Tag: case study

Case History

A 35 year old male presented to the emergency department with left-sided chest pain, a new cough and pain that gets worse with inspiration. The past medical history was significant for HIV, recurrent syphilis, rectal high-grade dysplasia, proctitis with possible rectal abscess with concomitant Herpes Simplex Viral infection and Cytomegalovirus colitis. This patient was not compliant with antiretroviral therapy (ART) and his CD4 count was <100 at admission. In the ED, a chest X-ray was performed which revealed bilateral patchy, peripheral mass-like opacities with ground glass halos (Figure 1). Routine respiratory cultures of sputum and bronchoalveolar lavage (BAL) revealed no significant observations; mainly respiratory flora was reported. However, hematology staining of BAL revealed multiple fungal elements consistent with Pneumocystis jirovecii organisms (Figure 2).

Discussion

Previously classified as a protozoa, Pneumocystis jirovecii (formerly known as Pneumocystis carinii) is currently considered a fungus based on nucleic acid and biochemical analysis. Stringer et al. proposed the change in nomenclature in early 2002, in honor of the Otto Jirovec, who was credited by some, as the original descriptor of the organism in human hosts.¹ A few Pneumocystis species have been described in a wide variety of mammalian hosts but P. jirovecii is only capable of infecting humans and is not capable of infecting other animals.⁴ P. jirovecii infection mostly affects the immunocompromised patients and can lead to severe, life-threatening disease. HIV is one of the most commonly encountered underlying diseases, but individuals with cancer, transplant recipients and hosts receiving immunosuppressive medication can be at risk. The route of transmission is thought to be person to person through air transmission. Immunocompetent hosts can act as reservoirs of the organisms and spread it to the immunocompromised. The use of antiretroviral therapy and prophylactic medication on HIV patients has substantially decreased the incidence of PJ infection in this population.^{2, 3} Defects in cellular immunity, specifically CD4+ T-cell-mediated immunity is a predisposing factor for the development of severe Pneumocystis infection. The disease is usually a pneumonia that can have a slow progression or progress rapidly. Fever, nonproductive cough, tachypnea, and severe dyspnea with hypoxia are the most common symptoms.

Induced sputum, bronchoalveolar lavage fluid, or lung tissue are the commonly accepted specimens received in clinical laboratories for direct diagnosis of P. jirovecii. Microscopically, the life cycle of Pneumocystis consists of at least two different life cycle forms of Pneumocystis organisms: the trophic form and the cyst form. The trophic form generally measures ∼2 µm in greatest diameter and in contrast, the cyst is significantly larger, measuring ∼8–10 µm in greatest diameter. The rigid Pneumocystis cyst wall is formed of β-glucan, which warrants detection of systemic Pneumocystis infections using Fungitell testing.⁴ Trophic and cyst forms can be detected with Papanicolaou, Gram-Weigert, or Wright Giemsa, Gomori methenamine silver (GMS), or calcofluor white. The sensitivity of the interpretation of these stains depends upon the expertise of the observed to differentiate Pneumocystis from artifacts and other fungi such asand Histoplasma capsulatum. The use of monoclonal antibodies with Immunofluorescent antibody stains directed against human Pneumocystis epitopes, can enhance direct detection of this organism in clinical specimens.⁵

Because the sensitivity of special stains and the microscopy depends, in part at least, on the experience and skill of the microscopist, polymerase chain reaction (PCR) has become a newer and promising testing method for P.jirovecii DNA detection. It is recommended that PCR should be done in cases with only mild to moderate immunosuppression because these individuals may have a lower burden of the fungus and clinical and radiologic findings are less developed compared to severely immunosuppressed patients.⁶ Another advantage of PCR is the ability to quantify the amount of P. jirovecii in the specimen, which has been suggested to help distinguish individuals who may be colonized versus those with true P. jirovecii associated pneumonia.⁷

The drug of choice for prophylaxis against or treatment of P. jirovecii  is trimethoprim-sulfamethoxazole. Prophylaxis may generally be started on HIV positive patients once the CD4+ is <200cells/microL, CD4% is <14%, and/or patients have a detectable viral load.⁸

-Rebecca Yee, PhD, D(ABMM), M(ASCP)^CM is the Chief of Microbiology, Director of Clinical Microbiology and Molecular Microbiology Laboratory at the George Washington University Hospital. Her interests include bacteriology, antimicrobial resistance, and development of infectious disease diagnostics.

Case History

A 25 year old male with severe right lower quadrant abdominal pain, fever and history of congenital neutropenia and thrombocytopenia presented to the emergency department. The patient reported experiencing similar episodes over the previous six months, sometimes requiring hospitalization. His symptoms would typically improve following several days of antibiotic therapy and were thought to be secondary to typhlitis. He reported that his current symptomology was more severe than any of the previous episodes. In the emergency department, the patient was found to be tachycardic and severely hypotensive, prompting admission for sepsis and empiric antimicrobial therapy with piperacillin/tazobactam and vancomycin. Imaging at the time revealed severe terminal ileitis with mild pancolitis, markedly worsened from a study obtained months prior during a previous episode. After failing to improve with conservative management, an exploratory laparotomy with total abdominal colectomy and end ileostomy was completed to achieve source control.

Laboratory workup

Anaerobic bottles from blood cultures collected at the time of hospital admission flagged positive in under 24 hours. Gram staining from the positive bottle broth revealed large, gram variable bacilli (Image 1A). Multiplex PCR performed on the positive blood culture broth failed to reveal the identity of the organism. After 24 hours, close observation was required to visualize bacterial growth on anaerobic blood culture media, which appeared as a thin, translucent film (Image 1B). To provide better visualization for this case, a loop was utilized to scrape the growth so a path could be observed within the biomass (Images 1B and 1C, dotted lines). The bacterium recovered was definitively identified as Clostridium septicum by MALDI-TOF MS, prompting continued coverage with piperacillin/tazobactam until discharge.

Discussion

Clostridium septicum is an anaerobic, Gram-positive spore-forming bacillus.^1,2 Colony morphology on solid media evolves over time, with a characteristic “medusa head” morphology at under 8 hours, a “sand grain” appearance at approximately 24 hours, and visible swarming after 48 hours (Image 1B and 1C).² The organism is found in the soil and the gastrointestinal tracts of both humans and animals with the potential to cause a variety of diseases. It is especially problematic as an infectious agent of livestock and other ruminants, poultry, and horses.¹ Clinical manifestations of infection with C. septicum in humans includes necrotizing enterocolitis, bacteremia, and clostridial myonecrosis.² Prompt identification of infection with Clostridium septicum is essential due to the rapidly fatal nature of untreated bacteremia with this organism. The mainstay of treatment is early initiation of antibiotic therapy and aggressive surgical debridement of affected tissue. The drug of choice for medical management is penicillin, although metronidazole and carbapenems may be used in patients with penicillin allergies.

C. perfringens and C. septicum are the two clostridial species most associated with bacteremia in neutropenic patients.⁵ Clostridium septicum bacteremia can allow for the hematogenous dissemination of infection and can be rapidly fatal.³ Infection of the bowels of a susceptible host and compromise to the bowel wall integrity leads to entry of bacteria into the circulation. In severe cases, this in turn can lead to seeding of distal sites with progression to sequelae including clostridial myonecrosis (gas gangrene). While classical traumatic myonecrosis associated with an infected wound becomes contaminated with clostridial spores from the external environment (most commonly C. perfringens), atraumatic (or spontaneous) myonecrosis is associated with C. septicum (among other clostridial species) and results from hematogenous seeding of distal sites during bacteremia. Virulence and tissue necrosis are mediated by a variety of exotoxins produced by the organism,¹ with alpha-toxin being the primary virulence determinant.⁴

Importantly, Clostridium septicum bacteremia is strongly associated with both hematogenous and gastrointestinal cancers. For this reason, detection of this pathogen in the blood may warrant further patient evaluation for potential sources of underlying pathology.² In this patient’s case, typhlitis and neutropenic enterocolitis were precipitating factors leading to his C. septicum bacteremia as this patient presented without evidence of gastrointestinal malignancy. Following the procedure, the patient stabilized, and his condition continued to improve through recovery. His antibiotics were eventually discontinued, and he was discharged.

References

1. Alves MLF, Ferreira MRA, Donassolo RA, Rodrigues RR, Conceição FR. Clostridium septicum: A review in the light of alpha-toxin and development of vaccines. Vaccine. 2021;39(35):4949-4956. doi:10.1016/j.vaccine.2021.07.019
2. Mallozzi MJG, Clark AE. Trusting your gut: Diagnosis and management of clostridium septicum infections. Clinical Microbiology Newsletter. 2016;38(23):187-191. doi:10.1016/j.clinmicnews.2016.11.001
3. Koransky JR, Stargel MD, Dowell VR Jr. Clostridium septicum bacteremia. Its clinical significance. Am J Med. 1979;66(1):63-66. doi:10.1016/0002-9343(79)90483-2
4. Kennedy CL, Krejany EO, Young LF, et al. The alpha-toxin of Clostridium septicum is essential for virulence. Mol Microbiol. 2005;57(5):1357-1366. doi:10.1111/j.1365-2958.2005.04774.x
5. Bennet JE, Dolin R, Blaser MJ, Onderdonk AB, Garrett WS. Diseases Caused by Clostridium. In Mandell, Douglas, and Bennett’s principles and practice of infectious diseases (2^nd ed., pp. 2960-2968). Elsevier.

-Amanda Means is a PGY-1 resident in Anatomic and Clinical Pathology at the University of Texas Southwestern Medical Center in Dallas, Texas.  Dr. Means did her undergraduate studies at Sam Houston St University in Huntsville, TX and received her medical degree from the University of Texas Health Sciences Center in San Antonio.

-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.

-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.

Case History

A 13 year old female presented to the emergency department with a painful left thumb swelling. Eight days ago, she picked out a hangnail from the medial side of her left thumb, resulting in a worsening pain and swelling. She went to urgent care five days ago and was prescribed Augmentin with no improvement. Physical examination showed a tender circumferential swelling of the right thumb past the flexion joint, with paronychia extending 1 cm in length with fluctuance extending an additional 0.5 cm. The wound was incised, and the drainage was sent to the microbiology laboratory for culture.

The culture grew Gram negative bacilli after 24 hours of incubation (Figure 1). The culture grew a moderate quantity of small nonhemolytic colonies that showed “pitting” appearance on blood (Figure 2) and chocolate (Figure 3) agar plates. The colonies notably smelled musty/bleachy. There was no growth on MacConkey agar.

Identification by Matrix-Assisted Laser Desorption Ionization – Time of Flight (MALDI-ToF) revealed Eikenella corrodens.

Discussion

Eikenella corrodens is a facultatively anaerobic, gram negative, oxidase positive, catalase negative, nonmotile, non-spore-forming, rod. It belongs to the HACEK group and is in the family Neisseriaceae. It is a part of the normal flora of the mouth and upper respiratory tract.

E. corrodens is an opportunistic pathogen that can lead to various infections including a variety of head and neck infections (ocular, mastoid, submandibular, thyroid), pleuropulmonary infections, skin and soft tissue infections, etc.). It can cause subcutaneous abscesses, cellulitis of soft tissues, and bacteremia in intravenous drugs users. E. corrodens also causes infections of the hand (i.e., ostomyelitis, cellulitis) because of chronic nail biting, human bite, or clenched-fist injury. The bacterium can gain access to the central nervous system by way of periodontal, middle ear, or sinus infections and cause meningitis, brain or spinal abscesses, subdural empyema, and osteomyelitis. In some predisposed individuals, endocarditis and bacteremia can also occur.

Under aerobic conditions, it grows slowly in blood and chocolate agar at 35–37℃ and does not grow on MacConkey Agar. It forms small, convex, round or irregular, gray, and non-hemolytic colonies. Most isolates may “pit” the agar although both pitting and non-pitting strains have similar biochemical characteristics. Most strains produce a musty or bleach-like odor.

E. corrodens is generally sensitive to ampicillin, amoxicillin, second- and third generation cephalosporins, tetracyclines, azithromycin, sulfamethoxazole, and fluoroquinolones. They are resistant to clindamycin, vancomycin, erythromycin, metronidazole, aminoglycosides, and penicillinase-resistant penicillins, with penicillin susceptibility varying from strain to strain. In clinical microbiology laboratories, the routine antimicrobial susceptibility testing for E. corrodens is not usually performed since it is generally responsive to beta-lactams. If necessary, susceptibility testing can be performed following the CLSI guidelines for fastidious organisms.

The disease spectrum of E. corrodens is increasing in complexity, and it is important to study its clinical characteristics for timely diagnosis, and effective treatment.

References

1. Chapter 9, Color Atlas and Textbook of Diagnostic Microbiology, Seventh Edition.
2. Li, L, Shi, Y-B, Weng, X-B. Eikenella corrodens infections in human: Reports of six cases and review of literatures. J Clin Lab Anal. 2022; 36:e24230. doi:10.1002/jcla.24230
3. Mühlhauser M. Eikenella corrodens. Rev Chilena Infectol. 2013. doi:10.4067/S0716-10182013000200007

-Fahad Sheikh is a 2^nd year AP/CP pathology resident in the Department of Pathology at Montefiore Medical Center in Bronx, NY.

-Phyu Thwe, Ph.D, D(ABMM), MLS(ASCP)^CM is Associate Director of Infectious Disease Testing Laboratory at Montefiore Medical Center, Bronx, NY. She completed her medical and public health microbiology fellowship in University of Texas Medical Branch (UTMB), Galveston, TX. Her interests includes appropriate test utilization, diagnostic stewardship, development of molecular infectious disease testing, and extrapulmonary tuberculosis.

Case Description

A 47 year old male presented to the emergency department with a two-week history of progressively worsening left-sided flank and abdominal pain with radiation to his back. He also endorsed associated nausea, vomiting, dizziness, lack of appetite, and a 1-month history of intermittent fever, chills, night sweats, cough, and chest pain. Patient history was also notable for travel throughout the Amazon basin in Peru and Colombia, then to Panama where he felt ill while hiking in the rainforest. He also had sustained injuries to his left flank and head while traveling.

Given his symptomology, further evaluation and management were undertaken. CBC showed a drop in hemoglobin from 10.3 g/dL to 8.5 g/dL, and imaging revealed splenomegaly with a caudally located subcapsular hematoma (Figure 1). Small hemoperitoneum on the pelvis with small non-loculated fluid along the bilateral paracolic gutters was also observed. The patient received two units of packed red blood cells to stabilize his hemoglobin levels.

Laboratory Diagnosis

Malaria smears were ordered given his history travel and evidence of anemia. Plasmodium vivax was identified on thin smear at a parasitemia of 0.1%. The Infectious Disease service was consulted and the patient received IV artesunate followed by oral artemether/lumefantrine and was also started on primaquine for hypnozoite eradication as he was not G6PD deficient. The malaria-associated splenic rupture was well managed with conservative treatment, and no surgical intervention was needed.

Discussion

Malaria is a severe and sometimes fatal tropical disease caused by Plasmodium sp. The World Health Organization (WHO) estimates 300-500 million humans suffer from malaria each year, of whom >1 million die.¹ Five species of Plasmodium cause human malaria: P. falciparum, P. malariae, P. vivax, P. ovale, and P. knowlesi. Patients with malaria initially present with a combination of non-specific symptoms such as fever, chills, headache, and general malaise. Moreover, it can cause various complications, including severe anemia, neurologic defects, nephrotic syndrome, hepatosplenomegaly, and even splenic rupture.

Splenic rupture is an infrequent but life-threatening complication of malaria. Due to a paucity of reported cases, the incidence of pathological splenic rupture in natural vector-transmitted malaria is poorly defined. Additionally, cases of splenic rupture in the setting of malaria are likely to be underreported due to a lack of diagnostic methods, especially in endemic regions.² One case series determined splenic rupture during malaria was fatal 22% of the collected cases, and it was likely to be the most frequent life-threatening issue of Plasmodium vivax infection reported worldwide.³ Similarly, P. vivax tends to cause more pronounced splenomegaly and a higher incidence of splenic rupture when compared to other Plasmodium species as noted in experimental and clinical studies.^2.4 However, the underlying mechanism is incompletely established.

The cause of splenic rupture in malaria infections is thought to be a complication of the macroscopic consequences of different microscopic infiltrative phenomena. Specificities of clotting regulation in the spleen red pulp and acute spleen-specific pooling/unpooling of platelets may lead to increase in intrasplenic tension, making the spleen prone to rupture.³ Although malaria-related splenic rupture is essentially a ‘pathological rupture’ in the absence of overt trauma, minor trauma can also be a triggering event, which possibly contributed to the splenic rupture in this case.

Malaria patients with splenic rupture may present with abdominal pain, hypotension, tachycardia, nausea, and vomiting, which can be difficult to distinguish from signs and symptoms of malaria. Referred left shoulder pain (Kehr sign) caused by diaphragmatic irritation from peri-splenic effusion may also occur. The physical examination can show left upper quadrant or diffuse abdominal tenderness, abdominal rigidity or guarding, and splenomegaly. Radiological studies (i.e., ultrasound or CT scan) play a critical role in diagnosing malaria-associated splenic rupture, and the main findings may include splenic enlargement, splenic tear, subcapsular/intrasplenic hematoma, peri-splenic effusion, and hemoperitoneum. Non-radiological workup by contrast (e.g., decreased hemoglobin/hematocrit level) is generally non-specific.

Management of malaria-associated splenic rupture generally follows the same principles as traumatic injuries. Early diagnosis and appropriate management are essential for a favorable prognosis. It is suggested that conservative treatment can be considered in patients with stable hemodynamics. However, the risk of delayed hemorrhage still exists, which makes strict monitoring crucial. Some data suggest surgical intervention should be considered a first-line treatment if tears involve the splenic hilum.⁵ Although it may be challenging to decide on surgery versus conservative strategy in clinical practice, there are several definitive surgical indications including signs of peritonitis and unstable hemodynamic status despite aggressive resuscitation. Of note, splenectomy may increase the risk of severe infection caused by encapsulated bacteria and complicated malaria; therefore, spleen-preserving procedures should be attempted in selected patients, such as frequent travelers to malarious regions.⁶

References

1. Guerra, C.A., et al., The limits and intensity of Plasmodium falciparum transmission: implications for malaria control and elimination worldwide. PLoS Med, 2008. 5(2): p. e38.
2. Zingman, B.S. and B.L. Viner, Splenic complications in malaria: case report and review. Clin Infect Dis, 1993. 16(2): p. 223-32.
3. Imbert, P., C. Rapp, and PA Buffet, Pathological rupture of the spleen in malaria: analysis of 55 cases (1958-2008). Travel Med Infect Dis, 2009. 7(3): p. 147-59.
4. Schmidt, L.H., Plasmodium falciparum and Plasmodium vivax infections in the owl monkey (Aotus trivirgatus). I. The courses of untreated infections. Am J Trop Med Hyg, 1978. 27(4): p. 671-702.
5. Fuks, D., et al., Spontaneous splenic rupture during a febrile crisis of Plasmodium falciparum malaria. J Chir (Paris), 2005. 142(6): p. 403-5.
6. Jimenez, B.C., et al., Spontaneous splenic rupture due to Plasmodium vivax in a traveler: case report and review. J Travel Med, 2007. 14(3): p. 188-91.

-Bo Zhang, MD is an AP/CP resident at UT Southwestern Medical Center in Dallas, Texas. He is a first year resident interested in different aspects of surgical pathology.

-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.

Case History

A middle-aged patient with a complex past medical history presented to the Emergency Department with the primary complaints of shortness of breath and cough. The patient had recently been admitted for community-acquired pneumonia and discharged with antibiotics 10 days ago. However, the patient continued to have a dry cough, a fever of 102 degrees F, and shortness of breath. On the new admission, they were noted to be hypotensive and labs showed elevated WBC (14.7), lactate of 7.3, proBNP of 852, and procalcitonin of 4.62. Bacterial blood cultures showed no growth. A chest x-ray showed worsening left lower lobe consolidation with extension to the left upper lobe, compared to the x-ray at the previous admission. A bronchoscopy was done and bronchoalveolar lavage (BAL) was submitted for Gram stain, aerobic bacterial culture, and fungal culture. The Gram stain and bacterial culture were negative. However, the fluorochrome stain showed many large budding yeast forms, most suggestive of Blastomyces dermatitidis. Lung tissue sample culture (Image 1), Gram stain (Image 2) and histopathology (Image 3) confirmed the identification as Blastomyces dermatitidis. The patient was expired before the results were released. Gross images of lungs are shown in image 4.

Discussion

Blastomyces dermatitidis is a dimorphic fungus found in soil and decaying wood. Often found in areas close to a water source such as a lake, river, or stream.¹ The fungus is endemic to parts of the United States, including parts of the Appalachian Mountains, the Great Lakes, and the Ohio and Mississippi River Valley.¹ Human infection occurs when airborne conidia are inhaled. Blastomycosis (aka Gilchrist’s disease) may cause a broad range of clinical presentations. The most affected organs are the lungs and the skin.² Osseous, genitourinary, central nervous system (CNS), and disseminated blastomycosis can also be seen, but at a lower frequency.² Unlike opportunistic fungal pathogens such as H. capsulatum, C. immitis, and C. neoformans, B. dermatitidis no more likely to cause disease in immunocompromised population compared to the non-immunocompromised populatin.³ However, the disease is more severe, with higher morbidity and mortality, and more likely to be disseminated in immunocompromised patients.³

Although growth of fungi took 2 days in our case, Blastomyces is a slow growing fungi in that mycelial forms mature in 14-21 days. In suspicious cases, cultures should be hold up to 8 weeks. Furthermore, Blastomyces should be cultured as soon as possible since it does not survive well in samples. Morphologically, Blastomyces colony appears as a mold, which is white, prickly, and cottony at 25-30 °C However, at 35-37 °C, the colony appears as a yeast, which is tan, wrinkled, and waxy. Microscopically, at 37 °C, Blastomyces appear as round to oval cells with refractile and thick cell walls and measure 8 – 15 uM in diameter. Each yeast cell produces only one, broad-based (4-5 uM), bud. At 25-30 °C, septate hyphae form with short or long conidiophores. Round to pear-shaped conidia attach to the apex, resembling lollipops (Image 5).⁴

History of recent travel to the endemic areas or already living in there usually triggers the suspicion with clinical findings. There are different auxiliary diagnostic modalities for B. dermatitidis including culture, cytology smear, histopathology, urine antigen test, serum antigen test, serum antibody test, and molecular techniques. Serum antibody test exhibits high degree of cross-reactivity with other endemic mycoses.⁵ Serum and urine antigen testing has a sensitivity of 89 % and specificity of 79 % and it is useful in diagnosis, monitoring treatment, and detecting recurrence.^5,6,7 Direct visualization of the distinctive yeast form with broad-based budding on a cytology smear of respiratory secretions or tissue samples using fluorochrome stain is considered as presumptive diagnosis and enough for initiation of antifungal therapy. However, a negative result in smear cannot exclude the diagnosis due to lack of sensitivity. Polymerase chain reaction (PCR) based assays have been developed to detect B. dermatitidis.⁸ However, although they are promising, utility has not been confirmed and there are no FDA approved assays.⁸

Only histopathology and culture can provide a definitive diagnosis. Although H&E may be enough in selected cases, periodic acid-Schiff (PAS) and Grocott’s methenamine silver (GMS) stains are useful to highlight the yeast form in tissue sections. In culture, seeing the characteristic morphologic and microscopic appearance is very useful for diagnosis. However, confirmatory testing with chemiluminescent DNA probe may still be necessary.⁹

Depending on the severity and site of the infection fluconazole, itraconazole, voriconazole, or amphotericin B can be used in treatment.¹⁰

References

1. Castillo CG, Kauffman CA, Miceli MH. Blastomycosis. Infect Dis Clin North Am. 2016;30(1):247-264.
2. Mazi PB, Rauseo AM, Spec A. Blastomycosis. Infect Dis Clin North Am. 2021;35(2):515-530.
3. McBride JA, Gauthier GM, Klein BS. Clinical Manifestations and Treatment of Blastomycosis. Clin Chest Med. 2017;38(3):435-449.
4. Maresca B, Kobayashi GS. Dimorphism in Histoplasma capsulatum and Blastomyces dermatitidis. Contrib Microbiol. 2000;5:201-216.
5. Wheat LJ. Antigen detection, serology, and molecular diagnosis of invasive mycoses in the immunocompromised host. Transpl Infect Dis. 2006;8(3):128-139.
6. Mongkolrattanothai K, Peev M, Wheat LJ, Marcinak J. Urine antigen detection of blastomycosis in pediatric patients. Pediatr Infect Dis J. 2006;25(11):1076-1078.
7. Tarr M, Marcinak J, Mongkolrattanothai K, et al. Blastomyces antigen detection for monitoring progression of blastomycosis in a pregnant adolescent. Infect Dis Obstet Gynecol. 2007;2007:89059.
8. Bariola JR, Hage CA, Durkin M, et al. Detection of Blastomyces dermatitidis antigen in patients with newly diagnosed blastomycosis. Diagn Microbiol Infect Dis. 2011;69(2):187-191.
9. Saccente M, Woods GL. Clinical and laboratory update on blastomycosis. Clin Microbiol Rev. 2010;23(2):367-381.
10. Chapman SW, Dismukes WE, Proia LA, et al. Clinical practice guidelines for the management of blastomycosis: 2008 update by the Infectious Diseases Society of America. Clin Infect Dis. 2008;46(12):1801-1812.

-Kadir Isidan, MS, MD is a pathology resident at University of Chicago (NorthShore). His academic interests include gastrointestinal pathology and cytopathology.

-Paige M.K. Larkin, PhD, D(ABMM), M(ASCP)^CM is the Director of Molecular Microbiology and Associate Director of Clinical Microbiology at NorthShore University HealthSystem in Evanston, IL. Her interests include mycology, mycobacteriology, point-of-care testing, and molecular diagnostics, especially next generation sequencing.

Case History

A 40-year-old woman with past medical history of polysubstance use disorder (cocaine, IVDU-heroin) presented with shortness of breath on exertion, weight loss, and weakness. Cardiac ultrasound showed aortic valve endocarditis with mild thickening of the aortic valve, vegetation and severe aortic regurgitation without stenosis. The patient was taken to the operating room for aortic valve replacement. A tissue biopsy was sent for surgical pathology workup and microbiology cultures. H&E staining of the right and left coronary cusp and noncoronary cusp and showed focal giant cell reaction, and acute inflamed granulation tissue consistent with vegetation/infective endocarditis. The Gram stain of the tissue specimen revealed gram positive cocci but no bacterial growth was seen. Fungal and mycobacterial cultures were also negative. Broad Range Bacterial PCR and Sequencing (BRBPS) of the heart valve detected Streptococcus mutans.

Discussion

The first step of BRBPS is performing polymerase chain reaction (PCR) targeting the 16S ribosomal RNA (rRNA), a conserved gene across many bacterial species including mycobacteria. If PCR is negative, then sequencing is not performed but if PCR is positive, sequencing such as Sanger sequencing or Next generation sequencing will be followed. Subsequent bioinformatics analysis of the sequencing results will allow identification of the specific bacteria.^1,2 In the patient here, the PCR for 16S rRNA was positive and sequencing revealed S. mutans.

S. mutans is part of the viridans-group of Streptococcus and can be identified as a gram positive cocci with growth that is alpha-hemolytic, optochin resistant, and bile insoluble. Viridans group Streptococcus invade the bloodstream following dental treatment or dental procedures and can be associated with high risk for infectious endocarditis in patients with underlying heart disorders. S. mutans first gained medical attention due to its role in dental caries.³ S. mutans is considered part of the normal flora of the oropharynx, more specifically the dental plaque, and can form biofilms on the hard surface of the tooth. Bacterial strains that cause endocarditis have been shown to be able to bind to type I, III, and IV collagen, which are major components of the host cardiovascular tissues.⁴ The bacteria also have virulence factors that can cause strong adhesion to human endothelial cells. Additionally, aggregation and interaction with fibrinogen, platelets, and completement allow this bacteria to successfully cause cardiovascular diseases.⁵  

In infective endocarditis, 20% of the cases are negative by conventional methods such microbiology cultures.⁶ Several studies have shown that in specimens from patients with endocarditis, 16s rRNA sequencing can correctly detect the organism that was grown in culture but also successfully detect organisms in specimens where there was no growth, allowing clinical teams to accurately treat patients, similar to our case here.^7,8 For prosthetic heart valve tissue, the sensitivity of sequencing versus culture is 93% and 35%, respectively. A study describing periprosthetic joint infections using elbow joint fluids showed that sequencing was positive in 47 specimens but 8% of those were negative by culture.¹⁰ Additionally, 16s rRNA sequencing has been useful in identifying bacterial tick-borne organisms not typically grown in culture such as Borrelia, Anaplasmsa, Ehrlichia, and Rickettsia].¹¹

The BRBPS test is validated for and ideally be tested on specimens from sterile sources (joint fluid, blood, heart valves, CSF) and ideal specimens are those where bacterial organisms can be visualized using microscopy. Limitations of BRBPS is that this test only detects bacterial organisms and will not detect viruses, fungi, and parasites. False-positive results are possible if the specimen is contaminated with patient flora. False-negative results may occur due to sequence variability affecting how the primers bind, presence of PCR inhibitors, or the quantity of nucleic acid material below the limit of detection. Clinical tests utilizing sequencing approaches may be costly at the moment in time; those who order sequencing tests need to understand the purpose of different sequencing tests so the most appropriate test is ordered. For example, if fungal pathogens are suspected, a sequencing test based on amplifying 28S rRNA or ribosomal ITS genes for the conserved genes found in fungal pathogens is appropriate.¹² Such tests where you selectively enrich for specific targets such as 16s or ITS are ‘targeted NGS tests’ which have higher sensitivity for detection of microorganisms in sample types with large amounts of DNA. In comparison, metagenomics is a more agnostic approach and allows for detection of all nucleic acid in the specimen (including both host and microbial reads). While metagenomics can successfully detect pathogens involved in an infection, it can also detect the microbiome present in the same specimen. Hence, the one limitation is the background noise from human nucleic acid and the microflora [13-14. Another type of sequencing is whole genome sequencing where the microbial genome of a particular organism is sequenced and assembled. WGS aids in identification, typing, and determining the microbial susceptibility. WGS is helpful in identifying outbreaks or for epidemiological purposes, but the limitation is that a pure culture is needed. WGS requires a pure culture so this is a limitation for organisms that are non-viable in culture [13-14].

References

1. Rosey AL, Abachin E, Quesnes G, Cadilhac C, Pejin Z, Glorion C, Berche P, Ferroni A. Development of a broad range 16S rDNA real-time PCR for the diagnosis of septic arthritis in children. J Microbiol Methods. 2007 Jan;68(1):88-93. doi: 10.1016/j.mimet.2006.06.010. Epub 2006 Aug 14. PMID: 16904782.
2. Broad Range Bacterial PCR and Sequencing, Varies. Mayo Clinic Laboratories. https://www.mayocliniclabs.com/test-catalog/Overview/65058
3. Loesche WJ. 1986. Role of Streptococcus mutans in human dental decay. Microbiol Rev 50:353–380.
4. Nomura R, Naka S, Nemoto H, Inagaki S, Taniguchi K, Ooshima T, Nakano K. 2013. Potential involvement of collagen-binding proteins of Streptococcus mutans in infective endocarditis. Oral Dis 19:387–393. doi: 10.1111/odi.12016.
5. Otsugu, M., Nomoura R., Matayoshi, S., Teramoto, N., Nakanoa, K. Contribution of Streptococcus mutans Strains with Collagen-Binding Proteins in the Presence of Serum to the Pathogenesis of Infective Endocarditis. Infect Immun. 2017 Dec; 85(12): e00401-17.
6. Baddour LM at al; American Heart Association Committee on Rheumatic Fever, Endocarditis, and Kawasaki Disease of the Council on Cardiovascular Disease in the Young, Council on Clinical Cardiology, Council on Cardiovascular Surgery and Anesthesia, and Stroke Council. Infective Endocarditis in Adults: Diagnosis, Antimicrobial Therapy, and Management of Complications: A Scientific Statement for Healthcare Professionals from the American Heart Association. Circulation. 2015 Oct 13;132(15)
7. Peeters, B., Herijgers, P., Beuselinck, K., Verhaegen, J., Peetermans, W.E., Herregods, M.-C., Desmet, S., Lagrou, K. Addd diagnostic value and impact on antimicrobial therapy of 16s rRNA PCR and amplicon sequencing on resected heart valves in infective endocarditis: a prospective cohort study. Clinical Microbiology and Infection. 2017 Nov; 23(11): 888.e1-888.e5
8. Premru, M.M, Zupanc, T.L., Klokocovnik, T., Sabljic, E.R., Cerar, T. Broad-Range 16s rRNA PCR on Heart Valves in Infective Endocarditis. J Heart Valve Dis. 2016 Mar; 25(2):221-22
9. Miller, R. J.H., Chow, B., Pillai, D., Church, D. Development and evaluation of a novel fast broad-range 16S ribosomal DNA PCR and sequencing assay for diagnosis of bacterial infective endocarditis: multi-year experience in a large Canadian healthcare zone and a literature review. BMC Infect Dis. 2016 April 12:16:146
10. Flurin, L.; Wolf, M.J.; Greenwood-Quaintance, K.E.; Sanchez-Sotelo, J.; Patel, R. Targeted next generation sequencing for elbow periprosthetic joint infection diagnosis. Diagn. Microbiol. Infect. Dis. 2021, 101, 115448.
11. Kingry, L.; Sheldon, S.; Oatman, S.; Pritt, B.; Anacker, M.; Bjork, J.; Neitzel, D.; Strain, A.; Berry, J.; Sloan, L.; et al. Targeted Metagenomics for Clinical Detection and Discovery of Bacterial Tick-Borne Pathogens. J. Clin. Microbiol. 2020, 58, e00147-20.
12. Yeo, S.F.; Wong, B. Current status of nonculture methods for diagnosis of invasive fungal infections. Clin. Microbiol. Rev. 2002, 15, 465–484.
13. Mitchell SL, Simner PJ. Next-Generation Sequencing in Clinical Microbiology: Are We There Yet? Clin Lab Med. 2019 Sep;39(3):405-418
14. Hilt, E.E., Ferrieri, P. Next Generation and Other Sequencing Technologies in Diagnostic Microbiology and Infectious Diseases. Genes (Basel). 2022 Aug 31;13(9):1566. doi: 10.3390/genes13091566.

–Rami Abdulbaki, MD is a Pathology Resident (PGY-4) at The George Washington University Hospital. His academic interest includes hematopathology and molecular pathology.

-Maikel Benitez Barzaga, MD is a Pathology Resident (PGY-2) at The George Washington University Hospital. His academic interest include hematology, microbiology, molecular and surgical pathology.

–Rebecca Yee, PhD, D(ABMM), M(ASCP)^CM is the Chief of Microbiology, Director of Clinical Microbiology and Molecular Microbiology Laboratory at the George Washington University Hospital. Her interests include bacteriology, antimicrobial resistance, and development of infectious disease diagnostics.

Microbiology Case: Lung nodules in a patient undergoing lung transplant evaluation

Case History 

A 71-year-old male with a past medical history of severe interstitial lung disease (ILD) presented for lung transplant evaluation. His chest CT demonstrated findings consistent with his known diagnosis of ILD, along with a 3.6 cm focal nodular calcific density near the right costophrenic angle, and additional scattered calcified lung nodules measuring up to 3 mm. Sputum cultures were obtained to evaluate the CT findings.

Laboratory Identification

Routine bacterial, fungal, and AFB sputum testing was performed.  No AFB were recovered, and a mixture of bacteria consistent with oral flora were found on blood, chocolate and MacConkey agars.  The fungal culture grew a moderate amount of round, non-hyphenated yeast which were encapsulated, urease-positive and reacted with caffeic acid (Image 1A and 1B) consistent with Cryptococcus species.  The organism was definitively identified as Cryptococcus gattii by MALDI-TOF mass spectrometry, which was subsequently confirmed by growth and the appearance of a deep blue color on Canavanine Glycine Bromothymol Blue (CGB) agar (Image 1C).  The patient was prescribed daily fluconazole to take daily for 6 months, and underwent a successful bilateral transplant two months after treatment initiation.

Discussion

Cryptococci are important pathogens of both immunocompetent and immunocompromised hosts.  While Cryptococcus neoformans causes most human cryptococcal disease, Cryptococcus gattii is also a clinically important cause of infections.  Though genetically similar, these two species exhibit important differences with respect to ecological niche, pathogenesis, and epidemiology.  Historically, trees (specifically eucalyptis) have been identified as environmental reservoirs of C. gattii, while C. neoformans is associated with pigeon guano.¹  Cryptococcus neoformans has a worldwide distrubtion, while C. gattii is thought to be geographically restricted to Australia, Western Canada and the Pacific Northwest of the United States, although this has become less clear in recent years.  Indeed, the patient in this case had not traveled to any of these locales; instead, he is from the southeastern United States, where the organism may be endemic.³

                There is an established association between C. gattii and infections in immunocompetent hosts, and recent evidence points to genetic and immunological factors which predispose some individuals to C. gattii infection.  Possible differences in clinical course and patient outcomes have been suggested to justify differentiation between C. gattii and C. neoformans in laboratory settings.  Importantly, routine laboratory methods such as commercial biochemical identification systems, morphological observations, and cryptococcal antigen testing lack the discriminatory power to distinguish these species.²  By contrast, MALDI-TOF MS and molecular methods, including some molecular panels performed on positive blood culture bottles, are able to discriminate between C. gattii and C. neoformans.  The use of glycine as a sole carbon and nitrogen source in the presence of canavanine allows biochemical differentiaton through the use of CGB agar.  The degredtation of L-canavanine to ammonia in the presence of glycine by C. gattii raises the pH and results in associated color change, while C. neoformans remains a yellow or green color (Image 1C).  While robust, this incubation can take up  to five days resulting in prolonged turn around times.²

Cryptococal infection begins through inhalation of the organism into the lungs, where the yeast then can dissemisate to other anatomical sites.  When compared to C. neoformans, C. gattii is less likely to present with central nervous system (CNS) involvement but exhibts a higher incidence of imaging abnormalities and mass lesions.  In pulmonary settings, C. neoformans infections commonly present with infiltrates while C. gattii infections are nodular² as seen in this case.  Irrespective of the species involved, cryptococcal infections can be asymptomatic or classically present as a meningoencephalitis, chronic or acute pneumonia, or in a number of cutaneous manifestations.  Fluconazole is the drug of choice for management of asymptomatic or mild to moderate pulmonary infections. Despite the removal of the infected lungs, it was determined that the patient should complete the entire six month course of fluconazole due to his immunosuppression post-transplant.

References

1. Beardsley, J., Dao, A., Keighley, C., Garnham, K., Halliday, C., Chen, S. C.-A., and Sorrell, T.C.  What’s New in Cryptococcus gattii: From Bench to Bedside and Beyond.  J. Fungi. 2023; 9, 41:1-16.
2. Butler-Wu, S. and Limaye, A.P.  Guideline: A Quick Guide to the Significance and Laboratory Identification of Cryptococcus gattii.  American Society for Microbiology. 2011.  https://asm.org/Guideline/A-Quick-Guide-to-the-Significance-and-Laboratory-I  Accessed: February 1^st, 2023.
3. Lockhart, S., Roe, C. C., and Engelthaler, D.M.  Whole-Genome Analysis of Cryptococcus gattii, Southeastern United States.  Emerg. Infect. Dis. 2016 Jun; 22(6): 1098-1101.

-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.

-Francesca Lee, MD, is an associate professor in the Departments of Pathology and Internal Medicine (Infectious Diseases) at UT Southwestern Medical Center

-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.