Microbiology Case Studies SET 1:
Microbiology Case Studies:
Case 1:
A 75-year-old man, presented to the Emergency Room with fever, shortness of breath,
chest pain, and severe, extremely productive cough. He had been a heavy smoker for
almost 50 years before he recently quit 7 years ago, when he was diagnosed with
emphysema. He occasionally used oxygen at home when he had difficulty breathing, and
on presentation he was using portable oxygen because of his severe respiratory distress.
A chest – x-ray revealed a right lower lobe infiltrate, and he was admitted to the hospital.
Sputum, urine, and blood cultures were collected.
The direct Gram stain of the sputum specimen revealed the following:
Many neutrophils (>25 per low power field)
Rare squamous epithelial cells (<10 per low power field)
Many gram-positive lancet-shaped diplococci and cocci in short chains
Few gram-negative diplococci
Few gram-positive bacilli
After overnight incubation at 35 °C in 5% CO2, a blood agar plate inoculated with the
specimen revealed a mixture of two colony types. Rare, non-hemolytic, tiny white, dry-
looking colonies were present. A predominance (3+) of small, mucoid, grey, convex,
alpha-hemolytic colonies were also seen.
The urine culture showed no growth at 24 hours. All blood cultures were negative after 5
days’ incubation.
1. Based on the direct Gram stain, is the specimen acceptable for culture? Explain.
Yes, this specimen is acceptable because of the minimal number of epithelial cells
and an appropriate amount of PMNs
2. Based on the colony and microscopic morphology, what organism is suspected?
Streptococcus pneumoniae
Bile solubility testing on the isolate showed the organism disintegrates.
3. Identify this isolate. Streptococcus pneumoniae _
4. Identify two virulence factors associated with this organism.
Capsular polysaccharide and C substance
5. Should antimicrobial susceptibility testing be performed on this pathogen? If so, what
antimicrobial agent(s) should be tested?
Penicillin and Ceftriaxone, Doxycycline, Erythromycin, Trimeth-sulfa, Levofloxacin,
and Vancomycin
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As an inpatient at University Hospital how would the physician empirically treat this
patient? Refer to the antibiogram and suggest two antibiotics.
Levofloxacin or vancomycin
6. Identify a mechanism for preventing this infection in this patient population?
Pneumovax vaccinations for adults
7. In this case, the patient’s symptoms were quite diagnostic of pneumonia. Why were
urine and blood cultures also collected?
Additional EIA, based on soluble antigens excreted in urine, works for heavy blood
infections
8. Identify the common normal flora found at the body site associated with this specimen
source that gives the same hemolysis type.
Viridans streptococcus
Microbiology Case Studies:
Case 2:
In mid-August, a 2-year-old boy is brought to his pediatrician presenting with a painful itch
and discharge from the left ear. The child had been playing several times in the last few
days in a shallow pool. The physician prescribes a topical antimicrobial for external otitis.
Two days later, the child returns with increased pain and a colored discharge draining from
the ear. A swab culture of the affected site is collected.
The direct gram stain revealed few polymorphonuclear (PMN) cells, many gram-negative
rods.
Growth at 18 hours incubation:
Blood agar: 3+ large, grey, flat colonies which emitted a fruit-like odor
Chocolate agar: equivalent to BA
MacConkey agar: NLF
1. Based on the patient’s age, history, direct smear, and culture results. Identify the
most likely pathogen. Is it necessary to do any additional testing for identification of this
organism?
Pseudomonas aeruginosa, can confirm identity with M-35 CLSI guidelines by
checking criteria matches ID and performing an oxidase test with a purple (+) result.
2. Susceptibility testing of the isolate revealed:
Aztreonam: S
Cefepime: S
Ciprofloxacin: S
Gentamicin: S
Imipenem: S
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Piperacillin/Tazobactam: S
Tobramycin: S
Levofloxacin: S
3. In this case, which of the antibiotics (above) are contraindicated for systemic
intravenous use in pediatric patients?
Ciprofloxacin and Levofloxacin
4. Refer to the antibiogram and suggest two antibiotics for treatment of the patient.
Circle the antibiotic that is the more cost-effective choice.
Amikacin and Ciprofloxacin
Microbiology Case Studies:
Case 3:
Two weeks until Christmas and 10-year old John is really looking forward to what gifts he
might receive. He has not had a break since Thanksgiving, which he spent on his uncle’s
pig farm. He heads home after school and suddenly he does not feel well: He has a bad
headache and feels chilled, his entire body hurts. When he gets home his mother takes his
temperature and it is at 102.3 °F. In the morning, John’s temperature is down to 100.5 °F.
and his headache is not as bad, but he still aches everywhere. He stays home from school
and spends most of the day sleeping. His temperature again increases in the afternoon to
103 °F.
Two days later, he finally gets in to see his family doctor. Again, his temperature is
elevated to 101.5 °F. His physical exam is unremarkable except for swollen cervical and
axillary lymph nodes. His lab results come back negative. John went home after being told
he most likely had a case of the flu. Two weeks into the New Year, John is still feeling
unwell, his fever again spikes and this time in the Emergency room he complains of a stiff
and rigid neck. The physician is now worried that John may have meningitis. Specimens
are collected but everything in the laboratory test results come back as normal. Some
specimens were sent to the Microbiology laboratory, but at 24 hours there was no growth.
1. What type of specimens were most likely collected based on John’s physical
symptoms?
Blood and CSF
2. Name the plates that this specimen would be plated on for culture and susceptibility?
BA, CHOC, Mueller Hinton
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3. At 48 hours, there was pinpoint growth on both the BA and CH. The primary culture
and gram stain are seen below:
Give a BAP colony morphology:
4+ pinpoint, non-hemolytic, gray
Give a gram stain report:
GNCB
4. What bacterial organisms may be suspected as the cause of the patient’s illness?
Brucella sp.
5. Identify a selective and differential media that may be used to isolate this organism.
List its primary ingredients. Describe the appearance of the above organism on this
media.
Brucella Blood Agar, containing casein, yeast, meat peptones, glucose, hemoglobin,
and microbial antibiotics. Brucella sp. appears as small, translucent, convex colonies.
6. What is the name of this patient’s disease?
Brucellosis
7. How did the patient most likely acquire this infection? Explain.
Contact with farm animals like the pigs at his uncle’s farm
8. What are the public health implications for this patient’s disease?
Send sample to LRN reference level laboratory and inform physician if it cannot be
ruled out, also cannot possess this microorganism without government permit as it is
a category B agent and easy to disseminate with a moderate morbidity and low
mortality.
9. Identify an appropriate antimicrobial treatment for this infection.
SXT and gentamicin to treat pediatric patient
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Microbiology Case Studies:
Case 4:
A 34-year-old Haitian male, living in a displaced persons’ camp went to see a medical
officer. For several days now, he has been experiencing severe abdominal cramps and
painful bouts of diarrhea. A liquid, bloody stool with mucus is cultured.
On MacConkey the colonies appeared NLF.
Manual biochemical testing on the isolate reveals:
TSI: K/A
Urea: Neg
LIA: P/Y
SIM: ===
Citrate: Neg
1. Identify this isolate. Shigella sp.
2. Is it a stool pathogen?
Yes
3. Describe the disease progression (at a cellular level) after initial infection.
After initial infection it will attach to mucosal surface of GI tract, penetrate the
epithelial cells, create localized inflammation, leading to shedding of intestinal lining and
formation of ulcers
4. How is this disease transmitted? Explain.
Person to person, fecal-oral route, or flies-vector
5. Identify two virulence factors associated with this disease.
Shigella toxin and adhesion to mucosal surfaces
6. In general terms, identify the infective dose for acquiring this infection.
The infective dose is only 10 organisms, making it easy for flies to cause disease from
contamination
7. The isolate is identified as serogroup B. Identify the species associated with this
serogroup.
S. flexneri
8. Identify a possible long-term complication associated with this infection.
Reiter’s syndrome: pain in joints, eye irritation, and painful urination
Chronic arthritis
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9. Identify an appropriate antimicrobial treatment for this infection.
SXT or Ciprofloxacin
Microbiology Case Studies:
Case 5:
Braden is an avid outdoorsman and is particularly fond of hunting ground squirrels. He
loves to have his wife prepare his favorite Southern style squirrel stew. Late one night,
Bubba was dragged to the Emergency Department by his wife when he experienced a
sudden onset of fever, headache, chills and weakness and he also had 1 swollen, tender
and painful lymph node. The physician collects blood cultures and sends them to the lab
for C & S. A Microbiology lab report for the blood cultures comes back “positive” for short,
pale-staining GNR – further testing and susceptibility to follow.
1. What is the most likely cause of this man’s disease (genus & species)?
Francisella tularensis
2. What is the name of the infection or disease in this patient?
Tularemia
3. List 3 manual laboratory tests that may be performed to identify this organism and
state the expected results.
Oxidase: neg
Urease: neg
Beta-lactamase: pos
4. How is this disease transmitted? Explain.
Can be transmitted by rabbit bite, arthropod bite, contact with infected tissue,
ingestion of wild animal carriers, and inhalation
Microbiology Case Studies:
Case 6:
Dawn, a 28-year-old farmwife who has had recent bouts of the “flu” is rushed to the
hospital where she delivers a 3-week premature male infant. The child appeared normal
until 5 days after his birth, he developed meningitis and dies 2 days later. Cultures from
the meninges and CSF reveal small translucent, grey colonies with beta-hemolysis on BA.
The gram stain reveals small GP rods. The Catalase test was positive.
1. What organism is the most likely cause of this infant’s death (genus & species)?
Listeria monocytogenes
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2. Name 3 confirmatory tests (not automated identification) that may be used in a
microbiology laboratory to identify this organism. Give the expected test results.
Bile esculin hydrolysis: pos
Hippurate: pos
Camp test: pos (block type hemolysis, q-tip shape)
3. How was this disease transmitted to both the mother and her infant? Explain.
Mother likely acquired disease by consuming food that is a reservoir for this
organism, including unpasteurized dairy products processed meats. The patient
history of being a farm wife leads me to believe she has consumed unpasteurized
dairy products. The disease is then transmitted to the infant through intrauterine
transmission from the mothers blood stream
4. This organism is easily confused with another organism. Name the organism.
Identify the testing that will distinguish the two organisms.
Streptococcus agalactiae (GBS) can distinguish by performing a CAMP test, L.
monocytogenes will create a unique Q-tip shape of hemolysis and GBS creates arrowhead
hemolysis
Microbiology Case Studies:
Case 7:
A 50-year-old white male presented to the emergency department in respiratory distress.
Three days before admission, he developed shortness of breath, fever, and a progressive
cough with blood tinged sputum. He had also experienced night sweats. His physical
examination was unremarkable, and he was taking no routine medications before
admission. He smoked a half a pack of cigarettes per day and stated that he did not use
illegal drugs. The only abnormal test results were his WBC count: 22.1 × 109/L and a urine
drug screen positive for cocaine, while the chest x-ray showed dense infiltrates in the left
middle and lower lung. He was admitted to the intensive care unit and started on broad-
spectrum antibiotics, including piperacillin/tazobactam 4.5 g every 6 hours and levofloxacin
750 mg every 24 hours.
On day 2 of admission, the patient developed progressive respiratory distress and it was
discovered that he had an ischemic infarct. On day 3, blood cultures were positive in 4
sets for Gram-positive cocci. An echocardiogram was performed and showed severe
mitral valve regurgitation, and vegetations on the mitral valve. The patient was diagnosed
with endocarditis, and vancomycin 1 g every 12 hours and gentamicin 60 mg every 8
hours were added to his antibiotic regimen. He was then scheduled for a mitral valve
replacement. He underwent the surgery successfully but then died 4 days later due to
another ischemic infarct.
1. List what organism(s) may be the most likely cause of this man’s endocarditis (genus
& species)?
Viridans Streptococcus, Coagulase Negative Staphylococcus, Micrococcus sp.
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2. The isolate was both catalase and oxidase negative. On blood agar, it was pinpoint
with slight alpha-hemolysis. Its gram stain is seen below: GPC in pairs, tetrads and short
chains.
Which organism most likely caused this man’s endocarditis? Explain your reasoning.
Viridans Streptococcus; organism is catalase and oxidase negative, ruling out any
Staphylococcus sp. The organism is commonly a cause for endocarditis, especially in
those with damaged heart valves like the patient in this case. Slight alpha hemolysis also
aligns with this organism.
3. Are automated identification instruments successful in identifying this organism?
Automated identification is unreliable because the instrument cannot differentiate the
species of the Viridans Streptococcus group.
4. Is this organism ever found as normal flora in humans? If so, state its usual habitat.
Yes, the mouth and oropharynx in humans
5. What is the antimicrobial treatment for this patient? Should his regime have been
changed?
A broad-spectrum treatment to begin with, then vancomycin and gentamicin would be
added after identifying GPC’s in sample. Once Viridans Streptococcus is identified, the
patients antimicrobial treatment would change to penicillin or ceftriaxone to target this
particular pathogen.
