Comparative genomic and phenotypic analyses of pathogenic fungi Neoscytalidium dimidiatum and Bipolaris papendorfii isolated from human skin scraping

Neoscytalidium dimidiatum and Bipolaris species are fungal plant pathogens that have been reported to cause human diseases. Recently, we have isolated numerous N. dimidiatum and Bipolaris species from the skin scrapings and nails of different patients. In this work, we have sequenced the genome of one strain of N. dimidiatum. The sequenced genome was compared to that of a previously reported Bipolaris papendorfii genome for a better understanding of their complex lifestyle and broad host-range pathogenicity. Both N. dimidiatum UM 880 (~ 43 Mb) and B. papendorfii UM 226 (~ 33 Mb) genomes include 11,015-12,320 putative coding DNA sequences, of which 0.51-2.49% are predicted transposable elements. Analysis of secondary metabolism gene clusters revealed several genes involved in melanin biosynthesis and iron uptake. The arsenal of CAZymes related to plants pathogenicity is comparable between the species, including genes involved in hemicellulose and pectin decomposition. Several important gene encoding keratinolytic peptidases were identified in N. dimidiatum and B. papendorfii, reflecting their potential pathogenic role in causing skin and nail infections. In this study, additional information on the metabolic features of these two species, such as nutritional profiling, pH tolerance, and osmotolerant, are revealed. The genomic characterization of N. dimidiatum and B. papendorfii provides the basis for the future functional studies to gain further insights as to what makes these fungi persist in plants and why they are pathogenic to humans.

Prevalence of Sarcoptes scabiei in Patients with Suspected scabies

Objective

Scabies is caused by an ectoparasite called Sarcoptes scabiei (S. scabiei), which penetrates the epidermis through skin folds and burrows in the stratum corneum, following the development of tunnels (sillion). The disease is specifically characterised by keratosis, allergy and itching that increases at night-time. This study aimed to investigate the frequency of S. scabiei in patients with a pro-diagnosis of scabies.

Objective

Between January 2012 and December 2019, a total of 746 [n=388 (52%), female; n=358 (48%) male] patients aged 0-80 years were admitted to Fırat University Hospital Parasitology-mycology Laboratory. Skin scrapings were taken from suspected lesions on anatomic regions such as the hands (wrist, interdigital skin, fingertip and palm), abdomen, penis and legs (thigh and bottom foot). They were examined under a light microscope after adding 15% potassium hydroxide solution.

Results

S. scabiei was positive in 139 (18.63%) of 746 patients including a mother and her daughter and a married couple, where 68 (9.11%) were female and 71 (9.52%) were male.

Conclusion

To our best knowledge, this is the first comprehensive study of scabies in Elazığ. Despite the recent socio-economic and cultural developments observed in our country, scabies and all other parasitic infestations still remain to be important problems. We believe that improvement of the public vigilance together with early diagnosis will improve sanitation and provide protection against scabies and parasitic infestations.

A Sarcoptes scabiei specific isothermal amplification assay for detection of this important ectoparasite of wombats and other animals

Background

The globally distributed epidermal ectoparasite, Sarcoptes scabiei, is a serious health and welfare burden to at-risk human and animal populations. Rapid and sensitive detection of S. scabiei infestation is critical for intervention strategies. While direct microscopy of skin scrapings is a widely utilised diagnostic method, it has low sensitivity. PCR, alternatively, has been shown to readily detect mite DNA even in microscopy-negative skin scrapings. However, a limitation to the latter method is the requirements for specialised equipment and reagents. Such resources may not be readily available in regional or remote clinical settings and are an important consideration in diagnosis of this parasitic disease.

Methodology

A Loop Mediated Isothermal Amplification (LAMP) assay targeting the ITS-2 gene for S. scabiei was developed and evaluated on clinical samples from various hosts, previously screened with conventional S. scabies-specific PCR. Species specificity of the newly developed LAMP assay was tested against a range of DNA samples from other arthropods. The LAMP assays were performed on a real-time fluorometer as well as thermal cycler to evaluate an end-point of detection. Using skin scrapings, a rapid sample processing method was assessed to eliminate extensive processing times involved with DNA extractions prior to diagnostic assays, including LAMP.

Results

The S. scabiei LAMP assay was demonstrated to be species-specific and able to detect DNA extracted from a single mite within a skin scraping in under 30 minutes. Application of this assay to DNA extracts from skin scrapings taken from a range of hosts revealed 92.3% congruence (with 92.50% specificity and 100% sensitivity) to the conventional PCR detection of S. scabiei. Preliminary results have indicated that diagnostic outcome from rapidly processed dry skin scrapings using our newly developed LAMP is possible in approximately 40 minutes.

Discussion

We have developed a novel, rapid and robust molecular assay for detecting S. scabiei infesting humans and animals. Based on these findings, we anticipate that this assay will serve an important role as an ancillary diagnostic tool at the point-of-care, complementing existing diagnostic protocols for S. scabiei.