Microbiology Case Study: 57 year old Female with Altered Mental Status and Declining Health

Case Description

A 57 year old female presents to the emergency department with altered mental status, decreased appetite and chest, abdominal and pelvic pain. She has a complex medical history including end-stage renal disease, cardiovascular disease with pacemaker placement, and recurrent ascites. Her physical exam was notable for hypotension (65/52), hypothermia (31.7°C), and abdominal distention. A CT of her abdomen and pelvis revealed marked ascites, and bloodwork indicated leukocytosis (12.81, ref 4.22-10.33), elevated lactate (4.1, ref 0.5-2.2), and acidemia (7.27). Given the concern for septic shock, an infectious workup was initiated. A diagnostic paracentesis was undertaken which revealed rare yeast forms by Gram stain (Figure 1). Routine and fungal cultures of the ascites fluid grew yeast which was identified as Cryptococcus neoformans by matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS). Bacterial blood cultures turned positive after 3 days and Cryptococcus neoformans was identified (Figure 2). Interestingly, serum cryptococcal antigen tests were negative.

The patient was treated with amphotericin B, vancomycin, and meropenem. Despite intervention, the patient’s clinical condition continued to deteriorate, leading to multiple organ failure. The patient was transitioned to comfort care and expired soon thereafter.

Figure 1. Gram stain of peritoneal fluid (ascites) demonstrating two yeasts with surrounding capsule and host cells (100x objective, oil immersion).
Figure 2.  Bacterial blood culture with encapsulated yeasts on Gram stain (100x objective, oil immersion).


This case highlights two significant points: 1) atypical presentation of a cryptococcal infection and 2) the value of complimentary approaches in the diagnostic workup of an infectious etiology.

Cryptococciare environmental fungi with worldwide distribution, classily causing opportunistic central nervous system infection in patients with either uncontrolled HIV or other significantly immunocompromising conditions. In this patient population, a staggering 70-90% of cryptococcal infections manifest as meningitis, with a one-year mortality rate as high as 70% in some regions.1 Meningitis caused by Cryptococcus sp. accounts for nearly 1 in 7 HIV-related deaths worldwide.2 This case and others,3 serve as an important reminder that cryptococcal disease may present in different ways, including peritonitis in a patient without significant immunosuppression.

Several methods are available to aid in the identification of Cryptococcus sp.4 Direct microscopic evaluation of Cryptococcus in fluid and tissue samples reveals round, narrow-based budding yeast of variable size (2-20 um). The capsule of Cryptococcus is classically seen with India ink, though recent work has shown that Gram stain is as effective.5 In our patient, direct microscopy of the peritoneal fluid provided the first clue that Cryptococcus was the causative agent. Other useful stains used for histopathological analysis include mucicarmine and Fontana-Masson, which stain the capsule and melanin, respectively. In culture, strains of Cryptococcus sp. typically elaborate a robust capsule leading to the formation of mucoid colonies. However, acapsular strains have also been identified.

Biochemical hallmarks of Cryptococcus sp. include the production of urease and phenoloxidase leading to the formation of melanin which is absorbed into the cell wall. Phenoloxidase activity is exploited for diagnostic purposes as it leads to melanized pigmentation in the presence of caffeic acid, such as in either a caffeic acid disk test or on Bird Seed agar.

Non-culture-based methods for the diagnosis of cryptococcal infections include detection of cryptococcal capsular antigens by either ELISA, latex agglutination, or a lateral flow immunoassay (LFA). The LFA is a cost-effective test with rapid turnaround time which exhibits strong agreement with other antigen detection methods. While the LFA has proven useful in a variety of settings,6 our patient’s LFA was negative, underlining the importance of using orthogonal methods in parallel to identify microbes. In cases where patients are infected with an acapsular strain of Cryptococcus, the antigen testing will be negative since the antigenic target (i.e the capsule) is missing. An important consideration when assessing discrepancies between Gram stain/culture and ancillary immunoassay testing is “prozone effect”. Prozone, or Hook effect, is a phenomenon where overwhelming amounts of analyte impairs immunocomplex formation, causing a lack of analyte detection (i.e false-negative test). To account for prozone, a serial dilution series of the sample with repeat testing should be performed to ensure accurate correlation.


  1. World Health Organization. Guidelines for the diagnosis, prevention, and management of cryptococcal disease in HIV-infected adults, adolescents and children, March 2018: supplement to the 2016 consolidated guidelines of the use of antiretroviral drugs for treating and preventing HIV infection.
  2. Rajasingham R, Smith RM, Park BJ, Jarvis JN, Govender NP, Chiller TM, Denning DW, Loyse A, Boulware DR. Global burden of disease of HIV-associated cryptococcal meningitis: an updated analysis. The Lancet infectious diseases. 2017 Aug 1;17(8):873-81.
  3. El-Kersh K, Rawasia WF, Chaddha U, Guardiola J. Rarity revisited: cryptococcal peritonitis. Case Reports. 2013 Jul 10;2013:bcr2013009099.
  4. Mais DD. Quick compendium of clinical pathology. American Society for Clinical Pathology Press; 2018.
  5. Coovadia YM, Mahomed S, Dorasamy A, Chang C. A comparative evaluation of the Gram stain and India ink stain for the rapid diagnosis of cryptococcal meningitis in HIV infected patients in Durban: brief report. Southern African Journal of Infectious Diseases. 2015 Jan 1;30(2):61-3.
  6. Perfect JR, Bicanic T. Cryptococcosis diagnosis and treatment: What do we know now. Fungal Genetics and Biology. 2015 May 1;78:49-54.


-Andrew T. Nelson, MD, PhD, is a Clinical Pathology resident at UT Southwestern Medical Center in his second year. He has an interest in Clinical Chemistry.

-Andrew Clark, PhD, D(ABMM) is an Assistant Professor at UT Southwestern Medical Center in the Department of Pathology, and Associate Director of the Clements University Hospital microbiology laboratory. He completed a CPEP-accredited postdoctoral fellowship in Medical and Public Health Microbiology at National Institutes of Health, and is interested in antimicrobial susceptibility and anaerobe pathophysiology.

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

One thought on “Microbiology Case Study: 57 year old Female with Altered Mental Status and Declining Health”

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s

This site uses Akismet to reduce spam. Learn how your comment data is processed.

%d bloggers like this: