Dermatophytes’ identification by Matrix-assisted laser desorption ionization-time of flight mass spectrometry. (MALDI-TOF MS) - the experience of a clinical laboratory

Objectives: Dermatophytes are a challenging group of fungi that infect the keratinized tissues. The taxonomy of these fungi has changed recently with the reclassification of some species and description of new ones. However, many clinical laboratories still base the identification of dermatophytes on their phenotype. Since dermatophytes are very pleomorphic, macro and micromorphology are often insufficient to reach a correct classification and may lead to misidentifications. The identification based on MALDI-TOF relies on the protein profile of the microorganism. Thus, this study aims to summarize our current laboratorial experience of dermatophyte identification using MALDI-TOF MS. Methods: From january to april 2018, 95 dermatophytes isolates, collected from human keratinized samples and also from quality control programs were characterized by phenotypic analysis, and by VITEK MS V3.2 bioMerieux. Before identification procedure, isolates were inoculated on Sabouraud Dextrose agar plates and incubated at 27°C during 5 to 10 days. Species were identified taking into account clinical features, as well as cultural, microscopic and physiological characteristics. Prior to MALDI-TOF MS analysis, the samples were pre-treated according to the manufacturer’s protocol for filamentous fungi. Molecular identification by sequencing of the internal transcribed spacer 1 (ITS1) was performed in 34 of those isolates Results: Through phenotypic analysis eight different species were identified (54 Trichophyton rubrum; 4 T.soudanense; 22 T.interdigitale; 1 T.mentagrophytes; 3 T.tonsurans; 7 Microsporum canis; 3 M.audouinii; 1 Microsporum spp.- (non canis or audouinii). MALDI-TOF analysis showed an identification agreement in 80 cases (84,2%) with a confidence level of 99,9%. Eight isolates showed divergent identification results: three T.rubrum were identified as T.violaceum, three T.soudanense were identified as T.rubrum, one T.mentagrophytes was identified as T.interdigitale and one T.tonsurans was identified as T.rubrum. In four cases MALDI-TOF analysis did not get a profile. The ITS sequencing analysis of discrepant results corroborated the MALDI-TOF identification in five of them. On the other hand, T.soudanense was only identified by phenotypic analysis since MALDI-TOF and ITS sequencing result was T.rubrum. MALDITOF identification of T.violaceum was not confirmed by ITS sequencing that identified T. rubrum instead, in accordance with the phenotypic identification. Conclusion: Correct identification of dermatophytes to species level requires sequencing of the ITS, LSU, and/or betatubulin regions. The implementation of this methodology in a clinical laboratory is expensive and time consuming. MALDI-TOF identification is a good option for dermatophytes’ identification performed in laboratory routine, since costs of consumables as well as time of sample preparation are lower than for PCR analysis and doesn’t require long training period as phenotypic identification does. In this study, however, both methods failed to identify some species variants like Trichophyton soudanense or T. violaceum. The combined use of both MALDI-TOF and phenotypic methods seems to be the better approach for dermatophytes’ identification since some species show significant phenotypic and clinical differences.info:eu-repo/semantics/publishedVersio

Frequency and molecular epidemiology of Aspergillus isolated from patients with suspicion of respiratory fungal infection

Objective: The aim of this study was to determine the frequency of Aspergillus detected in respiratory samples from a cohort of patients with suspicion of fungal infection of the respiratory tract as well as to determine the susceptibility to azoles of the isolates from the Fumigati section. Methods: A retrospective study was performed involving samples obtained from 16 hospitals covering different districts of continental Portugal and Azores islands. One hundred and eighty-seven respiratory samples (101 bronchoalveolar lavage fluids, 52 bronchial lavages, 27 bronchial secretions, 6 expectorations and 1 bronchial aspirate) were collected between November 2011 and December 2017 from a cohort of 146 patients with suspicion of respiratory fungal infection (ages ranging from 20 to 87 years old). Demographic and clinical data were recorded. Detection of Aspergillus was done by culture, immunoenzimatic assay and/or molecular techniques. Aspergillus molecular identification to species level was performed by sequencing of the calmodulin and β-tubulin genes. To detect possible resistance to azoles, isolates belonging to section Fumigati were inoculated into Sabouraud dextrose agar media supplemented with 1 µg/ml or 4 µg/ml of voriconazole, 4 µg/ml of itraconazole and 0.5 µg/ml of posaconazole and their growth was observed and recorded after 7 days of incubation at 27ºC. Doubtful results were confirmed when possible by E-test and by real-time multiplex PCR for the detection of mutations in the Cyp51A gene. Results: Fifty-seven (39.0%) of the studied patients were positive for Aspergillus. From the cases with a positive culture (n=58) the species were identified by sequencing and belonged to six different sections. The most frequently isolated was the section Nigri (42.1%) followed by the Fumigati (33.3%) and Flavi sections (8.6%). Regarding the species, the most frequent was A. niger sensu stricto (33.9%) followed by A. fumigatus sensu stricto (32.1%). Nine cryptic species were also identified which frequency was 21.4%. In order to study the frequency of azole resistance in Fumigati isolates collected from the samples of this cohort as well from other biological products, 52 isolates - Aspergillus fumigatus sensu stricto (n=45), A. lentulus (n=4), A. udagawae (n=2) and A. pseudofelis (n=1) – were tested. The tested A. fumigatus sensu stricto isolates did not show resistance to azoles. An A. udagawae strain revealed low susceptibility to voriconazole (MIC was not determined due to loss of strain viability). An A. pseudofelis strain also showed decreased susceptibility to voriconazole (MIC =1 μg/ml) as well as to and itraconazole (MIC = 2 μg/ml). Conclusion: In this study, the genus Aspergillus was frequently isolated in the respiratory samples tested and a high number of cryptic species was detected. Although resistance to azoles was not a problem identified in the tested isolates, determination of the in vitro susceptibility profile and molecular identification of the Aspergillus species is essential to improve the diagnosis and management of aspergillosis since several cryptic species have intrinsic resistance to antifungal drugs.info:eu-repo/semantics/publishedVersio

Polarons in Carbon Nanotubes

We use ab initio total-energy calculations to predict the existence of polarons in semiconducting carbon nanotubes (CNTs). We find that the CNTs' band edge energies vary linearly and the elastic energy increases quadratically with both radial and with axial distortions, leading to the spontaneous formation of polarons. Using a continuum model parametrized by the ab initio calculations, we estimate electron and hole polaron lengths, energies and effective masses and analyze their complex dependence on CNT geometry. Implications of polaron effects on recently observed electro- and opto-mechanical behavior of CNTs are discussed.Comment: Revtex preprint format, 12 pages, 2 eps figures, source in LaTeX. Accepted for publication in Physical Review Letter

AMADEOS SysML Profile for SoS Conceptual Modeling

International audienc

Understanding Urban Demand for Wild Meat in Vietnam: Implications for Conservation Actions

Vietnam is a significant consumer of wildlife, particularly wild meat, in urban restaurant settings. To meet this demand, poaching of wildlife is widespread, threatening regional and international biodiversity. Previous interventions to tackle illegal and potentially unsustainable consumption of wild meat in Vietnam have generally focused on limiting supply. While critical, they have been impeded by a lack of resources, the presence of increasingly organised criminal networks and corruption. Attention is, therefore, turning to the consumer, but a paucity of research investigating consumer demand for wild meat will impede the creation of effective consumer-centred interventions. Here we used a mixed-methods research approach comprising a hypothetical choice modelling survey and qualitative interviews to explore the drivers of wild meat consumption and consumer preferences among residents of Ho Chi Minh City, Vietnam. Our findings indicate that demand for wild meat is heterogeneous and highly context specific. Wild-sourced, rare, and expensive wild meat-types are eaten by those situated towards the top of the societal hierarchy to convey wealth and status and are commonly consumed in lucrative business contexts. Cheaper, legal and farmed substitutes for wild-sourced meats are also consumed, but typically in more casual consumption or social drinking settings. We explore the implications of our results for current conservation interventions in Vietnam that attempt to tackle illegal and potentially unsustainable trade in and consumption of wild meat and detail how our research informs future consumer-centric conservation actions

time and resilient master clocks in cyber physical systems

Since many years, it has been acknowledged that the role of time is fundamental to the design of distributed algorithms [21]. This is exacerbated in cyber-physical distributed systems, and consequently in Systems-of-Systems, where it is sometimes impossible to say which one of two observed environmental events occurred first

Paracoccidioidiomycosis: case report

Os autores reportam o caso clínico de um homem, 43 anos de idade, natural e residente na ilha da Madeira, emigrado na Venezuela até há 6 anos. Em Março 2009, observado por aparecimento de lesão pápulo-crostosa de bordos regulares eritematosos, indolor, pruriginosa, com dimensões de 4,5 x 3 cm, localizada no dorso, com 2 meses de evolução. Como antecedentes, refere história de lesão da mucosa bucal, com exame histopatológico compatível com paracoccidioidomicose (PCM). Foram efectuadas duas biópsias da lesão cutânea para avaliação histopatológica e micológica. O exame histopatológico revelou a presença de múltiplas células circulares, sugerindo distribuição característica de “roda de leme”. O estudo micológicos revelou, no exame directo, a presença de leveduras – algumas em gemulação. As culturas permitiram isolar o Paracoccidioides brasiliensis. A radiografia pulmonar apresentava infiltrado bilateral e simétrico, nos lobos centrais e basais. A Tomografia Axial Computadorizada torácica demonstrou múltiplos nódulos espiculados, áreas de opacidade e bronquiectasias. Foi efectuada broncofibroscopia (sem alterações) e simultaneamente foi obtido o lavado broncoalveolar (LBA). A cultura, a 25º C, revelou a presença de hifas e clamidósporos (forma filamentosa). Na cultura, a 37º C, não se obteve a forma leveduriforme. O tratamento efectuado foi o itraconazol 200 mg/dia, durante 6 meses, com regressão da lesão. Até à actualidade, nenhum caso de PCM foi reportado na ilha da Madeira, Portugal. Embora não seja frequente, fora das áreas endémicas, os dermatologistas devem ser capazes de reconhecer e diagnosticar micoses sistémicas, como a PCM.We report a case of a 43 years-old portuguese man, natural and resident in Madeira island, who was emigrated in Venezuela until 6 years ago. He was observed on March 2008 for a crusted papulo-nodular lesion with erythematous regular borders, pruritic and sized 4,5 x 3,0 cm, located on the dorsum, with a 2 month history. There was no palpable lymphadenopathy. He denied other simptomatology. On March of 1999, the patient had a mouth lesion which was compatible with paracoccidioidomycosis on histopathological examination. He was not aware of any associated pathologies. We performed two punch biopsies of the cutaneous lesion for histopathological and mycological examination. The histopathology showed the presence of multiple round cells of different size (yeast cells) in a narrow base suggesting the classic “pilot’s wheels”, on Hematoxiline & Eosine stain. On direct microscopic examination the mycology revealed yeast of different sizes – some of them on gemulation. The cultures, at 24º and 37º, isolated Paracoccidioides brasiliensis. The thoracic x-ray revealed a heterogeneous, bilateral and symmetric pattern located towards the central and basal portions. The CT scan of the chest showed multiple, micronodular and striated lesions (some of them with small cavities), with tendency to coalesce. To characterize better these lung abnormalities, the patient performed a fibrobronchoscopy of the respiratory tract which was normal. The culture, at 25 ºC, obtained from the sputum of the bronchoalveolar lavage fluid (BAL) showed Paracoccidioides brasiliensis. Routine laboratory studies were normal and serology negative for HIV and tuberculosis. The treatment of choice was itraconazol 200 mg/day, for 6 months. As far as we know no case of PCM has been reported in Madeira. Although it is not a frequent disease outside the endemic areas, dermatologists should be able to recognise and diagnose systemic mycosis like PCM.info:eu-repo/semantics/publishedVersio