Molecular methods for the diagnosis and characterization of Cryptococcus: a review

Diagnosis and management of Cryptococcus neoformans var. grubii detected in an oral mass in a pink-tongued skink (Cyclodomorphus gerarrdii)

Cryptococcus is an encapsulated yeast that is found in both yeast and hyphal forms. Cryptococcus neoformans and C. gattii are the most medically important species, causing disease in both immunocompromised and immunocompetent individuals. A large, friable, sublingual mass was surgically resected from the oral cavity of a pink-tongued skink (Cyclodomorphus gerarrdii). Histopathology, fungal culture and PCR testing with Sanger sequencing confirmed granulomatous inflammation containing large numbers of yeasts identified as Cryptococcus neoformans var. grubii. Surgical excision and treatment with oral amphotericin B and terbinafine was unsuccessful in managing the infection. On Day 67 after surgery, Cryptococcus DNA was detected by PCR in the blood but not oral, cloacal or skin swabs. The skink was euthanised 72 days after surgery due to anorexia, weight loss and progressive neurological signs of disease. Necropsy results showed disseminated cryptococcosis, including meningoencephalitis and ventriculitis. Two in-contact pink-tongued skinks remained asymptomatic and PCR-negative during 198 days of observation. This case suggests Cryptococcus infections should be considered for oral masses presenting with or without neurological signs in skinks. Further investigation is required to determine the best treatment options for disseminated cryptococcosis in reptiles. This report describes the third reported case of Cryptococcus in a reptile and the first case of cryptococcosis in a pink-tongued skink. It is also the first report of Cryptococcus in a reptile identified to the variety level using PCR, including in whole blood samples.

Comparative analysis of diagnostic methods for the detection of Cryptococcus neoformans meningitis

BACKGROUND

Cryptococcosis is a devastating opportunistic infection in immunocompromised individuals, primarily in people living with HIV/AIDS. This study evaluated a protocol for the early diagnosis of meningitis due to C. neoformans, utilizing established molecular techniques from serum and CSF samples.

METHODS

The 18S and 5.8S (rDNA-ITS) sequence-specific nested PCR assays were compared with direct India ink staining and the latex agglutination test for detection of C. neoformans in serum and cerebrospinal fluid (CSF) from 49 Brazilian suspected meningitis patients. Results were validated with samples obtained from 10 patients negative for cryptococcosis and HIV, and by analysis of standard C. neoformans strains.

PRINCIPAL FINDINGS

The 5.8S DNA-ITS PCR was more sensitive (89-100%) and specific (100%) than the 18S rDNA PCR and conventional tests (India ink staining and latex agglutination) for identification of C. neoformans. While the 18S PCR exhibited a sensitivity (72%) similar to that of the latex agglutination assay in serum samples, it was superior to the latex agglutination assay when testing CSF, with a sensitivity of 84%. However, the latex agglutination was superior to the 18SrDNA PCR in specificity in CSF (92%). The 5.8S DNA-ITS PCR yielded the highest levels of accuracy (96-100%) of any test for detection (serological and mycological) of C. neoformans in both serum and CSF.

CONCLUSION

Use of the nested 5.8S PCR was superior to other techniques for the diagnosis of cryptococcosis. The possibility of using serum, a non-invasively collected material, in a targeted 5.8S PCR analysis to identify Cryptococcus spp. is recommended, especially in immunosuppressed patients. Our results indicate that nested 5.8S PCR can increase the diagnostic capability of cryptococcosis, and we suggest its use to monitor patients in the future.

Pulmonary Cryptococcosis

Pulmonary cryptococcosis describes an invasive lung mycosis caused by Cryptococcus neoformans or Cryptococcus gattii complex. It is often a high-consequence disease in both immunocompromised and immunocompetent populations, and may be misdiagnosed as pulmonary malignancy, leading to a delay in therapy. Epidemiology follows that of cryptococcal meningoencephalitis, with C. gattii infection more common in certain geographic regions. Diagnostic tools include histopathology, microscopy and culture, and the detection of cryptococcal polysaccharide antigen or Cryptococcus-derived nucleic acids. All patients with lung cryptococcosis should have a lumbar puncture and cerebral imaging to exclude central nervous system disease. Radiology is key, both as an adjunct to laboratory testing and as the initial means of detection in asymptomatic patients or those with non-specific symptoms. Pulmonary cryptococcomas (single or multiple) may also be associated with disseminated disease and/or cryptococcal meningitis, requiring prolonged treatment regimens. Optimal management for severe disease requires extended induction (amphotericin B and flucytosine) and consolidation therapy (fluconazole) with close clinical monitoring. Susceptibility testing is of value for epidemiology and in regions where relatively high minimum inhibitory concentrations to azoles (particularly fluconazole) have been noted. Novel diagnostic tools and therapeutic agents promise to improve the detection and treatment of cryptococcosis, particularly in low-income settings where the disease burden is high.

Pleural involvement in cryptococcal infection

Pleural involvement of cryptococcal infection is uncommon and is more commonly observed in immunocompromised hosts than in immunocompetent ones. Pleural involvement in cryptococcal infections can manifest with or without pleural effusion. The presence of Cryptococcus spp. in the effusion or pleura is required for the diagnosis of cryptococcal pleural infection, which is commonly determined by pleural biopsy, fluid culture, and/or detection of cryptococcal antigen in the pleura or pleural fluid.

Granulomatous Sarcoidosis Mimics

Many granulomatous diseases can mimic sarcoidosis histologically and in terms of their clinical features. These mimics include infectious granulomatous diseases, granulomatous reactions to occupational and environmental exposures, granulomatous drug reactions, vasculitides and idiopathic granulomatous conditions. It is important to distinguish sarcoidosis from these mimics, as a misdiagnosis of these diseases may have serious consequences. This manuscript reviews numerous sarcoidosis mimics and describes features of these diseases that may allow them to be differentiated from sarcoidosis. Distinguishing features between sarcoidosis and its mimics requires a careful review of the medical history, symptoms, demographics, radiographic findings, histologic features, and additional laboratory data. Understanding the clinical characteristics of sarcoidosis and its mimics should lead to more accurate diagnoses and treatment of granulomatous disorders that should improve the care of these patients. As the diagnostic criteria of sarcoidosis are not standardized, it is possible that some of these sarcoidosis mimics may represent varied clinical presentations of sarcoidosis itself.

Molecular Markers Reveal Epidemiological Patterns and Evolutionary Histories of the Human Pathogenic Cryptococcus

The human pathogenic Cryptococcus species are the main agents of fungal meningitis in humans and the causes of other diseases collectively called cryptococcosis. There are at least eight evolutionary divergent lineages among these agents, with different lineages showing different geographic and/or ecological distributions. In this review, we describe the main strain typing methods that have been used to analyze the human pathogenic Cryptococcus and discuss how molecular markers derived from the various strain typing methods have impacted our understanding of not only cryptococcal epidemiology but also its evolutionary histories. These methods include serotyping, multilocus enzyme electrophoresis, electrophoretic karyotyping, random amplified polymorphic DNA, restriction fragment length polymorphism, PCR-fingerprinting, amplified fragment length polymorphism, multilocus microsatellite typing, single locus and multilocus sequence typing, matrix-assisted laser desorption/ionization time of flight mass spectrometry, and whole genome sequencing. The major findings and the advantages and disadvantages of each method are discussed. Together, while controversies remain, these strain typing methods have helped reveal (i) the broad phylogenetic pattern among these agents, (ii) the centers of origins for several lineages and their dispersal patterns, (iii) the distributions of genetic variation among geographic regions and ecological niches, (iv) recent hybridization among several lineages, and (v) specific mutations during infections within individual patients. However, significant challenges remain. Multilocus sequence typing and whole genome sequencing are emerging as the gold standards for continued strain typing and epidemiological investigations of cryptococcosis.

Prevalence of pulmonary mycoses in smear-negative patients with suspected tuberculosis in the Brazilian Amazon

BACKGROUND

Pulmonary mycoses resemble clinically and radiologically chronic pulmonary tuberculosis. Studies describing the prevalence, etiology and clinical features of pulmonary mycosis are of crucial importance in the Brazilian Amazon.

AIMS

To estimate the frequency of pulmonary mycoses in smear-negative tuberculosis patients; to describe their demographic, epidemiological, and clinical characteristics; and to evaluate diagnostic methods.

METHODS

A cross-sectional study was conducted at two tuberculosis reference institutions in Amazonas, Brazil. We included 213 patients and collected clinical data, blood and induced sputum to perform serological, direct microscopy, microbiologic culture and PCR-based assays to identify infections caused by Aspergillus fumigatus, Paracoccidioides brasiliensis, Histoplasma capsulatum, Cryptococcus, and HIV. Chest computed tomography was also performed.

RESULTS

Pulmonary mycoses were diagnosed in 7% (15/213) of the cases, comprising ten aspergillosis cases, three cases of paracoccidioidomycosis and one case each of histoplasmosis and cryptococcosis. Among the patients with pulmonary mycoses, 86.7% were former tuberculosis patients. The most significant clinical characteristics associated with pulmonary mycoses were cavity-shaped lung injuries, prolonged chronic cough and hemoptysis.

CONCLUSIONS

Our study confirmed the high prevalence of pulmonary mycoses in smear-negative tuberculosis patients in the Brazilian Amazon.

Occurrence and Distribution of Cryptococcus Species in Environmental Sources from Lower Assam Belt of India

Cryptococcus is a non-motile, gram positive, non-fermenting Basidiomycetous encapsulated yeast like fungus that causes respiratory, neurological and other systemic diseases in both humans and animals. Present study delineates the possible distribution of Cryptococcus species in pigeon droppings, excreta of other avian species, eucalyptus tree and contaminated soil specimens collected from different geographical co-ordinates of six geographical regions of the lower Brahmaputra Valley of Assam, India. The fungi were isolated through conventional methods of Sabouraud Dextrose Agar (SDA) and Bird Seed Agar (BSA) media and identified through negative staining of capsule as well as performing classical bio-chemical tests. Identity of the isolates was further confirmed through sequence analysis of ITS-1 and ITS-4 region of the 18S rDNA. Two pathogenic species of Cryptococcus were isolated from 67 (15.40%) of the 435 specimens. Of these positive isolates 41 (9.43%) belonged to Naganishia albida (Cryptococcus albidus) while 26 (5.98%) represented Papiliotrema laurentii (Cryptococcus laurentii). Both the species were recovered from 58 (18.35%) dry and 9 (7.56%) moist specimens. The percentage of prevalence of Naganishia albida in dry and moist specimens were 35 (11.07%) and 6 (5.04%) respectively. Contrary to this, the percentage of prevalence of Papiliotrema laurentii in dry and moist were 23 (7.28%) and 3 (2.52%) respectively. The findings indicate that Cryptococcus species have established a better ecological sustenance in dry specimens than moist. The findings of the investigation demonstrated that the prevalence of Cryptococcus albidus in attics, dovecotes / houses of pigeon fanciers, contaminated soil, eucalyptus tree and droppings of other birds were 11(12.36%) out of 89, 23(14.11%) of 163,2(3.23%) of 62,4(7.84%) of 51 and only 1(1.43%) out of 7 specimens respectively. The recovery of Papiliotrema laurentii in the above specimens were 3(3.37%), 20(12.27%), 1(1.61%), 1(1.96%) and 1(1.42%) respectively. The findings revealed that the prevalence of Naganishia albida is more than that of Papiliotrema laurentii in natural substrates. The notorious pathogenic fungi, Cryptococcus neoformans could not be isolated, indicative of the fact that the region selected for the study is not environmentally favorable for growth and sustenance of the species. Findings of the study clearly demonstrate the ecological and epidemiological significance of the non-neoformans species of the genus cryptococcus that needs further comprehensive studies to access the prevalence of the genus from public health point of view.

Targeting novel genes for simultaneous detection of five fungal and bacterial agents from BAL samples using multiplex PCR assay

The main purpose of our study was to evaluate multiplex PCR assay targeting novel genes for detection of five fungal and bacterial agents in BAL samples; because many fungi and bacteria that cause respiratory infections have similar clinical symptoms, diagnosing and differentiating them are therefore essential to controlling and treating them. A total of 100 BAL specimens from a mycobacterium and mycology laboratory were collected from patients suspected of having TB or other respiratory diseases. Novel DNA targets for Aspergillus, Nocardia, Cryptococcus, and Streptomyces were found using modified comparative genomic analysis. Afterward, the primers were designed based on novel targets, and the sensitivity and specificity of the newly designed primers were evaluated. These primers, along with specific primers for M. tuberculosis (SDR), were used in a multiplex PCR assay. The results showed the culture test to be more sensitive than the PCR assay in detecting M. tuberculosis. However, in the detection of Aspergillus, the PCR assay was more sensitive than the culture test. We also found one positive culture and two positive PCR assays for Nocardiosis. Cryptococcal infections and Streptomyces associated with lung diseases were not identified by the culture test nor by the PCR assay. The multiplex PCR is one of the cheapest molecular diagnostic tests readily available for BAL samples in clinical laboratories. This assay can be used for early reports of the causative agents and for treating patients with appropriate drugs at an early stage.

Identification of the environmental source of infection for a domestic ferret with cryptococcosis

Cryptococcosis, caused by the Cryptococcus gattii and C. neoformans species complexes, is an environmentally acquired mycosis affecting a broad range of host species. Among 9 communally housed ferrets, a 5-y-old castrated male ferret domiciled in an outdoor enclosure in Sydney, Australia was diagnosed with sinonasal cryptococcosis. Clinical signs resolved during 18 mo of itraconazole therapy, but the ferret was eventually euthanized because of splenic hemangiosarcoma. At postmortem, microscopic foci of persistent cryptococcosis were detected. The diagnosis raised concerns that the owners and other ferrets were exposed to a common environmental source of infection, thus prompting an investigation. Soil samples, swabs of a hollow eucalypt log (used for behavioral enrichment), and nasal swabs from 8 asymptomatic ferrets were collected. Nasal exudate (obtained at diagnosis) and tissues (collected at postmortem) were available from the clinical case. Bird seed agar culture resulted in a heavy growth of Cryptococcus spp. from one environmental site (the log), one nasal swab, and nasal exudate and tissues from the clinical case. All other samples were culture-negative. Sub-cultured isolates from the log were a mixture of C. gattii molecular type VGI and C. neoformans molecular type VNI. Ferret isolates were a similar mixture of C. gattii VGI (all disease isolates) and C. neoformans VNI (nasal-colonizing isolate). Multilocus sequence typing further revealed the ferret isolates as identical to environmental isolates collected from the log, confirming the log as the source of clinical disease and nasal colonization. The log was removed to prevent further exposure to a high environmental load of Cryptococcus spp.

Central Nervous System Cryptococcal Infections in Non-HIV Infected Patients

Central nervous system (CNS) cryptococcosis in non-HIV infected patients affects solid organ transplant (SOT) recipients, patients with malignancy, rheumatic disorders, other immunosuppressive conditions and immunocompetent hosts. More recently described risks include the use of newer biologicals and recreational intravenous drug use. Disease is caused by Cryptococcus neoformans and Cryptococcus gattii species complex; C. gattii is endemic in several geographic regions and has caused outbreaks in North America. Major virulence determinants are the polysaccharide capsule, melanin and several ‘invasins’. Cryptococcal plb1, laccase and urease are essential for dissemination from lung to CNS and crossing the blood–brain barrier. Meningo-encephalitis is common but intracerebral infection or hydrocephalus also occur, and are relatively frequent in C. gattii infection. Complications include neurologic deficits, raised intracranial pressure (ICP) and disseminated disease. Diagnosis relies on culture, phenotypic identification methods, and cryptococcal antigen detection. Molecular methods can assist. Preferred induction antifungal therapy is a lipid amphotericin B formulation (amphotericin B deoxycholate may be used in non-transplant patients) plus 5-flucytosine for 2–6 weeks depending on host type followed by consolidation/maintenance therapy with fluconazole for 12 months or longer. Control of raised ICP is essential. Clinicians should be vigilant for immune reconstitution inflammatory syndrome.

An Unusual Case of Pulmonary Cryptococcus

Cryptococcal infections are caused by encapsulated fungi Cryptococcus gattii and C. neoformans. Inhalation commonly causes innocuous colonization but may cause meningitis or disseminated disease via hematogenous spread. Cryptococcosis occurs most commonly in immunocompromised patients including those with acquired immunodeficiency syndrome, meningoencephalitis or disseminated disease. However, cryptococcosis can occur as asymptomatic isolated pulmonary nodules in immunocompetent patients. Here we present a unique retrospective case report of a 55-year-old immunocompetent man who presented with pleuritic chest pain, productive cough, dyspnea on exertion, chills, night sweats, and weight loss. A computed tomography scan of his chest revealed multiple ground-glass opacities throughout both lung fields. The results of his autoimmune evaluation and human immunodeficiency virus tests were negative. A biopsy obtained through video-assisted thoracoscopic surgery revealed mucicarmine staining capsules confirming Cryptococcus, requiring treatment with amphotericin, flucytosine, and fluconazole. This case highlights the rarely studied presentation of symptomatic diffuse pulmonary cryptococcal infection in an immunocompetent patient requiring treatment.

[Molecular characterization of Cryptococcus neoformans isolates from HIV patients, Guayaquil, Ecuador]

INTRODUCTION

Neurocryptococcosis is an opportunistic fungal infection that represents a high cost in human lives and for the economy of countries. Its causative agent, the Cryptococcus neoformans/Cryptococcus gattii species complex, has a sexual and an asexual phase, four major serotypes and seven molecular varieties with phenotypic, clinical-epidemiological and antifungal susceptibility differences.

OBJECTIVE

To characterize by molecular methods clinical isolates of C. neoformans from Guayaquil, Ecuador.

MATERIALS AND METHODS

We determined mating types, serotypes and molecular varieties by PCR and RFLP in 27 yeast isolates previously identified as C. neoformans by conventional methods. The isolates were recovered from cerebrospinal fluid of HIV seropositive patients with neurological syndrome admitted at "Dr. José Daniel Rodríguez Maridueña" Hospital from December, 2013, to January, 2015.

RESULTS

We established a wide prevalence of C. neoformans serotype A, MATα and genotype VNI among the studied isolates.

CONCLUSIONS

These data are similar to those obtained in other countries and the first identified by molecular characterization in Guayaquil, Ecuador. Therefore, they constitute an important contribution to the knowledge on cryptococcosis in this country.

Disseminated cryptococcosis presenting as mediastinal and hilar lymphadenopathy in an immunocompetent patient

We herein report a rare case of disseminated cryptococcosis presenting as mediastinal and hilar lymphadenopathy in a young immunocompetent man. A previously healthy 26‐year‐old man presented with persistent headache and nonproductive cough. Chest computed tomography indicated mediastinal and hilar lymphadenopathy. Cryptococcal lymphadenitis and meningitis was confirmed by endobronchial ultrasound‐guided transbronchial needle aspiration and central spinal fluid examination, respectively. He received liposomal amphotericin B and flucytosine followed by fluconazole and finally improved.

Method for identification of Cryptococcus neoformans and Cryptococcus gattii useful in resource-limited settings

AIMS

The high HIV/AIDS burden in Sub-Saharan Africa has led to cryptococcosis becoming a public health concern. In this resource-limited setting, conventional identification methods are mainly used to diagnose cryptococcal infections. However, these methods are often inconsistent, and importantly, cannot discriminate between the aetiological agents, Cryptococcus neoformans and C. gattii. Therefore, there is a need for an alternative reliable method to identify these species.

METHODS

We examined the usefulness of a PCR method, including a restriction digest, in identifying clinical C. neoformans and C. gattii isolates. In addition, matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-ToF MS) was performed for validation purposes.

RESULTS

The intraspecific variation between tested strains allowed for their delineation into three traditional varieties of C. neoformans, that is, varietal forms: neoformans, grubii and gattii. Furthermore, we uncovered a restriction site (signature sequence: 5'-AATATT-3') that is present only in the distinct species C. neoformans (varietal forms neoformans and grubii), and is, importantly, absent in the distinct species C. gattii (C. neoformans var. gattii). Thus, we were able to discriminate the distinct species by directly digesting the PCR amplicons using the endonuclease SspI. It was also possible to delineate some tested isolates as either C. neoformans or C. gattii using our MALDI-ToF MS data.

CONCLUSIONS

The possibility of performing only a restriction digest makes the outlined method, similar to conventional techniques, economical and easy to optimise for routine use in resource-limited settings.

Validation and clinical application of a molecular method for the identification of Cryptococcus neoformans/Cryptococcus gattii complex DNA in human clinical specimens

The diagnosis of cryptococcosis is usually performed based on cultures of tissue or body fluids and isolation of the fungus, but this method may require several days. Direct microscopic examination, although rapid, is relatively insensitive. Biochemical and immunodiagnostic rapid tests are also used. However, all of these methods have limitations that may hinder final diagnosis. The increasing incidence of fungal infections has focused attention on tools for rapid and accurate diagnosis using molecular biological techniques. Currently, PCR-based methods, particularly nested, multiplex and real-time PCR, provide both high sensitivity and specificity.

In the present study, we evaluated a nested PCR targeting the gene encoding the ITS-1 and ITS-2 regions of rDNA in samples from a cohort of patients diagnosed with cryptococcosis. The results showed that in our hands, this Cryptococcus nested PCR assay has 100% specificity and 100% sensitivity and was able to detect until 2 femtograms of Cryptococcus DNA.

Accurate and sensitive real-time PCR assays using intergenic spacer 1 region to differentiate Cryptococcus gattii sensu lato and Cryptococcus neoformans sensu lato

In this work, two accurate and sensitive real-time polymerase chain reaction (PCR) assays to differentiate pathogenic Cryptococcus gattii sensu lato (s.l.) and C. neoformans sensu lato (s.l.) targeting the intergenic spacer 1 (IGS1) region from rDNA locus were developed. Specific primers were designed based on their IGS1 sequence analyses and the optimal real-time PCR assays showed that the dissociation curves generated two different melting peaks, at 82.8 and 84.2ºC for C. gattii s.l. and C. neoformans s.l., respectively. No amplifications were observed in the negative template control. The minimum limit of detection of both primers was 100 plasmid copies per reaction, and they were highly specific when tested with a range of fungal DNAs. Overall, the results showed that the designed primers completely differentiated C. gattii s.l. and C. neoformans s.l. from clinical and environmental sources with great accuracy when compared to phenotypic identification, with no cross-reactivity to other fungal DNA.

Cryptococcus gattii infections

Understanding of the taxonomy and phylogeny of Cryptococcus gattii has been advanced by modern molecular techniques. C. gattii probably diverged from Cryptococcus neoformans between 16 million and 160 million years ago, depending on the dating methods applied, and maintains diversity by recombining in nature. South America is the likely source of the virulent C. gattii VGII molecular types that have emerged in North America. C. gattii shares major virulence determinants with C. neoformans, although genomic and transcriptomic studies revealed that despite similar genomes, the VGIIa and VGIIb subtypes employ very different transcriptional circuits and manifest differences in virulence phenotypes. Preliminary evidence suggests that C. gattii VGII causes severe lung disease and death without dissemination, whereas C. neoformans disseminates readily to the central nervous system (CNS) and causes death from meningoencephalitis. Overall, currently available data indicate that the C. gattii VGI, VGII, and VGIII molecular types more commonly affect nonimmunocompromised hosts, in contrast to VGIV. New, rapid, cheap diagnostic tests and imaging modalities are assisting early diagnosis and enabling better outcomes of cerebral cryptococcosis. Complications of CNS infection include increased intracranial pressure, severe neurological sequelae, and development of immune reconstitution syndrome, although the mortality rate is low. C. gattii VGII isolates may exhibit higher fluconazole MICs than other genotypes. Optimal therapeutic regimens are yet to be determined; in most cases, initial therapy with amphotericin B and 5-flucytosine is recommended.

Real-time PCR assays for genotyping of Cryptococcus gattii in North America

Background

Cryptococcus gattii has been the cause of an ongoing outbreak starting in 1999 on Vancouver Island, British Columbia and spreading to mainland Canada and the US Pacific Northwest. In the course of the outbreak, C. gattii has been identified outside of its previously documented climate, habitat, and host disease. Genotyping of C. gattii is essential to understand the ecological and geographical expansion of this emerging pathogen.

Methods

We developed and validated a mismatch amplification mutation assay (MAMA) real-time PCR panel for genotyping C. gattii molecular types VGI-VGIV and VGII subtypes a,b,c. Subtype assays were designed based on whole-genome sequence of 20 C. gattii strains. Publically available multilocus sequence typing (MLST) data from a study of 202 strains was used for the molecular type (VGI-VGIV) assay design. All assays were validated across DNA from 112 strains of diverse international origin and sample types, including animal, environmental and human.

Results

Validation revealed each assay on the panel is 100% sensitive, specific and concordant with MLST. The assay panel can detect down to 0.5 picograms of template DNA.

Conclusions

The (MAMA) real-time PCR panel for C. gattii accurately typed a collection of 112 diverse strains and demonstrated high sensitivity. This is a time and cost efficient method of genotyping C. gattii best suited for application in large-scale epidemiological studies.

Treatment and outcomes among patients with Cryptococcus gattii infections in the United States Pacific Northwest

Background

Cryptococcus gattii is a fungal pathogen causing an emerging outbreak in the United States Pacific Northwest (PNW). Treatment guidelines for cryptococcosis are primarily based on data from C. neoformans infections; applicability to PNW C. gattii infection is unknown. We evaluated the relationship between initial antifungal treatment and outcomes for PNW C.gattii patients.

Methods

Cases were defined as culture-confirmed invasive C. gattii infections among residents of Oregon and Washington States during 2004–2011. Clinical data were abstracted from medical records through one year of follow-up. Recommended initial treatment for central nervous system (CNS), bloodstream, and severe pulmonary infections is amphotericin B and 5-flucytosine; for non-severe pulmonary infections, recommended initial treatment is fluconazole. Alternative initial treatment was defined as any other initial antifungal treatment.

Results

Seventy patients survived to diagnosis; 50 (71%) received the recommended initial treatment and 20 (29%) received an alternative. Fewer patients with pulmonary infections [21 (64%)] than CNS infections [25 (83%)] received the recommended initial treatment (p = 0.07). Among patients with pulmonary infections, those with severe infections received the recommended initial treatment less often than those with non-severe infections (11% vs. 83%, p<0.0001). Eight patients with severe pulmonary infections received alternative initial treatments; three died. Four patients with non-severe pulmonary infections received alternative initial treatments; two died. There was a trend towards increased three-month mortality among patients receiving alternative vs. recommended initial treatment (30% vs. 14%, p = 0.12), driven primarily by increased mortality among patients with pulmonary disease receiving alternative vs. recommended initial treatment (42% vs. 10%, p = 0.07).

Conclusions

C.gattii patients with pulmonary infections – especially severe infections – may be less likely to receive recommended treatment than those with CNS infections; alternative treatment may be associated with increased mortality. Reasons for receipt of alternative treatment among C.gattii patients in this area should be investigated, and clinician awareness of recommended treatment reinforced.

Cryptococcus gattii infections: contemporary aspects of epidemiology, clinical manifestations and management of infection

Cryptococcus gattii is an important primary and opportunistic pathogen, predominantly causing meningoencephalitis and pulmonary disease with substantial mortality. Initially considered geographically restricted to immune-competent, highly exposed individuals in the tropics, an apparent epidemic in North America has led to new perspectives on its ecology, epidemiology and clinical associations, which are distinct from its sibling species Cryptococcus neoformans. The role of C. gattii molecular genotypes/subtypes in different settings is under investigation. Diagnostic and treatment strategies are similar to those for C. neoformans in immunocompetent hosts, although data indicate that more prolonged induction, as well as total duration of therapy, is required. Exclusion of CNS involvement is mandatory. Brain cryptococcomas are characteristic of C. gattii infection, and raised intracranial pressure is common, for which surgery is often required. Immune reconstitution syndrome may occur. Ongoing C. gattii research and greater awareness and availability of specific diagnostic tests are required to improve patient outcomes.

Use of denaturing gradient gel electrophoresis for the identification of mixed oral yeasts in human saliva

A PCR-denaturing gradient gel electrophoresis (DGGE) method was established for the simultaneous presumptive identification of multiple yeast species commonly present in the oral cavity. Published primer sets targeting different regions of the Saccharomyces cerevisiae 26-28S rRNA gene (denoted primer sets N and U) and the 18S rRNA gene (primer set E) were evaluated with ten Candida and four non-Candida yeast species, and twenty Candida albicans isolates. Optimized PCR-DGGE conditions using primer set N were applied to presumptively identify, by band matching, yeasts in the saliva of 25 individuals. Identities were confirmed by DNA sequencing and compared with those using CHROMagar Candida culture. All primer sets yielded detectable DGGE bands for all species tested. Primer set N yielded mainly single bands and could distinguish all species examined, including differentiating Candida dubliniensis from C. albicans. Primer set U was less discriminatory among species but yielded multiple bands that distinguished subspecies groups within C. albicans. Primer set E gave poor yeast discrimination. DGGE analysis identified yeasts in 17 of the 25 saliva samples. Six saliva samples contained two yeast species: three contained C. albicans and three C. dubliniensis. C. dubliniensis was present alone in one saliva sample (total prevalence 16 %). CHROMagar culture detected yeasts in 16 of the yeast-containing saliva samples and did not enable identification of 7 yeast species identified by DGGE. In conclusion, DGGE identification of oral yeast species with primer set N is a relatively fast and reliable method for the simultaneous presumptive identification of mixed yeasts in oral saliva samples.

Comparison of primers for RAPD-PCR from environmental isolates of Cryptococcus neoformans, Cryptococcus albidus and Cryptococcus laurentii complex

Various organisms have been characterized by molecular methods, including fungi of the genus Cryptococcus. The purposes of this study were: to determine the discriminatory potential of the RAPD (Random Amplified Polymorphic DNA) primers, the pattern of similarity of the Cryptococcus species, and discuss their useful application in epidemiological studies. We analyzed 10 isolates of each specie/group: C. albidus, C. laurentii complex, C. neoformans var. grubii, all from environmental source, and two ATCC strains, C. neoformans var. grubii ATCC 90112, and C. neoformans var. neoformans ATCC 28957 by RAPD-PCR using the primers CAV1, CAV2, ZAP19, ZAP20, OPB11 and SEQ6. The primers showed a good discriminatory power, revealing important differences between them and between species; the SEQ6 primer discriminated a larger number of isolates of three species. Isolates of C. laurentii showed greater genetic diversity than other species revealed by all six primers. Isolates of C. neoformans were more homogeneous. Only the primer CAV2 showed no amplification of DNA bands for C. albidus. It was concluded that the use of limited number of carefully selected primers allowed the discrimination of different isolates, and some primers (e.g., CAV2 for C. albidus) may not to be applied to some species.

MALDI-TOF MS enables the rapid identification of the major molecular types within the Cryptococcus neoformans/C. gattii species complex

Background

The Cryptococcus neoformans/C. gattii species complex comprises two sibling species that are divided into eight major molecular types, C. neoformans VNI to VNIV and C. gattii VGI to VGIV. These genotypes differ in host range, epidemiology, virulence, antifungal susceptibility and geographic distribution. The currently used phenotypic and molecular identification methods for the species/molecular types are time consuming and expensive. As Matrix-Assisted Laser Desorption Ionization-Time-of-Flight Mass Spectrometry (MALDI-TOF MS) offers an effective alternative for the rapid identification of microorganisms, the objective of this study was to examine its potential for the identification of C. neoformans and C. gattii strains at the intra- and inter-species level.

Methodology

Protein extracts obtained via the formic acid extraction method of 164 C. neoformans/C. gattii isolates, including four inter-species hybrids, were studied.

Results

The obtained mass spectra correctly identified 100% of all studied isolates, grouped each isolate according to the currently recognized species, C. neoformans and C. gattii, and detected potential hybrids. In addition, all isolates were clearly separated according to their major molecular type, generating greater spectral differences among the C. neoformans molecular types than the C. gattii molecular types, most likely reflecting a closer phylogenetic relationship between the latter. The number of colonies used and the incubation length did not affect the results. No spectra were obtained from intact yeast cells. An extended validated spectral library containing spectra of all eight major molecular types was established.

Conclusions

MALDI-TOF MS is a rapid identification tool for the correct recognition of the two currently recognized human pathogenic Cryptococcus species and offers a simple method for the separation of the eight major molecular types and the detection of hybrid strains within this species complex in the clinical laboratory. The obtained mass spectra provide further evidence that the major molecular types warrant variety or even species status.

Matrix-assisted laser desorption ionization-time of flight mass spectrometry-based method for discrimination between molecular types of Cryptococcus neoformans and Cryptococcus gattii

We evaluated the usefulness of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) for Cryptococcus identification at the species and subspecies levels by using an in-house database of 25 reference cryptococcal spectra. Eighty-one out of the 82 Cryptococcus isolates (72 Cryptococcus neoformans and 10 Cryptococcus gattii) tested were correctly identified with respect to their molecular type designations. We showed that MALDI-TOF MS is a practicable alternative to conventional mycology or DNA-based methods.

Amplified fragment length polymorphism confirms reciprocal monophyly in Chrysomya putoria and Chrysomya chloropyga: a correction of reported shared mtDNA haplotypes

Reinvestigation of mitochondrial haplotypes previously reported to be shared between the Afrotropical blowflies Chrysomya putoria Weidemann and Chrysomya chloropyga Weidemann (Diptera: Calliphoridae) revealed an error resulting from the misidentification of specimens. Preliminary amplified fragment length polymorphism (AFLP) analysis of the original and additional individuals again failed to find reciprocal monophyly, leading to a re-examination of the specimens for diagnostic male genitalic characters that were first described following the earlier study. Four of the original study specimens were found to have been misidentified, and definitive analysis of both mtDNA and AFLP genotypes using phylogenetic analysis and genetic assignment showed that each species was indeed reciprocally monophyletic. In addition to correcting the earlier error, this study illustrates how AFLP analysis can be used for efficient and effective specimen identification through both phylogenetic analysis and genetic assignment, and suggests that the latter method has special advantages for identification when no conspecific specimens are represented in the reference database.

Cryptococcus gattii: where do we go from here?

Infections caused by the emerging pathogen Cryptococcus gattii are increasing in frequency in North America. During the past decade, interest in the pathogen has continued to grow, not only in North America but also in other areas of the world where infections have recently been documented. This review synthesizes existing data and raises issues that remain to be addressed.

High-resolution melting analysis for identification of the Cryptococcus neoformans-Cryptococcus gattii complex

We have developed a two-step method based on high-resolution melting (HRM) that reliably identifies species from the Cryptococcus species complex (Cryptococcus neoformans var. grubii, Cryptococcus neoformans var. neoformans, and Cryptococcus gattii). Our results indicate that HRM can provide a fast protocol to identify and distinguish among the main Cryptococcus species.