Microbiology Case Study: An 18 Year Old with Gastrointestinal Bleeding

An 18 year old female with no significant past medical history experienced multiple episodes of gastrointestinal bleeding over the course of a few weeks. The most recent bout included a bloody episode that filled the toilet, for which she provided a picture for the clinician. She denies any other associated symptoms including epigastric pain, nausea, vomiting, fever, or chills. Her travel history is unknown.

Review of her history reveals an unremarkable family and social history. She has never had an incident similar to this in the past and no other family members have ever complained of similar symptoms. Review of systems was unremarkable and within normal limits. Physical exam was unremarkable. A rectal exam was performed and was noted to have brown stool that was guaiac (occult blood) positive. Non bleeding internal hemorrhoids were noted. There were no external hemorrhoids present.

Labs drawn including CBC were within normal ranges with the exception of absolute eosinophils which were at the upper limit of normal range at 0.6 x 103/µL [normal range= 0.0 – 0.6 103/µL].

The patient had an esophagogastroduodenoscopy (EGD) to further investigate the gastrointestinal bleed. The exam was otherwise normal with exception of the ascending colon where they noted a worm on the surface of the mucosa (Image 1-2). The worm was collected and transported to microbiology for examination (Image 3-4).

Image 1. View of a worm seen on the mucosal surface of the ascending colon.
Image 2. Another view of a worm seen on the mucosal surface of the ascending colon.
Image 3. Adult worm viewed under the dissecting microscope.
Image 4. Eggs viewed under the dissecting microscope.


Examination of the worm and eggs revealed morphology consistent with Trichuris trichiura, or whipworm.

T. trichiura is most prevalent in warm, moist regions. The worldwide prevalence of infection is estimated to be roughly 800 million, mostly among poorer populations. Infection from T. trichiura is spread via fecal-oral route and caused by ingesting embryonated eggs. This occurs when contaminated dirt is ingested or by consumption of vegetables or fruits that have not been carefully cooked, washed or peeled.

The male and female worms both have the long whip-like structures at the anterior end. T. trichiura worms are 30-50 mm in length and the average life span is 1 year but they can live up to 10 years. The females have a straight and thick head while the males have a curly ended head. The males are typically longer the females. The eggs classically have barreled shaped, brown eggs with thick shells that measure 50-55 µm long by 22-24 µm wide. At each pole is lucent mucoid plug. The can also vary in size as noted in Image 5.

The adult female T. trichiura produces 1,000-7,000 eggs per day. The life cycle begins as unembryonated eggs passed in feces into soil (Figure 1). It takes approximately 21 days in the soil for an unembryonated egg to go through the process of embryonation to become the infective form of the parasite. Once ingested, the embryonated eggs hatch in the human intestine.

Image 5. T. trichiura eggs (CDC DPDx website)
Figure 1. Lifecycle of T. trichiura (CDC, DPDx)

Clinically, symptoms vary depending on the worm biomass present with most infections being asymptomatic. Symptoms include cramping, weight loss, growth restriction in children, bloody stool, and anemia. It can also result in Trichuris dysentery syndrome, which is more common in children. Recurrent rectal prolapse has also been reported. Lab findings include peripheral eosinophilia. T. trichiura is treated with Albendazole for 5-7 days +/- Ivermectin. Our patient was then prescribed albendazole and is being followed in GI clinic.


  1. Centers for Disease Control and Prevention. “Laboratory Identification of Parasites of Public Health Concern: Trichuriasis”. https://www.cdc.gov/dpdx/trichuriasis/index.html
  2. Procop, G. W., Church, D. L., Hall, G. S., Janda, W. M., Koneman, E. W., Schreckenberger, P. C., & Woods, G. L. (2017). Koneman’s color atlas and textbook of diagnostic microbiology (Seventh edition.). Philadelphia: Wolters Kluwer Health.

-Sharif Nasr, MD, 4th year anatomic and clinical pathology resident at University of Chicago (NorthShore). Dr. Nasr has an interest in GI pathology.

-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. 

Hematopathology Case Study: An 80 Year Old Man with Rapid Onset Cervical Adenopathy

Case History

An 80 year old man presented with rapid onset of cervical adenopathy over a period of few months. The largest lymph node measuring 6 cm was biopsied and sent for histopathological evaluation.

Biopsy Findings

Sections from the lymph node showed effacement of the lymph node architecture by a fairly monotonous population of medium to large sized lymphoid cells arranged in vague nodular pattern. Focally, a starry sky pattern was observed. The cells were 1.5-2 times the size of an RBC, with high N:C ratio, irregular angulated nuclei and small nucleoli. A high mitotic rate of 2-3 mitoses/hpf was seen.


Immunohistochemical stains showed that the lymphoma cells were positive for CD20, CD5, SOX-11, and negative for Cyclin D1, CD10, CD23, CD30, BCL-1, and BCL-6. Ki67 index was about 70%.


A diagnosis of Mantle cell lymphoma, pleomorphic variant was made.


Mantle cell lymphoma is a peripheral B cell lymphoma, occurring in middle aged or older adults, with a male: female ratio of 7:1. Although Cyclin D1 expression is considered a hallmark of mantle cell lymphoma, yet about 7% cases are known to be Cyclin D1 negative. In these cases, morphological features and SOX-11 positivity helps in establishing a definitive diagnosis.

Differential Diagnosis

In the assessment of morphological features of lymphoma, the cell size is an important starting point. In this case, the lymphoma cells ranged from medium to large sized. The following differential diagnoses were considered:

  • Burkitt lymphoma

This case showed a “starry sky” pattern focally. A medium sized population of cells, high mitotic rate and a high Ki67 index (70%) favoured a Burkitt lymphoma. However, although commonly seen in Burkitt lymphoma, a “starry sky” pattern is not specific for this type of lymphoma. Also, the lack of typical “squaring off” of nuclei, basophilic cytoplasmic rim were against the diagnosis of Burkitt lymphoma. The nuclei in this case showed 0-1 small nucleoli, unlike the typical basophilic 2-3 prominent nucleoli of Burkitt lymphoma. Moreover, Ki67 index, even though high was not enough for Burkitt lymphoma where it approaches 100%. The cells were negative for CD10 and Bcl-6, which are almost always found in a Burkitt lymphoma. Hence, a diagnosis of Burkitt lymphoma was ruled out.

  • Diffuse Large B cell Lymphoma

The presence of interspersed large cells with nucleoli, irregular nuclei, high mitotic rate, and a high Ki67 index with a history of very rapid enlargement of lymph node suggested a diagnosis of Diffuse Large B cell lymphoma. However, the scant cytoplasm, lack of bizarre cells, and absence of CD10, BCl-2, BCl-6 were against a diagnosis of DLBCL.

  • Lymphoblastic lymphoma

A diagnosis of lymphoblastic lymphoma was favoured by the irregularly angulated nuclei, and presence of nucleoli. However, the cells of lymphoblastic lymphoma have a more delicate nuclear chromatin, higher mitotic rate as against the relatively condensed chromatin and the low to high variable mitotic rate of Mantle cell lymphoma. Also, lymphoblastic lymphomas are more commonly of the T cell subtype and occur commonly in younger individuals. In this case, B cell markers were positive (CD 20), and the patient was 80 year old, disfavouring a lymphoblastic lymphoma. The blastoid variant of mantle cell lymphoma is practically indistinguishable from lymphoblastic lymphoma, except that it is Tdt negative.

Cyclin D1 negativity in Mantle cell lymphoma

In the cases of Cyclin D1 negative mantle cell lymphomas, morphology plays a critical role in coming to a diagnosis of mantle cell lymphomas. In this case, points that favoured the diagnosis of mantle cell lymphoma were clinical features such as older age (80 years), and male gender, and morphological features such as a vaguely nodular pattern of growth, irregular nuclei, and 0-1 small nucleoli. Due to the presence of variably sized cells with distinct nucleoli, a pleomorphic variant was considered. Even though Cyclin D1 was found to be negative, the cells were positive for SOX-11.

SOX-11 is a transcription factor that is not normally expressed in B cells, but is sensitive and fairly specific for mantle cell lymphomas. It is important to note that SOX-11 is also positive in 25% Burkitt lymphoma, 100% lymphoblastic lymphoma, and 66% T-prolymphocytic leukemia. Herein lies the importance of recognising morphological features, as all of these lymphomas that may express SOX-11 were ruled on the basis of morphology. A more specific antibody, MRQ-58 may be used for greater specificity. The presence of SOX-11 is considered a specific biomarker for Cyclin-D1 negative mantle cell lymphomas. In these cases, there is upregulation of Cyclin D2 or D3 that may substitute for Cyclin D1 upregulation. But, immunohistochemical detection of Cyclin D2 or D3 is not helpful for establishing a diagnosis, as other lymphomas are commonly positive for these markers. Hence, it is important to perform SOX-11 immunohistochemistry to diagnose the Cyclin D1 negative variant of mantle cell lymphoma.

SOX-11 can be used not just for the diagnosis, but also for determining prognosis of mantle cell lymphoma. Indolent MCL usually lack SOX-11 expression. The pattern of SOX-11 staining has also been used a marker of prognosis. Cytoplasmic expression of MCl, seen in only a few cases was associated with a shorter survival as compared to the more common nuclear staining of SOX-11.


In this age, lymphoma diagnosis relies heavily on the use of immunohistochemical markers. However, this case highlights the importance of morphological features in diagnosing lymphomas with unusual immunohistochemical marker profile. Although, this case was negative for Cyclin D1, considered a hallmark of Mantle cell lymphoma, yet, the combination of morphological features with SOX-11 staining helped in clinching the diagnosis. To avoid a misdiagnosis, it would be prudent to perform SOX-11 staining in all lymphoma cases morphologically resembling MCL, but lacking Cyclin-D1.

-Swati Bhardwaj, MD has a special interest in surgical pathology and hematopathology. Follow her on Twitter at @Bhardwaj_swat.

–Kamran M. Mirza, MD, PhD, MLS(ASCP)CM is an Assistant Professor of Pathology and Laboratory Medicine, Medical Education and Applied Health Sciences at Loyola University Chicago Stritch School of Medicine and Parkinson School for Health Sciences and Public Health. A past top 5 honoree in ASCP’s Forty Under 40, Dr. Mirza was named to The Pathologist’s Power List of 2018 and placed #5 in the #PathPower List 2019. Follow him on twitter @kmirza.

Microbiology Case Study: A 70 Year Old Male with Multiple Myeloma

Case History

The patient is a 70 year old male who was diagnosed with Kappa free light chain multiple myeloma. He was initially seen after he had a fall in the woods and underwent imaging which showed multiple lytic lesions and blood work showing monoclonal proteins and thrombocytopenia. He was found to have a lesion on his right scapula for which he received radiation. Bone marrow biopsy was performed which showed 60% plasma cells. To date he has completed radiation therapy, 5 cycles of chemotherapy, and is in the process of collecting stem cells for autologous stem cell transplant. Routine fungal culture of the stem cell collection grew a single tan white dry appearing colony on potato flake agar. A Gram stain of the organism revealed gram positive cocci mixed with filamentous structures.

Laboratory Identification

Image 1. Single tan white dry colony on potato flake agar.
Image 2. Modified acid fast stain (left) and Gram stain (right).
Image 3. Filamentous branching on Gram stain.

Based on the colony morphology and Gram stain results the organism was suspected to be in the Streptomyces genus. Identification with MALDI-TOF was attempted and did not yield a result as this bacteria is not in the data base.


Streptomyces is a genus of gram positive aerobic saprophytic bacteria that grows in various environments, and has a filamentous form similar to fungi (1). The morphologic differentiation of Streptomyces involves identification of complex multicellular architecture with germinating spores that form hyphae, and multinuclear aerial mycelium, which forms septa at regular intervals, creating a chain of uninucleated spores (2,3). They are able to metabolize many different compounds including sugars, alcohols, amino acids, and aromatic compounds by producing extracellular hydrolytic enzymes (helping with degradation of organic matter). Their metabolic diversity is due to their extremely large genome which has hundreds of transcription factors that control gene expression, allowing them to respond to specific needs (3).

Streptomyces is also considered to be one of the most medically important bacteria because of its ability to produce bioactive secondary metabolites. These metabolites are used in the creation of antifungals, antivirals, antitumoral, anti-hypertensives, and many antibiotics and immunosuppressives. They are responsible for 2/3 of all the worlds naturally occurring antibiotics (1).

Streptomyces is usually considered a laboratory contaminant though they can cause infections in immunocompromised patients and are chiefly responsible for granulomatous lesions in skin also known as actinomycotic mycetomas (1,2). Invasive pulmonary disease has been seen in HIV patients, splenectomized patients with sarcoid, and rarely in immunocompetent hosts (1). More rare presentations include brain abscesses can be seen in patients with cerebral trauma, peritoneal infections have been shown to occur in patients undergoing multiple pericenteses, and bacteremia in patients with indwelling catheters (1). Infection with Streptomyces is not common so susceptibility data is limited. Available data shows that organisms were consistently susceptible to amikacin; frequently susceptible to imipenem, clarithromycin or erythromycin, minocycline, and trimethoprim-sulfamethoxazole; and infrequently susceptible to ciprofloxacin and ampicillin (4).

Our patient had not received the stem cell unit that this grew from, so another aliquot was requested. The second aliquot did not grow any organisms, so the Streptomyces was considered a contaminant.


  1. Procop, Gary W., et al. Konemans Color Atlas and Textbook of Diagnostic Microbiology. 7th ed., Wolters Kluwer Health, 2017.
  2. Tille, Patricia M. Bailey & Scotts Diagnostic Microbiology. 13th ed., Elsevier, 2014.
  3. Chater KF. Recent advances in understanding Streptomyces. F1000Res. 2016;5:2795. Published 2016 Nov 30. doi:10.12688/f1000research.9534.1
  4. Mona Kapadia, Kenneth V.I. Rolston, Xiang Y. Han, Invasive Streptomyces Infections: Six Cases and Literature Review, American Journal of Clinical Pathology, Volume 127, Issue 4, April 2007, Pages 619–624, https://doi.org/10.1309/QJEBXP0BCGR54L15

-Casey Rankins, DO, 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 Associate Professor at the University of Vermont.

Microbiology Case Study: A 40 Year Old Woman with Fever, Chills, and Leg Pain

Clinical History

A 40 year old African American female with a history of sickle cell disease presented to an outpatient clinic with fever, chills, and leg and back pain consistent with a sickle cell crisis. Her past medical history was also significant for asthma and seizures. She rated her pain as 10 out of 10, her vitals showed a temperature of 101.0°F, and she was also tachycardic and hypotensive. Her white blood cell count was 23.0 TH/cm2, hemoglobin 8.4 g/dL, hematocrit 26.0%, and platelets 619,000 TH/cm2. In clinic, she received pain medications and a fluid bolus, two sets of blood cultures were collected, and she was transferred to the emergency department for further work up.

Laboratory Identification

Image 1. Gram stain from a positive blood culture bottle showing small, gram positive budding yeast (1000x oil immersion).
Image 2. A mucoid, salmon-colored yeast grew on Sabouraud dextrose and chocolate agars.

Blood culture bottles were positive after approximately two days on the automated instrument. The Gram stain showed small, gram positive budding yeast (Image 1). The BioFire FilmArray for blood culture identification was negative for Candida albicans, C. glabrata, C. krusei, C. parapsilosis, and C. tropicalis. At this time, she was started on micafungin for antifungal therapy. A mucoid, salmon colored yeast grew on both Sabouraud dextrose and chocolate agars (Image 2) and was identified by Vitek 2 as Rhodotorula spp.


Rhodotorula spp. are basidiomycetous yeasts that make up the normal microbiota on moist skin and can be found in bathtubs and on shower curtains. Rhodotorula spp. are usually considered contaminants, but can rarely cause fungemia in patients with central lines, endocarditis, peritonitis, and meningitis, especially in those that are immunocompromised. R. mucilaginosa, R. glutinis, and R. minuta are the species commonly associated with human disease. 

In the laboratory, Rhodotorula spp. grow as a mucoid, salmon colored yeast within 1-3 days of incubation. On Gram stain or lactophenol cotton blue prep, the yeast is small and round to oval with multilateral budding. Pseudohyphae are not usually present. Rhodotorula spp. produce urease and fail to ferment carbohydrates. R. mucilaginosa is negative for nitrate assimilation. Identification can also be confirmed by commercial kits, automated systems, and MALDI-TOF mass spectrometry. Rhodotorula spp. are intrinsically resistant to echinocandins and fluconazole.

In the case of our patient, she was switched to intravenous amphotericin B after the identification of Rhodotorula spp. was made. Reference laboratory testing identified the isolate as R. mucilaginosa with high minimum inhibitory concentrations (MIC) to fluconazole and echinocandins. Amphotericin had an MIC of 0.5 µg/ml. She successfully completed a 14 day course with close monitoring of creatinine, electrolytes, and platelet count. Repeat blood cultures were negative and no other focuses of infection were found on CT scans, transthoracic echocardiogram, and ophthalmology exam.

-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. She is the Director of Clinical Pathology as well as the Microbiology and Serology Laboratories. Her interests include infectious disease histology, process and quality improvement, and resident education.

Hematology Case Study: Thrombocytopenia in a 4 Year Old Child

A 4 year old child was brought to the pediatrician by her mother with a complaint of new onset of severe bruising on her legs. The mother could not recall any falls or bumps that would have caused the bruising. On exam, the physician also noted mucosal bleeding in the oral cavity. Questioning revealed that the patient had experienced flu like symptoms several weeks earlier. The physical exam was normal except for the bleeding. There was no family history of bleeding disorders. A CBC was ordered.

Reported CBC Results

WBC, RBC, Hgb, Hct, RBC indicies normal

Platelet count 26 x 103/μL

IPF 22% (reference range IPF% 1.0-7.0%) The physician evaluated the results, noting the normal CBC but decreased platelet count. The above results also show the immature platelet fraction (IPF), an additional Advanced Clinical Parameter reported from the Sysmex XN hematology analyzer. A low platelet count, as seen in this patient, will reflex a fluorescent platelet count (PLT-F). The impedance count (PLT-I) can be falsely increased if small RBCs or fragments are counted as platelets. On the other hand, in an optical platelet count, when measuring platelets by size (PLT-O), large platelets can be missed, giving a falsely low count. In this case there was a low platelet count and an instrument flag for an abnormal platelet scattergram. The PLT-F, on the other hand, uses a platelet specific dye which eliminates interference seen with other methods. The fluorescent dye labels the RNA, and forward scatter is used to determine size while side fluorescence is used to measure RNA content. With gating set based on cell volume and RNA content, the PLT-F can be measured. Therefore, the reflexed and more reliable PLT-F was the reported count.

Figure 1. PLT-F scattergram. The PLT-F channel measures forward scatter (FSC) on the Y axis and side fluorescence (SFL) on the X axis.1

Additionally, when there is an abnormal scattergram or a low platelet count, the IPF% and IPF# are also reported. The immature platelet fraction is a measure of the youngest platelets, or reticulated platelets. These are the first circulating platelets, right out of the bone marrow. An increased IPF indicates an increase in platelet production, yet this child’s platelet count was very low. This suggests that the thrombocytopenia may be due to excessive destruction of platelets; the bone marrow was actively making platelets, but they were being destroyed, causing the low platelet count.

Figure 2. Platelet scattergrams from a healthy individual with a normal IPF (a) and a patient with a high IPF (b). Mature platelets appear as blue dots, green dots represent the IPF with increased cell volume and higher fluorescence intensity compared to mature platelets.1


Immune Thrombocytopenia- ITP.

Primary immune thrombocytopenia (ITP), formerly known as idiopathic thrombocytopenic purpura or immune thrombocytopenic purpura, is one of the most common bleeding disorders of children. In most cases, it presents with sudden onset of bruising and petechiae in an otherwise healthy child, with normal WBC and hemoglobin. ITP is an autoimmune bleeding disorder in which the immune system makes anti-platelet antibodies which bind to platelets and cause destruction. Even though the exact cause of ITP remains unknown, it is recognized that it can follow a viral infection or live vaccinations. While there are some similarities between pediatric ITP and ITP in adults, in children this tends to be an acute disease which is self-limiting and resolves itself in several weeks, with no treatment. However, in a small number of children, the disorder may progress to a chronic ITP. In contrast to ITP in children, a chronic form is more commonly seen in adults. It is usually a diagnosis of exclusion, does not follow a viral illness and requires treatment.

This patient recovered in a few weeks. One month after the initial episode, her PLT was 174 x 103/μL and her IPF% was 6.0%


An IPF reported with a CBC, in combination with a low platelet count, is fast, inexpensive, and can be extremely beneficial in aiding in a timely diagnosis. As the child’s platelet count recovered, the IPF% returned to normal range. ITP can therefore be monitored with a CBC. Thus, the IPF can be used not only to help diagnose but also as an indicator of remission.


  1. Sysmex America, 2019. www.sysmex.com/us. Used with permission
  2. Arshi Naz et al. Importance of Immature platelet Fraction as a predictor of immune thrombocytopenic purpura. Pak J Med Sci 2016 Vol 32 No 3:575-579
  3. Briggs,C. Assessment of an immature plateletfraction (IPF) in peripheral thrombocytopenia. Br J Haematol 2004Jul;126(1):93-9
  4. Sysmex White Paper. The role of the ImmaturePlatelet Fraction(IPF) in the differential diagnosis of thrombocytopenia. www.sysmex.com/us
  5. D-Orazio, JA, Neely, J, Farhoudi,N. ITP in children: pathophysiology and current treatment approaches.J Pediatr Hematol Oncol.2013 Jan;35(1): 1-13

-Becky Socha, MS, MLS(ASCP)CM BB CM graduated from Merrimack College in N. Andover, Massachusetts with a BS in Medical Technology and completed her MS in Clinical Laboratory Sciences at the University of Massachusetts, Lowell. She has worked as a Medical Technologist for over 30 years. She’s worked in all areas of the clinical laboratory, but has a special interest in Hematology and Blood Banking. When she’s not busy being a mad scientist, she can be found outside riding her bicycle.

Microbiology Case Study: A 35 Year Old Female with Post-Op Drainage

Case History

A 35 year old female with a history of BRCA-positive breast cancer (status-post right radical mastectomy February 2018) underwent prophylactic left mastectomy and revision of right mastectomy. She received prophylactic clindamycin and cefazolin. She was discharged on post-op day 5 with bacitracin and 3 weeks of cefadroxil. She initially healed well. On post-op day 43 she noted drainage from the left incision site. At presentation she was afebrile.  There was a 3.0 x 2.0 cm area of induration and erythema on the right lateral aspect of her abdominal incision with seropurulent drainage. Incision and drainage was performed in office and a swab of the fluid was sent to microbiology. The initial gram stain and cultures were negative for bacteria. The patient was placed on sulfamethoxazole-trimethoprim and levofloxacin. At follow up 7 days later, another abscess was medial to the prior site was incised and drained. A swab of the fluid was sent to microbiology for bacterial and fungal cultures.

Laboratory Identification

Fungal cultures grew at 36 hours on potato-flake agar. Gram stain revealed gram-variable bacilli. Growth on 7H10 agar produced colonies at 72 hours, and Kinyoun staining was positive for acid-fast bacilli. Matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF) at 72 hours identified Mycobacterium abscessus complex.

Image 1. Growth on 7H10 agar.
Image 2. Gram stain from 7H10 agar showing gram variable bacilli.
Image 3. Kinyoun stain showing acid-fast bacilli.


M. abscessus complex is a group of rapidly-growing, nontuberculous mycobacteria. As such they are acid-fast bacilli that grow within 7 days when transferred from solid media to solid media. The subspecies are M. abscessus abscessus, M. abscessus massiliense, and M. abscessus bolletii. The complex is known to cause progressive pulmonary disease in patients with underlying structural lung diseases. It has been estimated to comprise up to 13% of all mycobacterial pulmonary infections. It has also been implicated in skin and soft tissue infections (SSTIs) following surgical procedures or environmental exposure (i.e. spas). SSTIs can also occur by seeding from disseminated disease. Rarer manifestations include central nervous system (CNS) and ocular involvement. Identification is by culture and molecular techniques. It is classically resistant to many drug classes with limited consensus on appropriate therapy. It can harbor the erm gene, which confers inducible erythromycin resistance. Clarithromycin, amikacin, and cefoxitin tend to have the lowest rates of resistance. Long-term multidrug regimens are recommended, based on susceptibility testing. Changes to initial therapy are usually required due to side effects or lack of efficacy. Surgical therapy is often required, when possible. Mortality post therapy is approximately 15%.

At two-week follow up, the wound had no purulent drainage or erythema. The plan was for prolonged three-drug therapy tailored to susceptibility data.

  1. Griffith DE. Rapidly growing mycobacterial infections: Mycobacteria abscessus, chelonae, and fortuitum. Von Reyn CF and B A, eds. UpToDate. Waltham, MA: UpToDate Inc. https://www.uptodate.com (Accessed on May 21, 2019.)
  2. Lee MR, Sheng WH, Hung CC, Yu CJ, Lee LN, Hsueh PR. Mycobacterium abscessus Complex Infections in Humans. Emerg Infect Dis. 2015;21(9):1638–1646.
  3. Novosad SA, Beekmann SE, Polgreen PM, et al. Treatment of Mycobacterium abscessus Infection. Emerging Infectious Diseases. 2016;22(3):511-514.

-Jonathan Wilcock, 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: A 55 Year Old Male with Altered Mental Status

Case History

A 55 year old male presented to the emergency department (ED) with altered mental status (AMS). His past medical history includes stage 4 pancreatic cancer with known invasion into the distal splenic vein. Currently undergoing chemotherapy, his last infusion was one week prior to presentation. On physical exam, the patient is a cachectic male with dry mucous membranes, scleral icterus, hypotension (79/37), hypothermia (35o C), tachypnea (Respiratory Rate of 20/min) and tachycardia (pulse up to 130s). Initial labs were ordered including blood cultures and were significant for hypoglycemia (40mg/dL), pancytopenia, mild liver function test abnormalities, an ammonia level of 80 µmol/L and lactate of 11.2 mmol/L. It was concluded that the AMS resulted as a consequence of hypoglycemia. However, there was also concern for intracranial pathology vs. stroke vs. metastatic disease. Brain imaging showed no obvious lesion or mass. The cause of the hypotension was uncertain but could be a result of volume depletion or sepsis. Empiric vancomycin and cefepime were initiated in the ED. However, the patient decompensated, developing mid-abdominal and periumbilical ecchymoses suspicious for a retroperitoneal hemorrhage. Despite aggressive therapy, he expired in the ED.

Laboratory Identification

An anaerobic blood culture bottle flagged positive at 5 hours incubation. A gram stain showed large, boxy, gram positive rods without spores (Image 1). Brucella blood agar was inoculated and incubated anaerobically.  Following overnight incubation, the surface of the plate showed a subtle film of growth covering the plate and detectable hemolysis (Image 2). No discreet colonies were identified. A catalase test was performed and was negative. Definitive identification of Clostridium septicum was obtained by MALDI-TOF.

Image 1. Gram stain from the anaerobic blood culture bottle that flagged as positive following 5 hours of incubation. Boxy, large gram positive rods without spores are observed. Oil immersion photomicrograph (x100 objective).
Image 2. Brucella agar plate following 24 hours of incubation under anaerobic conditions at 35oC. Significant bacterial growth in a haze and detectable Beta hemolysis can be observed. No discreet colonies can be identified. Identification by MALDI-TOF was Clostridium septicum.


Clostridium septicum is an anaerobic gram positive bacillus that can produce spores; however, spores are not frequently seen, especially in nutrient-rich environments. Spores, when present, are typically oval and located subterminally. Infection by C. septicum was once thought to be extremely rare, but improvements in anaerobic laboratory techniques have allowed for the discovery of the true potential of this agent. C. septicum is one of several bacteria that can cause myonecrosis (i.e., gas gangrene). Infections are typically seen in settings of immunodeficiency, trauma, surgery, malignancy, skin infections/burns, and septic abortions. The colon may promote the growth of C. septicum better than other anatomic sites due to its anaerobic conditions. As one of the more aggressive etiologies of gas gangreneC. septicum infection progresses very rapidly, with a mortality rate of approximately 79% in adults, typically occurring within 48 hours of infection. Symptoms of infection include pain, described as a heaviness or pressure that is disproportionate to physical findings, tachycardia, and hypotension. Tissue necrosis then causes edema and ischemia resulting in metabolic acidosis, fever, and renal failure. The carbon dioxide and hydrogen produced during the growth of the organism move through tissue planes, causing their separation, producing features characteristic of palpable emphysema (i.e., crepitus). This also results in a magenta-bronze skin discoloration and bulla filled with a foul-smelling serosanguinous fluid.

Four toxins have been isolated from C. septicum: the lethal alpha toxin, DNase beta-toxin, hyaluronidase gamma toxin, and the thiol-activated/septicolysin delta toxin. Alpha toxin causes intravascular hemolysis and tissue necrosis and is well known as the primary virulence factor of C. septicum

C. septicum derived gas gangrene has shown strong correlations with increased levels of malignancy. Patients with C. septicum infections may have an occult colon cancer or a tumor that has metastasized to the colon. C. septicum bacteremia is also associated with typhlitis (defined as inflammation of the cecum that can extend proximally into the terminal ileum or distally into the ascending colon), which can develop in patients with hematologic malignancy receiving chemotherapy. Because the organism may be harbored in the gastrointestinal tract, the organism may gain access to the bloodstream through the ileocecal region.

Therapy includes antibiotics and surgical debridement (with occasional amputation). For antibiotic selection, typical anaerobic coverage includes piperacillin/tazobactam, ampicillin/sulbactam, metronidazole or meropenem. Vancomycin is also effective. Susceptibility testing is not typically performed; moreover, the CLSI makes an annual antibiogram which can be used as a guide. 

Key points

  • C. septicum often has swarming growth that covers the plate surface.
  • Spontaneous myonecrosis with C. septicum bacteremia can be an indicator of possible occult colonic malignancy.
  • C. septicum can be associated with typhlitis in neutropenic patients with hematologic malignancy undergoing chemotherapy.


  1. Smith-Slatas CL, Bourque M, and Salazar JC (2006). Clostridium septicum infections in children: a case report and review of the literature. Pediatrics 117(4): e796-e805.
  2. Alpern, RJ and Dowell, VR (1969). “Clostridium septicum infections and malignancy”. JAMA. 209: 385–388.
  3. Ballard, J, Crabtree, J, Roe, BA, and Tweten, RK (1995). “The primary structure of Clostridium septicum alpha-toxin exhibits similarity with that of Aeromonas hydrophila aerolysin”. Infection and Immunity. 63 (1):340–344.
  4. Sidhu JS, Mandal A, Virk J, and Gayam V (2019). “Early detection of colon cancer following incidental finding of Clostridium septicum bacteremia”. J Investig Med High Impact Case Rep. Jan-Dec;7:2324709619832050.
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Xiang Xu, MD, PhD and Dominick Cavuoti, DO contributed to this case.

-Clare McCormick-Baw, MD, PhD is an Assistant Professor of Clinical Microbiology at UT Southwestern in Dallas, Texas. he has a passion for teaching about laboratory medicine in general and the best uses of the microbiology lab in particular.