Amplification of coccidioidal DNA in clinical specimens by PCR

A multicentre external quality assessment: A first step to standardise PCR protocols for the diagnosis of histoplasmosis and coccidioidomycosis

BACKGROUND

In-house real-time PCR (qPCR) is increasingly used to diagnose the so-called endemic mycoses as commercial assays are not widely available.

OBJECTIVES

To compare the performance of different molecular diagnostic assays for detecting Histoplasma capsulatum and Coccidioides spp. in five European reference laboratories.

METHODS

Two blinded external quality assessment (EQA) panels were sent to each laboratory that performed the analysis with their in-house assays. Both panels included a range of concentrations of H. capsulatum (n = 7) and Coccidioides spp. (n = 6), negative control and DNA from other fungi. Four laboratories used specific qPCRs, and one laboratory a broad-range fungal conventional PCR (cPCR) and a specific cPCR for H. capsulatum with subsequent sequencing.

RESULTS

qPCR assays were the most sensitive for the detection of H. capsulatum DNA. The lowest amount of H. capsulatum DNA detected was 1-4 fg, 0.1 pg and 10 pg for qPCRs, specific cPCR and broad-range cPCR, respectively. False positive results occurred with high concentrations of Blastomyces dermatitidis DNA in two laboratories and with Emergomyces spp. in one laboratory. For the Coccidioides panel, the lowest amount of DNA detected was 1-16 fg by qPCRs and 10 pg with the broad-range cPCR. One laboratory reported a false positive result by qPCR with high load of Uncinocarpus DNA.

CONCLUSION

All five laboratories were able to correctly detect H. capsulatum and Coccidioides spp. DNA and qPCRs had a better performance than specific cPCR and broad-range cPCR. EQAs may help standardise in-house molecular tests for the so-called endemic mycoses improving patient management.

Diagnosis of Pulmonary Infections Due to Endemic Fungi

Endemic mycoses including Histoplasma, Blastomyces, Coccidioides, Paracoccidioides, and Talaromyces are dimorphic fungi that can cause a variety of clinical manifestations, including respiratory infections. Their pulmonary presentations are variable, and diagnosis is often delayed as they can mimic other infectious and non-infectious causes of pulmonary disease. Delay in diagnosis can lead to unnecessary antibiotic use, repeat hospitalizations, and increased morbidity and mortality. The diagnosis of endemic fungal pulmonary infections often relies on multiple diagnostic tests including culture, tissue histopathology, antigen assays, and antibody assays. Due to the increased use of immunosuppressive agents and the widening geographic ranges where these infections are being found, the prevalence of endemic fungal infections is increasing. Physicians need to be aware of the clinical manifestations of pulmonary infections due to endemic fungal in order to ensure that the proper diagnostic work up is obtained promptly. A high index of suspicion is particularly important in patients with suspected pulmonary infections who have failed to improve despite antibiotics in the appropriate setting. We present a review diagnostic testing for pulmonary infections due to endemic mycoses.

Disseminated coccidioidomycosis: Monitoring of serologic markers for treatment response

We describe a patient with a disseminated coccidioidomycosis. Biomarkers in serum during itraconazole therapy showed a rapid clearing of Coccidioides DNA as detected by PCR. Coccidioides antibody detection by lateral flow assay became negative after one year and decreased from 1:64 to 1:8 in the complement fixation test after two years. The (1 → 3)-ß-D-glucan levels normalised after two years without increase after cessation of antifungal therapy. Biomarkers in serum may guide treatment decisions in disseminated coccidioidomycosis.

Infectious Lung Disease

Infectious diseases are one of the main causes of morbidity and mortality worldwide. With new pathogens continuously emerging, known infectious diseases reemerging, increasing microbial resistance to antimicrobial agents, global environmental change, ease of world travel, and an increasing immunosuppressed population, recognition of infectious diseases plays an ever-important role in surgical pathology. This becomes particularly significant in cases where infectious disease is not suspected clinically and the initial diagnostic workup fails to include samples for culture. As such, it is not uncommon that a lung biopsy becomes the only material available in the diagnostic process of an infectious disease. Once the infectious nature of the pathological process is established, careful search for the causative agent is advised. This can often be achieved by examination of the hematoxylin and eosin-stained sections alone as many organisms or their cytopathic effects are visible on routine staining. However, ancillary studies such as histochemical stains, immunohistochemistry, in situ hybridization, or molecular techniques may be needed to identify the organism in tissue sections or for further characterization, such as speciation.

Coccidioidomycosis in pregnancy: Case report and literature review of associated placental lesions

BACKGROUND

Coccidioidomycosis is an endemic fungal infection found most commonly in the Southwestern United States, Northwestern Mexico, and parts of Central and South America. Although infection is relatively uncommon during pregnancy, it is imperative to have an index of suspicion in order to diagnose and begin timely treatment to prevent dissemination and dire consequences.

CASE REPORT

A 33-year-old Hispanic female was evaluated after she was involved in an automobile accident. Radiographic evaluation showed a 3.2 × 3.2 cm cavitary thick-walled lesion. A biopsy was negative for malignancy. Evaluation was positive for coccidioidomycosis by complement fixation reaction. Four months later, the patient presented 7 weeks into a pregnancy with massive hemoptysis. Bronchoscopy revealed bleeding from the right upper lobe and emergency embolization was performed. The patient had a spontaneous abortion 9 days after admission. The right upper and middle lobes of the lung were resected due to continuous bleeding. A subsequent pregnancy was un-eventful. Coccidioidomycosis titers remained negative throughout the second pregnancy.

DISCUSSION

This case demonstrates the potential for severe pulmonary coccidioidomycosis and vascular strain of pregnancy-associated vascular expansion in the first trimester of pregnancy and the possibility of a favorable pregnancy outcome in subsequent pregnancies after appropriate treatment. The route of feto-maternal transmission and placental lesions in coccidioidomycosis are discussed.

Cutaneous, Subcutaneous and Systemic Mycology

The first description of dermatophytosis was recorded by Celsus, a Roman encyclopaedist who described a suppurative infection of scalp (‘porrigo’ or ‘kerion of Celsus’) in De Re Medicina (30 A.D.). Throughout the middle ages, several descriptions of dermatophytosis were produced where it is described as ‘tinea’. The keratin-destroying moths which made circular holes in the woollen garments are known as Tinea. Due to similarity in the structure of circular lesion of dermatophytosis on the smooth skin with the circular hole made by moth, Cassius Felix introduced the term ‘tinea’ to describe the lesions. In 1806, Alibert used the term ‘favus’ to describe the honey-like exudate in some scalp infections. However, the fungal aetiology of tinea was first detected by Robert Remak, a Polish physician who first observed the presence of hyphae in the crusts of favus. This detection is also a landmark in medical history because this is the first description of a microbe causing a human disease. He himself did not publish his work, but he permitted the reference of his observations in a dissertation by Xavier Hube in 1837. Remak gave all the credits of his discovery to his mentor Schoenlein who first published the fungal etiological report of favus in 1839. He observed the infectious nature of the favus by autoinoculation into his own hands and also successfully isolated the fungus later (1945) and named Achorion schoenleinii (Trichophyton schoenleinii) in honour of his mentor. In 1844, Gruby described the etiologic agent of tinea endothrix, later became known as Trichophyton tonsurans. The genus Trichophyton was created and described by Malmsten (1845) with its representative species T. tonsurans. Charles Robin identified T. mentagrophytes in 1847 and T. equinum was identified by Matruchot and Dassonville in 1898. Raymond Jacques Adrien Sabouraud (France) first compiled the description of Trichophyton in his book (Les Teignes) in 1910 which was based on his observation in artificial culture. The sexual state of dermatophyte was described by Nannizzi (1927). Emmons (1934) first reported the classification of dermatophytes based on vegetative structures and conidia. Gentles (1958) established the successful treatment of tinea capitis with griseofulvin.

Recent advances in our understanding of the environmental, epidemiological, immunological, and clinical dimensions of coccidioidomycosis

Coccidioidomycosis is the endemic mycosis caused by the fungal pathogens Coccidioides immitis and C. posadasii. This review is a summary of the recent advances that have been made in the understanding of this pathogen, including its mycology, genetics, and niche in the environment. Updates on the epidemiology of the organism emphasize that it is a continuing, significant problem in areas of endemicity. For a variety of reasons, the number of reported coccidioidal infections has increased dramatically over the past decade. While continual improvements in the fields of organ transplantation and management of autoimmune disorders and patients with HIV have led to dilemmas with concurrent infection with coccidioidomycosis, they have also led to advances in the understanding of the human immune response to infection. There have been some advances in therapeutics with the increased use of newer azoles. Lastly, there is an overview of the ongoing search for a preventative vaccine.

Molecular markers in the epidemiology and diagnosis of coccidioidomycosis

The prevalence of coccidioidomycosis in endemic areas has been observed to increase daily. To understand the causes of the spread of the disease and design strategies for fungal detection in clinical and environmental samples, scientists have resorted to molecular tools that allow fungal detection in a natural environment, reliable identification in clinical cases and the study of biological characteristics, such as reproductive and genetic structure, demographic history and diversification. We conducted a review of the most important molecular markers in the epidemiology of Coccidioides spp. and the diagnosis of coccidioidomycosis. A literature search was performed for scientific publications concerning the application of molecular tools for the epidemiology and diagnosis of coccidioidomycosis. The use of molecular markers in the epidemiological study and diagnosis of coccidioidomycosis has allowed for the typing of Coccidioides spp. isolates, improved understanding of their mode of reproduction, genetic variation and speciation and resulted in the development specific, rapid and sensitive strategies for detecting the fungus in environmental and clinical samples. Molecular markers have revealed genetic variability in Coccidioides spp. This finding influences changes in the epidemiology of coccidioidomycosis, such as the emergence of more virulent or antifungal resistant genotypes. Furthermore, the molecular markers currently used to identify Coccidioides immitis and Coccidioides posadasii are specific and sensitive. However, they must be validated to determine their application in diagnosis. This manuscript is part of the series of works presented at the "V International Workshop: Molecular genetic approaches to the study of human pathogenic fungi" (Oaxaca, Mexico, 2012).

Molecular diagnosis of endemic and invasive mycoses: advances and challenges

The diagnosis of endemic and invasive fungal disease remains challenging. Molecular techniques for identification of fungi now play a significant and growing role in clinical mycology and offer distinct advantages as they are faster, more sensitive and more specific. The aim of this mini-review is to provide an overview of the state of the art of molecular diagnosis of endemic and invasive fungal diseases, and to emphasize the challenges and current need for standardization of the different methods. The European Aspergillus PCR Initiative (EAPCRI) has made significant progress in developing a standard for Aspergillus polymerase chain reaction (PCR), but recognizes that the process will not be finished until clinical utility has been established in formal and extensive clinical trials. Similar efforts should be implemented for the diagnosis of the other mycoses in order to fully validate the current methods or reinforce the need to design new ones. This manuscript is part of the series of works presented at the "V International Workshop: Molecular genetic approaches to the study of human pathogenic fungi" (Oaxaca, Mexico, 2012).

Coccidioidomycosis: adenosine deaminase levels, serologic parameters, culture results, and polymerase chain reaction testing in pleural fluid

BACKGROUND

In a patient with positive serum serology for coccidioidomycosis, the differential diagnosis of concurrent pleural effusions can be challenging. We, therefore, sought to clarify the performance characteristics of biochemical, serologic, and nucleic-acid-based testing in an attempt to avoid invasive procedures. The utility of adenosine deaminase (ADA), coccidioidal serology, and polymerase chain reaction (PCR) in the evaluation of pleuropulmonary coccidioidomycosis has not been previously reported.

METHODS

Forty consecutive patients evaluated for pleuropulmonary coccidioidomycosis were included. Demographic data, pleural fluid values, culture results, and clinical diagnoses were obtained from patient chart review. ADA testing was performed by ARUP Laboratories, coccidioidal serologic testing was performed by the University of California-Davis coccidioidomycosis serology laboratory, and PCR testing was performed by the Translational Genomics Research Institute using a previously published methodology.

RESULTS

Fifteen patients were diagnosed with pleuropulmonary coccidioidomycosis by European Organization for the Research and Treatment of Cancer/Mycoses Study Group criteria. Pleural fluid ADA concentrations were < 40 IU/L in all patients (range, < 1.0-28.6 IU/L; median, 4.7). The sensitivity and specificity of coccidioidal serologic testing was 100% in this study. The specificity of PCR testing was high (100%), although the overall sensitivity remained low, and was comparable to the experience of others in the clinical use of PCR for coccidioidal diagnostics.

CONCLUSION

Contrary to prior speculation, ADA levels in pleuropulmonary coccidioidomycosis were not elevated in this study. The sensitivity and specificity of coccidioidal serologic testing in nonserum samples remained high, but the clinical usefulness of PCR testing in pleural fluid was disappointing and was comparable to pleural fluid culture.

Viability and molecular authentication of Coccidioides spp. isolates from the Instituto de Medicina Tropical de São Paulo culture collection, Brazil

Coccidioidomycosis is an emerging fungal disease in Brazil; adequate maintenance and authentication of Coccidioides isolates are essential for research into genetic diversity of the environmental organisms, as well as for understanding the human disease. Seventeen Coccidioides isolates maintained under mineral oil since 1975 in the Instituto de Medicina Tropical de São Paulo (IMTSP) culture collection, Brazil, were evaluated with respect to their viability, morphological characteristics and genetic features in order to authenticate these fungal cultures. Only five isolates were viable after almost 30 years, showing typical morphological characteristics, and sequencing analysis using Coi-F and Coi-R primers revealed 99% identity with Coccidioides genera. These five isolates were then preserved in liquid nitrogen and sterile water, and remained viable after two years of storage under these conditions, maintaining the same features.

Biochemical characterization of an in-house Coccidioides antigen: perspectives for the immunodiagnosis of coccidioidomycosis

The objective of this study was to evaluate the reactivity of an in-house antigen, extracted from a strain of C. posadasii isolated in northeastern Brazil, by radial immunodiffusion and Western blotting, as well as to establish its biochemical characterization. The protein antigen was initially extracted with the use of solid ammonium sulfate and characterized by 1-D electrophoresis. Subsequently, it was tested by means of double radial immunodiffusion and Western blotting. A positive reaction was observed against the antigen by both immunodiagnostic techniques tested on sera from patients suffering from coccidioidomycosis. Besides this, two immunoreactive protein bands were observed and were revealed to be a β-glucosidase and a glutamine synthetase after sequencing of the respective N-terminal regions. Our in-house Coccidioides antigen can be promising as a quick and low-cost diagnostic tool without the risk of direct manipulation of the microorganism.

The public health impact of coccidioidomycosis in Arizona and California

The numbers of reported cases of coccidioidomycosis in Arizona and California have risen dramatically over the past decade, with a 97.8% and 91.1% increase in incidence rates from 2001 to 2006 in the two states, respectively. Of those cases with reported race/ethnicity information, Black/African Americans in Arizona and Hispanics and African/Americans in California experienced a disproportionately higher frequency of disease compared to other racial/ethnic groups. Lack of early diagnosis continues to be a problem, particularly in suspect community-acquired pneumonia, underscoring the need for more rapid and sensitive tests. Similarly, the inability of currently available therapeutics to reduce the duration and morbidity of this disease underscores the need for improved therapeutics and a preventive vaccine.

The diagnosis of coccidioidomycosis

Until recently, culture, microscopy, and serology have been the available methods for the diagnosis of coccidioidomycosis. While Coccidioides is frequently isolated by culture, special precautions must be taken because of the risk of laboratory infection and because Coccidioides is on the Select Agent list. Serology is useful but the sensitivity remains lower than desired. A commercially available test for coccidioidal galactomannan antigenuria now exists and appears useful for immunocompromised hosts with severe disease. Polymerase chain reaction assays targeting specific coccidioidal genes have demonstrated utility but are not commercially available. Moreover, their sensitivity and the best sample type remain unestablished.

Laboratory Aspects in the Diagnosis of Coccidioidomycosis

Coccidioides immitis and Coccidioides posadasii, the two recognized causes of coccidioidomycosis, may be detected by direct microscopy, culture, and serologic documentation. Two useful stains include the Grocott methenamine silver (GMS) and the calcofluor white (CFW). Other useful stains used in histopathologic studies include hematoxylin-eosin (H&E) and periodic acid Schiff (PAS). Nucleic acid amplification tests (NAATs) have been introduced for detection of Coccidioides spp. in specimens, but are not yet commercially available. Isolation of Coccidioides spp. by culture is not difficult as many fungal as well as routine bacteriologic media are available. For the safe isolation of Coccidioides spp., the laboratory should maintain a biological safety level 2 or 3. Identification of Coccidioides spp. uses the organisms' phenotypic or genotypic characteristics. Phenotypic identification to genus level may be achieved by visualization of spherules in specimens and/or by the presence of arthroconidia in culture. Isolates may be confirmed as Coccidioides spp. by molecular probes. Separation of species into C. immitis and C. posadasii is best achieved by specialized molecular techniques which are not normally available in routine clinical laboratories. Humoral antibodies can be used for the diagnosis and prognosis of coccidioidomycosis. Although positive serologic results may be helpful in the diagnosis of coccidioidomycosis, negative serologic results cannot be used to rule out the disease. Enzyme immunoassays (EIA) and immunodiffusion methods are commonly used for detection of both IgM and IgG antibody groups. Sequential complement fixation (CF) studies for IgG class of antibody are useful for the prognosis of coccidioidomycosis.

Serologic testing for symptomatic coccidioidomycosis in immunocompetent and immunosuppressed hosts

Serologic studies are an important diagnostic tool in the clinical evaluation and follow-up of persons with coccidioidomycosis. Numerous types of serologic tests are available, including immunodiffusion, enzyme immunoassay, and complement fixation. We conducted a retrospective review of the results of 1,797 serologic tests spanning 12 months from the onset of coccidioidomycosis in 298 immunocompetent and 62 immunosuppressed persons with symptomatic infection. Using the onset of symptoms as a reference point, we plotted the positive or negative serologic results over time for both groups. Compared with the immunocompetent group, immunosuppressed persons had lower rates of seropositivity for every type of test during the first year after onset of symptoms for coccidioidomycosis, although many results did not achieve statistical significance. Combining the results of these tests increased the sensitivity of the serologic evaluation in immunocompromised patients. Immunosuppressed persons have the ability to mount a serologic response to coccidioidomycosis, but in some circumstances, multiple methods may be required to improve detection.

Detection of Coccidioides species in clinical specimens by real-time PCR

Coccidioides spp. are dimorphic fungal pathogens endemic to the semiarid regions of North, Central, and South America. Currently, direct smear and culture are the most common means of identifying Coccidioides spp. While these methods offer relatively sensitive and specific means of detecting Coccidioides spp., growth in culture may take up to 3 weeks, potentially delaying the diagnosis and initiation of appropriate antifungal therapy. In addition, growth of the organism represents a significant safety risk to laboratory personnel. The need for a rapid and safe means of diagnosing coccidioidomycosis prompted us to develop a real-time PCR assay to detect Coccidioides spp. directly from clinical specimens. Primers and fluorescent resonance energy transfer (FRET) probes were designed to target the internal transcribed spacer 2 region of Coccidioides. The assay's limit of detection is below 50 targets per reaction. An analysis of 40 Coccidioides sp. clinical isolates grown in culture demonstrated 100% sensitivity of the assay. A cross-reactivity panel containing fungi, bacteria, mycobacteria, and viruses was tested and demonstrated 100% specificity for Coccidioides spp. An analysis of 266 respiratory specimens by LightCycler PCR demonstrated 100% sensitivity and 98.4% specificity for Coccidioides spp. compared with culture. Analysis of 66 fresh tissue specimens yielded 92.9% sensitivity and 98.1% specificity versus those of the culture method. The sensitivity of the assay testing 148 paraffin-embedded tissue samples is 73.4%. A rapid method for the detection of Coccidioides spp. directly from clinical material will greatly assist in the timely diagnosis and treatment of patients, while at the same time decreasing the risk of accidental exposure to laboratory personnel.

Novel approach to designing primers for identification and distinction of the human pathogenic fungi Coccidioides immitis and Coccidioides posadasii by PCR amplification

We developed a pair of primers that specifically identifies Coccidioides species, etiologic agents of the human fungal disease coccidioidomycosis. These primers could be used for distinguishing Coccidioides immitis and Coccidioides posadasii by simply comparing the amplicon sizes on an agarose gel.

Coccidioidomycosis and blastomycosis: Advances in molecular diagnosis

Clinical isolates of Coccidioides spp. and Blastomyces dermatitidis can be identified by chemiluminescent DNA probes and PCR assays targeting multicopy genes. In fixed tissue samples, cells of the two fungi are specified by in situ hybridization and PCR assays targeting 18S rDNA but sequencing of the products is mandatory. Nested PCR assays targeting genes encoding species- or genus-specific proteins like proline rich antigen of Coccidioides spp. and B. dermatitidis adhesin facilitate amplification of specific DNA from fixed tissue samples. The value of DNA amplification from native specimens of suspected cases of coccidioidomycosis or blastomycosis still needs to be determined.

Coccidioidomycosis of the lung contracted abroad

Coccidioides immitis is endemic in the southwestern United States. Coccidioidomycosis is rare in Japan, but the number of coccidioidomycosis cases from overseas is expected to increase markedly in the near future. A 33-year-old Japanese man with coccidioidomycosis who had lived in Arizona presented to our hospital. We performed wedge resection of the lung by video-assisted thoracoscopic surgery (VATS), and were able to completely remove the lesion. VATS wedge resection of the lung is effective in treating localized coccidioidomycosis. Before the operation, we could not confirm the existence of satellite lesions, but microscopically the main lesion was accompanied by several daughter lesions. It is very important that the surgical margin be sufficient to achieve complete resection.