Exam Questions Flashcards
(22 cards)
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. Logic: take blood sample from patient and add mycobacterium tuberculosis and measure the gamma interferons released from T cells of the patient.
5-CXR: look for cavitations, infiltrations or consolidations in upper lobes.
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
Urine dipstick test: for nitrites(bacterial metabolites) and search for any leukocyte esterase(detects WBCs)
Urine culture
Rule out ectopic pregnancy
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 due to mycoplasma pneumoniae
Why?
Children above 5yo most common causes of pneumonia due to bacterial or fungal.
Dry cough, normal WBC, clear mucus sputum, more suggestive of viral or atypical bacterial infection.
But hemolytic anemia is indicative for mycoplasma pneumoniae where IgM antibodies can trap RBCs.
Sample collection
Sputum, blood, urine and bronchial aspirate for molecular testing.
Microbiological tests:
1-microscopic examination of sputum with Gram staining= few neutrophils and no bacteria. Mycoplasma lack of a cell wall so cannot be stained with Gram.
2.culture
Culturing it’s important for isolate and identify bacterial pathogens and then antibiogram. But mycoplasma pneumoniae culture exam is negative, because these microbes do not grow on typical culture media. Similar to viral agents.
Molecular tests PCR (gold standard)
Performed on bronchial aspirate, was successful in identifying myco. Pneumoniae. Also syndromic panels can be used to look for multiple possible pathogens simultaneously.
Serology
Specifically looking for IgM and IgG can be detected by ELISA, but these test are slower because the body needs time to produce detectable amount of antibodies. Also cross reactions.
Cold agglutinins: if present often associated with myco.pneumoniae infection. It is non-specific (can be elevated in other conditions) and not all mycoplasma infections cause significant cold agglutinins.
Urine test
To rule out strep.pneumonia and legionella pneumophila infections. Quick and cheap.
A blood culture can be performed especially if there is suspicion of sepsis though it is less sensitive or mycoplasma.
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:
• Rapid immunoassays from throat swab: Strep A Rapid Test Card for Strep A antigen detection. If negative throat culture is recommended.
- Throat swab:
• Culture on blood agar (throat swab): Bacitracin susceptibility test and PYR test to distinguish S. pyogenes from other β-hemolytic streptococci. PYR positive for Strep.pyogenes.
• 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. Glutamate Dehydrogenase (GDH) test: first screening for CDI. GDH is a general antigen present in CD. It is a very sensitive test, meaning negative outcome rule of CDI. Easy, cheap and quick
if GDH positive: look for toxins by EIA. Toxin A and B, they are responsible for disease symptoms. These confirm the presence of active pathogenic toxins differentiating from asymptomatic colonization.
2. Molecular test: PCR for toxin genes in stools. Especially if GDH positive but EIA negative but clinical symptoms indicating CDI.
3.stool culture: although possible, culture is not the primary method for diagnosing C.difficile infection. Because it can be present in the gut microbiota of healthy individuals. Furthermore it is anaerobic which is very hard to culture.
4. Cytotoxicity test (not commonly used anymore)
Stool culture
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. They are not invading GI tract, instead invading RBCs so do not take stool sample
Microbiological tests:
-Blood test:
- Microscopic analysis on blood smear (gold standard)
Thick blood smear: best for detecting low parasitemia, highly sensitive.
Thin blood smear: species identification, parasite morphology. Quantify parasitemia levels for monitoring severity and treatment response. - Search malaria Ag with rapid immunochromatografic test (RDTs)
RDTs detect malaria antigens in blood (HRP2) and they give quick results. No need for skilled microscopy but they cannot quantify parasitemia levels. - DNA research in molecular biology on blood (PCR).
Additionally CBC may show anemia, thrombocytopenia and hypoglycemia.
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 (at least 2 different blood cultures)
• Lumbar puncture CSF analysis
Leukocyte count, protein and glucose concentration. CSF is typically turbid in bacterial infections with high leukocytes.
CSF gram stain and culture
PCR: rapid multiplex PCR, can even detect the pathogen after antibiotic administration.
• Skin biopsy of purpuric lesions, gram stain and culture for bacterial pathogens/PCR
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: first test to visualize the situation in the lungs. It reveals the presence of infection.
- Sputum test: collected early in the morning
A sample is considered appropriate if neutrophils outnumber epithelial cells by at least twice.
• Gram stain + microscopy
• Culture»_space; isolate/identify pathogen + antibiotic susceptibility (antibiogram)
• Molecular tests (PCR): most efficient strategy for diagnosis. Particularly important if viral agents are suspected. Syndromic panels can simultaneously detect multiple common respiratory pathogens. - Urinary test for Pneumococcal antigen and Legionella antigen
- Blood test - Hemoculture, 12% of pneumonia cases shows positive blood culture.
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: sudden onset of fever, headache, vomiting and arthralgia.
Normal blood procalcitonin rules out bacterial infection. Thrombocytopenia is a known feature of Dengue.
Differential diagnosis:
• Chikungunya Fever
• Zika Virus
• Malaria
Microbiological tests:
1. Blood test:
• Dengue NS1 antigen test
• Serology for Dengue antibodies (IgM and IgG). Serological tests have a lot of false positive due to cross reactivity thus need confirmation. Through PRNT. Time consuming
• NAAT: RT-PCR for viral RNA detection and identifying the viral agent. On blood samples.
DENV RNA in urine can be detected for a longer time than in blood.
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:
1-dark field microscopy: if active ulcer present-> direct visualization of T.pallidum.
1. Blood test:
-Serology:
• Non-treponemal: VDRL (detects antibodies against cardiolipin which is released from damaged host cells and bacteria during infection). Useful for screening, can be false positive.
• Treponemal: TPHA(antibodies specific to T.pallidum, high specificity, remain positive for life.
If both positive confirms active or recent syphilis.
- 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: especially important for pregnant women because can cause microcephaly in the fetus.
Differential diagnosis:
• Dengue fever
• Chikungunya fever
Microbiological tests:
-Blood test:
• RT-PCR for viral RNA detection (Zika, Dengue and Chikungunya)
• Serology
IgM ELSIA for Zika, Dengue and Chikungunya antibodies. Confirmed by PRNT
• 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.
WNW IgM and IgG antibodies= ELISA +PRNT
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+ antibiogram
PCR on blood samples to detect genetic material of the pathogen.
• Transesophageal echocardiogram (TEE) for viewing the vegetations on the valve.
Serological tests can be performed when the blood culture negative
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)
• Search of giardia antigens in faeces (rapid immunochromatographic tests)
• Molecular biology test (PCR) on faeces, syndromic panels.
-Widal-Wright to detect Salmonella infection
• Coproculture (stool culture) +antibiogram to rule out bacterial infection
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 only for HSV
• 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. Most common strategy
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
HPV - associated diseases and clinical relevance, diagnostic tools used for the identification of HPV infection and HPV - associated conditions
HPV is one of the most common STDs, often asymptomatic but sometimes persistent leading to;
-Benign lesions like genital warts(HPV-6,11)
-Precancerous and cancerous lesions- can progress to cervical cancer mainly types 16 and 18.
Anal, vulvar, vaginal, penile cancers.
Oropharyngeal squamous cell carcinoma (especially tonsils and base of the tongue)
Diagnosis
1. Cytology (Pap Smear)
• Screening tool for cervical dysplasia.
• Detects abnormal epithelial cells (koilocytes).
• Not specific for HPV type.
- HPV DNA Testing
• Detects viral DNA from cervical swabs (or other samples).
• Often done alongside a Pap smear (“co-testing”).
• Can identify high-risk HPV types.
• Used for:
• Screening in women >30 years
• Triage of abnormal Pap smears
• Follow-up after treatment of CIN - HPV mRNA Testing
• Detects E6/E7 mRNA, which are oncogenic transcripts from high-risk HPV.
• Higher specificity for clinically relevant infections (those with transformation potential). - Colposcopy and Biopsy
• Used when Pap smear or HPV test is abnormal.
• Allows visual inspection of the cervix and biopsy of suspicious areas. - In situ hybridization / Immunohistochemistry
• Used in tissue samples (e.g., cancer biopsies) to confirm HPV involvement.
Vaccines can prevent cervical and other anogenital cancers and also genital warts.
