Microbiology Case Study: A 27 Year Old Man with Lumbar Pain

Clinical History

A 27 year old male with past medical history of mixed connective tissue disease was transferred from an outside hospital where he had initially presented for 6 days of progressively worsening lumbar pain preceded by 1 day of fevers up to 104 F, as well as chills and rigors. Also noted was pain and swelling in his left thumb and a mild rash present on the hands and feet. It is notable that the patient has multiple pets, including a rat.

Workup at the outside hospital included and MRI showing facet arthrosis and effusions at L4-L5 with mass effect on the S1 nerve root. Neurosurgery recommended biopsy of the lumbar spine by Interventional Radiology.

Laboratory Findings

Two sets of blood cultures at the outside hospital showed no growth at 5 days. Two sets of blood cultures obtained at our institution were positive at 15 and 29 hours, with a smear showing gram negative bacilli. The blood culture media was tested by nucleic acid hybridization and no targets were detected. When subcultured, there was only significant growth on the blood plate, with very small gray-green colonies that were not well appreciated

Image 1. Gram stain showing gram negative bacilli.
Image 2. Blood agar plate showing difficult to discern growth of very small grayish colonies.

A sample was sent to a reference lab for testing, which identified Streptobacillus moniliformis.


In the United States, Streptobacillus moniliformis is the most common causative agent of rat bite fever, a relatively rare infectious systemic illness. This syndrome is also caused by infection with Spirillum minus, primarily seen in Asia, and rarely by Streptobacillus notomytis.1,2

S. moniliformis is a fastidious pleomorphic gram negative rod which grows slowly; in cases where there is clinical suspicion for rat bite fever, cultures can be held up to seven days. It is part of the normal nasal and oropharyngeal flora of rodents, with carriage rates of up to 100% in some rat populations. It can be found in oral, nasal, and conjunctival secretions, as well as urine, and can be transmitted to humans via bites, scratches, or oral contact. This includes kissing a pet rat or ingesting food or water that is contaminated with rat secretions.1,2

S. minus is a gram negative spirochete. It cannot be cultured on synthetic media, but may be visualized by Giemsa or Wright stain, or by using dark-field microscopy. Transmission of S. minus is similar to that of Steptobacillus spp., but has not been documented to be associated with contaminated food or water. (1, 2)

The clinical presentation of rat bite fever ranges from a mild case with only a flu-like illness to cases of severe sepsis. In untreated cases, the mortality rate is approximately 10 to 13 percent. Initial symptoms typically begin within 7 days of exposure for S. moniliformis and in 1 to 3 weeks for S. minus. These initial symptoms can include fever, myalgias, vomiting, pharyngitis, headache, and migratory arthralgias. If exposure was through a wound, it is typically resolved by the time symptoms develop, although it may reappear with ulceration, edema, and regional adenopathy in cases caused by S. minus. Cases associated with ingestion may have more severe vomiting and increased likelihood of developing pharyngitis.1,2

Symptoms may further develop to include a maculopapular rash on the extremities, and asymmetric polyarthralgias. The rash is seen most commonly on the extensor surfaces but can involve the palms and soles. Spontaneous remission may occur, but without treatment the fever can show a relapsing course, and the arthritis may last for several years. Possible complications include bacteremia, endocarditis, myocarditis, pneumonia, abscesses, septic arthritis, osteomyelitis, multiorgan failure, fulminant sepsis and death.1,2

Rat bite fever is usually diagnosed empirically based on consistent symptoms and history of rat exposure, because it is difficult or impossible to culture the causative organisms in the lab and there is no serologic test available. 16S rRNA sequencing can be used for definitive diagnosis, but only for certain sample types, and it is not always available.1,2

The empiric treatment of choice is penicillin, with the dose and duration being dependent on the clinical presentation. Ceftriaxone is also commonly used due to better ease of use in the outpatient setting, and tetracyclines are used in patients with beta-lactam allergies. For uncomplicated cases, most patients are treated for a total of 14 days; initially with IV antibiotics, and then transitioned to oral agents after 5 to 7 days if there is sufficient clinical improvement.1,2

Also remarkable in the patient’s history was a note indicating that they had been known to share drinks with his pets and instances of the pet rat licking the patient’s face. Initial treatment was vancomycin and cefepime, with vancomycin discontinued after the gram stain results. The patient was discharged before a definitive identification of the organism was made, with a plan for 6 weeks of outpatient treatment with ceftriaxone via infusion.


1.  King, Katherine Yudeh, MD, PhD “Rat Bite Fever.” UpToDate, Wolters Kluwer, 1 Jun. 2020. https://www.cdc.gov/rat-bite-fever/index.html

2.  “Rat-bite Fever (RBF).” Centers for Disease Control and Prevention, 1 Jun. 2020. https://www.uptodate.com/contents/rat-bite-fever?search=rat%20bite%20fever&source=search_result&selectedTitle=1~17&usage_type=default&display_rank=1

-Tom Koster, DO is a 1st year anatomic and clinical pathology resident at the University of Vermont Medical Center.


Microbiology Case Study: Elderly woman with Ear Pain

An elderly woman with a past medical history significant for end-stage renal disease status post deceased donor kidney transplant in 2018 (on immunosuppression), type 2 diabetes mellitus, and recurrent urinary tract infections presented to nephrology clinic with right ear pain and rash of three weeks. She was otherwise in her usual state of health. On physical exam, there were exophytic itchy papules with hemorrhagic crust and ulcerations on the ear (Image 1) and arm. A few of these papules showed central umbilication (Image 2). Erosions were also present on the upper back, face, neck, and forearms. Patient was referred to dermatology with concern for disseminated infection versus neoplasia. Complete blood count showed mildly elevated white cells. Serologies, cultures, imaging, lumbar puncture, and biopsy were performed.

Blood studies revealed a Cryptococcus antigen titer of 1:4096 along with a CSF antigen titer of 1:2048. Additionally, the CSF gram stain demonstrated yeast and cultures grew Cryptococcus neoformans. Opening pressure was normal and protein was slightly elevated to 53 mg/mL with 36 nucleated cells with a differential including 64% lymphocytes. Biopsy culture of the left cheek was positive for C. neoformans and a left forearm biopsy showed nodular aggregates of encapsulated yeasts, surrounded by relatively sparse lymphohistiocytic inflammation (Images 3-4). A CT of the chest showed innumerable pulmonary nodules concerning for infection.

Image 1. Erythematous and crusted pink plaque with ulceration on the pinna of the ear.
Image 2. Pink, domed papule on the arm with central umbilication and crust.
Image 3. Hematoxylin and eosin stain of the arm biopsy with Cryptococcus, low magnification. Note the loss of epidermis (left-hand side) and underlying foamy stroma with numerous yeasts within the dermis.
Image 4. Hematoxylin and eosin stain of Cryptococcus, high magnification. The yeasts show variable size and some demonstrate a halo of pale staining capsule. There is no significant inflammation in the background parenchyma.


Cryptococcus is an encapsulated basidiomycetous fungus typically found in soil and pigeon droppings.1 Two species comprise the majority of Cryptococcus infections: C. neoformans and C. gatti. C. neoformans is most commonly seen in immunosuppressed patients, particularly in the setting of AIDS.2 C. gatti infections may be seen in more immunocompetent patients and appears to be more geographically restricted to the tropics and Pacific Northwest.3 C. neoformans infections can present as lung disease associated with symptoms of fever, shortness of breath, or cough and characteristically may spread to the central nervous system to cause meningitis.4 Lumbar puncture may show significantly elevated opening pressures.5 Other features of disseminated Cryptococcus infections include rash, endocarditis, ocular lesions, or multiorgan failure.6

This case is a somewhat unusual presentation of disseminated Cryptococcus infection characterized only by skin findings without clinical features of pulmonary or CNS infection. Approximately 15% of patients with disseminated infection may show cutaneous findings but primary cutaneous cryptococcosis is rare.7 Cryptococcal skin findings are quite varied, but may present similar to molluscum contagiosum, as dome shaped papules with central umbilication.7,8 On microscopy, small variably sized round yeasts without hyphae are characteristic. These yeasts may show a clear or pale staining halo representing the capsule and are highlighted well on Grocott’s Methenamine Silver or Periodic Acid-Schiff stains. Histology may demonstrate innumerable extracellular yeasts accompanied by foamy stroma and minimal inflammation or more granulomatous tissue reaction with necrosis, ulceration, and mixed inflammation. In conclusion, disseminated Cryptococcus must be considered in the context of new skin findings in an immunocompromised patient even if typical pulmonary or CNS findings are not identified.


  1. Sorrell TC, Ellis DH. Ecology of Cryptococcus neoformans. Rev Iberoam Micol. 1997 Jun;14(2):42-3.
  4. Sabiiti W, May RC. Mechanisms of infection by the human fungal pathogen Cryptococcus neoformans. Future microbiol. 2012 Nov;7(11):1297-313.
  5. Abassi M, Boulware DR, Rhein J. Cryptococcal Meningitis: Diagnosis and Management Update. Curr Trop Med Rep. 2015;2(2):90–99. doi:10.1007/s40475-015-0046-y
  6. Clark RA, Greer D, Atkinson W, Valainis GT, Hyslop N. Spectrum of Cryptococcus neoformans infection in 68 patients infected with human immunodeficiency virus. Rev Infect Dis. 1990 Sep-Oct;12(5):768-77.
  7. Srivastava GN, Tilak R, Yadav J, Bansal M. Cutaneous Cryptococcus: marker for disseminated infection. BMJ Case Rep. 2015;2015:bcr2015210898. Published 2015 Jul 21. doi:10.1136/bcr-2015-210898
  8. Akram SM, Koirala J. Cutaneous Cryptococcus (Cryptococcosis) [Updated 2019 Aug 4]. In: StatPearls [Internet]. Treasure Island (FL): StatPearls Publishing; 2019 Jan-. Available from: https://www.ncbi.nlm.nih.gov/books/NBK448148/

-Dr. Stanton Miller is a second year AP/CP resident at UT Southwestern Medical Center who is interested in Dermatopathology.

-Dr. IJ Frame is a board-certified Clinical Pathologist who is completing his Medical Microbiology fellowship at UT Southwestern Medical Center.

-Dr. Dominick Cavuoti is a professor of AP and CP at UT Southwestern, specializing in infectious disease pathology, cytology and medical microbiology.


Microbiology Case Study: A 53 Year Old Man with an Aortic Valve Mass

Case History

The patient is a 53 year old male with a past medical history of chronic obstructive pulmonary disease, who presented to the emergency department with one day of right calf pain, worse with weight-bearing, with radiating paresthesias, and a pale, cold right foot. He also endorsed a history of intermittent fatigue and knee pain. The patient works on farm and has an 82 pack year smoking history. He was diagnosed with a right popliteal artery occlusion and started on IV heparin. A transthoracic echocardiogram revealed an aortic valve mass.

Five days after admission he underwent a thromboembolectomy of the occluded vessel. A further six days later he underwent a procedure to excise the aortic valve mass, but ended up having an aortic valve replacement. Cardiothoracic surgery described a friable mass with a large base, consistent with a vegetation that might be seen in infective endocarditis, and sent the mass for surgical pathology and aerobic and anaerobic cultures. He was started on empiric vancomycin by infectious disease.

The patient denied recent fevers, chills, sweats, weight loss or changes in appetite, cough, chest pain, abdominal pain, nausea, vomiting, diarrhea, constipation, painful urination, rash, or unusual bone or joint pain. Doxycycline and rifampin were added for further coverage.

Laboratory Identification

Blood cultures drawn on admission showed no growth at 5 days. Initial gram stain of tissue from the mass showed many gram positive beaded rods. Anaerobic cultures of this tissue grew a single colony of Micrococcus and a single colony of a gram positive bacilli, which also grew aerobically and was identified by Mayo as Corynebacterium spp., not jeikeium. Serology for Bartonella was negative. Q fever serology showed elevated titers of phase I Ab IgG only.

Surgical pathology of the aortic valve mass is shown below:

Image 1. H&E stain of the removed aortic valve, demonstrating foamy macrophages. Not shown are abundant necrotic debris and dystrophic calcifications. Photo taken by Jessica Crothers, MD.
Image 2. Periodic Acid-Schiff (PAS) stain of the area depicted in Figure 2. The foamy macrophages are diffusely PAS positive. Photo taken by Jessica Crothers, MD.

GMS, B&B, AFB, and Fite staining were negative for definitive organisms.

A second set of blood cultures showed no growth and 5 days, and AFB cultures were negative, and second Q fever serology showed a decrease in the titer of phase I Ab IgG.

A PCR of residual heart valve tissue identified Tropheryma whipplei.


The diagnosis of Tropheryma whipplei is made by T whipplei PCR, PAS stain, or T whipplei immunohistochemical staining.1 As these are all non-routine tests for a microbiology work-up, the diagnosis depends on high clinical suspicion.

Most often seen in the gut, T whipplei infection classically manifests as arthralgias, abdominal pain, weight loss, and diarrhea.2 However, it is also a rare source of culture-negative endocarditis, as seen in the case above.

The organism is a gram positive bacillus that is common in the environment and found in the saliva of up to 35% of healthy hosts.3 Furthermore, IgG antibodies to T whipplei have been detected in the blood of up to 70% of healthy individuals.4 Microscopically, there is minimal inflammatory response to this organism. Because of this and the classic symptoms, the characteristic foamy macrophages were initially thought to be indicative of a metabolic disorder.5 Once discovered and studied, it was found to most commonly affect males of European descent, which with the minimal inflammatory response to the organism led to the postulation that this population may have a heritable immunodeficiency.6 Others have suggested that the organism itself may have a role in down-regulating the immune response.7 A variety of immunologic disturbances have been associated with the disease, including down-regulation/absence of MHC II molecules and general dysfunction of monocytes/macrophages.1,7,8

Treatment varies by extent of disease, but it generally includes ceftriaxone or penicillin G followed by an extended course of TMP-SMX.1

In the case of our patient, he demonstrated symptomatic improvement after aortic valve repair followed by four weeks of ceftriaxone, with a plan to transition to TMP-SMX for one year.


  1. Apstein, MD, and T Schneider. “Whipple’s Disease.” UpToDate, Wolters Kluwer, 28 June 2019. Accessed 23 March 2020: https://www.uptodate.com/contents/whipples-disease?search=whipples%20disease%20children&source=search_result&selectedTitle=4~70&usage_type=default&display_rank=4#H703772001
  2. Durand DV, Lecomte C, Cathébras P. “Whipple disease. Clinical review of 52 cases.” Medicine (Baltimore). 1997;76(3):170.
  3. Street S, Donoghue HD, Neild GH. “Tropheryma whippelii DNA in saliva of healthy people.” Lancet. 1999;354(9185):1178.
  4. Raoult D, Birg ML, La Scola B, et al. “Cultivation of the bacillus of Whipple’s disease.” N Engl J Med. 2000;342(9):620.
  5. Whipple GH. “A hitherto undescribed disease characterized anatomically by deposits of fat and fatty acids in the intestinal and mesenteric lymphatic tissues.” Bull. Johns Hopkins Hosp. 1907; 18:382–391.
  6. Fenollar F, Puéchal X, Raoult D. “Whipple’s Disease.” N Engl J Med. 2007;356(1):55.
  7. Ectors NL, Geboes KJ, De Vos RM, et al. “Whipple’s disease: a histological, immunocytochemical, and electron microscopic study of the small intestinal epithelium.” J Pathol. 1994;172(1):73.
  8. Moos V, Schmidt C, Geelhaar A, et al. “Impaired immune functions of monocytes and macrophages in Whipple’s disease.” Gastroenterology. 2010;138(1):210. 

-Frederick Eyerer, MD is a 2nd year anatomic and clinical pathology resident at the University of Vermont Medical Center.

-Thomas Koster, DO is a 1st year anatomic and clinical pathology resident at the University of Vermont Medical Center.


Microbiology Case Study: A 70 Year Old with Altered Mental Status

Clinical History

A 70 year old patient with a history of sarcoidosis, diabetes mellitus type 2, and interstitial lung disease on prednisone presented to an outside hospital with subacute altered mental status and dizziness. Head imaging showed 3 ring-enhancing lesions most concerning for intracranial abscesses and the patient was transferred to a larger institution for management. Upon further imaging and physical examination, 3 additional lesions were found, one in the abdominal wall and two subcutaneous lesions on the extremities. An IR-guided biopsy of the abdominal wall lesion was performed and the specimen was sent for bacterial culture and smear.

Laboratory findings

An initial gram stain was interpreted as many neutrophils and no bacteria seen; however, Acridine Orange staining demonstrated the presence of fungi or bacteria on the smear. Further review of the gram stain showed many neutrophils with few filamentous beading and branching gram positive bacilli predominantly in the thick regions of the smear (image 1).

Image 1. A gram smear from the patient’s abdominal wall abscess at 100x magnification showing filamentous beading and branching gram positive organisms.
Image 2. A modified Kinyoun staining demonstrates that the organism is weakly acid fast positive (100x magnification).


Nocardia encompasses a group of delicate aerobic gram positive and weakly acid fast positive rod-shaped bacteria that, due to their branching appearance, were once thought to be fungi. The N. farcinica species are not found in normal flora, but instead in soil around the world and are most often associated with decaying vegetation. It is the bacteria’s ability to become airborne on dust particles that may result in inhalation and lead to the most common presentation, pulmonary nocardiosis. Other modes of entry include ingestion and cutaneous disease after traumatic inoculation. CNS involvement is a common site for secondary infection.1

The pathogenicity of Nocardia is the result of several mechanisms that the bacteria possess to evade the host’s defense system. Nocardia are often resistant to phagocytosis when they are in their log-phase. If the bacteria are phagocytosed, some species have the ability to inhibit the lysosome-phagosome fusion. Nocardia farcinica, in particular, is especially important to identify as it is more likely to progress to disseminated disease and has a higher rate of antimicrobial resistance.2

Most cases of nocardiosis, as with ours above, are in immunocompromised patients either by disease states such as HIV, diabetes, and malignancy or iatrogenically with corticosteroids or other immunosuppressing or immunomodulating drugs. The clinical presentation of nocardiosis is non-specific and is dependent on the site of infection, but the diagnosis should be on the differential for immunocompromised patients with a suspected CNS abscess, particularly if they have concurrent cutaneous, soft tissue, or pulmonary infections.3

Therapy is based on site of infection and species of nocardia isolated; however, trimethoprim-sulfamethoxazole is accepted as part of the first-line treatment. Severe disease, such as that exhibited in our patient, warrants combination therapy and may include a carbapenem, third generation cephalosporin, or an extended spectrum fluoroquinolone.4 Our patient was originally treated with trimethoprim-sulfamethoxazole and imipenem, but the trimethoprim-sulfamethoxazole was discontinued due to hyperkalemia and the patient was started on Linezolid.


  1. Spelman, Denis. “Microbiology, epidemiology, and pathogenesis of nocardia”. UpToDate, Wolters Kluwer, May 08, 2019. https://www.uptodate.com/contents/microbiology-epidemiology-and-pathogenesis-of-nocardiosis?search=nocardiosis&source=search_result&selectedTitle=3%7E94&usage_type=default&display_rank=3. Accessed on March 10, 2020.
  2. Bell M, McNeil MM, and Brown JM. Nocardia species (Nocardiosis). 2014. http://www.antimicrobe.org/b117.asp. Accessed on March 24, 2020.
  3. Spelman, Denis. “Clinical manifestations and diagnosis of nocardiosis”. UpToDate, Wolters Kluwer, May 08, 2019. https://www.uptodate.com/contents/clinical-manifestations-and-diagnosis-of-nocardiosis?search=nocardiosis&source=search_result&selectedTitle=1~94&usage_type=default&display_rank=1. Accessed on March 10, 2020.
  4. Spelman, Denis. “Treatment of nocardiosis”. UpToDate, Wolters Kluwer, November 11, 2019. https://www.uptodate.com/contents/treatment-of-nocardiosis?search=nocardiosis&source=search_result&selectedTitle=2~94&usage_type=default&display_rank=2. Accessed on March 24, 2020.

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


Microbiology Case Study: A 29 Year Old Man with Fevers and Chills

Case History

A 29 year old African American male presented to the emergency department for a 3 day history of fever, chills, and night sweats, approximately four weeks after returning home from a trip to Uganda. He denied any diarrhea, vomiting, cough, abdominal pain, nausea, or sick contacts. His past medical history was non-contributory. A complete blood count (CBC) was performed, which revealed anemia and low platelets. The patient’s blood was also analyzed through Giemsa stain on a thin smear preparation (Image 1). Findings revealed only several platelets present. In addition, the patient’s red blood cell morphology was varied and atypical. The cells appear smaller than normal (microcytic) with several shapes and form being present: acanthocytes (burr cells), schistocytes (fragmented red blood cells), and bite cells (red blood cells which appear as if a “bite” has been taken out of them). In addition, many red blood cells contained a delicate ring form with either a central chromatin dot or two dots in a “headphone” arrangement (Image 2). This ring form was the only form identified in the thin smear. In addition, it was only present inside the red blood cells (with no forms present outside the cells) and the red blood cells with the ring form were the same size as those blood cells without the ring form. Finally, several red blood cells were seen occupied by more than one ring form. A thick smear of the patient’s blood was prepared in order to lyse the red blood cells so that the cellular contents could be analyzed with increased sensitivity. Findings on the thick smear revealed the similar delicate ring form structure found inside the red blood cells on the thin smear. These were the only forms identified and they also contained either a central chromatin dot or two bi-lobed dots (“headphone” forms) (Image 3).

Image 1. Thin smear with variable red blood cell morphology (acanthocytes, schistocytes, and bite cells) and lowered platelet number.
Image 2. Delicate ring form with a central chromatin dot inside a red blood cell.
Image 3. Numerous delicate ring forms with either a central chromatin “dot” or bi-lobed “dots.”


The main differential diagnoses of ring forms present in red blood cells include two parasitic organisms: Babesia and Plasmodium species. Endemic regions for Babesia include the Midwest and Eastern United States, the majority of Europe, and parts of central Asia and Far East Asia. In addition, the ring forms of Babesia are pleomorphic (varying in size and shape from cell-to-cell) with rare distinctive “Maltese cross” forms (indicative of asexual budding).

Plasmodium, on the other hand, is endemic to South America, most of Sub-Saharan Africa (including Uganda), and parts of Asia (such as India, Southern China, and Indonesia). The most common Plasmodium sub-species in Uganda is P. falciparum, which accounts for over 90% of Plasmodium cases. The ring forms of Plasmodium are monomorphic. Considering the patient’s travel history, as well as the findings on the thin smear and thick smear of the patient’s blood, the organism was confirmed as Plasmodium falciparum through polymerase chain reaction (PCR).


Malaria is caused by the single-cell parasitic protozoan Plasmodium species, which is transmitted through an arthropod vector (Anopheles mosquito). Approximately 40% of the world’s population lives in endemic areas, 300-500 million clinical cases occur world-wide per year, resulting in 1.5-2.7 million deaths (90% of which are in Africa). However, this is an increasing problem even in non-endemic areas, considering the ease and flexibility of international travel, vague generalized clinical symptoms which could cause a delay in diagnosis, and drug resistance to the main active agents against the protozoan.

The Anopheles mosquito injects a sporozoite form of the parasite into humans, which then penetrates liver cells and matures into a schizont. The schizont then breaks through the liver cell and enters the blood stream as a merozoite, which invades red blood cells. The trophozoite form then matures in the red blood cells (as a “ring form”), which then re-enters the blood stream as a merozoite form. Finally, the merozoite matures into macrogametocytes and microgametocytes, which are taken up by the Anopheles mosquito.

The onset of symptoms usually occurs within 1 month (for patients that are not endemic to the region) or up to 6 months (for patients who have lived in Plasmodium regions and have presumably developed some sort of an immune tolerance to the parasite). These symptoms are characterized as “paroxysmal” and “cyclical,” which include chills, fever, sweats, and resolution, followed by another cycle of symptoms. Studies have shown that symptoms correlate with the release of merozoites into the blood stream, causing tissue necrosis factor release from circulating white blood cells. Patients may also develop anemia, splenomegaly, and acute renal failure. A unique complication of P. falciparum is its ability to infect a large number of mature red blood cells, rather than only young red blood cells. This results in high levels of parasitemia and increased clumping of red blood cells due to the induction of proteins in the cell that cause agglutination to other cells. This may result in “cerebral” malaria, which may cause altered mental status, coma, or even death.


  1. Laboratory diagnosis of malaria: Plasmodium falciparum. CDC Laboratory Identification of Parasites of Public Health Concern. https://www.cdc.gov/dpdx/resources/pdf/benchAids/malaria/Pfalciparum_benchaidV2.pdf
  2. Kerlin, Douglas and Gatton, Michelle. Preferential Invasion by Plasmodium Merozoites and the Self-Regulation of Parasite Burden. Public Library of Science. 2013; 8(2): e57434. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3584029/

Jamaal Rehman, MD is a 4th year anatomic and clinical pathology resident at University of Chicago (NorthShore) program based at Evanston Hospital, Evanston, IL. His academic interests include Surgical pathology, specifically Gastrointestinal pathology. He will be matriculating to the University of Iowa for a Gastrointestinal pathology fellowship following residency training.


Microbiology Case Study: A 57 Year Old Man with an Infected Drain Site

Clinical History

The patient is a 57 year old male with a history of traumatic brain injury in 2005 resulting in quadriplegia and subsequent neurogenic bladder with chronic spasms. In 2016 the patient underwent cystoprostatectomy, proctectomy, and ureteroenteric anastomosis to colon. The post-operative period was complicated by the formation of a presacral abscess consisting of MSSA and E. coli. Drain placement failed to resolve the abscess and drain studies showed the formation of a fistula to the patient’s rectal stump. The subsequent 3-year period consisted of repeat drain placements and laparotomy to drain and wash out multiple small collections of fluid seen on imaging. Bacterial cultures during this interval grew mixed gram positive and gram negative enteric bacteria, treated primarily with ertapenem. In January of 2020, the patient underwent exploratory laparotomy with debridement and drainage of pelvic abscess. Tissue cultures from the procedure grew MRSA and vancomycin was prescribed for treatment. Vancomycin was switched to daptomycin for more favorable dosing and ertapenem was added to his treatment plan. Four weeks after his operation, the patient reported pain at his drain site and the fluid in his Jackson-Pratt (JP) drain had turned green. Fluid from the JP drain was submitted for microbiological work-up.

Laboratory Findings

Gram stain of the fluid from the JP drain showed neutrophils, many gram negative bacilli, and beaded gram-positive bacilli. Modified Kinyuon testing was positive for acid-fast bacilli (AFB) and cultures were ordered for mycobacteria as well as Nocardia. The gram negative bacilli was isolated and identified as Pseudomonas aeruginosa by MALDI-ToF. The beaded gram-positive bacilli were isolated on CNA agar and identified by MALDI as Mycobacterium chelonae. Concordant morphology was observed on mycobacterial culture. Nocardia culture was overgrown by P. aeruginosa.

Image 1. Gram stain of specimen taken from the patient’s JP drain.
Image 2. CNA agar plate growing gram positive bacilli.
Image 3. 7H11 plate growing acid fast bacilli.


Rapidly growing mycobacteria (RGM) include the three most common clinically relevant species: Mycobacterium abscessus, Mycobacterium fortuitum, and Mycobacterium chelonae.

The RGM are environmental organisms found worldwide that usually grow in subculture within one week (eg, rapidly, as compared with other mycobacteria). M. abscessus is the most commonly encountered species of this group isolated from clinical respiratory specimens, M. fortuitum is the most common from non-respiratory specimens, and M. chelonae primarily impacts immunosuppressed patients and may also cause surgical wound infections.

Postoperative infections with RGM have occurred following various procedures including cosmetic surgery procedures, augmentation mammoplasty, laser in situ keratomileusis (LASIK), and heart surgery.1-8 Infection is characterized by multiple recurrent abscesses around the surgical wound.

Diagnosis for non-pulmonary disease is made by culture of the specific pathogen from drainage material or biopsy of the affected site. The isolation of organisms from sterile, closed sites, such as bone marrow or blood or from a skin biopsy (in the setting of multiple lesions), is diagnostic of the disease. Once an isolate has been identified as a nontuberculous mycobacteria (NTM), the species should be identified. However, identification of RGM in most laboratories is either incomplete or imprecise. M. abscessus isolates are frequently identified simply as “M. chelonae/abscessus complex,” or if they are specifically identified as “M. abscessus,” they are not accurately sub-speciated.

Susceptibility testing should be performed against a number of antibacterial agents, however, there is no established minimum inhibitory concentration (MIC) cutoff for susceptibility or resistance. M. chelonae is typically treated with Macrolide antibiotics, particularly azithromycin and clarithromycin. M. fortuitumM. abscessus, and M. chelonae are resistant to the antituberculosis agents rifampinethambutol, and isoniazid, so susceptibility testing of RGM should not be performed with these.

The clinicians in our case suspected that the M. chelonae culture from the patient’s JP drain was most likely a contaminant as the same organism was never isolated from previous tissue or fluid cultures. He was continued on daptomycin, ertapenem, and ciprofloxacin was added to cover P. aeruginosa. The patient responded well with resolution of his localized symptoms at the site of the JP drain. Unfortunately, he continues to suffer from multiple, recurring presacral abscesses.


  1. Rimmer J, Hamilton S, Gault D. Recurrent mycobacterial breast abscesses complicating reconstruction. Br J Plast Surg 2004; 57:676.
  2. John T, Velotta E. Nontuberculous (atypical) mycobacterial keratitis after LASIK: current status and clinical implications. Cornea 2005; 24:245.
  3. Freitas D, Alvarenga L, Sampaio J, et al. An outbreak of Mycobacterium chelonae infection after LASIK. Ophthalmology 2003; 110:276.
  4. Sampaio JL, Junior DN, de Freitas D, et al. An outbreak of keratitis caused by Mycobacterium immunogenum. J Clin Microbiol 2006; 44:3201.
  5. Edens C, Liebich L, Halpin AL, et al. Mycobacterium chelonae Eye Infections Associated with Humidifier Use in an Outpatient LASIK Clinic–Ohio, 2015. MMWR Morb Mortal Wkly Rep 2015; 64:1177.
  6. Toy BR, Frank PJ. Outbreak of Mycobacterium abscessus infection after soft tissue augmentation. Dermatol Surg 2003; 29:971.
  7. Centers for Disease Control and Prevention (CDC). Mycobacterium chelonae infections associated with face lifts–New Jersey, 2002-2003. MMWR Morb Mortal Wkly Rep 2004; 53:192.

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


An Asymptomatic 52 Year Old Female with a Surprise Finding on Colonoscopy

Case Presentation

A 52-year-old female with no significant past medical history is seen for a routine annual examination and is scheduled for a colonoscopy due to her age being over 50 years. The colonoscopy was performed and an isolated single worm was found within the cecum (Images 1-2). The worm was removed with cold forceps and subsequently placed in paraffin and sectioned (Images 3-5).

Image 1. The worm is depicted within the cecum attached to the mucosal wall by its anterior end.
Image 2. The worm is captured using cold forceps.
Image 3. Hematoxylin and eosin stained section of the worm.
Image 4. Higher power magnification, showing eggs with distinctive characteristic bilateral polar plugs and barrel shape.
Image 5. Higher power magnification, showing eggs with distinctive characteristic bilateral polar plugs and barrel shape.


The worm was identified as Trichuris trichiura. The common name for this organism is the whipworm. It belongs to the Nematode classification of parasites, which are commonly referred to as roundworms. Adults measure up to 5 cm in length and have a tapered or whip-like anterior end. The eggs measure 50 x 25 µm, and have brownish thick shells on stool smear. The eggs also have a barrel shape and distinctive protruding polar plugs at each end. These morphologic characteristics of the egg are diagnostic of Trichuris trichiura. The lack of a tissue migration phase and a relative lack of symptoms characterize whipworm infection, with only those with a heavy parasite burden becoming symptomatic. If these symptoms do arise, they are usually mild, ranging from loose stools with minimal blood loss and nocturnal stools, to iron deficiency anemia and vitamin deficiency. As parasite burden increases, however, symptoms can progress to dysentery, colitis, or rectal prolapse. Prolapse is more frequent in the Pediatric population, but has been described in adults as well.

Trichuris trichiura has one of the simplest of the Nematode life cycles. Eggs are unintentionally ingested, hatching in the small intestine by way of exploitation of signaling molecules from the intestinal microbiome. The larvae then burrow through the villi and continue maturing in the wall of the small intestine. They then return to the intestinal lumen, migrating to the cecum and subsequently into the large intestine, where they finish the process of maturation. Finally, the worm uses its anterior end to anchor into the bowel mucosa, where it feeds on tissue secretions and uses its posterior end for reproduction and laying eggs. Female worms can live from 1-5 years and can lay up to 20,000 eggs per day.

Whipworm infection is principally a problem in tropical Asia and, to a lesser degree, in Africa and South America. Children are most commonly infected, and can experience failure to thrive as well as cognitive and developmental defects. Transmission is by the fecal-oral route, explaining the large incidence of infection in children from developing countries, as they are far more likely to be in physical contact with soil and environmental contaminants, with subsequent placement of their fingers in their mouths. The fecal-oral route can also be facilitated by improper washing and cooking of fruits and vegetables, as well as overall poor hygiene, no matter what the geographical location. In the United States, whipworm infection is exceedingly rare. When it does happen, it is most commonly seen in the rural Southeast. Although it is rare, the incidence of infection is reported to be as high as 2.2 million individuals within the United States, with 1-2 billion cases worldwide.

Studies often reveal eosinophilia in nematode infections from ongoing tissue invasion. However, the lack of a tissue migration phase in Trichuris life cycles makes this a rare laboratory finding. Other studies such as anemia can give an indication to the presence of the worm. Characteristic egg morphology on stool smear remains the cheapest and easiest way to diagnose infection, but polymerase chain reaction using new sequencing techniques are now available in some laboratories to detect the presence of Trichuris with great sensitivity and specificity. The parasite burden can be quantified per gram of stool by the Kato-Katz technique. This procedure filters stool through mesh, with the filtered sample being placed within a template on a glass slide. The template is then removed and the remaining fecal material is removed with a piece of cellophane soaked in glycerol, leaving only eggs on the slide.

Discovery of T. trichiura in our patient was an unexpected finding, as our patient had no symptoms.  Asymptomatic detection of T. trichiura has been described in the past, so this finding is not unique. The medication of choice is mebendazole, showing a cure rate of 40-75%. The drug works well by inhibiting glucose uptake from the gastrointestinal tract of the helminth. However, this drug is very expensive, and as a result is difficult to obtain. The patient is currently receiving an alternative drug called albendazole as outpatient therapy and will be switched to mebendazole as soon as resources become available should the need remain. The patient is following up with her primary care physician and is expected to make a full recovery.


  1. Donkor, Kwame; Lundberg, Scott;
    https://emedicine.medscape.com/article/788570-overview. Trichuris trichiura (Whipworm) Infection (Trichuriasis).
  2. Sunkara T, Sharma SR, Ofosu A. Trichuris trichiura-An Unwelcome Surprise during Colonoscopy. Am J Trop Med Hyg. 2018 Sep;99(3):555-556. doi: 10.4269/ajtmh.18-0209. PubMed PMID: 30187847; PubMed Central PMCID: PMC6169157.

-Cory Gray, MD is a second year resident in anatomic and clinical pathology at the University of Chicago (NorthShore). His interests include hematopathology and molecular and genetic pathology, as well as medical microbiology.


Microbiology Case Study: 41 Year Old Male with Complaints of Abdominal Pain for One Month

Case History

A 41 year old African male presented to the ED with complaints of abdominal pain, weight loss, and decreased appetite over one month. He immigrated from Zimbabwe 10 years prior, and most recently visited 4 months ago. His past medical history is non-contributory. He was found to have microcytic anemia (Hgb 9.3 g/dL, MCV 77.0 fL), pneumonia, and focal small bowel dilation with thickening and inflammatory changes on abdominal CT.

Endoscopy revealed a large, villous, infiltrative mass in the third portion of the duodenum. On histologic examination of the duodenum biopsy, viable Schistosoma eggs were seen within the vessels in the lamina propria and associated with adenocarcinoma (Images 1 and 2). Schistosoma mansoni eggs were identified on stool ova and parasite exam (Image 3), and serology was positive for Schistosoma IgG antibody.

Image 1. 10x objective magnification of a hematoxylin and eosin stained histology slide of the duodenal biopsy with associated adenocarcinoma and multiple eggs can be visualized.
Image 2. 40x objective magnification of a hematoxylin and eosin stained slide from the duodenal biopsy of a man from Africa who presents with abdominal pain who is found to have a mass on endoscopy. Seen is a viable egg with intact miracidium and no evidence of calcification.
Image 3. 100x oil immersion objective magnification of an iodine prep from a concentrated formalin-fixed stool specimen demonstrating a Schistosoma mansoni egg with its characteristic large lateral spine.


Although this is not a common infection to encounter in the US, prevalence in endemic areas ranges from 30-100%. Infection occurs through contact with water contaminated with human feces; common circumstances are irrigation ditches as well as bathing and washing water.1

Schistosomiasis may be an indolent infection in many immunocompetent hosts. Chronic infection requires a shift from inflammatory TH1 response to a modulatory TH2 response.2 There is also evidence that Schistosoma infection may downregulate the immune response by inducing M2 differentiation of macrophages.3 These anti-inflammatory macrophages have been associated with a microenvironment favorable to malignancy. It has also been shown that S. mansoni is a risk factor for hepatocellular carcinoma (HCC) and colonic adenocarcinoma, possibly by altering p53 activation, initiation of chronic granulomatous response that blocks venules, increasing cell turnover, and promotion of ROS and RNOS production.4 Anti-idiotype antibodies produced in chronic infection may also down-regulate both specific and non-specific immune responses.5

This case is an unusual presentation in the US in that viable ova are typically not seen, and S. mansoni is more likely to involve the distal colon and liver rather than the small bowel. There is a known association between S. mansoni infection and HCC, and there are sporadic reports of association with tumors of the prostate, ovary, uterus, and cervix.5,6 To our knowledge however, there are no other reported cases of duodenal adenocarcinoma with concurrent schistosomiasis.


  1. Chai J and Jung B. Epidemiology of Trematode Infections: An Update. 2019. Adv Exp Med Biol. 1154:359-409.
  2. Barsoum RS, et al. Human Schistosomiasis: Clinical Perspective: Review. 2013. Journal of Advanced Research. 4:433-44.
  3. Hussaarts L, et al. Chronic helminth infection and helminth-derived antigens promote adipose tissue M2 macrophages and improve insulin sensitivity in obese mice. 2015. FASEB J. 29(7):3027-39.
  4. El-Tonsy MM, et al. Schistosoma mansoni infection: Is it a risk factor for development of hepatocellular carcinoma? 2013. Acta Trop. 128(3):542-7.
  5. Palumbo E. Association Between Schistosomiasis and Cancer. 2007. Infectious Diseases in Clinical Practice. 15(3):145-8.
  6. Peterson MR and Weidner N. Gastrointestinal neoplasia associated with bowel parasitosis: real or imaginary? 2011. J Trop Med. 2011:234254.

-Daniel Welder, MD is a second year Clinical Pathology resident at UT Southwestern Medical Center in Dallas, Texas. He has interests in Hematopathology, Transfusion Medicine and dabbles in Microbiology.



Microbiology Case Study: A 52 Year Old with a Liver Abscess

Clinical history

A 52 year old patient with a history of recent travel to India presented to interventional radiology from an outside hospital for aspiration of a liver abscess, and was subsequently returned to the outside hospital. The patient had spent 2 months in India before returning to the US, and about 1 month later developed right upper quadrant pain. Abdominal CT showed 2 cystic masses measuring 2-4cm. Aspiration of the cysts yielded 0.5mL of bloody fluid, which was sent for bacterial culture and smear. Infectious disease prescribed antimicrobial treatment consisted of ceftriaxone and metronidazole, followed by paromomycin and levofloxacin.

Laboratory findings

A gram smear of the patient’s liver mass aspirate showed few neutrophils and no bacteria. Culture of the aspirate showed no growth at 5 days. Multiple sets of blood cultures collected at the outside hospital all showed no growth at 5 days.

Image 1. Entamoeba coli trophozoite seen in the patient’s stool ova and parasite exam, demonstrating an eccentric karyosome and coarse, irregular peripheral chromatin.

A single ova and parasite exam of the patient’s stool was sent and showed few Entamoeba coli trophozoites. A sample of the patient’s blood was sent to the Mayo reference lab for serum Entamoeba histolytica antibody testing, which came back positive. Stool was sent for Entamoeba histolytica antigen testing which was negative.


Entamoeba coli is a non-pathogenic protozoan that can exist as a commensal organism in the human gastrointestinal tract. This organism has not been established to have any disease causing effect per se, but its presence may indicate exposure to water sources that could contain parasitic organisms. (3)

Entamoeba histolytica, by contrast, is a parasitic protozoal pathogen. Most infections are asymptomatic, but they can manifest as amebic dysentery or extraintestinal disease. The most common extraintestinal manifestation is amebic liver abscesses.1

Intestinal amebiasis occurs via ingestion of amebic cysts, typically through contaminated food or water, but also through other forms of fecal-oral contact. Infections are seen most commonly in areas with poor sanitation, but can be found in developed countries in patients who have migrated from or traveled to endemic areas.2

Once the amebic cysts pass into the small intestine, they form trophozoites, which are able to penetrate the mucous barrier of the gut and destroy intestinal epithelial cells. This leads to blood and mucus in the stool. (2) Once the amebae penetrate the gut wall, they are able to reach the blood and ascend through the portal system to the liver and form amebic liver abscesses.3

Clinical presentation of these abscesses typically includes right upper quadrant pain and fever in a patient with a history of travel to an endemic area. Serologic testing is used for confirmation if clinical presentation and imaging are suggestive, but this cannot distinguish between current infection and prior exposure, and up to 35 percent of uninfected inhabitants of endemic areas show positive serology.3 Stool microscopy may be the initial, and indeed only test available in some areas, but cannot differentiate E. histolytica from non-pathogenic E. dispar and E. moshkovskii strains.2

Image 2. E. histolytica trophozoite with ingested red blood cell, visible as a dark inclusion, as well as demonstrating a central karysome and fine, uniformly distributed chromatin. (CDC: https://www.cdc.gov/dpdx/amebiasis/index.html) Erythrophagocytosis is suggestive of E. histolytica.

Empiric treatment in the setting of consistent epidemiology, clinical picture, and radiology consists of metronidazole or tinidazole for tissue clearance followed by paromomycin, diiodohydroxyquin, or diloxanide furoate for intraluminal clearance.

Infectious diseases was taking care of this patient and decided her clinical syndrome is probably extraintestinal Entamoeba histolytica amoebiasis based on the results of the CT findings and the antibody in the right clinical setting.  Although her stool ova and parasite only showed Entamoeba coli, she clearly has been exposed to contaminated food or water.  In addition, the Entamoeba histolytica stool antigen was negative, but this can be an insensitive test.


  1. Leder, Karin, and Peter F. Weller. “Extraintestinal Entamoeba histolytica amebiasis.” UpToDate, Wolters Kluwer, 27 Jan. 2020, http://www.uptodate.com/contents/extraintestinal-entamoeba-histolytica-amebiasis?search=entamoeba%20histolyticatreatment&topicRef=5727&source=see_link. Accessed 4 Feb. 2020.  
  2. Leder, Karin, and Peter F. Weller. “Intestinal Entamoeba histolytica amebiasis.” UpToDate, Wolters Kluwer, 27 Jan. 2020, http://www.uptodate.com/contents/intestinal-entamoeba-histolytica-amebiasis?search=entamoeba%20histolyticatreatment&source=search_result&selectedTitle=1~46&usage_type=default&display_rank. Accessed 4 Feb. 2020.
  3. Weller, Peter F. “Nonpathogenic enteric protozoa.” UpToDate, Wolters Kluwer, 25 July 2019, http://www.uptodate.com/contents/nonpathogenic-enteric-protozoa?search=entamoeba%20coli%20treatment&source=search_result&selectedTitle=1~6&usage_type=default&display_rank=1. Accessed 4 Feb. 2020.

-Tom Koster, DO is a 1st year Anatomic and Clinical Pathology Resident at the University of Vermont Medical Center.


Microbiology Case Study: A Teenager with an Infected Wound

Case History

A male teenager presented to the emergency department following a 4 wheeler accident. He sustained extensive trauma to his right lower leg with a large, dirty laceration and grossly exposed muscle. His pulses were intact and motor & sensory nerve function were preserved. The wound was irrigated at the bedside and the patient was admitted with a plastic surgery consult for wound coverage. Cefepime was empirically started. After 10 days in the hospital and multiple surgeries to care for the wound, the patient developed a fever and increased pain, erythema, and swelling at surrounding the wound. The trauma service ordered blood and wound cultures.

Laboratory Identification

Image 1. The wound culture grew lavender-green colonies on blood agar (48 hours of incubation in CO2).
Image 2. Clear, lactose-negative colonies on MacConkey agar (48 hours of incubation in CO2).
Image 3. Gram stain from the blood agar plate showed gram negative rods (100x, oil immersion).

The oxidase reaction was negative. MALDI-TOF mass spectrometry identified the isolate as Stenotrophomonas maltophilia from the wound culture. Blood cultures were negative.


Stenotrophomonas maltophilia is a common non-fermenting gram negative rod that is ubiquitous in moist environments but is not commonly a member of human flora. S. maltophilia can readily be isolated from hospital surfaces and those with traumatic injuries, prolonged hospitalizations, on mechanical ventilation, and with in-dwelling devices are more susceptible to nosocomial infections by this organism. Those who are immunocompromised or have cystic fibrosis are also at an increased risk.  

In the laboratory, S. maltophilia is characterized as an aerobic, Gram-negative rod that grows as lavender-green colonies on blood agar (Image 1) and has an ammonia-like odor. This organism is catalase and oxidase negative and DNase positive. S. maltophilia is motile and is able to utilize glucose and maltose by oxidative fermentation. Current automated identification systems and MALDI-TOF mass spectrometry are able to accurately identify S. maltophilia.  

S. maltophilia is intrinsically resistant to many broad-spectrum antibiotics, including carbapenems and aminoglycosides. Beta-lactam resistance is due to two beta-lactamases and renders beta-lactam inhibitors ineffective. Trimethoprim-sulfamethoxazole (TMP-SMX) is the antibiotic of choice to treat S. maltophilia infections; however, resistance can develop. In the case TMP-SMX resistance, ceftazidime, minocycline, ticarcillin-clavulanate, ciprofloxacin, and levofloxacin can be tested. 

In the case of our patient, susceptibility testing was performed on the Vitek2 instrument and the isolate was susceptible to TMP-SMX. He was switched to TMP-SMX and underwent additional surgical procedures to wash out the infected area.

-Karla Perrizo, MD, is a Clinical Pathology resident at the University of Mississippi Medical Center.
