microbiology case study examples with answers

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Microbiology Cases

Microbiology/Pathology Case Descriptions

Micro Case 1

Over the course of 1 week, a 6-year-old boy develops 0.5- to 1.0-cm pustules on his face. During the next 2 days, some of the pustules break, forming shallow erosions covered by a honey-colored crust. New lesions then form around the crust. The boy's 40-yearold uncle develops similar lesions after visiting for 1 week during the child's illness.

m1-1 . What is the MOST LIKELY diagnosis?

m1-2. The Gram stain from a skin pustule showed gram positive cocci in clusters. The organism grew on sheep blood agar (SBA) and was catalase positive. What is the most likely microorganism?

A. Staphylococcus aureus B. Staphylococcus epidermidis C. Streptococcus pyogenes D. Streptococcus pneumonia

Micro Case 2 (Path Slide 18) [ImageScope] [WebScope]

Clinical History: This 29-year-old male's illness began 10 weeks prior to death, with an episode of "flu". Two weeks later his urine became "smoky". He was found to have hematuria, albuminuria and elevated BUN (180 mg/dl). He died from a pulmonary embolus.

Image Gallery:

The kidney excretes soluble waste from the body and controls electrolyte balance. It consists of the cortex and the medulla. Within the outer cortex, glomeruli with delicate capillary loops are seen. The basement membrane is thin and without inflammation or thickening. Bowman’s capsule that surrounds the glomerulus is thin. The interstitium demonstrates no evidence of inflammation or fibrosis. In the areas between the glomeruli, tubules and arterioles are seen. The tubules are intact. The vessels exhibit no narrowing or wall thickening. The inner medulla of the kidney contains only tubules and blood vessels. Larger arteries and veins are located at the interface between cortex and medulla.

m2-1. What is the BEST diagnosis at the time of death?

m2-2. The throat culture obtained exhibited gram positive cocci in chains. It also showed beta-hemolysis on sheep blood agar (SBA) and was catalase negative. What was the most likely organism?

Streptococcus pyogenes
Streptococcus viridans
Staphylococcus aureus

m2-3. An elderly wheelchair bound man had a history of recurrent urinary tract infections. He presents with new onset of fever, chills, and confusion. Blood cultures were drawn. The organism grown was non-hemolytic, catalase negative, and PYR positive. Gram stain showed gram positive cocci. What is the most likely organism?

Staphylococcus epidermidis
Staphylococcus saprophyticus
Enterococcus species

m2-4. An elderly wheelchair bound man had a history of recurrent urinary tract infections. He presents with new onset of fever, chills, and confusion. Blood cultures were drawn. The organism grown was non-hemolytic, catalase negative, and PYR positive. Gram stain showed gram positive cocci. What is the MOST LIKELY organism?

Micro Case 3 (Path Slide 51) [ImageScope] [WebScope]

Clinical History: A 45-year-old male became ill approximately 2 to 3 weeks ago following an alcoholic spree. He had nausea, vomiting, dehydration, confusion and high fever. He died suddenly shortly after admission.

microbiology case study examples with answers

What is the MOST LIKELY diagnosis AND the likely causative agent?

m3-1. These images depict pneumonia in the stage of:

Red hepatization
Gray hepatization
Abscess formation

m3-2. Community acquired atypical pneumonia can be caused by which of the following organisms?

Legionella pneumophilia
Klebsiella pneumoniae
Mycoplasma pneumoniae
Pseudomonas aeruginosa

Micro Case 4 (Path Slide 195) [ImageScope] [WebScope]

Clinical History: A 67-year-old male had rheumatic heart disease for thirty years. Three months prior to death he began to have episodes of fever and chills accompanied by signs of worsening congestive heart failure. Splinter hemorrhages and purpuric skin rashes were noted three weeks before death.

m4-1. What is the MOST LIKELY diagnosis?

m4-2. Most cases that present with these findings are caused by:

Rickettsiae

m4-3. In this particular patient the MOST LIKELY causative organism was:

Group A Streptococci
Viridans Streptococci

m4-4. The organism MOST LIKELY to infect normal heart valves is:

Group B Streptococci

m4-5. The organism MOST OFTEN associated with infective endocarditis in IV drug abusers is:

m4-6. The heart valve MOST OFTEN affected by infective endocarditis in IV drug abusers is the:

Aortic valve
Mitral valve
Pulmonic valve
Tricuspid valve

m4-7. Which of these organisms are normal flora of the throat and are associated with dental caries, brain abscesses, and endocarditis?

Streptococcus pneumoniae
Peptostreptococcus species

ANSWER

m4-8. A patient with suspected infectious endocarditis has a St. Jude’s prosthetic aortic valve and a fever of 38.6°C (101.5°F). Blood culture shows non-hemolytic, small, white colonies. The organism was Gram positive, catalase positive and coagulase negative. What is the MOST LIKELY organism?

Stapylococcus epidermidis

m4-9. A throat culture grows normal oropharyngeal flora. What alpha-hemolytic organism is most likely to be isolated on the blood agar?

A. Staphylococcus epidermidis B. Staphylococcus viridans C. Streptococcus pneumoniae D. Peptostreptococcus species

m4-10. A throat culture grows normal oropharyngeal flora. The coagulase test for the organism is positive. What is the genus and species of the organism?

A. Staphylococcus aureus B. Streptococcus agalactiae C. Streptococcus pyogenes D. Staphylococcus epidermidis

Micro Case 5

Clinical history: A 33-year-old female dairy farmer develops a severe headache and neck stiffness. On physical examination, her temperature is 38.2°C. She has no papilledema. A lumbar puncture is performed, and a Gram stain of the CSF obtained shows many short, gram-positive rods.

m5-1. Based on the clinical findings presented, what is the most likely causative agent in the case above?

m5-2. A sputum gram stain of an elderly person with cough and fever shows gram positive cocci in pairs. What is the most likely organism?

Haemophilus influenzae
Enterobacter species

m5-3. A 10-month-old child of a family from Mexico living in Durham was noted by his mother to have a grand mal seizure with shaking of arms and legs by the description given to the EMT. The EMTs found the child limp and unresponsive. In the emergency room the child’s fever was 39.5°C (103.1°F). Blood cultures and lumbar puncture were performed. CSF findings were as follows:

cell count of 4000
glucose 20mg/dl
protein 125mg/dl.

Gram stain showed PMNs and occasional Gram-negative coccobacillary organisms. The organism grew on chocolate agar but not on sheep blood agar or MacConkey’s agar. What is the most likely organism in this case?

Neisseria meningiditis
Moraxella catarrhalis
Streptococcus pneumonia

Micro Case 6 (Path Slide 123) [ImageScope] [WebScope]

Clinical History: A 25 year-old woman had pelvic pain, fever, and vaginal discharge for 3 weeks. On physical examination, she has lower abdominal adnexal tenderness and a painful, swollen left knee. Laboratory studies show WBC count of 11,875/mm 3 with 68% segmented neutrophils, 8% bands, 18% lymphocytes, and 6% monocytes.

The fallopian tube is lined by ciliated columnar epithelium that aid in transport of the ovum to the uterus. The epithelium is arranged in fronds that project into the lumen. The wall consists of smooth muscle and connective tissue.

m6-1. What is the MOST LIKELY diagnosis AND the likely causative agent?

m6-2. What is a likely complication of this disease?

Ectopic pregnancy
Infertility
Tubo-ovarian abscess
ALL of the above

m6-3. What organisms are most likely to cause this disease?

m6-4. Which of the following statement about this disease is FALSE ?

It is usually associated with endometriosis
May be complicated by strictures and infertility
May also involve the adjacent ovary
May result in a hydrosalpinx
May be complicated by septicemia
ALL of the above statements are false regarding this disease.
NONE of the above statements are false regarding this disease.

m6-5. The following organisms are commonly responsible for pelvic inflammatory disease EXCEPT :

Aspergillus
Streptococcus
Staphylococcus

m6-6. A 25-year-old male presents with urethritis. The Gram stain shows intracellular gram positive cocci. What is the most likely organism?

Chlamydia trachomatis
Ureaplasma species
Neisseria gonorrhoeae
Haemophilus ducreyi

Micro Case 7 (Path Slide 9) [ImageScope] [WebScope]

Clinical History: A 51-year-old male had a " neurogenic bladder ", caused by a spinal cord tumor. He had multiple bladder infections which were treated with antibiotics. He had surgery to remove the tumor. Postoperatively, he developed fever and costovertebral angle tenderness which did not respond to antibiotics. He expired and an autopsy was performed.

m7-1. What is the BEST diagnosis?

Acute pyelonephritis
Acute glomerulonephritis
Chronic pyelonephritis
Chronic glomerulonephritis

m7-2 . ALL of the following are risk factors for this condition EXCEPT :

Reflux nephropathy
Congenital vesicoureteral reflux
Posterior urethral valves
Acetaminophen (Paracetamol) overdose
Urolithiasis

m7-3 . A urine culture from an 18-year-old woman with similar symptoms also grew a pure culture of more than 100,000 colonies/ml of an organism on sheep blood agar (SBA) and MacConkey’s agar. The gram stain also showed gram negative rods. What is the most likely organism?

Escherichia coli

Micro Case 8 ( Pathology Slide 39) [ImageScope] [WebScope]

Clinical History: 58-year-old African American female had been hemiplegic on the right side for 3 months prior to death. She developed malaise, fever and chills after visiting with her grandchildren. Her infection progressed. She developed dyspnea and expired.

Image Gallery

m8-1. Based on these clinical findings, what is the best diagnosis and likely causative agent ?

m8-2. What is the most likely cause of this disease in most adults?

M8-2. What organism would be most likely to cause a persistent infection in cystic fibrosis?

Micro Case 9

Clinical history: A 52-year-old homeless, alcoholic man had a fever and a cough productive of thick sputum that worsened over several days. His temperature is 38.2°C. Diffuse crackles are heard at the right lung base. Laboratory studies are as follows:

hemoglobin: 13.3 g/dL
hematocrit: 40%
platelet count: 291,8000/mm 3
WBC count: 13,240/mm 3 with 71 segmented neutrophils, 7% bands, 16% lymphocytes, and 6% monocytes.

m9-1. Based on these clinical findings, what is the likely causative agent?

m9-2. An 18-year-old Duke freshman presented to student health with severe headache, fever, and disorientation. A lumbar tap was performed with the following results:

cell count: 300 with 100% PMN
glucose: 10 mg/dl
protein: 100 mg/dl.

The gram stain of the spinal fluid revealed numerous PMNs with intracellular gram-negative diplococci. What is the most likely organism?

H aemophilus influenza
Neisseria meningitides

Micro Case 10

Clinical history: A 66-year-old man incurs extensive thermal burns to his skin and undergoes skin grafting procedures in the surgical intensive care unit. Two weeks later, he has increasing respiratory distress. Laboratory studies show hemoglobin of 13.1 g/dL, hematocrit 39.2%, platelet count 222,200/mm 3 , and WBC count 4520/mm 3 with 15% monocytes. A chest radiograph shows extensive bilateral infiltrates with patchy areas of consolidation. Image Gallery:

m10-1. Based on these clinical findings, what is the likely causative agent?

m10-2. A sputum specimen from a cystic fibrosis patient grew Gram negative rods on sheep blood agar and MacConkey’s agar. The organism was oxidase positive. What is the most likely organism?

Micro Case 11

Clinical history: A suspicious envelope arrived for sorting at rural post office. The envelope was opened and found to contain white powder. Approximately two days later, the postal worker who handled the letter developed cutaneous boils, which were and 1 to 5 cm in diameter with central necrosis and eschars. He and his wife also developed a mild nonproductive cough with fatigue, myalgia for 72 hours, followed by severe dyspnea, diaphoresis and cyanosis. Temperature of 39.5°C, pulse 105/min, respiration 25/min, and blood pressure 85/45mm Hg. Crackles were heard at the lung bases. A chest xray shows a widened mediastinum and small pleural effusions. WBC count of 13,130/mm 3 , hemoglobin 13.7g/dL, hematocrit 41.2%, MCV 91 um 3 , and platelet count 244,000/mm 3 . Both died despite antibiotic therapy. Several cattle, horses, and sheep on the postal worker's farm also died.

m11-2. In a somewhat related case, when Pharaoh did not heed Moses to the let the captive Hebrews go, a series of plagues fell upon the land of Egypt. In the fifth plague, large domesticated mammals including cattle, horses, and sheep died. This was followed by a plague in which the Egyptians developed cutaneous boils. Some developed a mild nonproductive cough associated with fatigue, myalgia, and low grade fever over 72 hours, followed by a rapid onset of severe dyspnea with diaphoresis and cyanosis. Despite antibiotic therapy with both ciprofloxacin and doxycycline (had they been available), many of those affected would die. Which of the following organisms is most likely to have produced these findings?

Bacillus anthracis
Herpes simplex virus
Mycobacterium leprae
Yersinia pestis

Micro Case 12 (UMich Slide 017) [ImageScope] [WebScope]

Clinical history : A 45-year-old woman is being treated in the hospital for pneumonia complicated by septicemia. She has required multiple antibiotics and was intubated and mechanically ventilated earlier in the course. On day 20 of hospitalization, she has abdominal distention. Bowel sounds are absent, and abdominal radiograph shows dilated loops of small bowel suggestive of ileus. She has a low volume of bloody stool.

m12-1. Based on these clinical findings, what is the likely causative agent?

m12-2. Which of the following are appropriate specimen samples for anaerobe culturing:

blood, spinal fluid, abscess aspirate
deep tissue biopsy, sputum, blood
cerebrospinal fluid, tissue and debridement from decubitus ulcer, bile

Micro Case 13

Clinical history: A 25-year-old man is involved in an accident in which he is ejected from the vehicle. He sustains a compound fracture of the left humerus and undergoes open reduction with internal fixation of the humeral fracture. Several days later, he has marked swelling of the left arm and crepitus .

m13-1. In a similar case, a middle aged woman with type 2 diabetes presents to the emergency room with a very painful right lower leg. She has a wound on that extremity and stated that she stumbled on a fallen tree limb in her yard. You observe that her lower leg is discolored and swollen with several areas of crepitus . The abscess fluid was sent to the microbiology laboratory for aerobic and anaerobic culture. The organism grew best on anaerobic cultures and was lecithinase positive. Gram stain shows gram positive rods and the organism show anaerobic growth on egg yolk agar. What is the most likely organism?

Fusobacterium nucleatum
Bacteroides fragilis
Clostridium perfringens
Peptostreptococcus spp.

Micro Case 14 (Path Slide 451) [ImageScope] [WebScope]

Clinical History: A 4-year-old female had a gradual onset of fever, productive cough, anorexia and diarrhea about eleven days prior to death. The breath sounds were harsh, and a few cracking rales were heard over the right base posteriorly.

m14-1. Based on these clinical findings, what is the likely causative agent?

m14-1. Which of the following is the BEST diagnosis?

Ghon complex
Miliary (disseminated) tuberculosis
Foreign body reaction to talcum powder
Atypical pneumonia
H1N1 influenza

Micro Case 15

Clinical history: A 35-year-old man with HIV complains that he has had a "bad" taste in his mouth and discoloration of his tongue for the past 6 weeks.

m15-1. What is the MOST LIKELY diagnosis?

m15-2. In a separate case, a blood culture from a neutropenic (<100 neutrophils/ul) 50-year-old woman on broad spectrum antibiotics grew a yeast. Tests for germ tubes were positive in the microbiology laboratory. What is the likely organism?

Candida albicans
Candida tropicalis
Candida pseudotropicalis
Candida parapsilosis

Micro Case 16

Clinical history: A 44-year-old diabetic woman developed facial pain over the past 24 hours. She has become lethargic and obtunded. There is swelling with marked tenderness over the left and right maxilla, bilateral exophthalmos, diffuse abdominal pain, poor skin turgor, and dry mucous membranes. Her temperature is 37.7°C. She has tachycardia, but no murmurs, and tachypnea; the lung fields are clear.

m16-1. What is the MOST LIKELY diagnosis and the best treatment option?

m16-2. In a separate case, A 22-year-old with non-Hodgkins lymphoma was profoundly neutropenic after induction chemotherapy and developed fevers. Broad spectrum IV antibiotic therapy was administered, but fevers continued. Chest x-ray showed new bilaterial fluffy pulmonary infiltrates. A bronchoscopy was performed which showed hyaline, septate hyphae with acute-angle branching. What is the MOST LIKELY organism?

Blastomyces dermatitidis
Candida species
Aspergillus spp

Micro Case 17

Clinical history: A 50-year-old resident of Phoenix, Arizona, has a cough that has persisted for 1 month. On physical examination, his temperature is 38.1°C. A chest radiograph shows 3.5-cm opacity with central cavitation in the right apical region. An open lung biopsy is performed to exclude cancer.

m17-1. Which of the following organisms is MOST LIKELY to be responsible for these findings?

Aspergillus fumigates
Coccidioides immitis
Histoplasma capsulatum
Mycobacterium tuberculosis

Micro Case 18

Clinical history: For the past 3 weeks, a 52-year-old man has had a chronic cough with a low-grade fever. On physical examination, his temperature is 37.4°C. A chest radiograph shows bilateral, scattered, 0.3- to 2-cm nodules in the upper lobes and hilar adenopathy. A fine needle aspirate of one of the nodules shows inflammation with mononuclear cells, including macrophages that, with PAS or silver stains, show intracellular, 2- to 5-um, rounded, yeast-like organisms.

m18-1. Which of the following infectious diseases is MOST LIKELY to produce these findings?

Coccidioidomycosis
Candidiasis
Cryptococcosis
Histoplasmosis
Blastomycosis

Micro Case 19

Clinical history: For the past month, a 68-year-old patient has had painful oral abcesses, fever, and a cough productive of yellow sputum. On physical examination, there is dullness to percussion at the left lung base. A chest radiograph shows areas of consolidation in the left lower lobe. Despite antibiotic therapy, the course of the disease is complicated by abscess formation, and he dies.

m19-1. Based on these clinical findings, what is the BEST diagnosis AND the likely causative agent?

m19-2. In a separate case, a middle aged man presented to his physician with a persistent cough of two months following an extended overseas trip to visit relatives. He had also noted a 10 pound weight loss and night sweats. A sputum was sent to the microbiology laboratory for routine bacterial culture and AFB culture. Kinyoun stain of his sputum was positive. What is the likely causative agent?

Actinomyces spp
Nocardia spp.

Micro Case 20

Clinical history: A 50-year-old man post lung transplant was admitted to hospital with fever, chills and cough. Chest x-ray showed multiple small abscesses within a right middle lobe infiltrate. The patient had been treated with prednisone and azathioprine daily for rejection. Gram stain of a bronchoalveolar lavage of the right middle lobe shows gram positive rods. Modified acid fast stain shows partially acid fast bacilli.

m20-1. What is the most likely organism?

m20-2. Nocardia species are:

branching, gram negative bacilli
partially acid fast, beaded gram positive filaments
acid fast, branching gram negative filaments
partially acid fast, gram variable bacilli

Micro Case 21

Clinical history: An HIV positive male presented in clinic with confusion and disorientation. He had a fever 38.5°C and photophobia. His CD4 count was 80/ul. A lumbar puncture was performed. It showed 32 WBC/ul with 89% lymphocytes, and 6% monocytes, glucose of 22mg/dl, and protein of 89mg/dl. Gram stain showed yeast and India ink showed a thick capsule.

m21-1. Which of the following is the most likely pathogen?

Cryptococcus neoformans
Hemophilus infulenzae
West Nile virus

m21-2. In a separate case, A 35-year-old man who received kidney transplantation was being treated with cyclosporine, azathioprine, and high doses of corticosteroids. While on this regimen, the patient began to experience headaches and became lethargic. A clinical diagnosis of meningoencephalitis was made. He died 7 days later. Autopsy showed a gelatinous meningeal exudate, and on sectioning of the brain, multiple small cyst-like areas were seen. Microscopic examination showed areas containing rounded structures with a prominent capsule that stained brightly with mucicarmine.

What is the most likely organism?

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JAC Antimicrob Resist
v.3(1); 2021 Mar

Educational Resource Review : Clinical microbiology case studies

Graphical abstract.

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Object name is dlab006f1.jpg

LI, low-income countries; LMIC, low- and middle-income countries; HMI, high- and middle-income countries; HIC, high-income countries.

Resource web link: http://clinmicro.asm.org/index.php/explore-the-profession/what-is-clinical-microbiology/418-clinical-microbiology-case-studies-clinical-microbiology-case-studies (Full classification scheme available at: http://bsac.org.uk/wp-content/uploads/2019/03/Educational-resource-review-classification-scheme.pdf )

WHO region and country (World Bank): Region of the Americas, USA (HIC)

Peer review commentary

These clinical microbiology case studies are available on the American Society for Microbiology website. Each of the case studies is humorously named and free to download and use. As of December 2020, there were 14 case studies on the website, with each case study available for individual download. Topics include malaria, Streptococcus pyogenes , Legionella , Salmonella and Nocardia , among others.

Each case study details a patient’s history and presentation, the action(s) of the doctor, lab test results, diagnosis and treatment, as well as the final patient outcome. The case studies are in PowerPoint (.ppt) format and contain, on average, 12 slides. Each case study was developed by a different author.

Overall, the case studies are straightforward and would be easy for teachers and other medical professionals to use as part of medical education. Contact information for each of the authors is provided at the end of the case study, should the educator want additional information before using the case study.





















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Medical Lab Technology

Microbiology case studies with answers

Here’s the microbiology case studies with answers.

Case Study: A patient presents with fever, chills, and a history of camping near a freshwater lake. A blood smear reveals intraerythrocytic parasites. What is the most likely causative agent? a) Plasmodium falciparum b) Trypanosoma cruzi c) Toxoplasma gondii d) Giardia lamblia Answer: a) Plasmodium falciparum
Case Study: A patient experiences severe watery diarrhea after consuming contaminated food. Stool samples show motile, comma-shaped bacteria. Which pathogen is responsible? a) Salmonella enterica b) Escherichia coli (E. coli) c) Vibrio cholerae d) Clostridium difficile Answer: c) Vibrio cholerae
Case Study: A sexually active individual presents with painful genital ulcers. Dark-field microscopy reveals spiral-shaped bacteria. What is the likely causative agent? a) Treponema pallidum b) Neisseria gonorrhoeae c) Chlamydia trachomatis d) Herpes simplex virus Answer: a) Treponema pallidum
Case Study: A child develops a fever and a “strawberry tongue.” Examination shows enlarged lymph nodes. What is the most likely diagnosis? a) Streptococcus pneumoniae b) Streptococcus pyogenes c) Streptococcus mutans d) Streptococcus agalactiae Answer: b) Streptococcus pyogenes
Case Study: A patient with AIDS presents with a lung infection characterized by yeast-like cells in lung tissue. Which fungus is the probable causative agent? a) Candida albicans b) Aspergillus fumigatus c) Cryptococcus neoformans d) Histoplasma capsulatum Answer: c) Cryptococcus neoformans
Case Study: A patient presents with a high fever, joint pain, and a recent history of travel to a tropical region. Lab tests reveal thrombocytopenia and leukopenia. What is the most likely causative agent? a) Dengue virus b) Influenza virus c) Zika virus d) Epstein-Barr virus Answer: a) Dengue virus
Case Study: A patient develops a skin infection characterized by red, raised, and painful nodules with central pustules. What is the most likely causative bacterium? a) Staphylococcus aureus b) Streptococcus pneumoniae c) Clostridium perfringens d) Mycobacterium tuberculosis Answer: a) Staphylococcus aureus
Case Study: A patient presents with diarrhea containing blood and mucus. Stool samples reveal trophozoites with ingested red blood cells. What is the probable causative agent? a) Entamoeba histolytica b) Giardia lamblia c) Cryptosporidium parvum d) Trichomonas vaginalis Answer: a) Entamoeba histolytica
Case Study: A healthcare worker develops a respiratory infection with a “fried-egg” appearance on culture. What is the likely pathogen? a) Mycoplasma pneumoniae b) Legionella pneumophila c) Chlamydophila pneumoniae d) Pneumocystis jirovecii Answer: b) Legionella pneumophila
Case Study: A patient with a history of animal contact presents with fever, night sweats, and weight loss. Acid-fast bacilli are seen in sputum samples. What is the likely diagnosis? a) Tuberculosis (Mycobacterium tuberculosis) b) Leprosy (Mycobacterium leprae) c) Pertussis (Bordetella pertussis) d) Tetanus (Clostridium tetani) Answer: a) Tuberculosis (Mycobacterium tuberculosis)
Case Study: A patient develops a urinary tract infection. Urine culture reveals pink colonies on MacConkey agar. What is the likely causative bacterium? a) Escherichia coli b) Klebsiella pneumoniae c) Pseudomonas aeruginosa d) Enterococcus faecalis Answer: a) Escherichia coli
Case Study: A patient presents with a pruritic rash and clusters of fluid-filled vesicles on the skin. What virus is most likely responsible? a) Varicella-Zoster virus b) Measles virus c) Rubella virus d) Human papillomavirus Answer: a) Varicella-Zoster virus
Case Study: A patient presents with foul-smelling, frothy diarrhea and abdominal cramps. Microscopy reveals motile, pear-shaped trophozoites. What is the likely causative agent? a) Entamoeba histolytica b) Giardia lamblia c) Trichomonas vaginalis d) Cryptosporidium parvum Answer: b) Giardia lamblia
Case Study: A patient presents with a high fever, headache, and muscle pain. Recent travel history includes a camping trip in the woods. What is the likely causative agent? a) Borrelia burgdorferi b) Rickettsia rickettsii c) Anaplasma phagocytophilum d) Bartonella henselae Answer: a) Borrelia burgdorferi
Case Study: A patient presents with a wound infection after a dog bite. What bacterium is often associated with such infections? a) Streptococcus pneumoniae b) Staphylococcus epidermidis c) Pasteurella multocida d) Escherichia coli Answer: c) Pasteurella multocida
Case Study: A neonate presents with severe pneumonia and conjunctivitis. What is the likely causative agent? a) Chlamydia trachomatis b) Neisseria gonorrhoeae c) Mycoplasma pneumoniae d) Streptococcus pneumoniae Answer: b) Neisseria gonorrhoeae
Case Study: A patient develops a skin abscess with central necrosis. Gram stain shows gram-positive cocci in clusters. What is the likely bacterium? a) Streptococcus pyogenes b) Staphylococcus aureus c) Clostridium perfringens d) Escherichia coli Answer: b) Staphylococcus aureus
Case Study: A patient presents with diarrhea after eating undercooked poultry. Stool samples reveal gram-negative, spiral-shaped bacteria. What is the likely causative agent? a) Salmonella enterica b) Campylobacter jejuni c) Escherichia coli (E. coli) d) Shigella flexneri Answer: b) Campylobacter jejuni
Case Study: A patient presents with meningitis symptoms, and cerebrospinal fluid analysis shows gram-negative diplococci. What is the likely pathogen? a) Streptococcus pneumoniae b) Neisseria meningitidis c) Haemophilus influenzae d) Listeria monocytogenes Answer: b) Neisseria meningitidis
Case Study: A patient with a history of exposure to bat guano develops a severe respiratory illness. Which fungus is the probable causative agent? a) Aspergillus fumigatus b) Histoplasma capsulatum c) Cryptococcus neoformans d) Candida albicans Answer: b) Histoplasma capsulatum
Case Study: A patient presents with oral thrush and esophagitis. Which organism is often responsible for this condition in immunocompromised individuals? a) Candida albicans b) Aspergillus fumigatus c) Pneumocystis jirovecii d) Cryptococcus neoformans Answer: a) Candida albicans
Case Study: A patient presents with fever, jaundice, and hepatomegaly. Blood smears show intraerythrocytic parasites with a “ring form.” What is the likely causative agent? a) Plasmodium vivax b) Babesia microti c) Toxoplasma gondii
Case Study: A patient presents with a productive cough, night sweats, and weight loss. Chest X-rays reveal cavitary lesions in the lungs. What is the likely diagnosis? a) Tuberculosis (Mycobacterium tuberculosis) b) Influenza (Influenza virus) c) Aspergillosis (Aspergillus species) d) Histoplasmosis (Histoplasma capsulatum) Answer: a) Tuberculosis (Mycobacterium tuberculosis)
Case Study: A patient develops a foodborne illness with diarrhea and abdominal cramps after consuming contaminated poultry. Which bacterium is often responsible? a) Clostridium difficile b) Campylobacter jejuni c) Escherichia coli (E. coli) d) Salmonella enterica Answer: d) Salmonella enterica
Case Study: A patient with a history of cystic fibrosis presents with a chronic respiratory infection. What bacterium is commonly associated with these infections? a) Pseudomonas aeruginosa b) Streptococcus pneumoniae c) Mycoplasma pneumoniae d) Haemophilus influenzae Answer: a) Pseudomonas aeruginosa
Case Study: A patient develops a urinary tract infection. Urine culture reveals small, gram-negative rods. What is the likely causative bacterium? a) Escherichia coli b) Klebsiella pneumoniae c) Proteus mirabilis d) Enterococcus faecalis Answer: c) Proteus mirabilis
Case Study: A patient presents with a high fever, severe headache, and a petechial rash. What is the likely causative agent? a) Staphylococcus aureus b) Streptococcus pyogenes c) Rickettsia rickettsii d) Neisseria meningitidis Answer: c) Rickettsia rickettsii
Case Study: A patient with a compromised immune system presents with a severe lung infection. Chest X-rays show diffuse, bilateral infiltrates. What is the likely causative agent? a) Mycobacterium tuberculosis b) Pneumocystis jirovecii c) Streptococcus pneumoniae d) Chlamydia pneumoniae Answer: b) Pneumocystis jirovecii
Case Study: A patient presents with a cutaneous lesion at the site of a cat scratch. What bacterium is commonly associated with this condition? a) Staphylococcus aureus b) Streptococcus pyogenes c) Bartonella henselae d) Francisella tularensis Answer: c) Bartonella henselae
Case Study: A patient presents with a severe respiratory infection and a history of exposure to bird droppings. What fungus is commonly associated with this condition? a) Candida albicans b) Histoplasma capsulatum c) Aspergillus fumigatus d) Cryptococcus neoformans Answer: b) Histoplasma capsulatum
Case Study: A patient presents with severe watery diarrhea after a recent antibiotic treatment. Stool samples reveal the presence of gram-negative, rod-shaped bacteria. What is the likely causative agent? a) Clostridium difficile b) Salmonella enterica c) Escherichia coli (E. coli) d) Campylobacter jejuni Answer: a) Clostridium difficile
Case Study: A patient presents with a high fever, headache, and muscle pain. Recent travel history includes exposure to ticks. What is the likely causative agent? a) Borrelia burgdorferi b) Rickettsia rickettsii c) Anaplasma phagocytophilum d) Babesia microti Answer: a) Borrelia burgdorferi
Case Study: A patient presents with severe diarrhea, dehydration, and electrolyte imbalances. Stool samples reveal comma-shaped, gram-negative bacteria. What is the likely causative agent? a) Vibrio cholerae b) Salmonella enterica c) Campylobacter jejuni d) Shigella flexneri Answer: a) Vibrio cholerae
Case Study: A patient presents with a respiratory infection characterized by a barking cough and inspiratory stridor. What is the likely causative agent? a) Influenza virus b) Bordetella pertussis c) Respiratory syncytial virus d) Streptococcus pneumoniae Answer: b) Bordetella pertussis
Case Study: A patient with a compromised immune system develops a fungal infection characterized by septate hyphae on histopathology. What is the likely causative fungus? a) Candida albicans b) Aspergillus fumigatus c) Cryptococcus neoformans d) Histoplasma capsulatum Answer: b) Aspergillus fumigatus

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Microbiology Case Study: An 83 Year Old Male with Fever

Case History

The infectious disease service was consulted on an 83 year old male for fever.

His past medical history was significant for diabetes mellitus, anemia and renal insufficiency. He initially presented 3 weeks ago with chills, rigors and fever to 103 degrees Fahrenheit. For the past several months, the patient has had weight loss (10-20 pounds over an unspecified timeframe), fatigue and new iron deficiency anemia. A heart murmur was heard on physical exam. The patient was admitted for suspicion of sepsis and he was started on empiric antibiotics vancomycin and ceftriaxone. Three sets of blood cultures were drawn prior to initiation of antibiotics, which were all positive for gram positive cocci in pairs and chains. Transesophageal echocardiogram (TEE). TEE showed large vegetation on posterior mitral leaflet measuring 1cm x 1.8 cm, and a smaller mass on the anterior leaflet. A week after admission, a mitral valve replacement was performed followed and a portion of the valve was sent for culture (Figure 1).

Laboratory Identification

The gram positive organism from blood and mitral valve culture was identified as Streptococcus mitis by MALDI-TOF mass spectrometry. S. mitis is a member of the Streptococcus genus. Streptococci have a number of features that aid in laboratory identification: they are Gram positive, catalase-negative, spherical/ovoid, with organisms that are usually found in chains. They are facultative anaerobes.

More specifically, S. mitis belongs to the viridans streptococci group which includes Streptococcus mutans , Streptococcus sanguis , and Streptococcus salivarius , among many others. The most common infection caused by viridans streptococci is bacterial endocarditis, as in the case of this patient. Other infections can include brain abscesses, liver abscesses, dental caries, and bacteremia.

Patients with bacterial endocarditis have an infection of the heart valves or the endoecardial wall that leads to formations of vegetations. These vegetations are composed of thrombotic debris and organisms (Image 2), often associated with destruction of cardiac tissue. Its onset often involves severe symptoms including fever, chills, and weakness. Fever is the most consistent symptom of infective endocarditis, but it may be subtle or even absent in some cases, especially in older adults. Weight loss and flu-like symptoms may also be seen. Left-sided infective endocarditis, as in the case of our patient, will present with murmur in 90% of cases. In long-standing infective endocarditis, patients may present with Roth spots (retinal hemorrhages), Osler nodes (subcutaneous nodules in the digits), microthromboemboli (which appear as splinter hemorrhages under fingernails and toenails), and Janeway lesions (red nontender lesions on the palms or soles).

In the laboratory, the diagnosis of S. mitis and other viridians streptococci is often detected via blood culture as in the case of this patient. Once the blood culture bottle becomes positive, a Gram stain is performed, which shows Gram positive cocci in chains (Image 1). These features are helpful in differentiating Streptococcus from Staphylococcus (which appears as clusters instead of chains). Biochemical testing can be done to narrow down the species and identify S. mitis, which is optochin resistant (as opposed to S. pneumonia), acetoin negative (in contrast to most other viridans organisms), and urease negative (which differentiates it from S. vestibularis which is urease positive).

Surgical pathology can also aid in diagnosis by microscopically identifying vegetations on the affected valve (Image 2). Treatment of bacterial endocarditis is usually with penicillin or ceftriaxone, however susceptibility testing should be performed on S. mitis and other viridians streptococci because resistance can occur to penicillin. Blood cultures are followed until they are negative for 72 hours. In the case of our patient, his cultures became negative shortly after he started treatment. Susceptibility testing showed that the organism is sensitive to penicillin and ceftriaxone. The patient was continued on ceftriaxone and is clinically improving.

-Haytham Hasan, MD, is an Anatomic and Clinical Pathology resident at NorthShore Evanston Hospital (University of Chicago).

-Erin McElvania, PhD, D(ABMM), is the Director of Clinical Microbiology NorthShore University Health System in Evanston, Illinois. Follow Dr. McElvania on twitter @E-McElvania.

Medical Microbiology and Infection

At a glance, fourth edition stephen gillespie and kathleen bamford.

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Case Studies

Select a Case from the list below. Key in your answer before hitting ‘Show answer’ to view the correct answer. There is also a facility to print out the whole page with your own answers and the ideal answers.

Core Cases:

1. A young, previously fit man with a 1 week history of a ’flu-like illness
2. A patient presents at A&E following a coronary artery bypass graft
3. A 19-year-old woman with a shivers, severe headache and photophobia
4. A 68-year-old woman with a defunctioning colostomy to relieve bowel obstruction
5. A returning traveller with watery diarrhoea
6. A 65-year-old with cough, blood-stained sputum and occasional mild fevers
7. A 42-year-old woman with sweats, back ache, loin pain and fever
8. A 25-year-old student with a fever
9. A 61-year-old with a high fever with muscle aches and pains and coryzal symptoms
10. A 52-year-old dialysis patient with suspected tuberculosis
11. A 29-year-old man presents with fever and generalised lymphadenopathy
12. A 75-year-old man with suspected shingles
13. A 26-year-old woman who is 27 weeks pregnant presents in labour
14. A 36-year-old patient presents several hours after eating tinned fish
15. A 26-year-old man who had taken illicit drugs
16. An 18-year-old female ‘gap-year’ student with fever, myalgia and weakness
17. A 32-year-old man with fever, headache and myalgia
18. A 55-year-old woman with shortness of breath, fever, and cough
19. A 2-year-old child with a febrile convulsion
20. A 32-year-old man with a discharging sinus below his left knee
21. A 25-year-old man with end-stage renal failure
22. A 44-year-old man who presented with an episode of collapse
23. A 73-year-old woman in a care of the elderly ward develops diarrhea

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Case Studies: Microbiology

All microbiology case studies.

A Bioinformatic Investigation of a Mysterious Meningoencephalitis

By Sari Matar, Dyan Anore, Basma Galal, Shawn Xiong

Sarah’s Stomach

By Kelli M. Kinlen, David M. Zuckerman

Molly’s Medical Mission Maladies

By William M. Kolling, Catherine D. Santanello

A New York State of Mind

By Samantha N. Jewell, Julian A. Brix

What’s in Your Food?

By Bwalya Lungu

A Fatal Bite

By Obidimma Ezezika, Mona Jarrah, Shawanah Rahman

Troubled Waters

By Sebastian A. Schormann, James E. Boyett, Samiksha A. Raut

New Tricks for Old Drugs

By Carlos C. Goller, Stefanie H. Chen, Melissa C. Srougi

Stuck on You

By Brenda F. Canine, Michael L. Dini, Breanna N. Harris

Making Better Poison Eaters

By Kelsie J. Anson, Briana N. Van Treeck, Jake J. Flood

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Review of Medical Microbiology & Immunology: A Guide to Clinical Infectious Diseases, 16e

Part XI: Clinical Cases: Introduction

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Clinical cases: introduction.

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These brief clinical case vignettes are typical presentations of common infectious diseases. Learning the most likely causative organisms of these classic cases will help you answer the USMLE questions and improve your diagnostic skills. These cases are presented in random order similar to the way they are on the USMLE. The important features of the case are written in boldface.

A 22-year-old woman has a severe sore throat. Findings on physical examination include an inflamed throat, swollen cervical lymph nodes, and an enlarged spleen. Her heterophile agglutinin test (Monospot test) is positive.

Diagnosis: Infectious mononucleosis is caused by Epstein–Barr virus. Other viruses and bacteria, especially Streptococcus pyogenes, can cause pharyngitis and cervical lymphadenopathy, but an enlarged spleen and a positive Monospot test make infectious mononucleosis the most likely diagnosis. See page 295 for additional information.

A 5-year-old boy with diabetic ketoacidosis has ptosis of his right eyelid, periorbital swelling, and a black, necrotic skin lesion under his eye. Biopsy of the skin lesion shows nonseptate hyphae with wide-angle branching.

Diagnosis: Mucormycosis caused by Mucor or Rhizopus species. Diabetic ketoacidosis and renal acidosis predispose to mucormycosis. Fungal spores are inhaled into the sinuses, resulting in lesions on the face. See page 419 for additional information.

A 40-year-old man complains of watery, foul-smelling diarrhea and flatulence for the past 2 weeks. He drank untreated water on a camping trip about a month ago. See pear-shaped flagellated trophozoites in stool.

Diagnosis: Giardiasis caused by Giardia lamblia. Of the protozoa that are common causes of diarrhea, Giardia and Cryptosporidium cause watery diarrhea, whereas Entamoeba causes bloody diarrhea. See page 429 for additional information on Giardia, page 431 for additional information on Cryptosporidium, and page 425 for additional information on Entamoeba.

A 35-year-old man who is human immunodeficiency virus (HIV) antibody positive has had a persistent headache and a low-grade fever (temperature, 100°F) for the past 2 weeks. See budding yeasts with a wide capsule in India ink preparation of spinal fluid.

Diagnosis: Meningitis caused by Cryptococcus neoformans. The latex agglutination test, which detects the capsular polysaccharide antigen of Cryptococcus in the spinal fluid, is a more sensitive and specific test than is the test with India ink. See page 417 for additional information. If acid-fast rods are seen in spinal fluid, think Mycobacterium tuberculosis. See page 179 for additional information.

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Clinical Case Study

You are a pathologist working in the lab at Daigger Memorial Hospital (located in central Oregon). The emergency room is sending you cultures collected from patients. Your job is to determine:

The pathogenic bacteria causing the disease
What disease is being presented
What is the best treatment given the patient’s unique symptoms and history

Review the patient assessment form provided. Consider the type of sample taken and determine the relevant primary and secondary symptoms. Generally, samples taken in a clinical setting contain multiple organisms. In this case study, the sample will contain one contaminant organism and one causative agent.

Note: Watch for allergies. These may affect the appropriate treatment you will prescribe for the patient.

For some diseases, an irregularity in pulse or respiration, for example, may be indicative of the seriousness of the illness or may even be a direct indicator of the disease presented. Therefore, it is important that you understand what is considered “Within Normal Limits” for all assessment areas on the patient assessment form. Familiarize yourself with the acceptable normal ranges for pulse, respiration, oxygen saturation, blood pressure, and temperature for the age group your patient falls within.

Clinical Case Study Flowchart »

Patient Assessment Form »

Normal Flora According to Body System

Adapted from: Strohl, W.A. et.al. Lippincott's Illustrated Reviews: Microbiology. Lippincott Williams & Wilkins. Baltimore, MD. 2001 and Forbes, B.A. et.al. Bailey and Scott's Diagnostic Microbiology. Eleventh Edition. Mosby. St. Louis, MO. 2002

System	Common Normal (Resident) Flora	Rare Normal Flora & Comments
Ear	Coagulase neg. Staphylococci (most prevalent) spp. (most prevalent) Aspergillis, Alternaria, Penicillium, Candida	Bacillus, Micrococcus, Neisseria, Mycobacteria
Eye	(most prevalent) spp. (most prevalent) < 30% of population	, , Enterobacteriaceae, , , other alpha and gamma hemolytic Streptococcus spp., spp., spp. The bacteria inhibiting enzyme lysozyme is present in tears.
Genitourinary tract	spp., , spp. Coagulase negative spp. Microaerophilic & anaerobic spp. spp., spp., spp. spp., spp., , spp., yeasts
Intestinal tract	Over 98% of species in intestine are strict anaerobes. spp., , , , , spp. spp., (< 0.1%), spp. spp., spp. spp., spp.
Mouth and Nose	spp. (30-60% of bacterial flora of the mouth), , , , , spp., spp., spp., spp., spp., spp., spp., spp.	spp.
Skin	& coagulase negative account for 90% of resident flora. Hemolytic , spp. , , spp. Yeasts: Malassezia spp., Candida spp.	Transient flora either die or are removed by washing. Many organisms prefer specific sites.
Stomach	Generally low concentration of acid resistant species: , , , , fungi	spp.

Pathogenic Organisms According to Body System

Adapted from: Gilligan, P.H. et.al. Cases in Medical Microbiology and Infectious Diseases. 2nd ed. American Society for Microbiology, Washington, D.C. 1997. Murray, Patrick R. Editor. Manual of Clinical Microbiology. 8th ed. ASM Press. Washington, D.C. 2003. Strohl, W.A. et.al. Lippincott's Illustrated Reviews: Microbiology. Lippincott Williams & Wilkins. Baltimore, MD. 2001

System	Disease	Possible Causative Organism
Central Nervous System	Meningitis	Coagulase negative , , , , , , , , , , spp., Gram negative bacilli, Anaerobic bacteria, Coxsackievirus
Eye	Conjunctivitis	, , , , , , , , Fungi, Foreign body
Eye	Blepharitis	, , Herpes Simplex Virus,
Gastrointestinal tract	Diarrhea	spp., spp., , , , spp., , spp., , , , spp., , , Enterovirus, Norwalk agent (calicivirus), Rotavirus
Genitourinary tract	Urinary tract infection (uti) and urethritis	[n], [c,n], [c], spp. [n], spp., [c,n], [c,n], , spp., ,
Respiratory tract	Lung abscess	, spp. (from aspiration)
Respiratory tract	Pneumonia	spp [c], [n], including [n], [c,n], spp., spp., Non-fermenting Gram negative bacilli [n], and many more including fungi, bacteria, parasites and viruses.
Respiratory tract	Bronchitis	[c], [c], [c,n], [n]
Skin and Soft Tissue	Skin infections	(diaper rash), , Enteroviruses
Systemic	Endocarditis	, ,
Systemic	Bacteremia	Coagulase negative , spp., spp., spp., spp.,

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Case Study
Review the patient assessment form provided. Consider the type of sample taken and determine the relevant primary and secondary symptoms. Generally, samples taken in a clinical setting contain multiple organisms. In this case study, the sample will contain one contaminant organism and one causative agent. Note: Watch for allergies.