Rapid identification of Sporothrix schenckii in biopsy tissue by PCR

Development of loop-mediated isothermal amplification for rapid detection of sporotrichosis caused by Sporothrix schenckii

Background and Aim

Sporothrix schenckii is the causative agent of sporotrichosis, which most commonly causes lymphocutaneous infections in immunocompromised hosts. This pathogen infects dogs, cats, cattle, and buffaloes and can potentially infect humans. Diagnosis by fungal culture is lengthy, and although there are several clinical diagnoses and molecular methods, these are complicated and time-consuming for veterinarians. This study aimed to develop a visual diagnostic assay that is less time-consuming and can be used by veterinarians to screen for sporotrichosis.

Materials and Methods

To develop a loop-mediated isothermal amplification (LAMP) assay for sporotrichosis, primers specific for fragments of the 18S rRNA gene of S. schenckii were designed. Then, the time and temperature were optimized to successfully achieve LAMP. Ten-fold serial dilutions of DNA were used to determine the detection limit using both LAMP and nested polymerase chain reaction (nPCR) assays.

Results

The optimal LAMP conditions were incubation at 73°C for 30 min. Agarose gel electrophoresis revealed a ladder-like pattern of the LAMP product, and a sky-blue color indicated a positive result. A comparison of the LAMP assay with nPCR revealed that it was 10 times more sensitive than nPCR, with a detection limit of 10 pg. The use of a heat box compared with a thermocycler gave the same results.

Conclusion

Loop-mediated isothermal amplification gives good results and may represent a future alternative diagnostic tool for screening fungal pathogens before the results of conventional fungal cultures are received. However, this method should be further studied to clarify its use with clinical samples.

Trends in Molecular Diagnostics and Genotyping Tools Applied for Emerging Sporothrix Species

Sporotrichosis is the most important subcutaneous mycosis that affects humans and animals worldwide. The mycosis is caused after a traumatic inoculation of fungal propagules into the host and may follow an animal or environmental transmission route. The main culprits of sporotrichosis are thermodimorphic Sporothrix species embedded in a clinical clade, including S. brasiliensis, S. schenckii, S. globosa, and S. luriei. Although sporotrichosis occurs worldwide, the etiological agents are not evenly distributed, as exemplified by ongoing outbreaks in Brazil and China, caused by S. brasiliensis and S. globosa, respectively. The gold standard for diagnosing sporotrichosis has been the isolation of the fungus in vitro. However, with the advance in molecular techniques, molecular assays have complemented and gradually replaced the classical mycological tests to quickly and accurately detect and/or differentiate molecular siblings in Sporothrix. Nearly all techniques available for molecular diagnosis of sporotrichosis involve PCR amplification, which is currently moving towards detecting Sporothrix DNA directly from clinical samples in multiplex qPCR assays. From an epidemiological perspective, genotyping is key to tracing back sources of Sporothrix infections, detecting diversity in outbreak areas, and thus uncovering finer-scale epidemiological patterns. Over the past decades, molecular epidemiological studies have provided essential information to policymakers regarding outbreak management. From high-to-low throughput genotyping methods, MLSA, AFLP, SSR, RAPD, PCR-RFLP, and WGS are available to assess the transmission dynamics and sporotrichosis expansion. This review discusses the trends in the molecular diagnosis of sporotrichosis, genotyping techniques applied in molecular epidemiological studies, and perspectives for the near future.

Sporotrichosis in Mexico

Sporotrichosis is an endemic mycosis caused by the species of the Sporothrix genus, and it is considered one of the most frequent subcutaneous mycoses in Mexico. This mycosis has become a relevant fungal infection in the last two decades. Today, much is known of its epidemiology and distribution, and its taxonomy has undergone revisions. New clinical species have been identified and classified through molecular tools, and they now include Sporothrix schenckii sensu stricto, Sporothrix brasiliensis, Sporothrix globosa, and Sporothrix luriei. In this article, we present a systematic review of sporotrichosis in Mexico that analyzes its epidemiology, geographic distribution, and diagnosis. The results show that the most common clinical presentation of sporotrichosis in Mexico is the lymphocutaneous form, with a higher incidence in the 0-15 age range, mainly in males, and for which trauma with plants is the most frequent source of infection. In Mexico, the laboratory diagnosis of sporotrichosis is mainly carried out using conventional methods, but in recent years, several researchers have used molecular methods to identify the Sporothrix species. The treatment of choice depends mainly on the clinical form of the disease, the host's immunological status, and the species of Sporothrix involved. Despite the significance of this mycosis in Mexico, public information about sporotrichosis is scarce, and it is not considered reportable according to Mexico's epidemiological national system, the "Sistema Nacional de Vigilancia Epidemiológica." Due to the lack of data in Mexico regarding the epidemiology of this disease, we present a systematic review of sporotrichosis in Mexico, between 1914 and 2019, that analyzes its epidemiology, geographic distribution, and diagnosis.

Diagnosis of Breakthrough Fungal Infections in the Clinical Mycology Laboratory: An ECMM Consensus Statement

Breakthrough invasive fungal infections (bIFI) cause significant morbidity and mortality. Their diagnosis can be challenging due to reduced sensitivity to conventional culture techniques, serologic tests, and PCR-based assays in patients undergoing antifungal therapy, and their diagnosis can be delayed contributing to poor patient outcomes. In this review, we provide consensus recommendations on behalf of the European Confederation for Medical Mycology (ECMM) for the diagnosis of bIFI caused by invasive yeasts, molds, and endemic mycoses, to guide diagnostic efforts in patients receiving antifungals and support the design of future clinical trials in the field of clinical mycology. The cornerstone of lab-based diagnosis of breakthrough infections for yeast and endemic mycoses remain conventional culture, to accurately identify the causative pathogen and allow for antifungal susceptibility testing. The impact of non-culture-based methods are not well-studied for the definite diagnosis of breakthrough invasive yeast infections. Non-culture-based methods have an important role for the diagnosis of breakthrough invasive mold infections, in particular invasive aspergillosis, and a combination of testing involving conventional culture, antigen-based assays, and PCR-based assays should be considered. Multiple diagnostic modalities, including histopathology, culture, antibody, and/or antigen tests and occasionally PCR-based assays may be required to diagnose breakthrough endemic mycoses. A need exists for diagnostic tests that are effective, simple, cheap, and rapid to enable the diagnosis of bIFI in patients taking antifungals.

Comparative Genomic Data Provide New Insight on the Evolution of Pathogenicity in Sporothrix Species

Sporothrix species are commonly isolated from environmental and clinical samples. As common causes of zoonotic mycosis, Sporothrix species may result in localized or disseminated infections, posing considerable threat to animal and human health. However, the pathogenic profiles of different Sporothrix species varied, in virulence, geographic location and host ranges, which have yet to be explored. Analysing the genomes of Sporothrix species are useful for understanding their pathogenicity. In this study, we analyzed the whole genome of 12 Sporothrix species and six S. globosa isolates from different clinical samples in China. By combining comparative analyses with Kyoto Encyclopedia of Genes and Genomes (KEGG), Carbohydrate-Active enZymes (CAZy), antiSMASH, Pfam, and PHI annotations, Sporothrix species showed exuberant primary and secondary metabolism processes. The genome sizes of four main clinical species, i.e., S. brasiliensis, S. schenckii, S. globosa, and S. luriei were significantly smaller than other environmental and clinical Sporothrix species. The contracted genes included mostly CAZymes and peptidases genes that were usually associated with the decay of plants, as well as the genes that were associated with the loss of pathogenicity and the reduced virulence. Our results could, to some extent, explain a habitat shift of Sporothrix species from a saprobic life in plant materials to a pathogenic life in mammals and the increased pathogenicity during the evolution. Gene clusters of melanin and clavaric acid were identified in this study, which improved our understanding on their pathogenicity and possible antitumor effects. Moreover, our analyses revealed no significant genomic variations among different clinical isolates of S. globosa from different regions in China.

Fast diagnosis of sporotrichosis caused by Sporothrix globosa, Sporothrix schenckii, and Sporothrix brasiliensis based on multiplex real-time PCR

The accurate diagnosis of sporotrichosis and identification at the species level are critical for public health and appropriate patient management. Compared with morphological identification methods, molecular diagnostic tests are rapid and have high sensitivity and standardized operating processes. Therefore, we designed a novel multiplex real-time polymerase chain reaction (PCR) method based on the calmodulin (CAL) gene for the identification of clinically relevant Sporothrix species: S. globosa, S. schenckii s. str., and S. brasiliensis. We evaluated the assay with clinical and spiked samples and assessed its diagnostic performance by comparing the results to those of culture and species-specific PCR. Thirty-three DNA templates were used to detect assay specificity, and three plasmids were constructed to create a standard curve and determine the limits of detection (LODs). For nucleic acid detection, the sensitivity and specificity reached 100%. The LODs were 10 copies, 10 copies and 100 copies for S. globosa, S. schenckii s. str and S. brasiliensis, respectively. For the clinical samples, the positive detection rates by culture, species-specific PCR and the multiplex real-time PCR assay were 87.9% (29/33), 39.4% (13/33), and 93.9% (31/33), respectively. For the spiked samples, the positive detection rates were both 100% for S. schenckii s. str and S. brasiliensis. Based on the above results, compared with culture and other molecular diagnosis methods, the novel multiplex real-time PCR assay is effective, fast, accurate, and highly sensitive. It has a lower reaction cost and lower sample volume requirements, can detect co-infections, and allows for standardized operation and easier interpretation of results. In the future, this assay could be developed into a commercial kit for the diagnosis and identification of S. globosa, S. schenckii s. str, and S. brasiliensis.

Sporotrichosis is a subacute or chronic infectious disease caused by dimorphic fungi of Sporothrix spp. The genus Sporothrix consists of several species with different geographic distributions, virulence, and antifungal susceptibilities, making species-level identification necessary. S. brasiliensis, S. globosa, S. schenckii s. str and S. luriei make up the “pathogenic clade” of the genus Sporothrix. Importantly, S. luriei has a low clinical-epidemiological impact within this genus. Therefore, we designed a novel multiplex real-time PCR method using fluorescent probes for the identification of S. globosa, S. schenckii s. str, and S. brasiliensis. We designed a pair of primers based on the conserved sequence of the calmodulin gene of Sporothrix spp. and probes with different fluorescent signals based on the divergent sequences of S. globosa, S. schenckii s. str and S. brasiliensis. Through the verification of nucleic acid, clinical and spiked sample detection, the multiplex real-time PCR could quickly and accurately identify the three clinically relevant species of Sporothrix spp. with high sensitivity. This new assay could be applied in epidemiology, clinical diagnosis, and experiments with sporotrichosis to control new outbreaks, reduce diagnostic and identification time, and improve test efficiency.

Immunopathogenesis of Human Sporotrichosis: What We Already Know

Sporotrichosis is a subacute/chronic mycosis caused by dimorphic fungus of the genus Sporothrix. This mycosis may affect both human and domestic animals and in the last few years, the geographic dispersion and increase of sporotrichosis worldwide has been observed. The occurrence of cases related to scratching/bites of domestic felines have increased, characterizing the disease as predominantly a zoonosis. In humans, sporotrichosis mainly involves the cutaneous tegument of infected patients, but other tissues may also present the infection. The main forms of clinical presentation are lymphocutanous sporotrichosis (LC) and fixed sporotrichosis (F). Although less common, mucosal, cutaneous disseminated, and extracutaneous forms have also been described. Multiple factors from the fungus and host can play a role in driving the clinical evolution of sporotrichosis to benign or severe disease. In this review, we discuss the immunopathological aspects involved in human sporotrichosis. Putting together the two branches of knowledge—host immune response and fungal evading mechanisms—we may perceive new possibilities in understanding the fungus–host interaction in order to be in a position to go further in the control of sporotrichosis.

Endemic mycoses in immunocompromised hosts

Endemic mycoses remain a significant cause of morbidity and mortality among immunocompromised patients. As the number of immunosuppressed individuals increases worldwide, the incidence of endemic mycoses is also expected to rise. In immunocompromised patients, endemic mycoses can present in atypical fashion, cause more severe and/or disseminated disease, and result in higher mortality. Despite several noteworthy advances over the past decade, significant challenges remain with regard to the prevention, diagnosis, and therapy of endemic mycoses in immunocompromised hosts. This review highlights important developments related to the epidemiology, diagnosis, treatment, and prevention of commonly encountered endemic mycoses. We also discuss emerging topics, knowledge gaps, and areas of future research.

Molecular identification of the Sporothrix schenckii complex

Sporothrix schenckii, an ascomycetous dimorphic organism that for over a century was recognized as the sole agent of sporotrichosis, a subcutaneous mycosis with a worldwide distribution. However, it has been proposed, based on physiologic and molecular aspects, that S. schenckii is a complex of distinct species: Sporothrix brasiliensis, Sporothrix mexicana, Sporothrix globosa, S. schenckii sensu strictu, Sporothrix luriei, and Sporothrix albicans (formerly Sporothrix pallida). Human disease has a broad range of clinical manifestations and can be classified into fixed cutaneous, lymphocutaneous, disseminated cutaneous, and extracutaneous sporotrichosis. The gold standard for the diagnosis of sporotrichosis is the culture; however, serologic, histopathologic and molecular approaches have been recently adopted for the diagnosis of this mycosis. Few molecular methods have been applied to the diagnosis of sporotrichosis to detect S. schenckii DNA from clinical specimens, and to identify Sporothrix spp. in culture. Until now, Sporothrix is the unique clinically relevant dimorphic fungus without an elucidated genome sequence, thus limiting molecular knowledge about the cryptic species of this complex, and the sexual form of all S. schenckii complex species. In this review we shall focus on the current diagnosis of the sporotrichosis, and discuss the current molecular tools applied to the diagnosis and identification of the Sporothrix complex species. 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).