IMPatienT: An Integrated Web Application to Digitize, Process and Explore Multimodal PATIENt daTa.

Medical acts, such as imaging, lead to the production of various medical text reports that describe the relevant findings. This induces multimodality in patient data by combining image data with free-text and consequently, multimodal data have become central to drive research and improve diagnoses. However, the exploitation of patient data is problematic as the ecosystem of analysis tools is fragmented according to the type of data (images, text, genetics), the task (processing, exploration) and domain of interest (clinical phenotype, histology). To address the challenges, we developed IMPatienT (Integrated digital Multimodal PATIENt daTa), a simple, flexible and open-source web application to digitize, process and explore multimodal patient data. IMPatienT has a modular architecture allowing to: (i) create a standard vocabulary for a domain, (ii) digitize and process free-text data, (iii) annotate images and perform image segmentation, (iv) generate a visualization dashboard and provide diagnosis decision support. To demonstrate the advantages of IMPatienT, we present a use case on a corpus of 40 simulated muscle biopsy reports of congenital myopathy patients. As IMPatienT provides users with the ability to design their own vocabulary, it can be adapted to any research domain and can be used as a patient registry for exploratory data analysis. A demo instance of the application is available at https://impatient.lbgi.fr/.

Investigation of Azole Resistance Involving cyp51A and cyp51B Genes in Clinical Aspergillus flavus Isolates.

This study aimed to investigate azole resistance mechanisms in Aspergillus flavus, which involve cyp51A and cyp51B genes. Real-time Reverse Transcriptase qPCR method was applied to determine the overexpression of cyp51A and cyp51B genes for 34 A. flavus isolates. PCR sequencing of these two genes was used to detect the presence of gene mutations. Susceptibility test found sensitivity to voriconazole (VOR) in all strains. 14.7% and 8.8% of isolates were resistant to itraconazole (IT) and posaconazole (POS), respectively, with a cross-resistance in 5.8%. For the double resistant isolates (IT/POS), the expression of cyp51A was up to 17-fold higher. PCR sequencing showed the presence of 2 mutations in cyp51A: a synonymous point mutation (P61P) in eight isolates, which did not affect the structure of CYP51A protein, and another non synonymous mutation (G206L) for only the TN-33 strain (cross IT/POS resistance) causing an amino acid change in the protein sequence. However, we noted in cyp51B the presence of the only non-synonymous mutation (L177G) causing a change in amino acids in the protein sequence for the TN-31 strain, which exhibits IT/POS cross-resistance. A short single intron of 67 bp was identified in the cyp51A gene, whereas three short introns of 54, 53, and 160 bp were identified in the cyp51B gene. According to the models provided by PatchDock software, the presence of non-synonymous mutations did not affect the interaction of CYP51A and CYP51B proteins with antifungals. In our study, the overexpression of the cyp51A and cyp51B genes is the primary mechanism responsible for resistance in A. flavus collection. Nevertheless, other resistance mechanisms can be involved.

Chronic blepharitis due to Demodex: A prospective study in Sfax (Tunisia).

INTRODUCTION: Chronic blepharitis is a common cause of eye irritation and dryness. They are often treated without regard to causal factors such as parasites which are rarely mentioned. AIM: To describe the role of Demodex in the pathogenesis of chronic blepharitis, to analyze the epidemiological, clinical, diagnostic and therapeutic particularities. METHODS: This is a prospective, case-control study conducted in the mycology parasitology department at the Habib Bourguiba university hospital in Sfax covering 100 cases with chronic blepharitis and 87 control cases. Clinical examination and eyelash removal were performed with direct examination for qualitative and quantitative analysis, before and after treatment. RESULTS: Demodex was significantly more found in patients than in controls (48% vs 13.8%). The quantitative analysis showed a significant difference between the two groups with 52.1% of Demodex (+++) for patients versus 8.3% for controls. Demodex blepharitis were treated with yellow oxid mercure ophthalmic ointment with a good outcome in 81,3%. CONCLUSION: Although it is admitted to be a saprophyte of the skin, a large number of arguments argues for the incrimination of Demodex in the etiopathogenesis of chronic blepharitis, hence the interest of eyelashes examination and a parasitic research in front of any chronic blepharitis resistant to usual treatments. In case of positive research, a specific treatment should be prescribed. Its effectiveness is another argument for the etiological diagnosis.

Viability predictive factors of the daughter vesicles in hepatic cystic echinococcosis.

INTRODUCTION: Management of cystic echinococcosis (CE) requires knowledge of certain aspects related to the survival of Echinococcus granulosus. The viability of daughter vesicles (DV) is a determining factor in guiding therapeutic indications, particularly for transiently active Cysts type CE3b. PURPOSE: To determine the predictive factors of DV viability and its impact on the therapeutic management of CE3b type. MATERIALS AND METHODS: This is a prospective pilot study with an analytical aim on patients with cystic echinococcosis of the liver type CE2 and CE3b, operated in the General Surgery Department of Habib-Bourguiba Academic Hospital, Sfax-Tunisia for 22 months from March 2018 until December 2019. The unit of the study is the DV. A parasitological study of the DV was done in the parasitology laboratory. RESULTS: During the study period, 27 (40.9%) of 66 operated CE Disease from 21 patients containing 248 DV were explored. The median viability of DV protoscoleces was 16.7%. In bivariate analysis, factors for viability of DV protoscoleces were: fever, acute cholangitis, hyperbilirubinemia, left liver location, rock water and bilious echinococcal fluid (EF), cyst size ≥ 43 mm, Intracystic pressure ≥ 35 mmHg, DV size ≥ 6.5 mm, volume, number of DV/cyst ≥ 5, and opaque wall (p < 0.05). Predictive factors for the Non-viability of DV were: CE3b type, purulent EF, gelatinous EF. In multivariate analysis, only CE2 type, cyst size ≥ 43 mm, number of DV/cyst ≥ 5 and DV size ≥ 6.5 mm were factors significantly associated with the viability of DV protoscoleces. CONCLUSION: CE3b cysts without the criteria of viability of DV protoscoleces may become candidates for the 'Wait-and-Watch' procedure.

A case of pediatric primary osteolytic extradural and complicated hydatid cyst revealed by a skull vault swelling.

Hydatidosis is a parasitic infestation whose etiological agent is the larva of the cestode Echinococcus granulosus. It is a zoonosis, and the human being behaves as an accidental intermediate host in the parasitic cycle with pediatric predominance. The most frequent clinical presentation is hepatic, followed by pulmonary, with cerebral hydatidosis being extremely rare. Imaging is characteristic, generally dealing with single cystic lesion, usually unilocular and less frequently multilocular, located mainly intraaxially. Extradural hydatid cyst, whether primary or secondary, remains very rare or even exceptional. The primary disease remains extremely rare, and its clinical picture is related to the number, size, and location of the lesions. Infection within these cerebral hydatid cysts remains an extremely rare occurrence, and only few cases were reported previously in the literature. The authors report the nosological review of the clinical, imaging, surgical, and histopathological records of a pediatric primary osteolytic extradural and complicated hydatid cyst in a 5-year-old North African male patient coming from a rural area who presented for progressive onset of a painless left parieto-occipital soft swelling without any neurological disorder with good outcomes after surgery. The authors report this case due the fact that it had not been documented before in the pediatric population and to the success of the specialized treatment.

Early postoperative intra-axial dissemination of a pediatric extradural and complicated hydatid cyst.

Hydatid disease is very common around the Mediterranean basin and endemic in some parts of the world. Cerebral involvement remains rare, represents only about 2% of all hydatid localizations and mainly affects the pediatric population. Extradural hydatid cyst is very rare or even exceptional when it is associated with or followed by intracerebral disseminations. Here, the authors report a new exceptional case of an early multiple intra-axial hydatid dissemination in a 5-year-old North African male patient from a rural area who underwent surgery 3 months after a primary osteolytic extradural and complicated hydatid cyst with good clinical and radiological outcomes.

Genotypic Analysis of the Population Structure in Malassezia globosa and Malassezia restricta.

The molecular characterization of Malassezia spp. isolates from animals and humans has not been thoroughly studied. Although a range of molecular methods has been developed for diagnosing Malassezia species, they have several drawbacks, such as inefficiency in differentiating all the species, high cost and questionable reproducibility. The present study aimed to develop VNTR markers for genotyping Malassezia isolated from clinical and animal samples. A total of 44 M. globosa and 24 M. restricta isolates were analyzed. Twelve VNTR markers were selected on seven different chromosomes (I, II, III, IV, V, VII and IX), six for each Malassezia species. The highest discriminatory power for a single locus was obtained with the STR-MG1 marker (0.829) and STR-MR2 marker (0.818) for M. globosa and M. restricta, respectively. After the analysis of multiple loci, 24 genotypes were noted among 44 isolates in M. globosa, with a discrimination index D of 0.943 and 15 genotypes were noted among 24 isolates in M. restricta, with a discrimination index D of 0.967. An endogenous infection was detected in two patients. Different genotypes of M. globosa strains colonized one patient. Interestingly, VNTR markers analysis revealed a carriage between a breeder and his dog in three cases for M. globosa and two for M. restricta. The FST (0.018 to 0.057) values indicate a low differentiation between the three populations of M. globosa. These results suggest a dominant clonal mode of reproduction in M. globosa. The typing of M. restricta showed a genotypic diversity of the strains, which can cause various skin pathologies. However, patient five was colonized with strains having the same genotype collected from different body parts (back, shoulder). VNTR analysis was capable of identifying species with high accuracy and reliability. More importantly, the method would facilitate monitoring Malassezia colonization in domestic animals and humans. It was shown that the patterns are stable and the method is discriminant, making it a powerful tool for epidemiological purposes.

Production and Quantification of Virulence Factors in Malassezia Species.

Seventy-seven strains of Malassezia were included in this study. Biofilm and hydrolytic enzyme production were studied by using specific solid media. The Real-Time reverse transcriptase qPCR method was applied to determine the overexpression of genes encoding the extracellular enzymes. All included Malassezia species produced biofilms. No statistically significant difference was observed between Malassezia species in biofilm formation (p = 0.567). All Malassezia species produced lipase, and 95% of Malassezia globosa showed a strong enzymatic activity (Pz = 0.55 ± 0.02). A statistically significant difference was observed between the mean keratinase indices of Malassezia slooffiae and the other Malassezia species (p = 0.005). The overexpression of one or more genes was observed in 100% of strains isolated from patients with folliculitis, 87.5% - with pityriasis versicolor, and 57.14% of the control group isolates. A statistically significant difference in the lipase gene expression (p = 0.042) was between the strains from patients with folliculitis and the control group. This investigation provides more information about the frequency of the production of the major enzymes considered virulence factors of Malassezia species. Interestingly, the overexpression of one or more genes was observed in strains isolated from patients with Malassezia disorders.

OntoRepliCov: an Ontology-Based Approach for Modeling the SARS-CoV-2 Replication Process.

Understanding the replication machinery of viruses contributes to suggest and try effective antiviral strategies. Exhaustive knowledge about the proteins structure, their function, or their interaction is one of the preconditions for successfully modeling it. In this context, modeling methods based on a formal representation with a high semantic expressiveness would be relevant to extract proteins and their nucleotide or amino acid sequences as an element from the replication process. Consequently, our approach relies on the use of semantic technologies to design the SARS-CoV-2 replication machinery. This provides the ability to infer new knowledge related to each step of the virus replication. More specifically, we developed an ontology-based approach enriched with reasoning process of a complete replication machinery process for SARS-CoV-2. We present in this paper a partial overview of our ontology OntoRepliCov to describe one step of this process, namely, the continuous translation or protein synthesis, through classes, properties, axioms, and SWRL (Semantic Web Rule Language) rules.

MESOCOSM: A mesocosm database management system for environmental nanosafety.

Engineered nanomaterials (ENMs) are intentionally designed and produced by humans to revolutionize the manufacturing sector, such as electronic goods, paints, tires, clothes, cosmetic products, and biomedicine. With the spread of these ENMs in our daily lives, scientific research have generated a huge amount of data related to their potential impacts on human and environment health. To date, these data are gathered in databases mainly focused on the (eco)toxicity and occupational exposure to ENMs. These databases are therefore not suitable to build well-informed environmental exposure scenarios covering the life cycle of ENMs. In this paper, we report the construction of one of the first centralized mesocosm database management system for environmental nanosafety (called MESOCOSM) containing experimental data collected from mesocosm experiments suited for understanding and quantifying both the environmental hazard and exposure. The database, which is publicly available through https://aliayadi.github.io/MESOCOSM-database/, contains 5200 entities covering tens of unique experiments investigating Ag, CeO2, CuO, TiO2-based ENMs as well as nano-enabled products. These entities are divided into different groups i.e. physicochemical properties of ENMS, environmental, exposure and hazard endpoints, and other general information about the mesocosm testing, resulting in more than forty parameters in the database. The MESOCOSM database is equipped with a powerful application, consisting of a graphical user interface (GUI), allowing users to manage and search data using complex queries without relying on programmers. MESOCOSM aims to predict and explain ENMs behavior and fate in different ecosystems as well as their potential impacts on the environment at different stages of the nanoproducts lifecycle. MESOCOSM is expected to benefit the nanosafety community by providing a continuous source of critical information and additional characterization factors for predicting ENMs interactions with the environment and their risks.

Combination of amphotericin B and caspofungin in the treatment of mucormycosis.

We report a case of invasive mucormycosis in 52 year-old woman. CT-scan and magnetic resonance imaging found a partial right sinus thrombosis associated with homolateral ethmoidal and maxillary sinusitis with submucosal inflammation. Histopathological examination of excised tissue was positive for mucormycosis. Our patient was treated by surgical debridement and a combination of amphotericin B and caspofungin, with a good outcome.

Macrophage activation syndrome in a patient affected by Plasmodium falciparum Aeroport malaria.

Malaria is a worldwide problem. Infection with Plasmodium. falciparum that may cause a multi-organ-failure, especially if the diagnose wasn't at time. Macrophage activation syndrome is a clinical and biological syndrome caused by an excessive proliferation of T lymphocytes. Plasmodium falciparum infection was rarely reported as a cause of this syndrome reported in the literature. We report a case of severe airport malaria in a 62-year-old man complicated by Macrophage activation syndrome. The patient was treated with intravenous quinine for 7days, catecholamine, volume expansion, mechanical ventilation, sedation and dialysis. But the evolution was marked by a multi-organ failure leading to the death of the patient. The occurrence of airport malaria stresses the need for sensitization of clinicians for considering malaria in febrile individuals even when they have not traveled to an endemic area. Clinicians should be aware of Macrophage activation syndrome when malaria does not respond to conventional therapy, since early diagnosis and prompt treatment may dramatically reduce the mortality associated with this condition.

Molecular Genotyping of Candida parapsilosis Species Complex.

BACKGROUND: The Candida parapsilosis complex species has emerged as an important cause of human disease. The molecular identification of C. parapsilosis isolates at the species level can be helpful for epidemiological studies and then for the establishment of appropriate therapies and prophylactic measures. METHODS: The present study was undertaken to analyze 13 short tandem repeat (STR) markers (7 minisatellites and 6 microsatellites) in a global set of 182 C. parapsilosis complex isolates from different origins including invasive and superficial clinical sites. RESULTS: Upon the analysis of 182 strains of C. parapsilosis complex species, 10-17 haplotypes were detected for each minisatellite marker. The combination of 7 minisatellite markers yielded 121 different genotypes with a 0.995 D value. Upon the analysis of 114 isolates (68 from invasive infections and 46 from superficial infections), 21-32 genotypes were detected for each microsatellite marker. The combination of all 13 markers yielded 96 different genotypes among 114 isolates with a high degree of discrimination (0.997 D value). The same multilocus genotype was shared by isolates recovered from some patients and from the hand of theirs correspondent healthcare worker. For another patient, the same multilocus genotype of C. metapsilosis was detected in blood and skin confirming that candidemia usually arises as an endogenous infection following prior colonization. CONCLUSIONS: These STR markers are a valuable tool for the differentiation of C. parapsilosis complex strains, to support epidemiological investigations especially studies of strain relatedness and pathways of transmission.

Molecular epidemiology of a Malassezia pachydermatis neonatal unit outbreak.

The non-lipid-dependent yeast Malassezia pachydermatis is predominantly zoophilic but occasionally colonizes the human skin. This yeast caused an outbreak in a neonatal iIntensive care unit (NICU). This study aimed to describe the molecular epidemiology of this M. pachydermatis outbreak. All the M. pachydermatis isolates collected at a French University Hospital from January 2012 to April 2013 were included in the study. M. pachydermatis isolates, sampled from various biological samples sites in 25 patients, were identified via MALDI-TOF mass spectrometry and typed using intergenic-spacer 1 (IGS1) nucleotide sequence polymorphisms analysis. By analyzing 90 IGS1 sequences (including 43 deposited in GenBank), we found that of the 186 M. pachydermatis isolates, 47 were viable for typing and all of them clustered within type 3; 78.7% clustered within the 3D subtype; the remaining clustered within three newly described subtypes: 3E (4.3%), 3F (8.5%) and 3 G (8.5%). No particular subtype was associated with a collection site or a particular time period. This first molecular investigation of a M. pachydermatis outbreak in neonates showed that multiple genotypes can colonize the same neonate patient by. The source of this polyclonal outbreak could not be identified. It stopped after infection control measures, including the prohibition of a lipid-rich moisturizing hand cream used by the health care staff, had been implemented.

Antifungal, molluscicidal and larvicidal assessment of anemonin and Clematis flammula L. extracts against mollusc Galba truncatula, intermediate host of Fasciola hepatica in Tunisia.

OBJECTIVE: To investigate the potential of anemonin and Clematis flammula (C. flammula) extracts against infective organisms. METHODS: The molluscicidal activities of anemonin and C. flammula extracts against Galba truncatula Müll. (Lymnaeidae) and Fasciola hepatica larval stages contaminating this snail in Tunisia were assessed by testing six groups of snails in 250 mL of extracts and aqueous dechlorinated solutions with different concentrations (ranging from 2.5 to 20.0 mg/L) for 48 h. Besides, the antifungal potential of C. flammula leaves and flowers was evaluated by using the diffusion agar and broth dilution methods against four fungal strains: Aspergillus niger, Pythium catenulatum, Rhizoctonia solani and Fusarium phyllophilum. RESULTS: As a result, hexane and ethyl acetate flower extracts exhibited significant molluscicidal activities with LC50 median lethal concentrations values of 11.87 and 11.65 mg/L, respectively while LC50 value of anemonin was 9.64 mg/L after 48 h exposure. The flower extracts showed a larvicidal effect with a deterioration rate exceeding 35.39% where flower ethyl acetate residue gave a deterioration rate of cercariae close to 97%. Moreover, C. flammula extracts were not noxious to the associated fauna survival. All extracts inhibited the growth of P. catenulatum, the leaves and flowers methanolic extracts had the more important fungicide action with minimum inhibitory concentrations of 1.56 and 3.12 mg/mL together with minimum fungistatic concentrations of 3.12 and 6.25 mg/mL respectively. Only flower extracts were active against Rhizoctonia solani with minimum inhibitory concentrations varying between 0.70 and 1.56 mg/mL and 6.25 mg/mL of minimum fungistatic concentration. Phytochemical tests showed that the antifungal activity may be attributed to the presence of the flavonoids/saponins in the methanolic extracts and the molluscicide effects could be due to the richness of hexane and ethyl acetate extracts on sterols and triterpenoids. CONCLUSIONS: This study emphasizes the important molluscicidal and antiparasitic effects of flower ethyl acetate extracts and anemonin compound as well as the considerable antifungal activities of methanolic extracts. These results improve the therapeutic virtues of C. flammula aerial part extracts.

Virulence factors, antifungal susceptibility and molecular mechanisms of azole resistance among Candida parapsilosis complex isolates recovered from clinical specimens.

BACKGROUND: The aim of this study was to determine the biofilm formation, the extracellular enzymatic activities of 182 clinical isolates of the Candida parapsilosis complex. METHODS: Molecular identification of the C. parapsilosis species complex was performed using PCR RFLP of SADH gene and PCR sequencing of ITS region. The susceptibility of ours isolates to antifungal agents and molecular mechanisms underlying azole resistance were evaluated. RESULTS: 63.5% of C. parapsilosis were phospholipase positive with moderate activity for the majority of strains. None of the C. metapsilosis or C. orthopsilosis isolates was able to produce phospholipase. Higher caseinase activities were detected in C. parapsilosis (Pz = 0.5 ± 0.18) and C. orthopsilosis (Pz = 0.49 ± 0.07) than in C. metapsilosis isolates (Pz = 0.72 ± 0.1). 96.5% of C. parapsilosis strains and all isolates of C. metapsilosis and C. orthopsilosis produced gelatinase. All the strains possessed the ability to show haemolysis on blood agar. C. metapsilosis exhibited the low haemolysin production with statistical significant differences compared to C. parapsilosis and C. orthopsilosis. The biofilm forming ability of C. parapsilosis was highly strain dependent with important heterogeneity, which was less evident with both C. orthopsilosis and C. metapsilosis. Some C. parapsilosis isolates met the criterion for susceptible dose dependent to fluconazole (10.91%), itraconazole (16.36%) and voriconazole (7.27%). Moreover, 5.45% and 1.82% of C. parapsilosis isolates were respectively resistant to fluconazole and voriconazole. All strains of C. metapsilosis and C. orthopsilosis were susceptible to azoles; and isolates of all three species exhibited 100% of susceptibility to caspofungin, amphotericin B and 5-flucytosine. CONCLUSIONS: A combination of molecular mechanisms, including the overexpression of ERG11, and genes encoding efflux pumps (CDR1, MDR1, and MRR1) were involved in azole resistance in C. parapsilosis.

Real-Time PCR Identification of Six Malassezia Species.

Lipophilic yeast Malassezia species is widely found on the skin surface of humans and other animals. This fungus can cause pityriasis versicolor, Malassezia folliculitis, and seborrheic dermatitis. Still now, there is a problem with species identification of Malassezia with conventional methods. We developed a real-time polymerase chain reaction (PCR) assay with multiple hybridization probes for detecting M. globosa, M. furfur, M. restricta, M. sympodialis, M. slooffiae, and M. pachydermatis. The amplification curves and specific melting peaks of the probes hybridized with real-time PCR product were used for species identifications. The assay was further evaluated on 120 samples which were performed by swabbing from 60 domestic animals (23 goats, 10 dogs, 15 cows, 3 cats, 8 rabbits, and 1 donkey) and in 70 human samples (28 patients with pityriasis versicolor, 17 breeders, and 25 control group). Fifteen M. pachydermatis were identified from animals. From human, 61 isolates were identified as M. globosa (28), M. furfur (15), M. restricta (6), M. sympodialis (8), M. slooffiae (2), and M. pachydermatis (2). Eight cases of co-detection from 6 patients and 2 breeders were revealed. Our findings show that the assay was highly effective in identifying Malassezia species. The application of multiplex real-time PCR provides a sensitive and rapid identification system for Malassezia species, which may be applied in further epidemiological surveys from clinical samples.

First genotype identification of Trichosporon asahii in Sfax, Tunisia.

PURPOSE: The objectives of our study were species identification and genotyping of Trichosporon isolates collected at the Parasitology and Mycology Laboratory in Sfax, Tunisia. METHODOLOGY: Molecular identification was carried out by analysing the IGS1 regions of the rDNA of 30 Trichosporon isolates. RESULTS: Trichosporon asahii was the most frequent species detected. Furthermore, four genotypes were identified in Tunisia: 1 (46.4 %), 4 (35.7 %), 7 (14.3 %) and 3 (3.6 %). In vitro antifungal susceptibility testing of the isolates showed that voriconazole exhibited the highest activity. CONCLUSION: This is the first reported study of genotype identification of T. asahii in Tunisia and even in the African continent.

Molecular study of the Candida parapsilosis complex in Sfax, Tunisia.

Candida parapsilosis, which was previously considered to be a complex of three genetically distinct groups, has emerged as a significant agent of nosocomial infections. Recently, this complex was separated into three species: C. parapsilosis sensu stricto, C. orthopsilosis, and C. metapsilosis In Tunisia, data pertaining to these fungi are limited. Thus, the purpose of our study was to determine by BanI PCR-RFLP and ITS sequencing, the occurrence of Candida parapsilosis complex among 182 isolates identified as C. parapsilosis by phenotypical methods. C. parapsilosis sensu stricto represented 94.5% of all isolates, while C. metapsilosis and. C. orthopsilosis were identified in 3.3% and 2.2%, respectively. Sequence analysis of internal transcribed spacer region confirmed and revealed only one genotype among the C. parapsilosis sensu stricto strains, three genotypes among six C. metapsilosis strains and two genotypes among four C. orthopsilosis strains.