Metagenomics — MCQs

10 questions

A frequent traveler presented with 4 days of continuous fever, abdominal pain, and bradycardia. What is the best diagnostic test to confirm the pathogen?

Which is the correct sequence of steps in isolating desirable protein using recombinant DNA technology? 1. Expression of protein and lysis of the bacterial cell 2. Incorporation of genes into bacteria 3. SDS PAGE 4. Protein elution 5. Column chromatography

In a patient presenting with fever and suspected systemic infection, which of the following specimens is the most appropriate for the isolation of microorganisms in laboratory diagnosis?

Which of the following is a primarily RNA based technique?

Which of the following organisms is an obligate intracellular bacterium that commonly causes sexually transmitted infections?

All are true about culture media except:

MacConkey medium is primarily classified as which type of culture medium?

DNA amplification is done by all, except:

After 5 days of birth, a baby developed poor feeding, convulsions, fever, high protein, low sugar, and low chloride levels in the cerebrospinal fluid. This is most likely due to what?

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What does Polymerase Chain Reaction (PCR) detect?

Metagenomics Indian Medical PG Practice Questions and MCQs

Question 1: A frequent traveler presented with 4 days of continuous fever, abdominal pain, and bradycardia. What is the best diagnostic test to confirm the pathogen?

A. Widal test
B. Blood culture (Correct Answer)
C. Urine culture
D. Stool culture

Explanation: ***Blood culture*** - **Blood culture** is the most sensitive and specific test for confirming **typhoid fever** in the first week of illness. - The presence of **continuous fever** (step-ladder pattern), **abdominal pain**, and **relative bradycardia** in a traveler strongly suggests typhoid fever caused by *Salmonella Typhi*. *Widal test* - The **Widal test** detects antibodies against *Salmonella Typhi* antigens and is often positive later in the disease course. - It has **limited sensitivity and specificity**, especially in endemic areas or with prior vaccination, leading to false positives and negatives. *Urine culture* - **Urine culture** has a low yield for *Salmonella Typhi*, as bacteria are intermittently shed in urine, usually later in the disease. - It's primarily useful for diagnosing **urinary tract infections** or in chronic carriers of typhoid. *Stool culture* - **Stool culture** yield is higher in the later stages of typhoid fever, as *Salmonella Typhi* is shed in feces. - Its sensitivity is lower than blood culture in the early acute phase when bacteremia is most prominent.

Question 2: Which is the correct sequence of steps in isolating desirable protein using recombinant DNA technology? 1. Expression of protein and lysis of the bacterial cell 2. Incorporation of genes into bacteria 3. SDS PAGE 4. Protein elution 5. Column chromatography

A. 2,1,3,5,4 (Correct Answer)
B. 2,4,5,3,1
C. 1,2,4,3,5
D. 1,5,2,4,3

Explanation: ***2,1,3,5,4*** - This sequence accurately reflects the typical order of operations in **recombinant protein isolation**: first, the gene is introduced into bacteria, then protein is expressed and cells lysed, followed by **SDS-PAGE as an intermediate quality check** to confirm protein expression before proceeding to purification steps (column chromatography and elution). - The process starts with gene incorporation, includes an analytical checkpoint after lysis, and ends with purified protein elution. *2,4,5,3,1* - This sequence is incorrect because **protein elution (4)** and **column chromatography (5)** are purification steps that occur *after* protein expression and cell lysis. - **Lysis (1)** cannot happen after elution, as cells must be lysed first to release the protein for purification. *1,2,4,3,5* - This sequence is incorrect because **expression and lysis (1)** must occur *after* the gene has been **incorporated into bacteria (2)** - the gene must be present before it can be expressed. - Additionally, **protein elution (4)** should follow **column chromatography (5)**, as elution is the step where protein is collected from the chromatography column. *1,5,2,4,3* - This sequence is incorrect because **incorporation of genes (2)** must be the first step - the gene needs to be in the bacteria before any expression, lysis, or purification can occur. - Starting with **expression and lysis (1)** before gene incorporation is impossible.

Question 3: In a patient presenting with fever and suspected systemic infection, which of the following specimens is the most appropriate for the isolation of microorganisms in laboratory diagnosis?

A. Blood culture for isolation of bacteria (Correct Answer)
B. Stool sample in cases of gastroenteritis
C. Throat swab for suspected pharyngitis
D. Urine sample for urinary tract infection

Explanation: ***Blood culture for isolation of bacteria*** - For **systemic infection** and **fever**, **blood culture** is the most direct method to isolate and identify the causative microorganism disseminated throughout the body. - It helps guide **appropriate antibiotic therapy** by determining the pathogen's **susceptibility profile**. *Stool sample in cases of gastroenteritis* - This specimen is appropriate for diagnosing **gastrointestinal infections** where the pathogen primarily affects the digestive tract. - It is not the primary choice for suspected **systemic infection** unless GI symptoms are prominent and dissemination is suspected. *Throat swab for suspected pharyngitis* - A throat swab is specific for diagnosing **pharyngitis** or upper **respiratory tract infections**, localizing the infection to the pharynx. - It would not sufficiently identify a **systemic infection**, as the pathogen may not be present in the throat in such cases. *Urine sample for urinary tract infection* - A urine sample is indicated for diagnosing **urinary tract infections (UTIs)**, where the pathogen is concentrated in the urinary system. - While a UTI can lead to systemic symptoms, a urine sample alone is insufficient to confirm a generalized systemic infection unless the infection has specifically localized there.

Question 4: Which of the following is a primarily RNA based technique?

A. Western blotting
B. Northern blotting (Correct Answer)
C. Southern blotting
D. Sanger's technique

Explanation: ***Northern blotting*** - **Northern blotting** is a molecular biology technique used to study **gene expression** by detecting specific **RNA molecules** (mRNA) in a sample. - It involves separating RNA fragments by **gel electrophoresis**, transferring them to a membrane, and then detecting specific sequences using **labeled probes**. *Western blotting* - **Western blotting** is a technique used to detect specific **proteins** in a sample. - It involves separating proteins by **gel electrophoresis**, transferring them to a membrane, and then detecting specific proteins using labeled **antibodies**. *Southern blotting* - **Southern blotting** is a molecular biology method used for the detection of **specific DNA sequences** in DNA samples. - It involves separating **DNA fragments** by **gel electrophoresis**, transferring them to a membrane, and then hybridizing with a labeled probe. *Sanger's technique* - **Sanger sequencing**, or the **dideoxy chain-termination method**, is a widely used method for **DNA sequencing**. - It uses **dideoxynucleotides** to terminate DNA synthesis at specific bases, allowing the determination of the **DNA sequence**.

Question 5: Which of the following organisms is an obligate intracellular bacterium that commonly causes sexually transmitted infections?

A. Mycoplasma
B. Chlamydia (Correct Answer)
C. Rickettsia
D. Prion

Explanation: ***Chlamydia*** - **Chlamydia trachomatis** is a classic example of an **obligate intracellular bacterium** that is a leading cause of sexually transmitted infections (STIs). - It has a unique biphasic developmental cycle, alternating between an infectious **elementary body** and a replicative **reticulate body** within host cells. *Rickettsia* - **Rickettsia** species are also **obligate intracellular bacteria** but are primarily transmitted via **arthropod vectors** (e.g., ticks, fleas, lice), causing diseases like **Rocky Mountain spotted fever** and **typhus**. - They are not typically associated with **sexually transmitted infections** in humans. *Mycoplasma* - **Mycoplasma** species are bacteria characterized by the **absence of a cell wall**, but they are generally **extracellular** or **intracellular but not obligate**. - While some *Mycoplasma* species can cause STIs (e.g., *Mycoplasma genitalium*), they do not fit the description of an **obligate intracellular bacterium** in the same way *Chlamydia* does (which requires host cell machinery for energy production). *Prion* - A **prion** is an **infectious protein particle** that lacks genetic material (DNA or RNA) and causes transmissible spongiform encephalopathies (TSEs), such as **Creutzfeldt-Jakob disease**. - It is not a bacterium and is not associated with **sexually transmitted infections**.

Question 6: All are true about culture media except:

A. LJ medium is used for tubercle bacilli
B. Loeffler's serum slope is used for Corynebacterium diphtheriae
C. The best medium for anaerobes is chocolate agar (Correct Answer)
D. Blood agar supports fastidious organisms

Explanation: ***The best medium for anaerobes is chocolate agar*** - **Chocolate agar** is an enriched medium used for the isolation of **fastidious organisms** like *Haemophilus influenzae* and *Neisseria* species, but it is not optimized for anaerobic growth. - Anaerobes require **anaerobic specific media** (e.g., thioglycollate broth, blood agar with reducing agents) and conditions (e.g., anaerobic jar) for optimal growth. *LJ medium is used for tubercle bacilli* - **Lowenstein-Jensen (LJ) medium** is a primary isolation medium specifically formulated for the growth of **mycobacteria**, including *Mycobacterium tuberculosis*. - It contains **malachite green**, which inhibits the growth of most other bacteria, and nutrients like **egg and asparagine** to support mycobacterial growth. *Loeffler's serum slope is used for Corynebacterium diphtheriae* - **Loeffler's serum slope** is an enrichment medium used to isolate and presumptively identify *Corynebacterium diphtheriae*. - It enhances the production of **metachromatic granules (Babes-Ernst granules)** by *C. diphtheriae*, which are visible upon staining. *Blood agar supports fastidious organisms* - **Blood agar** is an enriched medium containing 5% sheep blood, providing essential growth factors for many bacteria, including some **fastidious organisms**. - It is used to detect **hemolytic reactions**, which are important for differentiating various bacterial species.

Question 7: MacConkey medium is primarily classified as which type of culture medium?

A. Selective media
B. Differential media (Correct Answer)
C. Enrichment media
D. Transport media

Explanation: ***Differential media*** - MacConkey medium contains a **pH indicator (neutral red)** that allows for the differentiation of bacteria based on their ability to **ferment lactose**, turning colonies pink or red. - This characteristic allows researchers to distinguish between different types of bacteria growing on the same plate, such as **lactose fermenters** versus **non-lactose fermenters**. *Selective media* - While MacConkey medium is also selective (containing **bile salts** and **crystal violet** to inhibit Gram-positive bacteria), its primary classification often highlights its ability to differentiate. - Its selective properties mainly focus on inhibiting unwanted bacterial growth, rather than classifying bacteria based on metabolic differences. *Enrichment media* - **Enrichment media** are designed to promote the growth of specific, fastidious bacteria while suppressing others, typically by providing specific nutrients. - MacConkey medium does not specifically enrich for fastidious organisms; rather, it primarily selects for Gram-negative enteric bacteria and then differentiates them. *Transport media* - **Transport media** are designed to maintain the viability of microorganisms during transport to the laboratory without allowing significant multiplication. - MacConkey medium is used for isolation and identification in the lab, not for preserving samples during transit.

Question 8: DNA amplification is done by all, except:

A. DNA sequencing (Correct Answer)
B. Loop-mediated isothermal amplification (LAMP)
C. Ligase chain reaction
D. Polymerase chain reaction

Explanation: ***DNA sequencing*** - **DNA sequencing** determines the **nucleotide base order** in a DNA molecule but does not increase the amount of DNA. - While requiring a DNA template, it is an **analytical technique** rather than an amplification method. *Loop-mediated isothermal amplification (LAMP)* - **LAMP** is an **isothermal DNA amplification** technique that amplifies target DNA sequences at a constant temperature (60-65°C). - It uses a DNA polymerase with strand displacement activity and 4-6 primers to produce large amounts of DNA rapidly. *Ligase chain reaction* - **LCR** is an amplification method that detects specific **DNA sequences** by ligating adjacent probes. - It amplifies the signal from a target DNA sequence rather than the DNA itself by creating many copies of joined probes. *Polymerase chain reaction* - **PCR** is a widely used technique for **amplifying** a specific segment of DNA to produce many copies. - It involves cycles of **denaturation**, **annealing**, and **extension** using a DNA polymerase.

Question 9: After 5 days of birth, a baby developed poor feeding, convulsions, fever, high protein, low sugar, and low chloride levels in the cerebrospinal fluid. This is most likely due to what?

A. Listeria monocytogenes infection (Correct Answer)
B. Tuberculosis infection
C. Leptospira infection
D. Mycoplasma pneumoniae infection

Explanation: ***Listeria monocytogenes infection*** - **Listeria meningitis** in neonates often presents with non-specific symptoms such as **poor feeding**, **convulsions**, and fever, typically in the **first week of life**. - The CSF profile of **high protein**, **low glucose**, and **low chloride** is characteristic of **bacterial meningitis**, which *Listeria* commonly causes in newborns. - *Listeria* is one of the leading causes of neonatal meningitis, particularly in early-onset sepsis (within 7 days of birth). *Tuberculosis infection* - **Tuberculous meningitis** typically has a more insidious onset and is less common in neonates unless there's significant maternal exposure. - While it can cause low glucose and high protein in CSF, the acute presentation in a 5-day-old neonate is atypical for TB. - TB meningitis has a longer incubation period and wouldn't typically present this early. *Leptospira infection* - **Leptospirosis** is rare in neonates and usually presents with symptoms like fever, headache, and muscle pain, sometimes leading to renal or hepatic involvement. - The CSF profile in leptospirosis would typically show **lymphocytic pleocytosis** with normal or slightly elevated protein, not the classic bacterial meningitis pattern. *Mycoplasma pneumoniae infection* - **Mycoplasma pneumoniae** is primarily a cause of **respiratory infections** (e.g., atypical pneumonia) in older children and adults. - It rarely causes meningitis in neonates, and neonatal infection is highly unusual. - When CNS involvement occurs, it's typically in older children with preceding respiratory symptoms.

Question 10: What does Polymerase Chain Reaction (PCR) detect?

A. Antigen
B. Antibody
C. Nucleic acid (Correct Answer)
D. All of the above

Explanation: **Explanation:** **Why Nucleic Acid is the Correct Answer:** Polymerase Chain Reaction (PCR) is a molecular technique used to **amplify specific sequences of DNA**. It utilizes a heat-stable DNA polymerase (like *Taq* polymerase) to create millions of copies of a target genetic sequence. In microbiology, PCR is used to detect the **nucleic acid** (DNA or RNA) of a pathogen. For RNA viruses (like HIV or SARS-CoV-2), a variation called Reverse Transcription-PCR (RT-PCR) is used to first convert RNA into complementary DNA (cDNA) before amplification. **Why Other Options are Incorrect:** * **Antigens (Option A):** These are proteins or polysaccharides on the surface of a pathogen. They are detected using immunological assays like **ELISA** (Enzyme-Linked Immunosorbent Assay) or Lateral Flow Assays (Rapid Antigen Tests), not PCR. * **Antibodies (Option B):** These are host proteins produced by B-cells in response to an infection. They are detected via **Serology** (e.g., ELISA, Western Blot, or Agglutination tests) to identify past or current exposure, whereas PCR identifies the presence of the organism itself. **High-Yield Clinical Pearls for NEET-PG:** * **Steps of PCR:** Denaturation (94-96°C) → Annealing (50-65°C) → Extension (72°C). * **Real-Time PCR (qPCR):** Allows for **quantification** of the microbial load (e.g., Viral Load in Hepatitis C or HIV). * **Multiplex PCR:** Can detect multiple different pathogens in a single clinical sample simultaneously using different primers. * **Sensitivity:** PCR is highly sensitive, making it the "Gold Standard" for diagnosing organisms that are difficult to culture (e.g., *M. tuberculosis*, *Chlamydia*, or viral infections).

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