Fast and Sustainable Thermo-osmotic DNA Extraction Protocol for Trans-spectrum Contingency and Field Use

In the field of molecular genetics, DNA extraction protocols and kits are sample-specific and proprietary, preventing lateral distribution among similar facilities from different sectors to alleviate supply shortages during a crisis. Expanding upon previous fast extraction protocols such as alkaline- and detergent-based ones, the use of boiling-hot water to rupture cells, virions, and nuclei, as proposed during the COVID-19 pandemic, might alleviate shortages and costs. Different soft, relatively abundant (highly enriched), and uncomplicated (genomically homogenous and with few inhibitors) biosamples are collected in 1.5 mL tubes, mixed with boiling-hot water, and stirred vigorously, so as to have membranes lysed and proteins deactivated; mechanical disruption may be used as well if necessary. Incubation in boiling water bath for 20-30 min follows. Depending on sample type and quantity, which affects the total extraction volume, 2-5 μL are pipetted off for direct PCR and the same volume for two decimal serial dilutions. The latter are intended to optimize the crude extract to a workable DNA/inhibitor concentration balance for direct PCR. Uncomplicated, highly enriched samples such as mycelial growth in fruits and human swab samples can be processed, contrary to complicated samples such as blood and physically unyielding samples such as plant tissue. The extract can be used for immediate PCR in both benchtop and portable thermocyclers, thus allowing nucleic acid amplification tests (NAAT) being performed in resource-limited settings with low cost and waste footprint or during prolonged crises, where supply chain failures may occur. Key features DNA extraction from different sample types using only boiling water and occasional mechanical assistance. Crude extract serially diluted twice, 10- and 100-fold, to bypass purification and quantification steps. Direct PCR for 2-10 μL of crude lysate and dilutions (conditional to sample type and quantity) to enhance probability of workable DNA-inhibitors' concentrations. Lowers the cost and curtails the overall footprint of testing to increase sustainability in field operations and in standard lab environments under supply chain derailment.

Historical microbiology: researching past bioevents by integrating scholarship (re)sources with paleomicrobiology assets

The analysis of past epidemics and pandemics, either spontaneous or of human origin, may revise the physical history of microbiota and create a temporal context in our understanding regarding pathogen attributes like virulence, evolution, transmission and disease dynamics. The data of high-tech scientific methods seem reliable, but their interpretation may still be biased when tackling events of the distant past. Such endeavors should be adjusted to other cognitive resources including historical accounts reporting the events of interest and references in alien medical cultures and terminologies; the latter may contextualize them differently from current practices. Thus 'historical microbiology' emerges. Validating such resources requires utmost care, as these may be susceptible to different biases regarding the interpretation of facts and phenomena; biases partly due to methodological limitations.

Treatment of nail clippings with ethyl alcohol improves the efficacy of Raman spectroscopy in the diagnosis of Trichophyton rubrum onychomycosis

The purpose of this work was to enhance the diagnostic accuracy of nail Raman spectroscopy for fungal nail infections, specifically onychomycosis caused by Trichophyton rubrum. The study assessed the different ethyl alcohol retention rates between control and infected nails after soaking nail clippings in ethanolic solutions and drying. Results revealed that ethyl alcohol completely evaporated from infected nail samples, while significant amounts were still present in control samples. Principal component analysis (PCA) was applied to discriminate control from infected nails and showed superior group separation when nails were treated with ethyl alcohol. PCA loadings plot attributed the efficient classification to the ν_s (CCO) Raman vibrational mode of ethyl alcohol. As Raman spectroscopy can detect minute concentration changes of ethyl alcohol in nails and the deterioration caused by onychomycosis accelerates its evaporation, a simple and rapid method for detecting T. rubrum onychomycosis is proposed.

Environmental and bioclimatic factors influencing yeasts and molds distribution along European shores

The present study employed data collected during the Mycosands survey to investigate the environmental factors influencing yeasts and molds distribution along European shores applying a species distribution modelling approach. Occurrence data were compared to climatic datasets (temperature, precipitation, and solar radiation), soil datasets (chemical and physical properties), and water datasets (temperature, salinity, and chlorophyll-a concentration) downloaded from web databases. Analyses were performed by MaxEnt software. Results suggested a different probability of distribution of yeasts and molds along European shores. Yeasts seem to tolerate low temperatures better during winter than molds and this reflects a higher suitability for the Northern European coasts. This difference is more evident considering suitability in waters. Both distributions of molds and yeasts are influenced by basic soil pH, probably because acidic soils are more favorable to bacterial growth. Soils with high nitrogen concentrations are not suitable for fungal growth, which, in contrast, are optimal for plant growth, favored by this environment. Finally, molds show affinity with soil rich in nickel and yeasts with soils rich in cadmium resulting in a distribution mainly at the mouths of European rivers or lagoons, where these metals accumulate in river sediments.

Beyond the Microbiome: Germ-ganism? An Integrative Idea for Microbial Existence, Organization, Growth, Pathogenicity, and Therapeutics

The advances made by microbiome research call for new vocabulary and expansion of our thinking in microbiology. For example, the life-forms presenting in both unicellular and multicellular formats invite us to rethink microbial existence, organization, growth, pathogenicity, and therapeutics in the 21st century. A view of such populations as parts of single organisms with a loose, distributed multicellular organization, introduced here as a germ-ganism, rather than communities, might open up interesting prospects for diagnostics and therapeutics innovation. This study tested and further contextualized the concept of germ-ganism using solid cultures of bacteria and fungi. Based on our findings and the literature reviewed herein, we propose that germ-ganism has synergy with a systems medicine approach by broadening host-environment interactions from cells and microorganisms to a scale of biological ecosystems. Germ-ganism also brings about the possibility of studying the multilevel impacts of novel therapeutic agents within and across networks of microbial ecosystems. The germ-ganism would lend itself, in the long term, to a veritable biocybernetics system, while in the mid-term, we anticipate it will contribute to new diagnostics and therapeutics. Biosecurity applications would be immensely affected by germ-ganism. Industrial applications of germ-ganism are of interest as a more sustainable alternative to costly solutions such as tampered strains/microorganisms. In conclusion, germ-ganism is informed by lessons from microbiome research and invites rethinking microbial existence, organization, and growth as an organism. Germ-ganism has vast ramifications for understanding pathogenicity, and clinical, biosecurity, and biotechnology applications in the current historical moment of the COVID-19 pandemic and beyond.

Evidence for the presence of a human saprophytic oral bacterium, Mycoplasma faucium, in the skin lesions of a psoriatic patient

Psoriasis is currently regarded a mixed autoimmune and autoinflammatory disease. This report describes for the first time the detection of a saprophytic, human oral Tenericutes species, Mycoplasma faucium, in the skin lesions of a patient presenting initially guttate and later plaque psoriasis. An unusual finding in standard histopathology investigation consisted of round and oval thinly stained or unstained, possibly intracellular structures, apparently directly pressing on keratinocyte nuclei of the psoriatic stratum spinosum. In ultrastructural study, wall-less bacteria were present intracellularly in the keratinocytes, mainly of the psoriatic stratum spinosum, and extracellularly in the upper dermis of the psoriatic lesions. M. faucium was consistently detected and identified in the psoriatic skin by general Tenericutes polymerase chain reaction and sequencing in two biopsies performed 31 months apart. This case raises new questions concerning the pathogenesis of psoriasis and its accepted autoimmune/autoinflammatory nature.

Mycosands: Fungal diversity and abundance in beach sand and recreational waters - Relevance to human health

The goal of most studies published on sand contaminants is to gather and discuss knowledge to avoid faecal contamination of water by run-offs and tide-retractions. Other life forms in the sand, however, are seldom studied but always pointed out as relevant. The Mycosands initiative was created to generate data on fungi in beach sands and waters, of both coastal and freshwater inland bathing sites. A team of medical mycologists and water quality specialists explored the sand culturable mycobiota of 91 bathing sites, and water of 67 of these, spanning from the Atlantic to the Eastern Mediterranean coasts, including the Italian lakes and the Adriatic, Baltic, and Black Seas. Sydney (Australia) was also included in the study. Thirteen countries took part in the initiative. The present study considered several fungal parameters (all fungi, several species of the genus Aspergillus and Candida and the genera themselves, plus other yeasts, allergenic fungi, dematiaceous fungi and dermatophytes). The study considered four variables that the team expected would influence the results of the analytical parameters, such as coast or inland location, urban and non-urban sites, period of the year, geographical proximity and type of sediment. The genera most frequently found were Aspergillus spp., Candida spp., Fusarium spp. and Cryptococcus spp. both in sand and in water. A site-blind median was found to be 89 Colony-Forming Units (CFU) of fungi per gram of sand in coastal and inland freshwaters, with variability between 0 and 6400 CFU/g. For freshwater sites, that number was 201.7 CFU/g (0, 6400 CFU/g (p = 0.01)) and for coastal sites was 76.7 CFU/g (0, 3497.5 CFU/g). For coastal waters and all waters, the median was 0 CFU/ml (0, 1592 CFU/ml) and for freshwaters 6.7 (0, 310.0) CFU/ml (p < 0.001). The results advocate that beaches should be monitored for fungi for safer use and better management.

Fast, Scalable, and Practical: An Alkaline DNA Extraction Pipeline for Emergency Microbiomics Biosurveillance

Pandemics and environmental crises evident from the first two decades of the 21st century call for methods innovation in biosurveillance and early detection of risk signals in planetary ecosystems. In crises conditions, conventional methods in public health, biosecurity, and environmental surveillance do not work well. In addition, the standard laboratory amenities and procedures may become unavailable, irrelevant, or simply not feasible, for example, owing to disruptions in logistics and process supply chains. The COVID-19 pandemic has been a wakeup call in this sense to reintroduce point-of-need diagnostics with an eye to limited resource settings and biosurveillance solutions. We report here a methodology innovation, a fast, scalable, and alkaline DNA extraction pipeline for emergency microbiomics biosurveillance. We believe that the presented methodology is well poised for effective, resilient, and anticipatory responses to future pandemics and ecological crises while contributing to microbiome science and point-of-need diagnostics in nonelective emergency contexts. The alkaline DNA extraction pipeline can usefully expand the throughput in emergencies by deployment or to allow backup in case of instrumentation failure in vital facilities. The need for distributed public health genomics surveillance is increasingly evident in the 21st century. This study makes a contribution to these ends broadly, and for future pandemic preparedness in particular. We call for innovation in biosurveillance methods that remain important existentially on a planet under pressure from unchecked human growth and breach of the boundaries between human and nonhuman animal habitats.

Brainstem phaeohyphomycosis due to Curvularia lunata (Cochliobolus lunatus) in a cat

A 13-year-old female neutered domestic short-hair cat was presented with chronic progressive vestibular ataxia, lethargy and anorexia. Clinical examination revealed bilateral mucopurulent nasal discharge. Neurological examination revealed obtundation, a right head tilt, ambulatory tetraparesis, generalised vestibular ataxia, decreased postural reactions in all limbs, right Horner's syndrome, spontaneous conjugate jerk rotatory nystagmus and right positional ventral strabismus. Neuroanatomical localisation was observed in the right central vestibular system. Computed tomography revealed a solitary ill-defined contrast-enhancing mass lesion at the level of the right cerebellopontine angle. Cerebrospinal fluid (CSF) analysis revealed mild mononuclear pleocytosis and fungal elements. CSF culture was positive for Curvularia spp. Further tests for underlying diseases were all negative. The cat was treated with antibiotic and antifungal treatment, but it deteriorated rapidly and was euthanased. Necropsy of the brainstem mass lesion revealed pyogranulomatous inflammation. Panfungal polymerase chain reaction (PCR) targeting the internal transcribed spacer (ITS) region and subsequent sequencing identified Curvularia lunata in the formalin fixed brain tissue. This is the first report of brainstem phaeohyphomycosis by Curvularia lunata (Pleosporales) in a cat. In addition, this is the first report among animal and humans where fungal elements of Curvularia lunata were found in the CSF cytology. Opportunistic fungal pathogens should be always considered within the differential diagnoses list in cats with neurological signs and advanced imaging findings compatible with solitary mass lesions in the brain. In feline patients with pyogranulomatous meningoencephalitis and a suspicion of a fungal aetiology, panfungal PCR for the ITS region and sequencing should be performed regardless of the absence of fungal elements in histopathology.

Isolation of Candida auris from cystic fibrosis patient, Greece, April 2019

We report the first isolation of Candida auris in Greece from a sputum culture of a cystic fibrosis patient in their 20s under posaconazole treatment. The pathogen was identified as C. duobushaemulonii by VITEK2YST, but as C. auris by MALDI-TOF MS. This case underscores the need for species-level identification of all non-albicans Candida (NAC) isolates from cystic fibrosis patients and patients with predisposing factors to fungal infection.

Variation of cultured skin microbiota in mothers and their infants during the first year postpartum

BACKGROUND/OBJECTIVES

The establishment of newborn skin flora depends on the ongoing skin maturation and the existence of potential microbial colonizers within the environment of the infant during a period of intense mother-infant physical interaction. This longitudinal study assessed culturable skin bacteria in the mother-infant dyad during the first year of life.

METHODS

A total of 17 mother-infant dyads were swabbed within 24 hours postpartum and at 3, 6, 9, and 12 months. Skin swabbing was performed on two anatomical areas per individual (mothers: chest-abdomen; infants: forehead-buttocks) and were incubated in five different solid culture media to optimize yield. Isolated bacterial species were identified to genus or species level using the API system (BioMeriéux, Marcy l'Etoile, France).

RESULTS

A total of 444 microbial strains were isolated belonging to 22 genera: 6 "frequent" (isolated from > 5% samples: S aureus, Proteus, Klebsiella, Pseudomonas, Enterobacter, and Enterococcus) and 16 "infrequent." Isolated genera per individual peaked at 6 months postpartum for mothers and infants (P < 0.05). Enterobacter, Enterococcus, Klebsiella, and Pseudomonas isolation rates varied significantly as a function of sampling time contrary to the rather constant isolation rates of Proteus and S aureus. The rates of concordant isolation of the same microbial species within the mother-infant dyad tended to drop from birth to the end of the first year postpartum.

CONCLUSIONS

Distinct variations in the isolation rates of skin commensals from specific anatomical sites of the mother-infant dyad indicate bidirectional microbial transmission. Increasing skin flora individuality of the growing infant was recorded, manifested by declining rates of concordant isolation of the same microbial species from mother and her infant.

The lipid profile of three Malassezia species assessed by Raman spectroscopy and discriminant analysis

Malassezia yeasts constitute the major eukaryotic cutaneous flora of homoeothermic vertebrates. These lipophilic yeasts are able to cause, trigger, or aggravate common skin diseases under favorable conditions. Species identification and subspecies differentiation is currently based on morphological characteristics, lipid assimilation profile, and molecular tests. Mass spectrometry has been also reported as a reliable, yet costly and labor-intensive, method to classify Malassezia yeasts. Here, we introduce Raman spectroscopy as a new molecular technique able to differentiate three phylogenetically close Malassezia species (M.globosa, M.pachydermatis, and M.sympodialis) by examining their lipid metabolic profile. Using Raman spectroscopy, lipid fingerprints of Malassezia cultures on Leeming-Notman agar, were analyzed by spectral bands assignment and partial least squares discriminant analysis. Our results demonstrate differential utilization of lipid supplements among these three species and the ability of Raman spectroscopy to rapidly and accurately discriminate them by predictive modelling.

Genotypes and population genetics of cryptococcus neoformans and cryptococcus gattii species complexes in Europe and the mediterranean area

A total of 476 European isolates (310 Cryptococcus neoformans var. grubii, 150 C. neoformans var. neoformans, and 16 C. gattii species complex) from both clinical and environmental sources were analyzed by multi-locus sequence typing. Phylogenetic and population genetic analyses were performed. Sequence analysis identified 74 sequence types among C. neoformans var. neoformans (VNIV), 65 among C. neoformans var. grubii (56 VNI, 8 VNII, 1 VNB), and 5 among the C. gattii species complex (4 VGI and 1 VGIV) isolates. ST23 was the most frequent genotype (22%) among VNI isolates which were mostly grouped in a large clonal cluster including 50% of isolates. Among VNIV isolates, a predominant genotype was not identified. A high percentage of autochthonous STs were identified in both VNI (71%) and VNIV (96%) group of isolates. The 16 European C. gattii species complex isolates analyzed in the present study originated all from the environment and all belonged to a large cluster endemic in the Mediterranean area. Population genetic analysis confirmed that VNI group of isolates were characterized by low variability and clonal expansion while VNIV by a higher variability and a number of recombination events. However, when VNI and VNIV environmental isolates were compared, they showed a similar population structure with a high percentage of shared mutations and the absence of fixed mutations. Also linkage disequilibrium analysis reveals differences between clinical and environmental isolates showing a key role of PLB1 allele combinations in host infection as well as the key role of LAC1 allele combinations for survival of the fungus in the environment. The present study shows that genetic comparison of clinical and environmental isolates represents a first step to understand the genetic characteristics that cause the shift of some genotypes from a saprophytic to a parasitic life style.

Changing Epidemiology of Invasive Candidiasis in Children during a 10-Year Period

Candida species are a common cause of invasive infection in neonates and children. The aim of our study was to evaluate the epidemiology and microbiology of invasive candidiasis (IC) in the largest tertiary Greek pediatric hospital during a 10-year period. A retrospective cohort study was performed from January 2008 to December 2017. Identification of species and antifungal susceptibility testing was performed according to the Clinical and Laboratory Standards Institute (CLSI) methodology. During the study period, 178 cases of IC were recorded. The tissue distribution included blood (87.1%), cerebrospinal (7.9%), peritoneal (3.9%) and pleural fluids (1.1%). Candida albicans and Candida parapsilosis (sensu lato) were the most frequently isolated species (47.8% and 28.7% respectively). From period 2008⁻2012 to period 2013⁻2017, a significant decrease in IC rates was detected (0.21 cases/1000 hospitalization days VS 0.11 cases/1000 hospitalization days, P = 0.040), while median minimum inhibitory concentrations (MICs) of amphotericin B were significantly increased for both C. albicans and C. parapsilosis (sl) (P = 0.037 and P = 0.004 respectively). The decrease in IC rates may reflect the increased awareness as well as the effective infection control initiatives and antifungal interventions. However, the significant increase in the MICs for amphotericin B and echinocandins such as caspofungin, raises concerns about their common use as first-line treatment. Epidemiologic monitoring is, therefore, critically important in order to evaluate and optimize therapeutic protocols for IC in pediatric populations.

Septic shock due to Candida famata (Debaryomyces hansenii) candidemia in an ICU immunocompetent trauma-patient

Sepsis related to Candida famata (C. famata) fungemia is extremely rare in immunocompetent patients. Moreover, septic shock has not been reported due to this yeast. A previously healthy young multi-trauma male, presented septic shock from C. famata, after he had been admitted in the Intensive Care Unit (ICU) due to haemorrhagic shock. Risk factors for candidemia in ICU patients are the presence of a central venous catheter (CVC), Total Parenteral Nutrition (TPN), use of broad-spectrum antimicrobials, immunosuppression and the length of ICU stay. The presence of CVCs, prior use of antibiotics, prolonged hospitalization, disruption of skin flora and immunocompromised states have been identified as predisposing risk factors for C. famata fungemia. It is worth noting that the present case concerns a non-immunocompromised patient, but long ICU stay and brain injury may indicate a state of immunoparalysis. Identification of the yeast was performed by partial amplification and sequencing of the 26S ribosomal DNA gene [hypervariable region D1/D2; partial sequencing of the act1 gene confirmed the identity of the strain as Debaryomyces hansenii (GenBank submission ID: 1688297)] The patient quickly recovered from sepsis after initiation of amphotericin B and was discharged on the 60th day.

High variability within Candida albicans transcription factor RLM1: Isolates from vulvovaginal infections show a clear bias toward high molecular weight alleles

Previous studies have correlated the severity of recurrent vulvovaginal Candida infections (VVC) and balanitis in patients from China with the presence of some dominant genotypes at the ORF RLM1. Here we tested VVC vs non-VVC isolates from Portugal, Brazil and Greece and, although the same genotypes were identified in VVC isolates, they were present in only five out of 150 strains. However, this analysis showed that VVC isolates presented a higher percentage of genotypes with similar high molecular weight alleles, in comparison with strains isolated from other biological sources.

Humanome Versus Microbiome: Games of Dominance and Pan-Biosurveillance in the Omics Universe

Global governance of pathogens such as Ebola virus and infectious diseases is central to global health, and to innovation in systems medicine. Worrisomely, the gaps in human immunity and healthcare services combined with novel pathogens emerging by travel, biotechnological advances, or the rupture of the host-species barrier challenge infectious diseases' global governance. Such biorisks and biothreats may scale up to global catastrophic biological risks (GCBRs) spatiotemporally, either as individual or as collective risks. The scale and intensity of such threats challenge current thinking on surveillance, and calls for a move toward pan-biosurveillance. New multilayered, cross-sectoral, and adaptable strategies of prevention and intervention on GCBRs should be developed, considering human hosts in entirety, and in close relationship with other hosts (plants and animals). This also calls for the "Humanome," which we introduce in this study as the totality of human subjects plus any directly dependent biological or nonbiological entities (products, constructs, and interventions). Surveillance networks should be implemented by integrating communications, diagnostics, and robotics/aeronautics technologies. Suppression of pathogens must be enforced both before and during an epidemic outbreak, the former allowing more drastic measures before the pathogens harbor the host. We propose in this expert review that microbiome-level intervention might particularly prove as an effective solution in medical and environmental scales against traditional, currently emerging, and future infectious threats. We conclude with a discussion on the ways in which the humanome and microbiome contest and cooperate, and how this knowledge might usefully inform in addressing the GCBRs, bioterrorism, and associated threats in the pursuit of pan-biosurveillance.

Phytochemical Analysis and Antimicrobial Activity of Origanum dictamnus Traditional Herbal Tea (decoction)

In the framework of the re-evaluation of chemistry and biological properties of Greek herbal teas (decoctions), the objective of this study was the estimation of the total phenolic content and the antimicrobial activity as well as the chemical analysis of the water extracts (decoction) of three samples of Cretan dittany ( Origanum dictamnus L) prepared in the traditional way to be used (drunk). Ten secondary metabolites were isolated and elucidated on the basis of spectral evidence for the first time from O. dictamnus drinkable decoction: carvacrol (1), β-sitosterol (2), uvaol (3), ursolic acid (4), rosmarinic acid (5), lithospermic acid (6), ferulic acid (7), cafeic acid (8), p-coumaric acid (9) and apigenin-7- O-glucoside (10). The samples showed a high total phenolic content (185.5-139.7 mg CAE/g) and an interesting antibacterial profile against Gram positive and negative human pathogenic microorganisms. Furthermore, the bioactivity against a panel of Malassezia strains was estimated.

Culturomics: A New Kid on the Block of OMICS to Enable Personalized Medicine

This innovation analysis highlights the underestimated and versatile potential of the new field of culturomics and examines its relation to other OMICS system sciences such as infectiomics, metabolomics, phenomics, and pharmacomicrobiomics. The advent of molecular biology, followed by the emergence of various disciplines of the genomics, and most importantly metagenomics, brought about the sharp decline of conventional microbiology methods. Emergence of culturomics has a natural synergy with therapeutic and clinical genomic approaches so as to realize personalized medicine. Notably, the concept of culturomics expands on that of phenomics and allows a reintroduction of the culture-based phenotypic characterization into the 21st century research repertoire, bolstered by robust technology for automated and massive execution, but its potential is largely unappreciated at present; the few available references show unenthusiastic pursuit and in narrow applications. This has not to be so: depending on the specific brand of culturomics, the scope of applications may extend to medicine, agriculture, environmental sciences, pharmacomicrobiomics, and biotechnology innovation. Moreover, culturomics may produce Big Data. This calls for a new generation of data scientists and innovative ways of harnessing and valorizing Big Data beyond classical genomics. Much more detailed and objective classification and identification of microbiota may soon be at hand through culturomics, thus enabling precision diagnosis toward truly personalized medicine. Culturomics may both widen the scope of microbiology and improve its contributions to diagnostics and personalized medicine, characterizing microbes and determining their associations with health and disease dynamics.

Wireless electrostimulation: a new approach in combating infection?

Electrostimulation (ES), hitherto successfully employed in wound treatment, has shown potential in antimicrobial applications, suggesting its use as synergistic to or replacement of antibiotics. The differential susceptibility of pathogens and host tissue and organs to various ES modalities might allow selective use against specific infections. The use of ES is cheaper in terms of development/testing, routine application and environmental footprint. If extensive substitution of chemical compounds is achieved, the development of resistance might be reversed through negative selection. A promising setup of ES seems to be the noncontact current transfer, due to low amperage similar to innate bioelectricity, painlessness, simple logistics and low risk for treatment-caused infection.

Cornus mas L. (cornelian cherry), an important European and Asian traditional food and medicine: Ethnomedicine, phytochemistry and pharmacology for its commercial utilization in drug industry

ETHNOPHARMACOLOGICAL RELEVANCE

Cornus mas L. (cornelian cherry) fruits have been used for centuries as traditional cuisine and folk medicine in various countries of Europe and Asia. In folk medicines, the fruits and other parts of the plant have been used for prevention and treatment of a wide range of diseases such as diabetes, diarrhea, gastrointestinal disorders, fevers, rheumatic pain, skin and urinary tract infections, kidney and liver diseases, sunstroke, among others. This review provides a systematic and constructive overview of ethnomedicinal uses, chemical constituents and pharmacological activities of this plant as well as future research need for its commercial utilization as nutraceutical food supplement and medicine.

MATERIALS AND METHODS

This review is based on available literature on ethnomedicinal uses, phytochemical, pharmacological, toxicity and clinical studies on Cornus mas L. (cornelian cherry) fruits and other organs that was collected from electronic (SciFinder, PubMed, Science Direct and ACS among others) and library searches of books and journals.

RESULTS

Versatile ethnomedicinal uses of the plant in different European and Asian countries have been reported. Phytochemical investigations on different parts of this plant have resulted in the identification of 101 compounds, among which anthocyanins, flavonoids and iridoids are the predominant groups. The crude extracts of fruits and other parts of the plant and their pure isolates exhibit a broad spectrum of pharmacological activities such as anti-microbial, anti-diabetic, anti-atherosclerotic, cyto-, hepato-, neuro- and renalprotective, antiplatelet and antiglaucomic activities. Anthocyanins, flavonoids, iridoids and vitamin C are the major bioactive constituents of the fruits. Fruits are non-toxic and safe food on acute toxicity studies in rat and human models. Clinical trials in diabetic type2 and hyperlipidemic patients showed significant trends of amelioration in sugar level, insulin secretion in diabetic patients and amelioration of lipid profile, apolipoprotein status and vascular inflammation in hyperlipidemic patients.

CONCLUSION

Based on our review, Cornus mas L. (cornelian cherry) fruits and leaves can be used mainly in the treatment of diabetes, obesity, atherosclerosis, skin diseases, gastrointestinal and rheumatic problems. Some indications from ethnomedicines have been validated by pharmacological activities of the fruits and its extracts/pure isolates. The reported data reveal that the fruits are a potential source for treatment of diabetes, obesity, hyperlipidemia and gastrointestinal disorders. Unfortunately, the pharmacological studies in these areas are still insufficient to substantiate these preventive effects in confirmatory trials on the mass-scale clinical settings. Future studies on mechanisms of action, bioavailability, pharmacokinetics and adverse effects of the extracts and their bioactive constituents as well as their effective doses and long term toxic effects in humans are needed for commercial applications of these extracts/isolates in modern medicines. The available literature showed that most of the activities of the extracts are due to their constituents, anthocyanins, flavonoids and other phenolics, iridoids and vitamins for their antioxidant and other properties.

Identification and Characterization of VNI/VNII and Novel VNII/VNIV Hybrids and Impact of Hybridization on Virulence and Antifungal Susceptibility Within the C. neoformans/C. gattii Species Complex

Cryptococcus neoformans and C. gattii are pathogenic basidiomycetous yeasts and the commonest cause of fungal infection of the central nervous system. Cryptococci are typically haploid but several inter-species, inter-varietal and intra-varietal hybrids have been reported. It has a bipolar mating system with sexual reproduction occurring normally between two individuals with opposite mating types, α and a. This study set out to characterize hybrid isolates within the C. neoformans/C. gattii species complex: seven unisexual mating intra-varietal VNI/VNII (αAAα) and six novel inter-varietal VNII/VNIV (aADα). The URA5-RFLP pattern for VNII/VNIV (aADα) differs from the VNIII (αADa) hybrids. Analysis of the allelic patterns of selected genes for AD hybrids showed 79% or more heterozygosis for the studied loci except for CBS132 (VNIII), which showed 50% of heterozygosity. MALDI-TOF MS was applied to hybrids belonging to different sero/mating type allelic patterns. All hybrid isolates were identified as belonging to the same hybrid group with identification scores ranging between 2.101 to 2.634. All hybrids were virulent when tested in the Galleria mellonella (wax moth) model, except for VNII/VNIV (aADα) hybrids. VNI/VGII hybrids were the most virulent hybrids. Hybrids recovered from larvae manifested a significant increase in capsule and total cell size and produced a low proportion (5-10%) of giant cells compared with the haploid control strains. All strains expressed the major virulence factors-capsule, melanin and phospholipase B-and grew well at 37°C. The minimal inhibitory concentration of nine drugs was measured by micro-broth dilution and compared with published data on haploid strains. MICs were similar amongst hybrids and haploid parental strains. This is the first study reporting natural same sex αAAα intra-varietal VNI/VNII hybrids and aADα inter-varietal VNII/VNIV hybrids.

T2Candida Provides Rapid and Accurate Species Identification in Pediatric Cases of Candidemia

OBJECTIVES

The goal of this study is to assess the ability of the T2Candida platform (T2 Biosystems, Lexington, MA) to accurately identify Candida species from pediatric blood specimens with low volumes.

METHODS

Whole blood from 15 children with candidemia was collected immediately following blood culture draw. The amount of blood required by the system was reduced by pipetting whole blood directly onto the T2Candida cartridge. Specimens were subsequently run on the T2Dx Instrument (T2 Biosystems).

RESULTS

The T2Candida panel provided the appropriate result for each specimen compared with blood culture-based species identification and correctly identified 15 positive and nine negative results in 3 to 5 hours. While the time to species identification for blood culture was not reported, the T2Candida results include species data.

CONCLUSIONS

T2Candida can be used to efficiently diagnose or rule out candidemia using low-volume blood specimens from pediatric patients. This could result in improved time to appropriate antifungal therapy or reduction in unnecessary empirical antifungal therapy.

Environmental distribution of Cryptococcus neoformans and C. gattii around the Mediterranean basin

In order to elucidate the distribution of Cryptococcus neoformans and C. gattii in the Mediterranean basin, an extensive environmental survey was carried out during 2012-2015. A total of 302 sites located in 12 countries were sampled, 6436 samples from 3765 trees were collected and 5% of trees were found to be colonized by cryptococcal yeasts. Cryptococcus neoformans was isolated from 177 trees and C. gattii from 13. Cryptococcus neoformans colonized 27% of Ceratonia, 10% of Olea, Platanus and Prunus trees and a lower percentage of other tree genera. The 13 C. gattii isolates were collected from five Eucalyptus, four Ceratonia, two Pinus and two Olea trees. Cryptococcus neoformans was distributed all around the Mediterranean basin, whereas C. gattii was isolated in Greece, Southern Italy and Spain, in agreement with previous findings from both clinical and environmental sources. Among C. neoformans isolates, VNI was the prevalent molecular type but VNII, VNIV and VNIII hybrid strains were also isolated. With the exception of a single VGIV isolate, all C. gattii isolates were VGI. The results confirmed the presence of both Cryptococcus species in the Mediterranean environment, and showed that both carob and olive trees represent an important niche for these yeasts.

Effects of Yeast and Bacterial Commensals and Pathogens of the Female Genital Tract on the Transepithelial Electrical Resistance of HeLa Cells

Commensals of the human body can shift to a pathogenic phase when the host immune system is impaired. This study aims to investigate the effect of seven yeast and two bacterial commensals and opportunistic pathogens isolated from blood and the female genital tract on the transepithelial electrical resistance (TER) of human cervical epithelial cell cultures (HeLa). The pathogens Candida tropicalis, C. parapsilosis,C. glabrata, C. krusei, C. albicans and Saccharomyces cerevisiae, caused a significant decrease in TER as compared to the controls; Lactobacillus spp caused a significant increase in TER versus the controls and Escherichia coli had no effect on the TER of the cell monolayers. The above data show that Candida spp., S. cerevisiae and Lactobacillus spp. have a non-selective effect on the TER of HeLa cell monolayers. These results are consistent with the in vivo non-selective action of these microorganisms on the various human mucosal epithelia.

Multilocus sequence typing analysis reveals that Cryptococcus neoformans var. neoformans is a recombinant population

Cryptococcus neoformans var. neoformans (serotype D) represents about 30% of the clinical isolates in Europe and is present less frequently in the other continents. It is the prevalent etiological agent in primary cutaneous cryptococcosis as well as in cryptococcal skin lesions of disseminated cryptococcosis. Very little is known about the genotypic diversity of this Cryptococcus subtype. The aim of this study was to investigate the genotypic diversity among a set of clinical and environmental C. neoformans var. neoformans isolates and to evaluate the relationship between genotypes, geographical origin and clinical manifestations. A total of 83 globally collected C. neoformans var. neoformans isolates from Italy, Germany, France, Belgium, Denmark, Greece, Turkey, Thailand, Japan, Colombia, and the USA, recovered from different sources (primary and secondary cutaneous cryptococcosis, disseminated cryptococcosis, the environment, and animals), were included in the study. All isolates were confirmed to belong to genotype VNIV by molecular typing and they were further investigated by MLST analysis. Maximum likelihood phylogenetic as well as network analysis strongly suggested the existence of a recombinant rather than a clonal population structure. Geographical origin and source of isolation were not correlated with a specific MLST genotype. The comparison with a set of outgroup C. neoformans var. grubii isolates provided clear evidence that the two varieties have different population structures.

A Prospective, International Cohort Study of Invasive Mold Infections in Children

BACKGROUND

Invasive mold infections (IMIs) are a leading cause of mortality in immunocompromised children, yet there has never been an international epidemiologic investigation of pediatric IMIs.

METHODS

This international, prospective cohort study was performed to characterize the epidemiology, antifungal therapy, and outcomes of pediatric IMIs. Children (≤18 years) with proven or probable IMIs were enrolled between August 2007 and May 2011 at 22 sites. Risk factors, underlying diagnoses, and treatments were recorded. Outcomes were assessed at 12 weeks after diagnosis using European Organization for Research and Treatment of Cancer/Mycoses Study Group response criteria.

RESULTS

One hundred thirty-one pediatric patients with IMIs were enrolled; the most common IMI was invasive aspergillosis ([IA] 75%). Children with IA and those with other types of IMIs had similar underlying risk factors, except that children with IMIs caused by non-Aspergillus species were more likely to have received mold-active antifungal agents preceding diagnosis. The most commonly used antifungal classes after diagnosis were triazoles (82%) and polyenes (63%). Combination therapy was used in 53% of patients. Use of combination therapy was associated with an increased risk of adverse events (risk ratio, 1.98; 95% confidence interval, 1.06-3.68; P = .031), although there was no detectable difference in outcome.

CONCLUSIONS

Although risk factors for IMIs are similar across specific subtypes, preceding antifungal therapy may be an important modifier. Combination antifungal therapy requires further study to determine its true risks and benefits.

Performance of three small-scale wastewater treatment plants. A challenge for possible re use

The study focused on the assessment of the performance of three WWTPs in Greece by the estimation of the microbiological and chemical quality of influent and effluent sewage. Physicochemical parameters were recorded (temperature, pH, COD, BOD, suspended solids, conductivity), and meteorological data were collected (air temperature, rain). Microbiological parameters were analyzed (Escherichia coli, total coliforms, bacteriophages, Salmonella, human adenoviruses, Candida, Pseudallescheria boydii, helminths, parasites Cryptosporidium ssp., and Giardia spp.). Statistically significant correlations among the various aforementioned parameters were investigated, in an attempt to propose appropriate processing performance indicators. Furthermore, the study aimed to assess current joint ministerial decision (JMD) on wastewater reuse, for irrigation purposes; to evaluate its practicability and its potential for public health protection. In the vast majority, outlet samples from all three studied WWTPs were not appropriate for irrigation reuse purposes based on BOD50 and suspended solids limit values, set by the current JMD, for both limited and unrestricted irrigation applications. Reductions for E. coli, total coliforms, and bacteriophages were found to range between 2-3, 1.5-2.5, and 2-4 log10 values, respectively. Salmonella spp. was detected in outlet sewage samples from Patra (PAT), Arachova (ARH), and Livadeia (LEV), at 23% (3/13), 33% (4/12), and 38% (5/13), respectively. Molds were detected at 92.3% (12/13), 100% (13/13), and 91.6% (11/12), respectively, while Candida was found at 85% (11/13), 67% (8/12), and 46% (6/13). A high prevalence of Pseudallescheria boydii, in outlet samples from all studied WWTPs is an important public health issue, which underlines the need for further studies on this emerging fungal pathogen in wastewater reuse applications. Pseudallescheria boydii was found at 85% (11/13), 67% (8/12), and 46% (6/13), respectively. Helminths were found in both inlet and outlet samples, of all studied WWTPs, at 100%. Human adenoviruses, were detected at high percentages in outlet samples at 76.9% (10/13), 92.3% (12/13), 84.6% (11/13), respectively, while no influence of UV irradiation was recorded on the entry and exit loads of human adenoviruses. No influence of meteorological parameters was found on the microbiological and chemical parameters, with the exception of a weak positive correlation between environmental temperature and bacteriophages. A moderate positive correlation was found between BOD and suspended solids, bacteriophages, and total coliforms, bacteriophages and E. coli, and bacteriophages and adenoviruses. A significant positive correlation was found between total coliforms and E. coli, COD and BOD, and suspended solids and COD. No correlations were proved between human pathogens and bacterial indicator parameters. Collectively, our findings underlined the unsuitability of the current JMD on wastewater reuse in Greece, or public health protection. The study is expected to support the development of a public health risk assessment model based on quantitative risk assessment on the use of treated wastewater for irrigation purposes in Greece.

International Society of Human and Animal Mycology (ISHAM)-ITS reference DNA barcoding database--the quality controlled standard tool for routine identification of human and animal pathogenic fungi

Human and animal fungal pathogens are a growing threat worldwide leading to emerging infections and creating new risks for established ones. There is a growing need for a rapid and accurate identification of pathogens to enable early diagnosis and targeted antifungal therapy. Morphological and biochemical identification methods are time-consuming and require trained experts. Alternatively, molecular methods, such as DNA barcoding, a powerful and easy tool for rapid monophasic identification, offer a practical approach for species identification and less demanding in terms of taxonomical expertise. However, its wide-spread use is still limited by a lack of quality-controlled reference databases and the evolving recognition and definition of new fungal species/complexes. An international consortium of medical mycology laboratories was formed aiming to establish a quality controlled ITS database under the umbrella of the ISHAM working group on "DNA barcoding of human and animal pathogenic fungi." A new database, containing 2800 ITS sequences representing 421 fungal species, providing the medical community with a freely accessible tool at http://www.isham.org/ and http://its.mycologylab.org/ to rapidly and reliably identify most agents of mycoses, was established. The generated sequences included in the new database were used to evaluate the variation and overall utility of the ITS region for the identification of pathogenic fungi at intra-and interspecies level. The average intraspecies variation ranged from 0 to 2.25%. This highlighted selected pathogenic fungal species, such as the dermatophytes and emerging yeast, for which additional molecular methods/genetic markers are required for their reliable identification from clinical and veterinary specimens.

Pityriazepin and other potent AhR ligands isolated from Malassezia furfur yeast

Malassezia furfur yeast strains isolated from diseased human skin preferentially biosynthesize indole alkaloids which can be detected in the human skin and are highly potent activators of the aryl hydrocarbon receptor (AhR) and AhR-dependent gene expression. Chemical analysis of an EtOAc extract of a M. furfur strain obtained from diseased human skin and grown on l-tryptophan agar revealed several known AhR active tryptophan metabolites along with a previously unidentified compound, pityriazepin. While its structure resembled that of the known alkaloid pityriacitrin, the comprised pyridine ring had been transformed into an azepinone. The indoloazepinone scaffold of pityriazepin is extremely rare in nature and has only been reported once previously. Pityriazepin, like the other isolated compounds, was found to be a potent activator of the AhR-dependent reporter gene assay in recombinant cell lines derived from four different species, although significant species differences in relative potency were observed. The ability of pityriazepin to competitively bind to the AhR and directly stimulate AhR DNA binding classified it as a new naturally-occurring potent AhR agonist. M. furfur produces an expanded collection of extremely potent naturally occurring AhR agonists, which produce their biological effects in a species-specific manner.

Soluble urokinase plasminogen activator receptor level is an independent predictor of the presence and severity of coronary artery disease and of future adverse events

Introduction

Soluble urokinase plasminogen activator receptor (suPAR) is an emerging inflammatory and immune biomarker. Whether suPAR level predicts the presence and the severity of coronary artery disease (CAD), and of incident death and myocardial infarction (MI) in subjects with suspected CAD, is unknown.

Methods and Results

We measured plasma suPAR levels in 3367 subjects (67% with CAD) recruited in the Emory Cardiovascular Biobank and followed them for adverse cardiovascular (CV) outcomes of death and MI over a mean 2.1±1.1 years. Presence of angiographic CAD (≥50% stenosis in ≥1 coronary artery) and its severity were quantitated using the Gensini score. Cox's proportional hazard survival and discrimination analyses were performed with models adjusted for established CV risk factors and C‐reactive protein levels. Elevated suPAR levels were independently associated with the presence of CAD (P<0.0001) and its severity (P<0.0001). A plasma suPAR level ≥3.5 ng/mL (cutoff by Youden's index) predicted future risk of MI (hazard ratio [HR]=3.2; P<0.0001), cardiac death (HR=2.62; P<0.0001), and the combined endpoint of death and MI (HR=1.9; P<0.0001), even after adjustment of covariates. The C‐statistic for a model based on traditional risk factors was improved from 0.72 to 0.74 (P=0.008) with the addition of suPAR.

Conclusion

Elevated levels of plasma suPAR are associated with the presence and severity of CAD and are independent predictors of death and MI in patients with suspected or known CAD.

Invasive Candida infections in surgical patients in intensive care units: a prospective, multicentre survey initiated by the European Confederation of Medical Mycology (ECMM) (2006-2008)

A prospective, observational, multicentre study of invasive candidosis (IC) in surgical patients in intensive care units (ICUs) was conducted from 2006 to 2008 in 72 ICUs in 14 European countries. A total of 779 patients (62.5% males, median age 63 years) with IC were included. The median rate of candidaemia was 9 per 1000 admissions. In 10.8% the infection was already present at the time of admission to ICU. Candida albicans accounted for 54% of the isolates, followed by Candida parapsilosis 18.5%, Candida glabrata 13.8%, Candida tropicalis 6%, Candida krusei 2.5%, and other species 5.3%. Infections due to C. krusei (57.9%) and C. glabrata (43.6%) had the highest crude mortality rate. The most common preceding surgery was abdominal (51.5%), followed by thoracic (20%) and neurosurgery (8.2%). Candida glabrata was more often isolated after abdominal surgery in patients ≥60 years, and C. parapsilosis was more often isolated in neurosurgery and multiple trauma patients as well as children ≤1 year of age. The most common first-line treatment was fluconazole (60%), followed by caspofungin (18.7%), liposomal amphotericin B (13%), voriconazole (4.8%) and other drugs (3.5%). Mortality in surgical patients with IC in ICU was 38.8%. Multivariate analysis showed that factors independently associated with mortality were: patient age ≥60 years (hazard ratio (HR) 1.9, p 0.001), central venous catheter (HR 1.8, p 0.05), corticosteroids (HR 1.5, p 0.03), not receiving systemic antifungal treatment for IC (HR 2.8, p <0.0001), and not removing intravascular lines (HR 1.6, p 0.02).

Skin diseases associated with Malassezia yeasts: facts and controversies

The implication of the yeast genus Malassezia in skin diseases has been characterized by controversy, since the first description of the fungal nature of pityriasis versicolor in 1846 by Eichstedt. This is underscored by the existence of Malassezia yeasts as commensal but also by their implication in diseases with distinct absence of inflammation despite the heavy fungal load (pityriasis versicolor) or with characteristic inflammation (eg, seborrheic dermatitis, atopic dermatitis, folliculitis, or psoriasis). The description of 14 Malassezia species and subsequent worldwide epidemiologic studies did not reveal pathogenic species but rather disease-associated subtypes within species. Emerging evidence demonstrates that the interaction of Malassezia yeasts with the skin is multifaceted and entails constituents of the fungal wall (melanin, lipid cover), enzymes (lipases, phospholipases), and metabolic products (indoles), as well as the cellular components of the epidermis (keratinocytes, dendritic cells, and melanocytes). Understanding the complexity of their interactions will highlight the controversies on the clinical presentation of Malassezia-associated diseases and unravel the complexity of skin homeostatic mechanisms.