Rapid molecular diagnostics and syndromic testing

39 NEET-PG practice questions on Rapid molecular diagnostics and syndromic testing, part of Microbiology. The first 25 are below; the first 5 with answers and explanations (tap Show answer after you have chosen), the rest in Learn with a free account.

1. Question 1 · Medium

   Statements about CBNAAT: 1. It detects rifampicin resistance through rpoB mutations. 2. A positive result distinguishes live from dead bacilli. 3. It can be used on cerebrospinal fluid and lymph node aspirates. 4. It replaces culture for monitoring treatment response. Which combination is correct?

   1. A1 and 3 only
   2. B1 and 4 only
   3. C1, 2 and 3 only
   4. D2 and 4 only

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   Answer: A · 1 and 3 only

   The assay targets rpoB mutations for rifampicin resistance and is validated on several extrapulmonary specimens including cerebrospinal fluid and lymph node aspirates. It cannot distinguish viable from dead bacilli, so it stays positive during successful treatment and is unsuitable for monitoring, which uses smear and culture. Key point: CBNAAT detects rpoB mutations and works on extrapulmonary samples, but cannot monitor treatment.

   • B: Statement 4 is wrong, though statement 1 is correct.
   • C: Statement 2 is wrong: DNA from dead bacilli is also amplified.
   • D: Statement 4 is wrong: monitoring uses smear and culture.

2. Question 2 · Medium

   In a neonatal intensive care unit, blood cultures from a 9-day-old baby with suspected late-onset sepsis flag positive after 14 hours, and the Gram stain of the broth shows gram-positive cocci in clusters. The baby has an umbilical venous catheter and is on piperacillin-tazobactam. Which test will most rapidly guide the choice between cloxacillin and vancomycin?

   1. AConventional disc diffusion testing after overnight subculture
   2. BSerum procalcitonin with a repeat value after 24 hours
   3. CMolecular detection of mecA from the positive broth
   4. DA second blood culture drawn from another peripheral site

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   Answer: C · Molecular detection of mecA from the positive broth

   Molecular detection of mecA, performed directly on the positive broth, tells within an hour whether a staphylococcus is methicillin-resistant, which is precisely the decision to be made, and mass spectrometry alongside identifies the species. Conventional susceptibility testing adds a further day. Key point: mecA detection from a positive blood culture distinguishes MRSA within an hour.

   • A: Disc diffusion needs overnight incubation after subculture.
   • B: Procalcitonin suggests bacterial infection but says nothing about resistance.
   • D: A repeat culture repeats the same delay.

3. Question 3 · Medium

   Which limitation is most important to state when reporting a positive result from a highly sensitive amplification test on a respiratory sample?

   1. AA positive result always indicates severe disease
   2. BThe result cannot be repeated on the same specimen
   3. CDetection may reflect colonisation or recent infection
   4. DAmplification tests are unable to detect respiratory viruses

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   Answer: C · Detection may reflect colonisation or recent infection

   High analytical sensitivity means organisms present in small numbers, including commensals and residual nucleic acid from a recent illness, are detected. Reports therefore need clinical correlation, and local protocols often restrict panels to defined indications to limit misinterpretation. Key point: A positive amplification result may mean colonisation or recent infection, so correlate it clinically.

   • A: Detection says nothing about severity.
   • B: Results are reproducible; that is not the limitation.
   • D: Amplification tests are the mainstay of viral detection.

4. Question 4 · Medium

   Which advantage of MALDI-TOF identification over conventional biochemical identification matters most in bloodstream infection?

   1. AIt removes the need to take blood cultures at all
   2. BIt provides complete antibiotic susceptibility results in one run
   3. CIt detects resistance genes directly from the patient's blood
   4. DIt shortens the time to targeted therapy

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   Answer: D · It shortens the time to targeted therapy

   In bacteraemia, outcome depends on how early appropriate therapy starts. Identifying the isolate within minutes of growth allows therapy to be narrowed or corrected a day earlier than with biochemical panels, which is why many hospitals pair it with rapid resistance-gene testing. Susceptibility testing itself still follows. Key point: MALDI-TOF shortens time to targeted therapy in bacteraemia by identifying isolates in minutes.

   • A: Cultures are still required to obtain the isolate.
   • B: It identifies organisms but does not report susceptibility.
   • C: Resistance genes need molecular assays; mass spectrometry does not report them routinely.

5. Question 5 · Easy

   Which statement about multiplex PCR panels for syndromic testing is correct?

   1. ASeveral pathogens causing one syndrome are detected in a single run
   2. BThey detect host antibodies rather than pathogen nucleic acid
   3. CThey remove the need for any antimicrobial susceptibility testing
   4. DOnly one organism can be detected in each reaction run

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   Answer: A · Several pathogens causing one syndrome are detected in a single run

   Syndromic multiplex panels amplify many targets simultaneously, for example the common bacterial, viral and parasitic causes of acute diarrhoea or of meningitis, and report them together within hours. They do not provide full susceptibility data, so culture is still needed for most bacterial isolates. Key point: Multiplex panels detect many pathogens of one syndrome at once but do not replace culture.

   • B: These panels detect nucleic acid, not antibodies.
   • C: Limited resistance markers are reported; full susceptibility still needs culture.
   • D: Detecting multiple targets in one reaction is the defining feature of multiplex PCR.

6. Question 6 · Medium

   Sputum from a man who completed tuberculosis treatment two years ago and now has six weeks of cough, haemoptysis and weight loss is reported as 'MTB detected, rifampicin resistance indeterminate'. The sample was scanty and blood-stained. Which action follows?

   1. ARecord him as rifampicin-sensitive and begin the first-line regimen
   2. BRecord him as rifampicin-resistant and begin a second-line regimen
   3. CRepeat the test only if he deteriorates over the next two months
   4. DRepeat on a fresh specimen and send for culture-based susceptibility testing

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7. Question 7 · Hard

   A district laboratory notices that its molecular tuberculosis assay gives invalid or error results on 18% of sputum samples from one peripheral centre, against 2% from all others, over the same two months and on the same instrument. Samples from that centre arrive each afternoon in a shared bag without ice packs. Which explanation should be investigated first?

   1. ASpecimen quality and transport conditions from that centre
   2. BA change in the organism's genome across the country
   3. CInsufficient clinical suspicion among staff at that centre
   4. DThe age distribution of patients attending that centre

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8. Question 8 · Easy

   A line probe assay is requested on sputum from a man whose CBNAAT has already shown rifampicin resistance, before his regimen is decided at the district drug-resistant tuberculosis centre. What additional information will the assay provide?

   1. AThe bacillary load in the submitted sputum sample
   2. BResistance to isoniazid and to second-line drugs
   3. CSusceptibility to each of the four first-line drugs
   4. DSpecies identification of all mycobacteria including atypical ones

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9. Question 9 · Hard

   Which explanation best accounts for a molecular assay reporting rifampicin resistance when the same organism tests susceptible by phenotypic methods?

   1. AContamination of the specimen with a rifampicin-containing drug
   2. BDelayed transport of the specimen to the laboratory
   3. CA very low bacillary load in the submitted specimen
   4. DA silent or disputed rpoB mutation

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10. Question 10 · Medium

    A medical college introduces a rapid respiratory panel in its emergency department and audits the service after six months. Which outcome best shows that the test is being used appropriately?

    1. AA shorter laboratory turnaround time for each panel
    2. BFewer unnecessary antibiotic courses with no missed bacterial infection
    3. CAn increase in admissions for overnight observation
    4. DA rise in the number of panels performed per patient

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11. Question 11 · Hard

    A rapid molecular test for a respiratory pathogen has a sensitivity of 90% and a specificity of 98%. It is applied in a community screening programme where the pre-test probability of infection is 1%. Roughly what proportion of positive results will be true positives?

    1. AAbout nine tenths
    2. BAbout one twentieth
    3. CAbout two thirds
    4. DAbout one third

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12. Question 12 · Medium

    A medical college laboratory installs a mass spectrometer, and the residents are taught what it can and cannot do. Statements about MALDI-TOF: 1. It identifies organisms by comparing protein mass spectra with a database. 2. Accurate identification needs an adequate reference database. 3. It reliably separates all closely related species. 4. It can be applied to positive blood culture broths after processing. Which combination is correct?

    1. A2 and 3 only
    2. B1, 2 and 4 only
    3. C1, 3 and 4 only
    4. D1 and 3 only

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13. Question 13 · Medium

    A fine-needle aspirate from a cervical lymph node in a young woman with matted nodes, evening fever and weight loss shows granulomas with caseation on cytology, and the smear for acid-fast bacilli is negative. She has lost 4 kg in two months and her chest radiograph is normal. Which test on the same aspirate best confirms the organism and its rifampicin susceptibility together?

    1. ACBNAAT on the aspirate
    2. BZiehl-Neelsen staining repeated on fresh smears
    3. CTuberculin skin test with 5 tuberculin units
    4. DInterferon-gamma release assay on whole blood

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14. Question 14 · Medium

    At a screening camp during an outbreak, a medical officer has to decide how far the camp can rely on antigen testing. Statements about rapid antigen tests: 1. A positive result during an outbreak is usually reliable. 2. Sensitivity is generally lower than that of nucleic acid amplification. 3. They detect organism components rather than host antibodies. 4. A negative result in a symptomatic contact excludes infection. Which combination is correct?

    1. A2 and 4 only
    2. B1, 2 and 3 only
    3. C3 and 4 only
    4. D1 and 4 only

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15. Question 15 · Medium

    Laboratory results on the second hospital day for a man with two days of coryza, sore throat and dry cough: respiratory multiplex PCR positive for rhinovirus; blood cultures sterile at 48 hours; procalcitonin 0.08 ng/mL (reference below 0.5); total leucocytes 7,200/microL; chest radiograph clear. He is 36 years old with well-controlled hypertension, has no sputum and no breathlessness, and his oxygen saturation is 98% on room air. He was started on piperacillin-tazobactam in casualty and is now afebrile, comfortable and eating normally. What is the most appropriate action?

    1. AContinue piperacillin-tazobactam to complete seven days
    2. BStop the antibiotic and continue supportive care
    3. CAdd azithromycin to cover atypical organisms
    4. DEscalate to meropenem and repeat the cultures

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16. Question 16 · Medium

    At a PHC in a district whose nearest molecular testing laboratory is 60 km away, a man with two weeks of cough is found to be a household contact of a patient on treatment for rifampicin-resistant tuberculosis. He is ambulant and willing to come back, has lost 3 kg, and has had evening fever for ten days. Which arrangement serves him best?

    1. ACollect sputum and transport it to the molecular testing site
    2. BRepeat sputum smear microscopy at the PHC every week
    3. CBegin the standard first-line regimen today and review him after two months
    4. DRefer him for a chest radiograph at the district hospital alone

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17. Question 17 · Medium

    On the eighth day of an intensive care stay a woman develops fever of 39.2 degrees C and blood pressure of 82/48 mmHg. A rapid molecular panel run directly on blood reports Klebsiella pneumoniae carrying the blaNDM gene, while her blood culture bottles are still incubating. Her total leucocyte count is 18,600/microL, lactate 3.8 mmol/L and urine output 20 mL in the last hour; she is on meropenem and had an infected abdominal drain removed on the previous day. Which empirical choice follows best from this result?

    1. ACeftriaxone combined with amikacin
    2. BMeropenem continued alone at a higher dose
    3. CA colistin-based regimen
    4. DPiperacillin-tazobactam by extended infusion

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18. Question 18 · Medium

    Cerebrospinal fluid from a 4-year-old with two days of fever, headache and one brief generalised seizure shows 40 cells/microL with a lymphocyte predominance, protein 45 mg/dL and glucose 62 mg/dL against a blood glucose of 98 mg/dL. The Gram stain is negative and the meningitis panel is positive for enterovirus. He received one dose of ceftriaxone in casualty, is now alert and playful, has had all his routine immunisations, and three other children in his locality have had a similar brief illness this month. What is the most appropriate decision?

    1. AStop ceftriaxone and continue supportive care
    2. BAdd intravenous acyclovir to cover the enterovirus
    3. CContinue ceftriaxone to complete ten days of treatment
    4. DStart four-drug antituberculous treatment empirically

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19. Question 19 · Medium

    Cerebrospinal fluid from a child with four weeks of fever, headache, vomiting and a sixth nerve palsy shows 120 cells/microL with 85% lymphocytes, protein 220 mg/dL and glucose 28 mg/dL against a blood glucose of 96 mg/dL. The fluid forms a cobweb clot on standing, and the child's mother is on treatment for sputum-positive pulmonary tuberculosis. Which single test best confirms the clinical suspicion fastest?

    1. AIndia ink preparation of the fluid
    2. BLatex agglutination for cryptococcal antigen
    3. CHerpes simplex virus PCR on the fluid
    4. DCBNAAT on concentrated cerebrospinal fluid

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20. Question 20 · Medium

    Which situation is the clearest indication for a syndromic multiplex panel rather than conventional testing alone?

    1. AFollow-up of a treated lower urinary tract infection
    2. BRoutine throat swab in uncomplicated acute pharyngitis
    3. CScreening of healthy voluntary blood donors
    4. DEncephalitis with a wide treatable differential

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21. Question 21 · Easy

    Sputum CBNAAT from a newly diagnosed man at a district hospital reports 'MTB detected, rifampicin resistance detected'. He has not been treated for tuberculosis before. What is the correct next step under the programme?

    1. ATreat as drug-sensitive disease and review at the end of treatment
    2. BRefer for second-line resistance testing and start an appropriate regimen
    3. CRepeat the same cartridge test after two months of therapy
    4. DStart the standard first-line four-drug regimen today

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22. Question 22 · Easy

    In a hospital laboratory, MALDI-TOF mass spectrometry is used chiefly for which purpose?

    1. ADirect detection of viral RNA in serum samples
    2. BHistological grading of biopsy tissue
    3. CRapid identification of cultured bacteria and yeasts
    4. DMeasurement of antibody titres in paired sera

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23. Question 23 · Medium

    During an outbreak of acute watery diarrhoea in a flood relief camp, stool from several children is tested by a syndromic gastrointestinal panel. For one child with profuse rice-water stools and severe dehydration the panel reports both Vibrio cholerae and enteroaggregative Escherichia coli, while the camp has notified forty similar cases in two days and one death. How should this be interpreted?

    1. AOnly the pathogen listed first on the report is relevant
    2. BBoth results are false positives and should be ignored
    3. CThe panel result effectively excludes cholera in this child
    4. DCorrelate clinically and treat the dominant pathogen

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24. Question 24 · Medium

    On the fourth day after an emergency laparotomy, a man in the surgical ward has fever, headache, neck stiffness and drowsiness. Lumbar puncture yields cloudy fluid with 1,800 cells/microL, 90% of them neutrophils, protein 180 mg/dL and glucose 22 mg/dL against a blood glucose of 110 mg/dL. The Gram stain shows no organisms and cultures are sterile at 48 hours; he had received a dose of ceftriaxone at another hospital before transfer. The computed tomogram of the head is normal and he has had no neurosurgery. Which test is most likely to identify the cause?

    1. ACerebrospinal fluid adenosine deaminase estimation
    2. BPaired blood cultures from two peripheral sites
    3. CRepeat Gram stain on the same fluid after 24 hours
    4. DMultiplex PCR meningitis panel on the CSF

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25. Question 25 · Easy

    Which test best suits a bedside decision at night in a febrile child in a malaria-endemic block where microscopy is unavailable?

    1. ABlood culture in a paediatric bottle
    2. BSerology for antimalarial antibodies
    3. CMalaria rapid diagnostic test
    4. DNested PCR for Plasmodium species

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