Microbiology Case Study: A 24 Year Old Refugee with Eye Irritation

Case History

A twenty-four year-old male Kenyan refugee had been in the United States for about a month when he received a mandatory health screen for infectious diseases. He had no complaints and stated that overall, he was generally healthy. Physical exam was significant only for bilateral red conjunctiva. He stated at times his eyes get irritated and have since birth. As part of routine work-up, an ova and parasite stool exam was ordered. Organisms were detected as seen in Image 1.

Image 1. Trichrome stained slides of patient’s stool sample.



The patient’s stool examination showed Giardia cysts. Two nuclei are visible in the figure above with centrally located karyosomes. Also visible are the intracytoplasmic fibrils, seen as a darker purple area.

Giardia is a flagellated protozoan that causes giardiasis, a diarrheal illness. It is the most commonly diagnosed intestinal parasitic disease in the United States. It is known as Giardia intestinalis, Giardia lamblia, or Giardia duodenalis. The most common mode of transmission is drinking water contaminated with feces from infected mammals (1).

Symptoms vary and can last 1 week to years if untreated (2). Typical symptoms of giardia are “greasy, foul-smelling, frothy stools that float.” Interestingly, less common symptoms can be itchy skin, hives, eye and joint swelling (3). Retinal arteritis and iridocyclitis has been noted as well (4). It is possible that this patient’s eye irritation is due to a chronic giardiasis infection. Common treatment is usually with an antibiotic/antiparasitic drug like metronidazole (Flagyl).

Diagnosis of Giardia can be made by demonstrating the pear shaped trophozoites and/or ovoid cysts in feces. A key identifier for this parasite is the presence of the two to four nuclei with a central karyosome and intracytoplasmic fibrils that make the parasite look like a face under the microscope. However, because Giardia is excreted intermittently, it is recommended to sample three stool specimens on separate days (5). Due to problems in concentrating the organism for identification on a trichrome stain, a fecal immunoassay is available that is more sensitive and specific (5).


  1. https://www.cdc.gov/parasites/giardia/index.html
  2. Robertson LJ, Hanevik K, Escobedo AA, Mørch K, Langeland N. Giardiasis–why do the symptoms sometimes never stop?. Trends Parasitol. 2010;26(2):75-82.
  3. https://www.cdc.gov/parasites/giardia/illness.html#seven
  4. Wolfe MS. Giardiasis.[PDF – 8 pages] Clin Microbiol Rev. 1992;5(1):93-100
  5. https://www.cdc.gov/parasites/giardia/diagnosis.html


-Angela Theiss is a pathology resident at the University of Vermont Medical Center.


-Christi Wojewoda, MD, is the Director of Clinical Microbiology at the University of Vermont Medical Center and an Associate Professor at the University of Vermont.

Microbiology Case Study: An 8 Year Old with Acute Appendicitis

Case History

An 8-year-old female presented to an outside hospital with appendicitis-like clinical symptoms and underwent a laparoscopic appendectomy. Gross examination of the appendix (7.2 cm in length x 0.5 cm in diameter) wall was unremarkable and the lumen contained a minimal amount of hemorrhage. The specimen was entirely submitted for microscopic evaluation.


Image 1. Cross section of appendix containing two intra-luminal helminths (H & E stain).


Image 2. Cross section of female Enterobius vermicularis containing eggs (H & E stain).


Image 3. Cross section of male Enterobius vermicularis (H & E stain).


Enterobius vermicularis (human pinworm) is an intestinal nematode (roundworm) with a worldwide distribution that is most prevalent among school-age children. Cross sections of the nonsegmented, cylindrical worms demonstrate a well-developed digestive tract, reproductive system, and two lateral alae (Images 1-3). E. vermicularis has two sexes and Image 1 demonstrates that the male is smaller than the female. Humans are directly infected upon ingestion of E. vermicularis eggs (fecal-oral route of transmission). The eggs then hatch and immature worms undergo maturation within the human gastrointestinal tract (Image 1). Eggs are shed in stool and the typical E. vermicularis eggs (Image 2) are thick-shelled with one flattened aspect, described as “D-shaped”. Patients with the infection are commonly asymptomatic or may complain of perianal pruritus. Rarely, patients present with abdominal pain secondary to E. vermicularis-associated acute appendicitis (1).


  1. Arca MJ, Gates RL, Groner JI, Hammond S, Caniano DA. 2004. Clinical manifestations of appendiceal pinworms in children: an institutional experience and a review of the literature. Pediatr Surg Int 20(5):372-5.


-Adina Bodolan, MD is a 1st year anatomic and clinical pathology resident at the University of Vermont Medical Center.


-Christi Wojewoda, MD, is the Director of Clinical Microbiology at the University of Vermont Medical Center and an Associate Professor at the University of Vermont.

Microbiology Case Study: Specimen Referral from a 20 Month Old Male

Case History

A 20 month old male presented to an outside hospital with symptoms unknown to our laboratory. That laboratory sent us the specimen recovered from a diaper (Image 1).

Image 1.


The nematode Ascaris lumbricoides is one of the most common helminth infections in the United States. It can grow to be 20-35 cm long. Infection occurs when an egg is ingested, usually in a small child eating dirt contaminated with human feces. When the larvae hatch they penetrate the duodenal wall. From there, the larvae go into the blood stream and eventually end up in the pulmonary circulation where the larvae grow in the alveoli.  In about three weeks, the larvae are coughed up from the lungs and swallowed.  The worms then mature in the jejunum (primarily).  Infection most often shows no symptomatology. If symptoms are present, they can range from mild abdominal discomfort to intestinal blockage and even cough as the worms migrate to the lungs [1].

Diagnosis can be made by examining concentrated stool for knobby-coated, bile-stained eggs that are oval [2].  However, some of the adult worms can pass with the feces.


  1. https://www.cdc.gov/parasites/ascariasis/index.html
  2. Murray PR, Rosenthal KS, Pfaller MA. Medical Microbiology, Seventh Edition. Elsevier Health Sciences; 2012.


-Angela Theiss, MD is a 1st year anatomic and clinical pathology resident at the University of Vermont Medical Center.


-Christi Wojewoda, MD, is the Director of Clinical Microbiology at the University of Vermont Medical Center and an Associate Professor at the University of Vermont.

Microbiology Case Study: An 18 Year Old with Vaginal Discharge

Case Presentation

An 18 year old girl presents to her pediatrician with her mother for her pre-college check-up. She has no past medical history. After her mother leaves the room for the social history component, the girl admits to having sex with her boyfriend for the first time two weeks ago and complains of a yellow green malodorous vaginal discharge that started a week ago. She endorses mild pelvic pain. A pelvic exam is performed and mild cervical tenderness is noted. The cervix is pink, nulliparous, inflamed and is covered by small red punctate spots. A thin yellow green frothy discharge of fishy odor is also detected. A wet prep is made and reveals squamous cells and numerous motile organisms.

Figure 1.  Trichomonas vaginalis in a Pap test. The protozoa are often found next to squamous cells. (ThinPrep)

Figure 2.  Collection of Trichomonas vaginalis parasites eating at a squamous cell in a Pap (ThinPrep)


Our patient was diagnosed with Trichomonas vaginalis (TV). TV is a flagellated parasitic protozoan for which humans are the only known host. It is 10-20 um long and 2-14 um wide with multiple flagella projecting from the anterior and posterior sides. It has a single trophozoite stage and does not survive well outside of its host. TV is a predatory obligate parasite that eats bacteria, vaginal epithelial cells, and red blood cells. It uses fermentative metabolism to produce the carbohydrates needed for fuel. TV is a sexually transmitted disease; however, because it is not reportable to local health departments, the true epidemiologic incidence rate is unknown. Its prevalence is highly variable by population and location. For example, some studies cite a prevalence of 3.1% of American pre-menopausal women (2.3% of adolescents) [1], while in certain high-risk populations the rate might be as high as 47% [2]. Most affected patients are asymptomatic; about a third of females become symptomatic within six months of infection. Symptoms for females include vulvar and vaginal irritation and itching, pain with urination and a diffuse, malodorous, yellow-green vaginal discharge. The cervix becomes reddened in a punctuated fashion causing the well-known strawberry cervix seen on colposcopy. In males, urethritis can develop. TV is often diagnosed via wet mount microscopy, where the protozoa can be seen moving around (Video 1). However, the sensitivity is relatively low, especially among males. Detection by nucleic acid probe from urine, endocervical, and vaginal swabs are considered more sensitive. TV can also be incidentally discovered on Pap tests (Figures 1 and 2). Treatment typically consists of a single dose of metronidazole [1,2]. It is critical that partners be treated as well, because otherwise reinfection may occur.



  1. Kissinger P. Trichomonas vaginalis: a review of epidemiologic, clinical and treatment issues. BMC Infectious Diseases. 2015; 15(307): 1-8.
  2. Meites E et al. A review of evidence-based care of symptomatic trichomoniasis and asymptomatic Trichomonas vaginalis infections. Clinical Infectious Diseases. 2015; 61(S8): S837-48.



-Amanda Strickland, MD, is a 2nd year Anatomic and Clinical Pathology Resident at UT Southwestern Medical Center.

Erin McElvania TeKippe, PhD, D(ABMM), is the Director of Clinical Microbiology at Children’s Medical Center in Dallas Texas and an Assistant Professor of Pathology and Pediatrics at University of Texas Southwestern Medical Center.


Microbiology Case Study: A 22 Year Old Female with Recent Travel

Case History

A 22 year old female with recent travel to Nicaragua noted passage of a 10-12 cm long worm in her stool. She also noted some intermittent hematochezia over the past several days and had developed an itchy eczematous rash on her extremities.

Laboratory Diagnosis

Stool sample was submitted for ova and parasite exam. Stool sediment exam showed the presence of multiple fertilized eggs measuring 50 microns (Image 1). Based on the size of the egg, and the presence of the thick and yellow mammelated coat, she was diagnosed with an Ascaris lumbricoides infection.


Image 1.


Ascaris is the largest of the common nematode parasites of humans with females measuring 20-35 cm long and males measuring 15-31 cm. Notably, males have a curved posterior end. Infection is acquired through ingestion of the embryonated eggs from contaminated soil. In the larval migration phase of infection, diagnosis can be made by finding the larvae in sputum or in gastric washings. One female worm can lay up to 20,000 eggs, therefore enumeration of eggs does not correlate with worm burden. Both fertilized and unfertilized eggs can be easily be recovered using the sedimentation concentration from a fecal sample. It is estimated that 25% of the world population is infected with Ascaris and since transmission depends on fecal contamination of the soil, in areas where infection rates are high, mass population treatment plans with Abendazole have been successful.


-Agnes Balla, MD is a 3rd year anatomic and clinical pathology resident at the University of Vermont Medical Center.


Christi Wojewoda, MD, is the Director of Clinical Microbiology at the University of Vermont Medical Center and an Assistant Professor at the University of Vermont.

Microbiology Case Study: A 50 year Old Man with Dysuria and Hematuria

Case History

A 50 year old healthy man presented with dysuria and hematuria for 4 months. He had briefly lived in the Middle East 3 years ago. The patient underwent cystoscopy which demonstrated a solid mass in the lateral wall of the bladder. Bladder biopsies were performed and showed invasive squamous cell carcinoma associated with ova consistent with Schistosoma haematobium (Figures 1&2).


Figure 1. H&E of bladder biopsy showing invasive squamous cell carcinoma and ova of Schistosoma haematobium.


Figure 2. High power view of Schistosoma haematobium ova.


Schistosomiasis is caused by blood flukes of the genus Schistosoma. There are three major species related to human disease: S. haematobium, S. japonicum, and S. mansoni. Clinical presentation of schistosomiasis depends on the species. S. haematobium infection causes urinary schistosomiasis. Urinary schistosomiasis can range from asymptomatic to gross hematuria and possible obstruction resulting in renal failure.  S. haematobium is geographically distributed primarily in Africa and the Middle East. Transmission to humans requires direct contact with water harboring snails infected with S. haematobium. The cercaria that are released from infected snails penetrate human skin and then migrate to venules of the bladder and ureters. The cercaria develop into adult male and female flukes.  The adult schistosomes reside in the bloodstream and lay eggs that pass through the urine. The eggs are highly immunogenic and produce an intense inflammatory response resulting in hematuria and dysuria. Progression to fibrosis, renal failure and carcinoma may occur as in our patient with squamous cell carcinoma of the bladder. In addition to detection in surgical specimens, S. haematobium may be detected by identification of ova in urine. The ova of S. haematobium are oval and 112-170 µm x 40-70 µm in size with a characteristic terminal spine.  In patients with a high clinical suspicion of S. haematobium, serology may be useful when ova are not identified in urine or surgical specimens. The recommended treatment for schistosomiasis is praziquantel.  The timing of treatment is important because praziquantel is most effective against the adult worm and requires a mature antibody response to the parasite. The Centers for Disease Control and Prevention recommend starting treatment for infected travelers at least 6-8 weeks after the last exposure to contaminated water.


-Jill Miller, MD is a 4th year anatomic and clinical pathology resident at the University of Vermont Medical Center.


-Christi Wojewoda, MD, is the Director of Clinical Microbiology at the University of Vermont Medical Center and an Assistant Professor at the University of Vermont.

Microbiology Case Studies: Babesia vs. Malaria

Patient History: Case 1

A 55 year old Asian woman presented to an emergency department in southern New England in September with complaints of a high fever with chills for the past 5 days. She noted feelings of excessive tiredness, muscle aches, and headache. She also described a decrease in appetite and nausea with vomiting and diarrhea. On physical exam, she was febrile (103.8°F) and scleral icterus was identified. Laboratory workup revealed findings suggestive of hemolysis including increased LDH (401 U/L) and increased unconjugated bilirubin (1.7 mg/dL), despite hemoglobin & hematocrit values in the normal range (13.7 g/dL & 39.3%, respectively). Elevated liver enzymes were also noted; AST 81 U/L and ALT 72 U/L. When questioned regarding traveling history, she reported a trip to Spain and Portugal 5 months earlier. Though she acknowledged living in a rural area of the Northeastern U.S. and indicated that her husband was diagnosed with Lyme disease one year earlier, she denied both recent time outdoors and arthropod or mosquito bites.

Patient History: Case 2

A 31 year old African American woman with a history of sickle cell trait presented to an emergency department in southern New England in September complaining of fevers of 5 days duration. She described being asymptomatic in the mornings followed by high spiking fevers with muscle aches and dull frontal headaches in the evenings. A physical exam revealed a fever (103°F), but no evidence of meningismus. Laboratory workup revealed a mild, microcytic anemia (hemoglobin & hematocrit: 10.7 g/dL & 32.5%, MCV: 76.3 fL), a decreased absolute lymphocyte count and increased band neutrophils. When questioned regarding recent travel, she reported having returned from Africa 10 days earlier. While abroad, she had primarily been in Nigeria’s capital, but she had also visited rural areas. She did not recall having been bitten by mosquitos, but she did not take any anti-malarial prophylaxis. Further, she denied both recent travel to the woods in the Northeastern U.S. and recent arthropod bites.


Figure 1. Peripheral blood smear from patient 1 showing ring-like forms which contain a small amount of cytoplasm and a chromatin dot as illustrated by the arrows. Both intra-erythrocytic and extra-cellular forms are present. Platelets are denoted by arrowheads.


Figure 2. BinaxNOW lateral flow assay from patient 1 is negative for the various Plasmodium spp.


Figure 3. Peripheral blood smear from patient 2 showing ring forms and trophozoites within red blood cells as denoted by arrows. Inset illustrates a scattered gametocyte. Platelets are denoted by arrowheads.


Figure 4. BinaxNOW lateral flow assay from patient 2 is positive for non-falciparum malaria species as indicated by the faint positive reaction denoted by the red arrow in the T2 region.


For patient 1, given the results from the peripheral blood (Figure 1), the negative BinaxNow results (Figure 2) and her lack of recent travel to malaria endemic regions, her illness was attributed to infection by Babesia spp. Further serologic testing was positive for Babesia microti. She was seronegative for Anaplasma phagocytophilum, Borrelia burgdorferi, Ehrlichia chaffeenesis. This finding was confirmed by PCR of her blood, which detected B. microti, but failed to detect B. duncani or B. divergens/MO-1. Approximately 3% of her red blood cells contained intracellular parasites.

For patient 2, her disease was most consistent with an infection by a non-falciparum species of malaria, including P. ovale, P. vivax or P. malariae, given her recent travel to Nigeria and advanced forms seen in the peripheral blood (Figure 3). Further speciation was uncertain due to low parasitemia levels (<1%) and the findings were unable to exclude a mixed infection with a low P. falciparum burden.


The clinical and laboratory presentations of babesiosis and malaria are quite similar despite the fact that each infection is caused by a distinct and highly unique microorganism. As seen in the two cases above, both illnesses often begin insidiously with fevers, headache and muscle & joint aches. The non-specific nature of the patient’s symptoms results in an unclear etiology unless key elements of the patient’s history, including exposure to insect and arthropod vectors and travel or habitation in endemic areas, are provided.

Examination of thick and thin blood smears is useful in the diagnosis of these two diseases. While both organisms have a very similar sized lifecycle forms which selectively infect red blood cells and prompt hemolysis, there are a few useful distinguishing characteristics. In the case of babesiosis, which is transmitted by the Ixodes scapularis tick in the United States, there are small ring like structures, both within red blood cells and extra-cellularly. The diagnostic tetrad form, known as a Maltese Cross, is helpful if identified but is not frequently observed in human infections. No advanced forms or pigment is present. In the case of malaria, which is transmitted via the female anopheline mosquito, protozoa are only found within red blood cells and advanced forms, including schizonts or gametocytes, are helpful in further speciation, if present. Other features, such as size of the infected red cell, number of merozoites, level of parasitemia and gametocyte shape, are helpful in the morphologic assessment of the Plasmodium spp.

Due to the pathogenic severity of P. falciparum, it is important that the microbiology laboratory has the ability to make the diagnosis in real time across all shifts. The BinaxNOW is an FDA approved lateral flow assay that is simple to perform and provides rapid diagnostics, though it isn’t as sensitive as microscopy. The test is comprised of two antigens: one specific to P. falciparum (T1) and one antigen common to all Plasmodium spp. (T2). The test will be positive for levels of parasitemia greater than 5,000 parasites per microliter.

As utilized in the above cases, other various laboratory modalities can aid in the diagnosis of babesiosis and malaria, including serologic tests and PCR, however, these tests may not be available in STAT situations. Using a variety of tests and obtaining a thorough travel history, will help the provider arrive at the correct diagnosis of blood protozoa.



-JP Lavik, MD, PhD, is a 3rd year Anatomic and Clinical Pathology Resident at Yale New Haven Hospital.


-Lisa Stempak, MD, is an Assistant Professor of Pathology at the University of Mississippi Medical Center in Jackson, MS. She is certified by the American Board of Pathology in Anatomic and Clinical Pathology as well as Medical Microbiology. Currently, she oversees testing performed in both the Chemistry and Microbiology Laboratories. Her interests include infectious disease histology, process and quality improvement and resident education.