Microbiology Case Study: A 21 Year Old With Chronic Kidney Disease

Case History

The patient is a 21 year old male with a history of developmental delay and chronic kidney disease secondary to posterior urethral valves, status post kidney transplant at age 14, who presents for a routine office visit with his pediatric nephrologist. In the past year, he has had chronic antibody-mediated transplant rejection despite immunosuppression. In addition, he drinks 1-1.5 gallons of water daily, self-catheterizes every three hours, and has an indwelling Foley at night. During the office visit, he denies any urinary symptoms, including dysuria, hematuria, cloudy urine, reduced output, or fever. However, given his significant risk factors for urinary tract infection, his provider orders a urinalysis and urine culture.

Laboratory Identification

The urine was noted to be cloudy, was positive for nitrites and leukocyte esterase, and had 11-50 white blood cells per high-powered field. 

Urine culture demonstrated the growth of two organisms, one of which was identified to be greater than 100,000 CFU of Proteus miribalis, and the second of which grew 10,000-100,000 CFU, was isolated, and is shown below:

Image 1. Appearance of the second organism’s growth on blood agar after the bile solubility test.
Image 2. Gram stain showing gram positive diplococci.

Mass spectrometry by MALDI-TOF confirmed that this second organism is Streptococcus pneumoniae, a bile-soluble gram positive diplococci. 


S pneumoniae is implicated in a number of diseases, but it is an uncommon pathogen in the urine. Several case-series and case reports have been published demonstrating a predilection of pathogenic urinary S pneumoniae for pediatric patients with urinary tract abnormalities. In one series, 26 urine cultures from 18 patients were identified as growing S pneumoniae, with CFU counts ranging from 100 to 100,000. Sixteen of the 26 cultures grew only S pneumoniae. Of the 18 patients, only six were adults, eight had had a kidney transplant, and four others had chronic problems with their kidneys (1). In another series of three pediatric cases, one patient had congenital bilateral duplication of the renal collecting system, one had a “congenital imperforate anus (high type 1A) with a rectovesical fistula and grade 4 bilateral vesicoureteral reflux,” and the third had bilateral renal dysplasia (2). Neither case series was able to identify a specific serotype of S pneumoniae responsible for these infections.

As discussed by Choi et al, the altered flow dynamics of the abnormal urinary systems in these patients may be compromising normal host immune clearance mechanisms, thereby increasing the susceptibility to infection (2, 3). However, it is unclear why S pneumoniae infections have a predilection for congenital urinary tract abnormalities, as opposed to all urinary tract abnormalities. Choi et al postulate that some of the gene polymorphisms known to predispose individuals to UTI or pneumococcal infections could be genetically linked to genes responsible for urinary tract abnormalities, thus increasing the probability that an individual with a congenital urinary tract abnormality would have an S pneumoniae urinary tract infection (2,4).

Given the patient’s history and risk factors, the presence of S pneumoniae in his urine was found to be significant. Treatment of both organisms and appropriate follow-up was recommended.


  1. Burckhardt, Irene, Jessica Panitz, Mark van der Linden, and Stefan Zimmermann.  “Streptococcus pneumoniae as an agent of urinary tract infections – a laboratory experience from 2010 to 2014 and further characterization of strains.”  Diagnostic Microbiology and Infectious Disease.  2016; 86: 97-101.
  2. Choi, Rihwa, Youngeun Ma, Kyung Sun Park,  Nam Yong Lee, Hee Yeon Cho, and Yae-Jean Kim.  “Streptococcus Pneumoniae as a uropathogen in children with urinary tract abnormalities.”  The Pediatric Infectious Disease Journal.  2013; 32(12): 1386-1388.
  3. Bogaert, D, R de Groot, PWM Hermans.  “Streptococcus pneumoniae colonization: the key to pneumococcal disease.”  The Lancet Infectious Diseases.  2004; 4(3): 144-154.
  4. Yuan, Fang Fang, Katherine Marks, Melanie Wong, Sarah Watson, Ellen de Leon, Peter Bruce McIntyre, John Stephen Sullivan.  “Clinical relevance of TLR2, TLR4, CD14, and Fc gamma RIIA gene polymorphisms in Streptococcus pneumoniae infection.”  Immunology and Cell Biology.  2008; 86(3): 268-270.

-Fritz Eyerer, MD is a first 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.

Hematopathology Case Study: A 54 Year Old Woman with a Bone Fracture

Case History

The patient is a 54 year old woman who presented to the hospital after a fall, which revealed a pathologic fracture of T1 and a spinal lesion from C6/C7 to T2. CT of the chest/abdomen and pelvis at the time showed a large mass in the anterior mediastinum with extensive lymphadenopathy and lytic lesions in the spine and ribs.

C7-T1 Soft Tissue Excision

H&E 20X
H&E 50X
H&E 100X


Sections show sheets of large epithelioid-like cells with segmented nuclei with variably prominent nucleoli and ample amounts of eosinophilic cytoplasm.A majority of these larger cells have abundant cytoplasm and lobulated nucle iwith multiple nucleoli and a surrounding halo. They are consistent with Lacunar cells. These cells form large aggregates and are admixed with numerous neutrophils, histiocytes and scattered lymphocytes.

Occasional Hodgkin cells and multi-nucleated Reed-Sternberg cells are seen, as well as scattered medium size hyper chromatic cells with irregular nuclear contours and scant cytoplasm consistent with mummy cells.

Immunohistochemical staining revealed that the largea typical cells are immunoreactive for CD30, CD15 and PAX5/BSAP. CD45 highlighted background lymphocytes but showed infrequent dim staining in the large atypical cells. By Ki-67, the proliferation index is 50-60% in the large atypical cells. Taken together, the findings are consistent with Classic Hodgkin Lymphoma, nodular sclerosis, syncytial variant.


Classic Hodgkin lymphoma (CHL) has four distinct subtypes including nodular sclerosis, lymphocyte-rich, mixed cellularity and lymphocyte-depleted. These subtypes differ based on characteristics of the background non-neopalastic reactive cells and the histomorphology of the Hodgkin/Reed-Sternberg cells (HRS). Nodular sclerosis Classic Hodgkin lymphoma accounts (NSCHL) for approximately 70% of all CHLs. The mediastinum is the most commonly involved site and it generally occurs in people between the ages of 15-34 years old. Generally, the histology shows nodules with surrounding fibrosis. There are a variable number of Hodgkin/Reed-Sternberg (HRS) cells mixed with other inflammatory cells. The characteristic HRS cell is called a lacunar cell. This is a type of HRS cell with more cytoplasm, less prominent nucleoli and can show retraction of the cytoplasm in formalin-fixed tissue that gives the cell a halo or “lacunae.”1

The syncytial variant (SV) of CHL, nodular sclerosis was first described in the 1980s. It presents in 5-15% of cases of NS CHL. It is characterized by sheets and clusters of “lacunar cells” typical of the type of HRS cell most commonly seen in NS CHL. Previous studies had determined the SV of CHL to have a worse prognosis and more aggressive course than other subgroups. In a more recent study by Sethi, et. al. the clinical features and response to treatment of patients with SV were compared to patients with typical NS CHL. Within the cohort, 43 patients with SV were compared to 124 patients with typical NS CHL. The study found that there was no significant difference in age, sex, performance status, stage, bulky disease, number of nodal sites and chemotherapy regimens used between the two groups.2

As far as treatment outcomes, the rate of complete response in the SV group was 74% vs. 87% in the NS group. This result approached statistical significance with a p=0.05. The medium progression-free survival in the SV group was significantly shorter compared with the NS group. The overall survival, however was not statistically different, indicating that salvage chemotherapy was ultimately able to match the clinical outcomes for patients with SV type to patients with NS type. 2

Currently, all CHLs are treated with adriamycin, bleomycin,vinblastine, decarbazine (ABVD) chemotherapy regimen plus or minus radiation therapy regardless of subtype. Patients with relapsed or refractory disease are treated with a “salvage” chemotherapy regimen followed by an autologous stem cell transplant. Emerging therapies including PD-1 inhibitor nivolumab have shown great effect in patients with CHL. PD-1 or programmed death ligand 1 is overexpressed on HRS cells. This ligand binds with receptorson T-cells to prevent the T-cell immune response and reduce cytokine activation and targeted  response against the proliferating HRS cells. By using an antibody against the PD-1 ligand in CHL,the ability of the tumor to suppress the immune response is decreased and patients have been shown to have better clinical response rates.3

Patients with SV do need to be recognized as a distinct subgroup that may have a higher risk of disease progression with first line chemotherapy agents.  Due to the high numbers of HRS cells seen in patients with SV and the increased failure rate of initial chemotherapy agents, antibody therapies such as PD-1 inhibitors may be even more successful in those patients.


  1. Swerdlow SH, Campo E, Harris NL, et al. WHO Classification of Tumours of Haematopoetic and Lymphoid Tissues (Revised 4thedition). IARC: Lyon 2017.
  2. Sethi, T.K.,  et al. Differences in Outcome of Patients with Syncytial Variant Hodgkin Lymphoma (HL) Compared with Typical Nodular Sclerosis HL. Blood. 2015;126(23),1441. Retrieved from http://www.bloodjournal.org/content/126/23/1441.
  3. Bond DA, Alinari L. Emerging treatment options for the management of Hodgkin’s lymphoma:clinical utility of nivolumab. J Blood Med. 2017;8:41-54. Published 2017 May 11. doi:10.2147/JBM.S117452.

Chelsea Marcus, MD is a third year resident in anatomic and clinical pathology at Beth Israel Deaconess Medical Center in Boston, MA and will be starting her fellowship in Hematopathology at BIDMC in July. She has a particular interest in High-grade B-Cell lymphomas and the genetic alterations of these lymphomas.

Microbiology Case Study: A 44 Year Old Man with Severe Back Pain

Case History

A 44 year old male presented to the emergency department with severe, throbbing back pain in his mid-thoracic spine. He states the pain began a couple weeks ago and noted no recent fevers or night sweats, but does admit to chills. His past medical history is significant for end stage renal disease requiring dialysis, insulin dependent diabetes mellitus, and multiple amputations. On physical examination, there was tenderness to palpation along spine in mid-thoracic region. Lab work showed a normal white blood cell count, C reactive protein of 0.90 mg/dL (0.00 – 0.50 mg/dL), and an erythrocyte sedimentation rate of 60.0 mm/hr  (0.0 -10.0 mm/hr). MRI of the spine was consistent with discitis and osteomyelitis at T7-8 with compression fractures causing spinal stenosis and cord compression. Given the concern for an infection process, blood cultures were collected and interventional radiology performed a bone biopsy. The specimen was sent for bacterial, fungal, and AFB cultures as well as for histology.

Laboratory Identification

Image 1. Discrete, creamy colonies growing on blood agar (left) and Sabouraud dextrose agar (right) after 48 hours of incubation at 35°C.
Image 2. Fragments of bone with focal necrosis, foci of acute and chronic inflammation with clusters of yeast forms and pseudohyphae consistent with a Candida spp. infection.

The organism grew as discrete, creamy colonies growing on blood agar and Sabouraud dextrose agar after 48 hours of incubation at 35°C and resembled a yeast. MALDI-TOF mass spectrometry identified the isolate as Candida parapsilosis.  Similarly, the surgical pathology specimen showed necrotic bone with inflammation and yeast forms and pseudohyphae consistent with a Candida spp. infection. Blood cultures were negative. On chart review from an outside hospital, it was discovered the patient had an episode of candidemia ten months ago which was thought to be related to his dialysis port.


Yeasts are ubiquitous in the environment and make up the normal microbiota of human skin as well as the oral cavity, gastrointestinal tract and genitourinary tract. In general, when Candida spp. cause infections it is thought to an opportunistic infection acquired endogenously and due to exposure to prolonged antibiotics, suppressed immune system, or as a result of intravascular catheters. Those with diabetes mellitus, mucositis, bowel perforations, and intravenous drug users are most susceptible. Infections with Candida parapsilosis are becoming more common, and have the potential to cause invasive disease, such as fungal endocarditis and severe infections in the neonatal population. 

In the microbiology laboratory, C. parapsilosis grows rapidly as discrete, creamy colonies on a variety of agars. On cornmeal-Tween 80 agar, C. parapsilosis grows as short, curved pseudohyphae with blastoconidia arranged singly or in small clusters at points of constriction. The arrangement is sometimes described as resembling a sage bush. C. parapsilosis is germ tube negative and is negative for urease. In many laboratories currently, identification is achieved by automated methods, such as Vitek 2, or mass spectrometry, allowing for more rapid and accurate identification.  

Anti-fungals, such as echinocandins, azoles, and amphotericin B, are all potential therapeutic options to treat C. parapsilosis infections. CLSI C.parapsilosis specific breakpoints exist for fluconazole, voriconazole,micafungin, caspofungin, and anidulafungin in the M27-S4. Susceptibility testing should be performed on significant isolates from normally sterile sites.

In the case of our patient, infectious disease was consulted and he was started on IV micafungin and then transitioned to oral fluconazole. He had a transesophgeal echo and eye exam performed to ensure he didn’t have endocarditis or an invasive eye infection due to hematogenous spread of the yeast. He was discharged home on long term oral fluconazole.  

-Rim Alkawas, MD, is a second year Anatomic and Clinical Pathology resident at the University of Mississippi Medical Center. 

-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.

Microbiology Case Study: A Young Adult with A Skin Lesion

Case History

A young adult female presents to an urgent care clinic with the chief complaint of a “bump and surrounding redness” on her right medial thigh. The patient reports the bump had been present without change for 1 year. Approximately 2 days prior to presenting at the urgent care clinic the patient states she nicked the bump while shaving, and subsequently the bump became tender with surrounding erythema and produced purulent drainage. The patient denies any similar prior lesions and denies any significant past medical history. On physical exam, the lesion measured 1 cm with the surrounding erythema measuring 5cm. The urgent care physician performed an incision and drainage and noted a scant amount of white purulent material within the lesion. A cyst wall was identified and was removed as much as possible. A swab of the purulent material was collected and submitted to microbiology for culture.

Laboratory Identification

The primary gram smear of the swab specimen was interpreted as no bacteria or polys seen. Routine culture media including blood, chocolate, MacConkey, and CNA agar were inoculated and incubated aerobically. Following incubation, the blood agar showed few gram positive cocci consistent with usual skin flora and few single morphology of medium to large sized gray colonies without hemolysis. On the MacConkey agar, few single morphology non-lactose fermenting colonies were identified. The gray colonies identified on the blood agar gram stained as gram negative bacilli with unremarkable morphology. An oxidase test was performed and the bacteria was found to be oxidase positive. The key biochemical and physiologic characteristics of the isolate included: good growth on thiosulfate citrate bile salts and sucrose (TCBS) agar with yellow colonies, good growth in 6% NaCl nutrient broth, and no growth in 0% NaCl nutrient broth. The organism was identified by matrix-assisted laser desorption/ionization time of flight (MALDI-TOF) as Vibrio alginolyticus.

Image 1. Blood agar isolate of medium sized gray colonies.

Image 2. MacConkey agar with non-lactose fermenting colonies.


Vibrio spp. are water organisms commonly found in marine or brackish water environments. These organisms are gram negative bacilli which classically have “comma” shaped morphology on gram smear, though this is not an absolute. On sheep blood agar, these organisms are variably beta hemolytic medium to large gray colonies and on MacConkey agar are non-lactose fermenting (with the exception of Vibrio vulnificus)Vibrio spp. are oxidase positive, ferment glucose, and readily grow on most isolation media with growth being enhanced with the addition of 1% NaCl to the media. The growth characteristics on media containing different concentrations of NaCl can be used in differentiating the different Vibrio spp. Thiosulfate Citrate Bile Salts and Sucrose (TCBS) agar is both selective and differential for Vibrio spp. with sucrose fermentation being detected as yellow colony formation.

Vibrio angiolyticus typically causes extraintestinal infections, with wound infections and otitis externa being the most frequent. Transmission frequently occurs via traumatic aquatic injuries in contaminated water. Vibrio angiolyticus rarely causes intestinal disease and is isolated in less than 5% of stool cultures in patients with Vibrio associated diarrhea. Growth characteristics of Vibrio alginolyticus include yellow colonies on TCBS due to its ability to ferment sucrose and good growth on 6% NaCl and no growth on 0% NaCl. Additional key biochemical characteristics of Vibrio alginolyticus include oxidase positivity, nitrite positivity, negative for myo-Inositol fermentation, negative for arginine dihydrolase, positive for lysine decarboxylase, and variable positivity for ornithine decarboxylase. Most wound infections due to Vibrio alginolyticus are non-severe, and most mild infections will clear without antibiotic therapy.


  1. Procop GW, Koneman EW. Koneman’s Color Atlas and Textbook of Diagnostic Microbiology, North American Edition. LWW; 2016.
  2. Morris, J., Calderwodd, S., and Bloom, A. Minor Vibrio and Vibrio-like species associated with human disease. In: UpToDate, Post, TW (Ed), UpToDate, Waltham, MA, 2017.


-Justin Rueckert, DO is a 3nd 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.

Gram Stain Examination – Beyond Infectious Organisms

Case History

A 72 year old female with past medical history of stage IV ovarian adenocarcinoma treated with chemotherapy and interval debulking surgery, presented to emergency room with a one week history of confusion and worsening balance.

CT scan of the head showed new communicating hydrocephalus.  A magnetic resonance imaging couldn’t be performed initially because of patient’s uncontrolled agitation.  Lumbar puncture (LP) was performed.  Following this procedure the patient’s mental status showed some improvement and therefore neurosurgery team decided to insert ventriculoperitoneal (VP) shunt to treat her hydrocephalus and prevent recurrence of seizures.

It was Friday afternoon when a microbiology technologist brought the patient’s cerebrospinal fluid (CSF) gram stain to be reviewed.  It was confirmed that no inflammatory cells and organisms were present.  However, cells in the background looked very atypical (Image 1a, b).

Image 1:  Gram stain of CSF showing atypical epithelial cells at (a) 40x and (b) 100x with oil.

Image 1b.


The gram stain is used to provide preliminary information about the microorganism present in the specimen.  Gram stain differentiates bacteria into two fundamental varieties of cells.  Bacteria that retain the initial crystal violet stain (purple) are said to be “Gram-positive,” whereas those that are decolorized and stain red with carbol fuchsin (or safranin) are said to be “Gram-negative” (1).  An adequate examination of a gram-stained smear includes observing numerous representative fields and the fields containing neutrophils yield the most information (2).  Gram stain provides information about number of bacteria present, gram reaction and shape of the bacteria.  In background we can also see epithelial cells and inflammatory cells.  However, it’s a good practice to also appreciate and investigate any odd looking findings.

To investigate further, we visited the hematology laboratory to view their CSF slide to determine if these cells were a processing artifact.  After it was confirmed that hematopathology saw the same atypical cells, a cytopathologist was requested to review the gram stain since patient’s CSF cytology specimen was to be processed after the weekend.  Cytopathologist favored our suspicion and decided to process the cytology specimen late in the day on Friday and it was confirmed that those atypical cells were consistent with the metastatic adenocarcinoma.

Neurosurgery team was immediately contacted to reconsider insertion of the VP shunt as the shunt would drain fluid from the CSF into the peritoneal cavity and thus there was concern for transferring of malignant cells from central nervous system into abdomen/pelvis. However, after consulting oncology team it was later decided to proceed with the procedure since patient’s primary tumor originated in abdomen/pelvis and current intraabdominal tumor burden was not significant as compared to the symptoms driven by CNS involvement. Proceeding with this procedure was considered to be palliative and the best course of action to improve the patient’s quality of life.


  1. Beveridge TJ. Use of the gram stain in microbiology. Biotech Histochem.2001 May;76(3):111-8.
  2. Barenfanger J, Drake C. Interpretation of gram stains for the nonmicrobiologist. 2001 July;32(7):368–375.


-Kiran Manjee, MD, is a 1st year anatomic and clinical pathology resident at University of Chicago (NorthShore).

-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: A 56 Year Old Man with Sinus Congestion and Axillary Adenopathy

Case History

A 56 year old male presented to his PCP complaining of sinus congestion, rhinorrhea, night sweats, decreased appetite and fevers of up to 101-102 every evening. Hematologic evaluation revealed a neutropenia and a lymphopenia. An infectious disease work up was negative. His LDH was elevated. Physical examination reveals an enlarged left axillary lymph node. An excisional biopsy was performed.

Biopsy Findings

Figure 1.jpg

Figure 2.jpg

H&E stained sections demonstrate an enlarged node with effaced architecture and scattered residual follicles with small, mature cells. There is a proliferation of intermediate to large, to very large, atypical and highly pleomorphic cells many of which demonstrate bizarre forms, irregular nuclear morphology and acidophilic nucleoli. The lymphoma cells are noted to focally traverse through adipose tissue. Occasional hallmark cells are appreciated.

To further characterize the infiltrate, immunohistochemical stains were performed and interpreted with appropriate controls. The lymphoma cells were diffusely positive for CD45 (LCA), CD43, and CD30 (membranous and Golgi) with a Ki-67 of 80-90%. These cells were negative for CD20, PAX-5, CD3, CD4, CD8 (mostly), CD5, D10, BCl-2, BCl-6 and ALK1.

The morphologic features and immunophenotype of the cells was diagnostic of anaplastic large cell lymphoma, ALK negative.


Anaplastic Large Cell Lymphoma (ALCL), ALK-negative (ALK-) is defined as a CD30+ T-cell neoplasm that morphologically resembles ALK-positive ALCL, but lacks ALK protein expression. It most commonly affects adults (aged 40-65 years), and has a slight male preponderance with a male-to-female ratio of 1.5:1. T. Most patients present with advanced disease (stage III-IV), lymphadenopathy and B symptoms. The most common differential diagnosis is ALK-positive ALCL.

The molecular deciphering of ALCL began in the 1990s with the discovery of a recurrent t(2;5) (p23;q35) translocation fusing the ALK gene and the nucleophosmin gene generating a NPM-ALK fusion protein, as well as other ALK translocations resulting in a high ALK kinase activity. This triggers the major oncogenic pathway in ALK-positive ALCL. Pharmacologic therapy has been developed to target ALK, and has shown efficacy. Thus, compared with ALK-negative cases, ALK-positive occurs in younger patients and has a better prognosis. ALK-negative ALCL also tends to involve both lymph nodes and extranodal tissues, although extranodal sites are less commonly involved than in ALK+ ALCL.

The other differential diagnoses of ALK- ALCL includes, primary cutaneous ALCL (C-ALCL), other subtypes of CD30+ T-cell or B-cell lymphoma with anaplastic features and classic Hodgkin Lymphoma. If a single lymph node or cutaneous cases are suggestive of ALK- ALCL, C-ALCL needs to be considered. Any cases that involve the gastrointestinal tract need to be distinguished from CD30+ enteropathy-associated and other intestinal T-cell lymphomas.

Molecular analysis of ALK- ALCL shows characteristic strong expression of CD30, in equal intensity in all the cells. Loss of T-cell markers is frequently seen, however, more than half of all cases express one or more T-cell markers. CD2 and CD3 are more commonly expressed than CD5, and CD43 is almost always expressed. CD4+ is frequently positive, while CD8+ is rare. Many cases also express cytotoxic markers TIA1, granzyme B, and/or perforin.

The genetic profile in ALK-negative ALCL has been found to be pretty heterogenous. Most notably, activating mutations of JAK1 and/or STAT3 have been shown to lead to activation of the JAK/STAT3 pathway. Chromosomal rearrangements of DUSP22 (i.e. chromosomal rearrangements in or near the DUSP22-IRF4 locus on 6p25.3) occur in 30% of the cases, and rearrangements of TP63 occur in about 8% of cases. Neither of the rearrangements have been reported in ALK+ ALCL.

From a prognostic standpoint, studies have shown that the rearrangements have effects on the survival rate. TP63-rearranged cases were shown to have an unfavorable prognosis worse than ALK- ALCL with neither rearrangement, while DUSP22-rearranged cases were shown to have favorable outcomes similar to ALK-positive ALCLs.


  1. Gaulard P, de Leval L. ALK-negative anaplastic large-cell lymphoma. 2016 Jan 14;127(2):175-7.
  1. Edgardo R. Parrilla Castellar et al., ALK-negative anaplastic large cell lymphoma is a genetically heterogeneous disease with widely disparate clinical outcomes Blood. 2014 Aug 28; 124(9): 1473–1480.


Bradon Zelman

-Brandon Zelman is 4th year medical student at the Philadelphia College of Osteopathic Medicine and an aspiring pathologist. You can follow Brandon on Twitter @ZelmanBrandon.


-Kamran M. Mirza, MD PhD is an Assistant Professor of Pathology and Medical Director of Molecular Pathology at Loyola University Medical Center. He was a top 5 honoree in ASCP’s Forty Under 40 2017. Follow Dr. Mirza on twitter @kmirza.

Microbiology Case Study: A 64 Year Old Man with Metastatic Colon Cancer

Case History

A 64 year old man with metastatic colon cancer and a history of recent motor vehicle collision with polytrauma presented from a rehabilitation facility with fever up to 105 degrees Fahrenheit. Two months prior to admission he was hospitalized for the motor vehicle collision in which he sustained orthopedic injuries to multiple extremities. In addition to external fixation of several injuries, he returned to the operating room on multiple occasions for additional incision and drainage of a wrist wound which demonstrated gross purulence with cultures growing Enterococcus, Prevotella, and an extended spectrum beta-lactamase-producing Morganella morganii. Antimicrobial regimen initially consisted of surgically placed antibiotic beads and broad-spectrum therapy with vancomycin, piperacillin-tazobactam, and then meropenem. The patient was eventually transitioned to an oral antibiotic regimen consisting of linezolid and ciprofloxacin for an anticipated course of six weeks and he was discharged to a rehabilitation facility.

After several weeks at the rehabilitation facility, the patient became febrile and was admitted for workup of his fever. Initially the fever was of uncertain origin with malignancy (rectal cancer with metastasis to the liver), drug fever (linezolid), and wound site infection on the differential. Linezolid was discontinued, daptomycin initiated, and ciprofloxacin maintained. Fever persisted and ciprofloxacin was discontinued as another possible source of drug fever. Ertapenem was initiated. Initially, prior wounds and surgical sites appeared well-healing. Blood cultures all yielded no growth. However, on day five of this hospitalization, purulent drainage was noted from the site of a left leg surgical wound. Arthrocentesis yielded 0.5 mL of bloody fluid which was sent for cell count, differential, and culture.

Laboratory Findings

Initial Gram stain showed few polymorphonuclear leukocytes with no bacteria seen. Cell count was unable to be performed due to viscosity of the specimen but differential showed 80% neutrophils. There was no growth on aerobic blood, chocolate, or MacConkey agars. Anaerobic Schaedler (non-selective) agar grew 1-2 mm brownish colonies (Image 1). Gram stain of this isolate revealed gram variable bacilli forming long filaments (Image 2). The isolate was identified using MALDI-TOF MS (Vitek) as Clostridium ramosum.

Image 1. 1-2 mm brownish colonies on anaerobic Schaedler agar

Image 2. Gram stain showing gram variable bacilli in filamentous chains

The patient was taken to the operating room for incision and drainage of the left knee with two additional samples sent for culture which grew Clostridium ramosum.


Clostridium species are anaerobic, spore-forming, gram positive bacilli. C. ramosum is non-motile and is normally found in the human colon and the environment. One study identified C. ramosum in the feces of 83% of sampled adults. Former names include Eubacterium filamentosum, Ramibacterium ramosum, Actinomyces ramosus, and Eubacterium ramosum. Figure 2 demonstrates a notable characteristic of C. ramosum, i.e. its variable appearance on Gram stain. The morphology here may be described as gram negative or “over-decolorized”, though gram positive bacilli are clearly seen forming many of the filaments. Its terminal endospores are often difficult to identify on Gram stain and this is true of Figure 2. These characteristics on Gram stain have historically made identification difficult, though use of MALDI-TOF MS facilitated identification in our case. Biochemically, C. ramosum ferments glucose and hydrolyzes esculin; it is negative for lecithinase and lipase.

C. ramosum possesses an IgA protease though it is not commonly pathogenic. When it is pathogenic, the spectrum of disease overlaps with that of other anaerobes and includes deep-seated abscesses, e.g. intra-abdominal abscess secondary to trauma. Osteomyelitis and primary bacteremia are also possible, particularly in immunocompromised patients. Otitis media in children is another possible clinical scenario.

Septic arthritis due to Clostridium ramosum

A 2016 case report described two cases of septic arthritis due to C. ramosum. In one case, a patient with rheumatoid arthritis on methotrexate and prednisone and history of revision knee arthroplasty eight years prior presented with knee swelling. Synovial fluid aspirate was consistent with an infectious process; the prosthesis was removed but synovial and intraoperative cultures were negative. Antimicrobial therapy with linezolid and ciprofloxacin was administered for six weeks with clinical improvement. Two weeks after discontinuation of antibiotics the patient became febrile. Blood cultures were negative but culture of synovial fluid grew C. ramosum. The patient required multiple operations due to joint destruction and was ultimately managed with intravenous penicillin and clindamycin with transition to oral metronidazole for three months of therapy. The second case of C. ramosum septic arthritis presented in this report was ultimately managed with surgical debridement and amoxicillin-clavulanate. Both cases presented in patients with immunocompromising comorbidities and the course of their septic arthritis was chronic, recurring, and destructive but non-fatal with both patients dying from other causes.

These clinical and laboratory characteristics are consistent with the case of C. ramosum septic arthritis identified at our institution. The case of septic arthritis presented here involved an immunocompromised host (malignancy) with history of trauma, foreign body placement (external fixator), and long-term antibiotic therapy. This patient’s wound required debridement in the operating room on three occasions. Once clinically stable, the patient was discharged to a subacute rehabilitation facility and continued on ertapenem with amoxicillin for an expected duration of six weeks with the plan to switch to amoxicillin-clavulanate and ciprofloxacin for suppressive therapy.


  1. Forrester JD, Spain DA. Clostridium ramosum bacteremia: case report and literature review. Surg Infect (Larchmt). 2014 Jun;15(3):343-6. doi: 10.1089/sur.2012.240. Epub 2013 Nov 27. Review. PubMed PMID: 24283763.
  2. García-Jiménez A, Prim N, Crusi X, Benito N. Septic arthritis due to Clostridium ramosum. Semin Arthritis Rheum. 2016 Apr;45(5):617-20. doi: 10.1016/j.semarthrit.2015.09.009. Epub 2015 Oct 1. PubMed PMID: 26546506.
  3. Procop, Gary W et al. Koneman’s Color Atlas and Textbook of Diagnostic Microbiology. Seventh ed., 2017.


-Benjamin F. Smith is a Pathology Student Fellow at 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.