Her temperature is 38.1°C (100.6°F), pulse is 75/min, and blood pressure is 130/80 mm Hg. Bowel sounds are normal. The abdomen is soft. There is tenderness to palpation in the left lower quadrant with guarding and no rebound. She receives appropriate treatment and recovers. Two weeks later, colonoscopy shows polypoid growths flanked by linear ulcers. A colonic biopsy specimen shows mucosal edema with distorted crypts and inflammatory cells in the lamina propria. Which of the following is the most appropriate recommendation for this patient?
- A. Obtain genetic studies now
- B. Obtain barium follow-through radiography in 1 year
- C. Obtain glutamate dehydrogenase antigen immunoassay now
- D. Start annual magnetic resonance cholangiopancreatography screening in 10 years
- E. Start annual colonoscopy starting in 8 years (Correct Answer)
Methods for studying the microbiome Explanation: ***Start annual colonoscopy starting in 8 years***
- The patient's presentation with bloody diarrhea, abdominal cramps, and repetitive episodes is consistent with <b>inflammatory bowel disease (IBD)</b>, specifically likely <b>ulcerative colitis</b> given the left lower quadrant tenderness and colonic biopsy findings (distorted crypts, inflammatory cells in lamina propria).
- Patients with IBD, particularly ulcerative colitis affecting a significant portion of the colon and diagnosed at a younger age, are at increased risk for <b>colorectal cancer</b>. Annual colonoscopy screening is recommended 8–10 years after diagnosis for early detection and prevention.
*Obtain genetic studies now*
- While genetic factors play a role in IBD susceptibility, <b>genetic studies are not routinely indicated for diagnosis or management</b> of inflammatory bowel disease, nor do they guide current screening recommendations for colorectal cancer in IBD patients.
- Genetic studies would not provide immediate clinical benefit for this patient's acute symptoms or long-term management plan regarding cancer surveillance.
*Obtain barium follow-through radiography in 1 year*
- <b>Barium follow-through radiography</b> is primarily used to evaluate the small intestine, often in suspected Crohn's disease. This patient's symptoms and colonoscopy findings point towards colonic involvement, making this less appropriate.
- Furthermore, this imaging modality uses <b>ionizing radiation</b> and is less sensitive for detecting mucosal changes indicative of dysplasia or early cancer compared to colonoscopy.
*Obtain glutamate dehydrogenase antigen immunoassay now*
- <b>Glutamate dehydrogenase antigen immunoassay</b> is a test for <b><i>Clostridioides difficile</i> infection</b>. While C. difficile can cause severe diarrhea and colitis, the patient's history of recurrent episodes over 8 months and the specific colonoscopy findings (polypoid growths, linear ulcers, distorted crypts) are more characteristic of IBD.
- Although C. difficile infection can exacerbate IBD, it does not explain the chronic, recurrent nature of her illness or the long-term cancer surveillance needs.
*Start annual magnetic resonance cholangiopancreatography screening in 10 years*
- <b>MRCP screening</b> is used to monitor for <b>primary sclerosing cholangitis (PSC)</b>, a condition associated with IBD, particularly ulcerative colitis. However, PSC screening is performed <b>when clinically indicated</b> (e.g., elevated alkaline phosphatase, cholestatic symptoms), not as routine scheduled surveillance.
- This patient has no clinical features suggesting PSC at present, and there is no guideline recommending routine MRCP screening at a predetermined time interval for all IBD patients.
Methods for studying the microbiome US Medical PG Question 7: An investigator is processing a blood sample from a human subject. A reagent is added to the sample and the solution is heated to break the hydrogen bonds between complementary base pairs. This solution is then cooled to allow artificial DNA primers in the solution to attach to the separated strands of the sample DNA molecules. An enzyme derived from the thermophilic bacterium Thermus aquaticus is added and the solution is reheated. These steps are repeated multiple times until the aim of the test is achieved. The investigator most likely used which of the following laboratory procedures on the test sample?
- A. Northern blot
- B. Western blot
- C. Polymerase chain reaction (Correct Answer)
- D. Immunohistochemistry
- E. Fluorescence in-situ hybridization
Methods for studying the microbiome Explanation: ***Polymerase chain reaction***
- The process described, including **denaturation** by heating, **annealing** of primers upon cooling, and **extension** by a heat-stable DNA polymerase (like from *Thermus aquaticus*), are the hallmark steps of **Polymerase Chain Reaction (PCR)**.
- PCR is used to **amplify specific DNA sequences** exponentially, making it possible to detect and analyze even minute amounts of genetic material.
*Northern blot*
- **Northern blot** is a laboratory technique used to detect specific **RNA molecules** among a mixture of RNA. It involves electrophoresis, transfer to a membrane, and hybridization with a probe.
- It does not involve repetitive heating, cooling, or the use of DNA primers and heat-stable polymerases for amplification.
*Western blot*
- **Western blot** is a widely used analytical technique in molecular biology and immunogenetics to detect specific **proteins** in a sample of tissue homogenate or extract.
- This method separates proteins by size using gel electrophoresis, transfers them to a membrane, and then detects the target protein using specific antibodies. It does not involve DNA denaturation or amplification.
*Immunohistochemistry*
- **Immunohistochemistry (IHC)** is a histological technique that uses the principle of specific antibody-antigen binding to **detect specific antigens (proteins) in cells or tissues**.
- It involves staining tissues with antibodies labeled with a chromogenic reporter or fluorophore to visualize the location and distribution of target proteins within preserved tissue sections.
*Fluorescence in-situ hybridization*
- **Fluorescence in-situ hybridization (FISH)** is a cytogenetic technique used to detect and **localize specific DNA or RNA sequences within cells or tissues** using fluorescent probes that bind to parts of the chromosome.
- While it involves hybridization, it is primarily for visualizing genetic material within its cellular context, not for amplifying DNA like PCR.
Methods for studying the microbiome US Medical PG Question 8: You are interested in studying the etiology of heart failure reduced ejection fraction (HFrEF) and attempt to construct an appropriate design study. Specifically, you wish to look for potential causality between dietary glucose consumption and HFrEF. Which of the following study designs would allow you to assess for and determine this causality?
- A. Cross-sectional study
- B. Case series
- C. Cohort study (Correct Answer)
- D. Case-control study
- E. Randomized controlled trial
Methods for studying the microbiome Explanation: ***Cohort study***
- A **cohort study** observes a group of individuals over time to identify risk factors and outcomes, allowing for the assessment of **temporal relationships** between exposure (dietary glucose) and outcome (HFrEF).
- This design is suitable for establishing a potential **causal link** as it tracks participants from exposure to outcome, enabling the calculation of incidence rates and relative risks.
*Cross-sectional study*
- A **cross-sectional study** measures exposure and outcome simultaneously at a single point in time, making it impossible to determine the **temporal sequence** of events.
- This design can only identify **associations** or correlations, not causation, as it cannot establish whether high glucose consumption preceded HFrEF.
*Case series*
- A **case series** describes characteristics of a group of patients with a particular disease or exposure, often to highlight unusual clinical features, but it lacks a **comparison group**.
- It cannot assess causality because it does not provide information on the frequency of exposure in healthy individuals or the incidence of the disease in unexposed individuals.
*Case-control study*
- A **case-control study** compares individuals with the outcome (cases) to those without the outcome (controls) to determine past exposures, which makes it prone to **recall bias**.
- While it can suggest associations, it cannot definitively establish a temporal relationship or causation as the outcome is already known when exposure is assessed.
*Randomized controlled trial*
- A **randomized controlled trial (RCT)** is the gold standard for establishing causation by randomly assigning participants to an intervention or control group, but it may not be ethical or feasible for studying long-term dietary exposures and chronic diseases like HFrEF due to the long follow-up period and complexity of diet.
- While ideal for causality, directly controlling and randomizing dietary glucose intake over decades to observe HFrEF development might be practically challenging or unethical.
Methods for studying the microbiome US Medical PG Question 9: A hospital implements a bundle to reduce catheter-associated bloodstream infections. Components include: chlorhexidine bathing, antibiotic-impregnated catheters, antiseptic catheter site dressings, and daily line necessity assessment. After implementation, bloodstream infections with coagulase-negative staphylococci decrease by 60%, but Candida bloodstream infections increase by 40%. Evaluate the microbiological mechanisms underlying these divergent outcomes and synthesize an optimal prevention strategy.
- A. Antibiotic-impregnated catheters select for resistant Candida; use non-antibiotic catheters
- B. The bundle successfully reduced bacterial infections, revealing underlying fungal infections; add antifungal prophylaxis
- C. Multiple interventions disrupted skin flora creating ecological niche for Candida; modify bundle to preserve some commensal bacteria while maintaining antisepsis (Correct Answer)
- D. Chlorhexidine bathing eliminates bacterial skin flora but promotes fungal colonization; discontinue chlorhexidine
- E. Candida increase represents surveillance bias from increased culturing; no change needed
Methods for studying the microbiome Explanation: ***Multiple interventions disrupted skin flora creating ecological niche for Candida; modify bundle to preserve some commensal bacteria while maintaining antisepsis***
- Aggressive use of **chlorhexidine bathing** and **antibiotic-impregnated catheters** eliminates commensal bacterial flora that provide **colonization resistance** against opportunistic fungi.
- The reduction in **Coagulase-negative staphylococci** creates an available **ecological niche**, allowing *Candida* species to proliferate and colonize the catheter site more effectively.
*Antibiotic-impregnated catheters select for resistant Candida; use non-antibiotic catheters*
- While **antibiotic-impregnated catheters** reduce bacterial biofilm, they do not directly "select" for resistance in fungi, as antibiotics have no biochemical target in *Candida*.
- Removing them entirely may lead to a rebound in **staphylococcal infections**, failing to address the need for a balanced antiseptic strategy.
*The bundle successfully reduced bacterial infections, revealing underlying fungal infections; add antifungal prophylaxis*
- Adding **antifungal prophylaxis** as a routine measures increases the risk of developing **drug-resistant fungal strains** like *Candida auris*.
- This approach ignores the ecological disruption caused by the bundle and instead layers on more **antimicrobial pressure**, which is rarely a sustainable prevention strategy.
*Chlorhexidine bathing eliminates bacterial skin flora but promotes fungal colonization; discontinue chlorhexidine*
- Discontinuing **chlorhexidine bathing** would likely reverse the 60% reduction in **coagulase-negative staphylococcal** infections, which are a major source of morbidity.
- The goal should be optimization (e.g., targeted use or modified frequency) rather than total discontinuation of an effective **infection control** tool.
*Candida increase represents surveillance bias from increased culturing; no change needed*
- A 40% increase in **Candida bloodstream infections** is a significant clinical shift that requires a root-cause analysis rather than dismissal as **surveillance bias**.
- "No change needed" is incorrect because the bundle has created a new, clinically significant risk for **iatrogenic candidemia**.
Methods for studying the microbiome US Medical PG Question 10: A 68-year-old man develops Clostridioides difficile infection after hospitalization for pneumonia. He is treated with oral vancomycin with resolution of diarrhea. Two weeks later, he has recurrent C. difficile infection. After a second vancomycin course, he has a third recurrence. His physician must choose between extended vancomycin taper, fidaxomicin, or fecal microbiota transplantation (FMT). Synthesize the microbiological rationale for selecting FMT over continued antibiotic therapy in recurrent C. difficile infection.
- A. FMT restores colonization resistance that prevents C. difficile recurrence better than antibiotics that further disrupt flora (Correct Answer)
- B. FMT treats antibiotic-resistant C. difficile strains unresponsive to vancomycin
- C. FMT provides immune modulation that antibiotics cannot achieve
- D. FMT eradicates C. difficile spores more effectively than antibiotics
- E. FMT is more cost-effective than prolonged antibiotic courses
Methods for studying the microbiome Explanation: ***FMT restores colonization resistance that prevents C. difficile recurrence better than antibiotics that further disrupt flora***
- Recurrent **Clostridioides difficile** infection (CDI) is driven by a persistent state of **dysbiosis** where the normal gut microbiome fails to inhibit spore germination and vegetative growth.
- **Fecal Microbiota Transplantation (FMT)** reintroduces a diverse ecosystem of commensal bacteria that compete for nutrients and restore **secondary bile acid metabolism**, effectively restoring the gut's **colonization resistance**.
*FMT treats antibiotic-resistant C. difficile strains unresponsive to vancomycin*
- CDI recurrence is rarely due to **antibiotic resistance**; C. difficile remains highly susceptible to **vancomycin** and **fidaxomicin** in vitro.
- The failure of therapy is due to the survival of **dormant spores** in a disrupted microbiome, not the presence of resistant vegetative cells.
*FMT provides immune modulation that antibiotics cannot achieve*
- While the microbiome does interact with the immune system, the primary mechanism of FMT in treating CDI is **microbial competition** and metabolic restoration rather than systemic **immune modulation**.
- Antibiotics like **fidaxomicin** can also have minor anti-inflammatory effects, but this is not the rationale for choosing FMT over pharmacological therapy.
*FMT eradicates C. difficile spores more effectively than antibiotics*
- Neither antibiotics nor FMT directly "kill" or **eradicate spores**; spores are biologically inert and resistant to most environmental stressors.
- FMT works by preventing those spores from **germinating** into toxin-producing vegetative cells by restoring the inhibitory environment of a healthy gut.
*FMT is more cost-effective than prolonged antibiotic courses*
- While FMT may be **cost-effective** in the long term by preventing further hospitalizations, this is a pharmacoeconomic rationale rather than a **microbiological** one.
- The question specifically asks for the **microbiological rationale**, which pertains to the restoration of the ecological balance of the gut flora.
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