Detection of gp43 and ITS1-5.8S-ITS2 ribosomal RNA genes of Paracoccidioides brasiliensis in paraffin-embedded tissue

PbGP43 Genotyping Using Paraffin-Embedded Biopsies of Human Paracoccidioidomycosis Reveals a Genetically Distinct Lineage in the Paracoccidioides brasiliensis Complex

Paracoccidioidomycosis (PCM) is a systemic mycosis caused by a group of cryptic species embedded in the Paracoccidioides brasiliensis complex and Paracoccidioides lutzii. Four species were recently inferred to belong to the P. brasiliensis complex, but the high genetic diversity found in both human and environmental samples have suggested that the number of lineages may be higher. This study aimed to assess the 43-kilodalton glycoprotein genotypes (PbGP43) in paraffin-embedded samples from PCM patients to infer the phylogenetic lineages of the P. brasiliensis complex responsible for causing the infection. Formalin-fixed, paraffin-embedded (FFPE) tissue samples from patients with histopathological diagnosis of PCM were analyzed. DNAs were extracted and amplified for a region of the second exon of the PbGP43 gene. Products were sequenced and aligned with other PbGP43 sequences available. A haplotype network and the phylogenetic relationships among sequences were inferred. Amino acid substitutions were investigated regarding the potential to modify physicochemical properties in the proteins. Six phylogenetic lineages were identified as belonging to the P. brasiliensis complex. Two lineages did not group with any of the four recognized species of the complex, and, interestingly, one of them comprised only FFPE samples. A coinfection involving two lineages was found. Five parsimony-informative sites were identified and three of them showed radical non-synonymous substitutions with the potential to promote changes in the protein. This study expands the knowledge regarding the genetic diversity existing in the P. brasiliensis complex and shows the potential of FFPE samples in species identification and in detecting coinfections.

Molecular Tools for Detection and Identification of Paracoccidioides Species: Current Status and Future Perspectives

Paracoccidioidomycosis (PCM) is a mycotic disease caused by the Paracoccidioides species, a group of thermally dimorphic fungi that grow in mycelial form at 25 °C and as budding yeasts when cultured at 37 °C or when parasitizing the host tissues. PCM occurs in a large area of Latin America, and the most critical regions of endemicity are in Brazil, Colombia, and Venezuela. The clinical diagnosis of PCM needs to be confirmed through laboratory tests. Although classical laboratory techniques provide valuable information due to the presence of pathognomonic forms of Paracoccidioides spp., nucleic acid-based diagnostics gradually are replacing or complementing culture-based, biochemical, and immunological assays in routine microbiology laboratory practice. Recently, taxonomic changes driven by whole-genomic sequencing of Paracoccidioides have highlighted the need to recognize species boundaries, which could better ascertain Paracoccidioides taxonomy. In this scenario, classical laboratory techniques do not have significant discriminatory power over cryptic agents. On the other hand, several PCR-based methods can detect polymorphisms in Paracoccidioides DNA and thus support species identification. This review is focused on the recent achievements in molecular diagnostics of paracoccidioidomycosis, including the main advantages and pitfalls related to each technique. We discuss these breakthroughs in light of taxonomic changes in the Paracoccidioides genus.

Paracoccidioidomycosis: Detection of Paracoccidioides brasiliensis´ genome in biological samples by quantitative chain reaction polymerase (qPCR)

Paracoccidioidomycosis (PCM) is a chronic mycosis caused by the saprobic and dimorphic species Paracoccidioides brasiliensis and P. lutzii. This disease is prevalent in Latin American countries. PCM appears as a relevant concern and challenge for the mycologists, since until now there is no a methodology suitable for an efficient and safe diagnosis and species identification. Thus, the present study aimed to validate a methodology for PCM´s diagnosis, using quantitative Polymerase Chain Reaction (qPCR) through target amplification of the gene encoding the recombinant protein Pb27, a common protein to the both species Paracoccidioides brasiliensis and P. lutzii. The experiments were performed in vitro to determine the specificity, efficiency and detection limit of qPCR assay, using specific primers and probe, which sequences were subject to a patent deposited in Brazilian CTIT, under the registration number: BR1020160078830. According to the results the technique showed sensitivity of 94% and specificity of 100%, demonstrating that it will be possible to develop a new fast and safe diagnostic PCM and can be standardized in order to present a low cost, accessible to the patient served by the public health system in Brazil and Latin America.

Two Cases of Lacaziosis in Bottlenose Dolphins (Tursiops truncatus) in Japan

Lacaziosis, formerly called lobomycosis, caused byLacazia loboi, is a zoonotic mycosis found in humans and dolphins and is endemic in the countries on the Atlantic Ocean. Although the Japanese coast is not considered an endemic area, photographic records of lacaziosis-like skin lesions were found in bottlenose dolphins (Tursiops truncatus) that were migrating in the Goto Islands (Nagasaki Prefecture, Japan). We diagnosed 2 cases of lacaziosis in bottlenose dolphins captured simultaneously at the same coast within Japanese territory on the basis of clinical characteristics, cytology, histopathology, immunological tests, and detection of partial sequences of a 43 kDa glycoprotein coding gene (gp43) with a nested-PCR system. The granulomatous skin lesions from the present cases were similar to those found in animals from endemic areas, containing multiple budding and chains of round yeast cells and positive in the immune-staining with anti-Paracoccidioides brasiliensisserum which is a fungal species related toL. loboi; however, thegp43gene sequences derived from the present cases showed 94.1% homology toP. brasiliensisand 84.1% toL. loboi. We confirmed that the causative agent at the present cases was different genotype ofL. loboifrom Amazon area.

A semi-nested PCR assay for molecular detection of Paracoccidioides brasiliensis in tissue samples

INTRODUCTION

Paracoccidioidomycosis is a systemic infection caused by Paracoccidioides brasiliensis.

METHODS

In this study, a semi-nested PCR for paracoccidioidomycosis diagnosis was developed. The primers ITS1 and ITS4 were used in the first reaction, while the primers MJ03 and ITS1 primer were used in the second reaction. The semi-nested PCR was used to investigate biopsies of five patients with oral lesions that resembled paracoccidioidomycosis.

RESULTS

The semi-nested PCR was positive for four samples and negative for a sample from a patient later diagnosed with leishmaniasis.

CONCLUSIONS

The new semi-nested PCR describe is useful for paracoccidioidomycosis diagnosis.

An atypical Paracoccidioides brasiliensis clinical isolate based on multiple gene analysis

An atypical isolate of Paracoccidioides brasiliensis (IFM54648), recovered from the sputum of a Brazilian man, was not detected in immunodiffusion tests for paracoccidioidomycosis and in species-specific PCR for the major antigen 43-kDa glycoprotein coding gene (gp43). The mycological characteristics of the isolate were similar to those of a typical P. brasiliensis. A total of 8 genes were sequenced from IFM54648, and the sequences were compared between the new isolate and other reference isolates and database sequences. We analyzed fragments of the gene sequences that code for gp43, the internal transcribed spacer regions of ribosomal RNA, the D1/D2 domains of the large subunit ribosomal RNA, glucan synthase, chitin synthase, glyoxalase I mRNA, 70-kDa heat-shock protein mRNA and urease. The gene sequences were 98.9-100% identical between IFM54648 and Pb01 (another atypical isolate). When compared to the other typical isolates, the identities were generally lower than 98%. A phylogenetic tree constructed using gp43 sequences showed that IFM54648 clustered with Pb01 at a considerable distance from other isolates. Therefore, this isolate is likely related to Pb01, which has recently been shown to be genetically distinct from other isolates of this species.

Molecular approaches for eco-epidemiological studies of Paracoccidioides brasiliensis

Medical mycology has greatly benefited from the introduction of molecular techniques. New knowledge on molecular genetics has provided both theoretical and practical frameworks, permitting important advances in our understanding of several aspects of pathogenic fungi. Considering Paracoccidioides brasiliensis in particular, important eco-epidemiological aspects, such as environmental distribution and new hosts were clarified through molecular approaches. These methodologies also contributed to a better understanding about the genetic variability of this pathogen; thus, P. brasiliensis is now assumed to represent a species complex. The present review focuses on some recent findings about the current taxonomic status of P. brasiliensis, its phylogenetic and speciation processes, as well as on some practical applications for the molecular detection of this pathogen in environmental and clinical materials.

Applications of Loop-Mediated Isothermal Amplificaton Methods (LAMP) for Identification and Diagnosis of Mycotic Diseases: Paracoccidioidomycosis and Ochroconis gallopava infection

Loop-mediated isothermal amplification (LAMP) methods are now useful for the detection of a specific gene in infectious diseases, genetic diseases, and/or genetic disorders in the large number of medical fields, and it was recently introduced to fungal investigation. It is characterized by the use of four different primers specifically designed to recognize six distinct regions of the target gene, and the reaction process proceeds at a constant temperature using strand displacement reaction. Quickness and simplicity is the advantage of the method. Amplification and detection of gene can be completed in a single step, by incubating the mixture of samples, primers, DNA polymerase with strand displacement activity and substrates at a constant temperature. The method was applied to two fungal infections; paracoccidioidomycosis (PCM), a deep mycosis caused by Paracoccidioides brasiliensis and Ochroconis gallopava infection. For PCM a combination of F3, B3, FIP, and BIP primers designed from the partial sequence of P. brasiliensis gp43 gene was used. The PCR products amplified by the primer set; F3 and B3 showed species specificity for P. brasiliensis and the detection limit of the PCR was 100 fg of fungal genomic DNA. The specific DNA banding pattern of P. brasiliensis was detected in the clinical and nine-banded armadillo derived isolates, paraffin-embedded tissue sample or sputum from PCM patient. LAMP method was used also for the identification of O. gallopava by using species-specific primer sets based on the D1/D2 domain of the LSU rDNA sequence. The method successfully detected the gene from both fungal DNA derived from brains and spleens of experimentally-infected mice with O. gallopava and environmental isolates. In conclusion, LAMP method for PCM and O. gallopava seemed to be useful for identification, diagnosis or retrospective study with advantage in the quickness and simplicity procedure, but require strictly-controlled environments.

Central nervous system paracoccidioidomycosis: diagnosis and treatment

BACKGROUND

Paracoccidioidomycosis (PCM) is a systemic mycosis caused by Paracoccidioides brasiliensis. The involvement of the central nervous system (CNS) in paracoccidioidomycosis is higher than previously thought and 2 clinical presentations have been reported, meningitis and pseudotumoral.

METHODS

Twenty medical records of patients with CNS paracoccidioidomycosis treated from 1986 to 2003 were analyzed. The follow-up ranged from 1 to 18 years (mean = 8.9 +/- 4.2).

RESULTS

Besides CNS paracoccidioidomycosis, all patients but one had the chronic systemic form and the pseudotumoral clinical presentation was the most frequent. Based on computed tomography scan findings, 4 image patterns were identified: low-density lesion with ring enhancement, lesion with calcification and ring enhancement, multiloculated low-density lesion with ring enhancement, and diffuse subarachnoid enhancement. The magnetic resonance imaging was performed in 3 patients and showed subarachnoid enhancement in 1 patient and heterogeneous lesion with ring enhancement in 2 patients. Eleven patients were submitted to medical treatment and 9 needed neurosurgical treatment; ventriculoperitoneal shunts in 4 patients, brain lesions resection in 3 patients, and partial resection of spinal cord lesions in 2 patients. Eleven patients had excellent outcome, 4 patients died, 3 are in good clinical condition with residual pulmonary dysfunction, and 1 patient was lost to follow-up.

CONCLUSIONS

The diagnosis of paracoccidioidomycosis with involvement of the CNS is difficult and clinical suspicion is a key point to achieve the correct diagnosis. Patients with early diagnosis have a favorable outcome with clinical or surgical treatment.

Comparison of the sequences of the internal transcribed spacer regions and PbGP43 genes of Paracoccidioides brasiliensis from patients and armadillos (Dasypus novemcinctus)

Paracoccidioides brasiliensis isolates from 10 nine-banded armadillos (Dasypus novemcinctus) were comparable with 19 clinical isolates by sequence analysis of the PbGP43 gene and ribosomal internal transcribed spacer 1 (ITS1) and ITS2 and by random amplified polymorphic DNA. In this original ITS study, eight isolates differed by one or three sites among five total substitution sites.