Exam Questions Flashcards
A 32-year-old Ukrainian woman comes to the emergency room reporting cough for several weeks accompanied by weight loss. Assuming the patient has tuberculosis, what microbiological tests should be done?
1- Sputum Collection and Microscopy
• Acid-Fast Bacilli (AFB) Staining and microscopic examination: Perform a Ziehl-Neelsen or Auramine stain. This test helps identify acid-fast bacilli, indicative of Mycobacterium tuberculosis.
2- Sputum Culture
• Solid Culture (Lowenstein-Jensen Medium) or Liquid Culture (BACTEC MGIT) + Antibiogram: These cultures allow for bacterial growth, detection of Mycobacterium tuberculosis and test drug effectiveness by antibiogram. Solid culture requires up to 6 weeks to visualise growth but liquid culture (BACTEC MGIT) can give results in 10-14 days. In BACTEC MGIT, decrease of oxygen and increase in flourescense indicate mycobacterial growth, positive culture identification is done by rapid immunochromatographic test. Gold standard for identification of TB
3- Molecular test (PCR) on sputum: NAATs (Nucleic Acid Amplification Tests) can confirm TB and detect rifampicin resistance, providing results within a few hours. It’s highly sensitive and should be done if available.
4- Blood test - QuantiFERON: QuantiFERON test allows us to diagnose both active and latent TB by doing quantitative determination of the production of y-interferon by lymphocytes.
27-year-old woman presents to the ER for pain in the lower abdominal quadrants, dysuria.
• She shows symptoms of vaginal discharge, fever and chill.
• Denies having previously contracted sexually transmitted diseases
• In the previous year she had 4 sexual partners, using the condom only occasionally
Which microbiological tests are done for diagnosis, and which pathogen is likely to be the cause?
Diagnosis: Salpingitis (Pelvic Inflammatory Disease)
Pathogens likely to be the cause: Most likely Chlamydia trachomatis or Neisseria gonorrhoeae (gonococcus) and maybe mycoplasma genitalium.
Microbiological tests:
Vaginal-Cervical swab for the detection of chlamydia, gonococcus and mycoplasma by:
- Cytological examination + Gram stain and Giemsa staining on cells obtained with cervical swab / endo-urethral scraping. Direct light microscopy.
- Cultural examination for Chlamydia trachomatis and gonococcus
- Molecular probes - NAATs (PCR)
- Antigenic tests: Rapid immunochromatographic test for the qualitative determination of Chlamydia trachomatis
Michelle, a 7-year-old girl, suddenly develops fever, headache, dry cough. Strong breathing difficulty convinces the parents to take her to the pediatric ER. Physical examination reveal fever, breathing difficulty with breathing rate 40 / min; Urgency lab tests: Hb 9.5g/dl (>11 g/dl) with increased reticulocytes. Assuming that the patient has pneumonia, which microbiological tests can you request to confirm the diagnosis and identify the pathogen to undertake targeted therapy?
Diagnosis: Pneumonia
Pathogens likely to be the cause: S. pneumoniae, Mycoplasma pneumoniae, or Chlamydia pneumoniae
Microbiological tests:
- Sputum test:
• Microscopic examination after Gram staining
• Culture examination
• Molecular test (PCR - NAATs): Excellent sensitivity, performed on sputum or bronchoaspirate - Blood test - hemoculture and serology for the detection of anti-Mycoplasma pneumoniae antibodies:
• ELISA for IgG and IgM
• Cold agglutinins - Urinary Antigen Tests for detection of Streptococcus pneumoniae antigen
6 year old girl with fever, sore throat (Difficulty swallowing food), pharynx erythema and swollen tonsils, no cough. What microbiological tests you request to confirm the diagnosis? What pathogen can cause this clinical scenario?
Diagnosis: Strep throat, pharyngitis
Pathogens likely to be the cause: Streptococcus pyogenes
Microbiological tests:
- Throat swab:
• Culture on throat swab: Bacitracin susceptibility test and PYR test to distinguish S. pyogenes from other β-hemolytic streptococci. PYR positive for Strep.pyogenes.
• Rapid immunoassays from throat swab: Strep A Rapid Test Card for Strep A antigen detection
• Molecular Tests (PCR - NAATs) from throat swab: GASDirect test and POC tests - fast results with high sensitivity and specificity. Rapid antigen detection test is the first line of diagnosis.
A 79-year-old woman hospitalized in a rehabilitation facility develops diarrhea seven day after discontinuation of an antibiotic course for a urinary infection. She refers abdominal pain, present fever, neutrophilic leukocytosis, and increase in CRP. Assuming that the patient has antibiotic-induced diarrhea, which microbiological tests can you request to confirm diagnosis, and identify the pathogen to undertake targeted therapy?
Diagnosis: Enteritis - antibiotic-induced diarrhea
Pathogen likely to be the cause: Clostridium difficile
Microbiological tests:
• Stool test
1. GDH search on faeces, if positive: look for toxins by EIA
2. Stool culture
3. Molecular test (PCR NAAT - Film array)
4. Cytotoxicity test (not commonly used anymore)
Child of 2 years and 8 months, coming from Burkina Faso, in Italy for about 10 days, is taken to the pediatric ER for fever. Assuming he has malaria, which are the diagnostic tests that have to be performed?
Diagnosis: Malaria
Pathogen likely to be the cause: Plasmodium species
Microbiological tests:
-Blood test:
- Search malaria Ag with rapid immunochromatografic test
- Microscopic analysis on blood smear
- DNA research in molecular biology on blood (PCR)
A 59-year-old woman presented to the emergency room (ER) with an 18 hours history of fatigue, lethargy and frequent vomiting. Starting 2 hours before arrival, she developed respiratory ditress and a facial purpuric rash. At the ER, the patient presented with an elevated respiratory rate, hypoxaemia, and severe hypotension, but no fever. In the first 4 hours after admission, the purpuric rash became disseminated and the general condition worsened to shock. What is the most probable microbiological aetiology? What is the differential diagnosis? What microbiological tests should be performed?
Most probable microbiological etiology: Meningococcal sepsis caused by Neisseria meningitidis because the disseminated intravascular coagulation cause purpuric rash
Differential diagnosis:
• Other bacterial sepsis such as Gram + sepsis (septic shock) like S. aureus and S. pyogenes or Gram - sepsis like E. coli
• Thrombotic thrombocytopenic purpura
• Viral hemorrhagic fevers
Microbiological tests:
• Blood culture for N. meningitidis
• Lumbar puncture CSF analysis (CSF gram stain, culture and PCR) for identification of bacteria
• Skin biopsy of purpuric lesions, gram stain and culture for bacterial pathogens
Male 67 years old is brought to the ER by the wife for chills, fever and pain to the right hemi-thorax since the day before. What is the most likely cause? What is the differential diagnosis? Which microbiological tests should be performed?
Most likely cause: Community-acquired pneumonia
Differential diagnosis: Acute heart failure, pulmonary embolism, acute bronchitis, hypersensitivity pneumonitis
Possible pathological agents:
-Bacterial: Strep. pneumoniae, Pseudomonas aeruginosa, Mycoplasma pneumoniae, Haemophilus influenzae, Legionella pneumophila, S. aureus
-Viral: Respiratory syncytial virus, Adenovirus, Flu virus etc.
Microbiological and diagnostic tests:
- Chest X-ray
- Sputum test:
• Gram stain + microscopy
• Culture»_space; isolate/identify pathogen + antibiotic susceptibility (antibiogram)
• Molecular tests (PCR) - Urinary test for Pneumococcal antigen and Legionella antigen
- Blood test - Hemoculture
A 22yo male has an unpainful rectal ulcer, inguinal adenopathy and no penile discharge. What is the probable diagnosis, differential diagnosis and microbiological tests prescribed?
Probable diagnosis: Lymphogranuloma Venereum (LGV) by Chlamydia trachomatis
Differential diagnosis:
-Gonorrhea
-Primary Syphillis
-HSV (Herpes Simple Virus) infection
Microbiological tests:
- Swab from rectal ulcer:
• Molecular test - Multiplex PCR on rectal ulcer swab for Chlamydia trachomatis, Neisseria gonorrhoeae and HSV
• Dark-field microscopy for Treponema pallidum in syphilis - Blood tests:
• Serology for Syphilis: Non-treponemal (VDRL) and treponemal (TPHA) tests for detecting syphilis
• HIV serology
87 year old, csf cloudy, high neutrophils, previous respiratory infection. Tests and probable
pathogens.
Case strongly suggests bacterial meningitis. Why? Cloudy CSF: indicates significant inflammation, likely due to the bacterial infection. High neutrophils= bacterial
Probable pathogens possible:
• Streptococcus pneumoniae
• Neisseria meningitidis
• Listeria monocytogenes
Tests:
- Lumbar puncture
•CSF gram stain
•CSF culture: Definitive diagnosis by isolating the pathogen
•CSF biochemical analysis
•CSF PCR: detects bacterial DNA, especially if prior antibiotic use affects culture yield.
-Blood tests, blood culture and serology tests
16 year old boy returns from scout camp in Colli Euganei, Padova. 3 days later, he develops fever (38C), intense headache, neck stiffness, photophobia, confusion, conjunctival hyperemia, mild leukopenia, elevated erythrocyte sedimentation rate and normal blood calcitonin (also BP 120/70 and HR 90). Principle diagnosis? Differential diagnosis? What microbiological tests you request to confirm the diagnosis?
Principle diagnosis: Tick-borne Encephalitis (TBE) by Tick-borne encephalitis virus (TBEV)
Differential diagnosis:
• Viral meningitis/encephalitis
• Bacterial meningitis
• Leptospirosis
• Rickettsial infections
Microbiological tests:
-Lumbar puncture (CSF analysis):
• PCR for TBE virus and other viral pathogens such as (HSV-1, HSV-2 or VZV) in CSF (gold standard in the early neurologic phase)
• Cell count, glucose, protein biochemistry analysis
• Gram stain and culture for ruling out bacterial meningitis
-Serology for TBE virus antibodies
On February 25, 2023, a 28-year-old man presented to the emergency room with the sudden onset of fever, headache, vomiting, and joint pain. The patient had returned the previous day from a 15-day trip to Brazil. Physical examination revealed hyperpyrexia (38°C), blood pressure of 140/80, and a heart rate of 98, and joint stiffness. Hematochemical tests showed mild leukopenia and thrombocytopenia, a slight increase in erythrocyte sedimentation rate and a normal level of blood procalcitonin. What is the most probable diagnosis? What is the differential diagnosis? Which microbiological tests should be done?
Most probable diagnosis: Dengue Fever
Differential diagnosis:
• Chikungunya Fever
• Zika Virus
• Malaria
Microbiological tests:
1. Blood test:
• Dengue NS1 antigen test
• Serology for Dengue antibodies
• NAAT: RT-PCR for viral RNA detection and identifying the viral agent
38 M maculopapular rashes, bisexual, used condom, rectal bleeding, rectal pain, proctitis traveled across Italy as a salesman. Had gonorrhea a few years back. Ulcers on hand, palms, soles, feets trunk. Erythematous lesions. What is the most probable diagnosis? What is the differential diagnosis? Which microbiological tests should we use to confirm the diagnosis?
Most probable diagnosis: Secondary syphilis by Treponema pallidum
Differential diagnosis:
• HSV infection
• LGV
• Gonorrhea
• HIV related conditions
Microbiological tests:
- Blood test:
-Serology:
• Non-treponemal: VDRL
• Treponemal: TPHA - Rectal swab:
-Dark-field microscopy or PCR (NAAT) on rectal swab for identifying the pathogen (HSV, Gonococcus, Chlamydia trachomatis) if serology is inconclusive
A 28 y/o pregnant woman, after a 2 weeks trip to Argentina, refers headache, athralgia, fever 39°, and after 2 days she also presents a skin rash. What is the most probable diagnosis and which tests would you perform?
Most probable diagnosis: Zika virus infection
Differential diagnosis:
• Dengue fever
• Chikungunya fever
Microbiological tests:
-Blood test:
• RT-PCR for viral RNA detection (Zika, Dengue and Chikungunya)
• Serology for Zika, Dengue and Chikungunya antibodies
• Complete blood count if needed
A 78 year old male was admitted to the Neurology Department of the Padua hospital because of the sudden onset of fever (38° C), maculopapular rash, confusion and aphasia. The patient reported no recent travel history. What is the most likely etiology of this condition? What is the differential diagnosis? What microbiological and virological tests should be done?
Diagnostic hypothesis: Viral encephalitis
Most likely etiology: Herpes Simple Virus (HSV-1) Encephalitis or WNV
Differential diagnosis:
• Varicella-Zoster Virus (VZV) Encephalitis
• Enteroviral Encephalitis
• Bacterial meningoencephalitis
Microbiological tests:
-Lumbar Puncture (CSF Analysis):
• Cell count
• Protein and glucose biochemistry analysis
• PCR for HSV (gold standard for diagnosis) and viral PCR panel
• Bacterial culture/Gram stain for bacterial meningitis
-Blood test (Serology or complete blood count if needed)
A woman with type 2 diabetes and who has been on oral anticoagulants for a few years and has a prosthetic mitral valve is hospitalized after 10 days of fever, asthenia and dyspnea at rest. What is the diagnostic hypothesis, differential diagnosis and microbiological tests prescribed?
Diagnostic hypothesis: Endocarditis in mechanical valve
Differential diagnosis:
•Non-bacterial Thrombotic Endocarditis (NBTE)
Microbiological tests:
• Blood culture for identifying the infectious agent
• Transesophageal echocardiogram (TEE) for viewing the vegetations on the valve
Lorenzo 15 years old, goes to the emergency room accompanied by his guardian for acute diarrhea and vomiting. What is the diagnostic hypothesis and microbiological tests prescribed?
Diagnostic Hypothesis: Enteritis due to Salmonella or Protozoa (giardia)
Microbiological tests:
1. Stool test
• Faecal exam for parasites, microscopic research (gold standard for parasites)
• Coproculture (stool test) and Widal-Wright to detect Salmonella infection
• Search of giardia antigens in faeces
• Molecular biology test (PCR) on faeces
A 3 days old boy presents with respiratory problems, fever, feeding intolerance + some other symptoms. Which is the most probable diagnosis? What is the most probable etiological agent? What is the differential diagnosis? Which microbiological tests should be done?
Most probable diagnosis and agent: Early-onset neonatal sepsis by Group B Streptococcus (Strep. agalactiae) or E. coli
Differential diagnosis:
• Early-onset neonatal sepsis from other pathogens, such as viral and fungal agents
• Neonatal pneumonia
Microbiological tests:
• Blood test, blood cultures for identifying the infectious agent
• Maternal vaginal/rectal swab
• Maternal blood test
• Lumbar puncture CSF analysis; gram stain, culture and PCR
Describe the workflow and microbiology tests for the WNV?
-Isolation of WNV from blood or CSF
-Detection of WNV nucleic acid in blood or CSF
-WNV specific antibody response (IgM) in CSF. (Cross reactivity and non-specific responses excluded)
-WNV IgM high titre and detection of WNV IgG, and confirmation by neutralization.
ChatGPT: symptoms; fever,headache, muscle weakness,encephalitis, meningitis.
Serology: for IgM and IgG in serum or CSF.(ELISA)
PRNT:measures neutralizing antibodies, confirms WNV if serology unclear. Serum sample.
Real time PCR:detects WNV RNA best for early infection, Sample from serum, CSF, whole blood, urine.
Public health reporting
Cross-reactivity: WNV antibodies may cross react with other flaviviruses(Dengue and Zika) requiring PRNT for confirmation.
Describe the pathogens that cause acute meningitis and the microbiology tests for the diagnosis.
Bacterial meningitis:
1-Neisseria Meningitidis
2-Streptococcus pneumoniae
3-Haemophilus influenza
4-Listeria monocytogenes
5-Streptococcus Agalactiae
Others: Borrelia burgdorferi, treponema pallidum, pseudomonas aeruginosa.
Viral meningitis:
1-enteroviruses like coxsackieviruses and echovirus
2-HSV1 and HSV2. Can cause recurrent meningitis
3-varicella-zooster
From what we already mentioned: WNV,TOSV and TBEV.
Fungi:cryptococcus neoformans
Protozoa: Toxoplasma gondii
Tests for Diagnosis
1-CSF examination: opening pressure, WBC count, protein and glucose levels.
2-direct microscopy: gram staining
3-CSF and Blood culture: gold standard
4-PCR: specifically important for viral causes, because culturing turns out negative.
5-Serology: antibody detection in serum.
Patient enters ER with epigastric pain. No ulcerations are present. The patient is no vomiting and does not have diarrhea. What diagnostic testing should be ordered to aid in the therapy of the patient?
H.pylori infection diagnostic approaches;
Non-invasive
1-Urea Breath Test: detect urease activity of the bacteria by radio labeled C02 in exhaled breath. Requires specialized equipment.
2-serology: looking for antibodies against h.pylori infection, useful in the first diagnosis not in follow-ups.
3-stool antigen test: detects bacterial antigens in feces.
Invasive tests
1-Gastroscopy: allows direct visualization of gastric mucosa and potential lesions.
2-rapid urease test: biopsy sample is placed in a urea-containing medium, detecting ammonia production via pH change.
3-histology
4-culture and antibiogram
