Estudis sobre la contaminació i desinfecció de virus entèrics en contexts d'ajuda humanitària

[cat] L’objectiu general plantejat en aquesta tesi és contribuir a millorar el control de la qualitat de l’aigua de beguda per reduir el risc de malalties infeccioses especialment en els contexts d’ajuda humanitària. Inclou una part on s'avaluen els nivells de contaminació fecal en aigües utilitzades com a fonts d’aigua potable en contexts d'ajuda humanitària: a l’àrea metropolitana de Port-au Prince, Haití, després del terratrèmol 2010 i en els camps de refugiats de Maban, Sudan del Sud, durant l’epidèmia causada pel Virus de l'Hepatitis E (VHE) l’any 2013. Els resultats del estudi a Haití reflecteixen com les aigües superficials i fonts de beguda de l’àrea metropolitana de Port-au-Prince, Haití, després del terratrèmol l'any 2010, presenten altes concentracions de virus transmesos per l'aigua. Es detecten adenovirus i norovirus humans, importants patògens causants de gastroenteritis. En el cas dels camps del Sudan del Sud afectats per l'epidèmia causada pel VHE els resultats indicaven que tot i que les fonts d'aigua eren negatives, les mostres d’aigua i aliments de les llars presentaven contaminació per adenovirus humans, identificant d'una possible ruta de transmissió viral intradomiciliar. Una segona part de la tesi consta del desenvolupament de nous filtres d’aigua ceràmics, com a tecnologia de potabilització de baix cost, per la reducció de virus contaminants. Aquest nou prototip de Filtre d’Aigua Ceràmic proposat, cuit en atmosfera reductora, millora l'eficiència d'eliminació de virus fins a 3 logaritmes, en compliment dels requisits de l'OMS per a aquestes tecnologies sense incrementar el cost del producte. I finalment, s'inclouen estudis sobre la reducció del VHE, com a virus emergent causant d'epidèmies, davant processos de desinfecció d'aigua de beguda com la radiació UV i els sobres de floculació-cloració utilitzats en crisis humanitàries. Les dades experimentals obtingudes en els experiments d’inactivació del VHE per radiació UV indiquen que una reducció de 99,99% es pot aconseguir utilitzant radiacions relativament baixes que oscil·len entre 195-269 J/m2. Aquestes radiacions són inferiors a les normalment utilitzades en els sistemes de tractament per radiació UV (400 J/m2). Pel que fa als sobres de floculació-cloració els resultats indiquen que les reduccions pel VHE són entre 0.8 i 1.6 logaritmes tot i que són dades només basades en quantificació genòmica. El bacteriòfag MS2 avaluat per a la infectivitat va mostrar reduccions logarítmiques entre 2.3 a 3.5. Aquests nivells d’eliminació viral estan per sota dels suggerits per l’OMS (4.5 logaritmes) per aquests tipus de tractaments.[eng] The overall objective raised in this doctoral thesis is to help improving the quality control of drinking water to reduce the risk of infectious diseases especially in the context of humanitarian crisis. The first part consists on the evaluation of faecal contamination in drinking water on humanitarian contexts: in the metropolitan area of Port au Prince, Haiti, after the earthquake in 2010 and in the refugee camps of Maban, South Sudan, during the epidemic in 2013 caused by Hepatitis E Virus. Secondly, a new prototype of Ceramic Water Filter was developed to reduce viral contaminants in drinking water. Finally, the reduction of hepatitis E virus in water was studied in front of disinfection processes such UV radiation and Flocculation-Chlorination sachet

Atypical enteropathogenic Escherichia coli (aEPEC) in children under five years old with diarrhea in Quito (Ecuador)

Enteropathogenic Escherichia coli (EPEC) remain one the most important pathogens infecting children and they are one of the main causes of persistent diarrhea worldwide. In this study, we have isolated EPEC from 94 stool samples of children under five years old with diarrheal illness in the area of Quito (Ecuador), and we have determined the occurrence of the two subtypes of EPEC, typical EPEC (tEPEC) and atypical (aEPEC), by PCR amplification of the genes eae (attaching and effacing) and bfp (bundle- forming pilus). Typical EPEC is positive for eae and bfp genes while aEPEC is positive only for eae. Our results suggest that aEPEC is the most prevalent subtype in Quito (89.36 %), while subtype tEPEC is less prevalent (10.64 %). [Int Microbiol 19(3):157-160 (2016)]Keywords: Escherichia coli · atypical EPEC · genes eae and bfp · diarrhea in children · Quito (Ecuador

Development of improved low-cost ceramic water filters for viral removal in the Haitian context

Household-based water treatment (HWT) is increasingly being promoted to improve water quality and, therefore, health status in low-income countries. Ceramic water filters (CWFs) are used in many regions as sustainable HWT and have been proven to meet World Health Organization (WHO) microbiological performance targets for bacterial removal (24 log); however, the described viral removal efficiencies are insufficient to significantly reduce the associated risk of viral infection. With the objective of improving the viral removal efficiencies of ceramic water filters, new prototypes with different oxide compositions and firing atmospheres have been developed and evaluated. For removal efficiencies human adenoviruses, MS2 bacteriophage and Escherichia coli were quantified in all prototypes. A new model of CWF that was fired in a reductive atmosphere presented virus and bacteria removal efficiencies greater than 3.0 log and 2.5 log, respectively, which would fulfill the viral targets that are recommended by the WHO. Ceramic characterization of the selected filters, which were fired in a reductive atmosphere, showed that a larger specific surface area than those of control filters and higher fraction of a positive Z-potential fraction are the most likely explanations for this increase in virus removal

Development and validation of a high performance liquid chromatography method to determine linezolid concentrations in pig pulmonary tissue

Background: linezolid is the first synthetic compound of a new group of antimicrobials, the oxazolidinones, which inhibit protein synthesis. It shows a broad spectrum of activity against Gram positive organisms. With respect to its pharmacokinetics, linezolid shows a relatively high volume of distribution and good penetration into inflammatory fluids, bone, fat and muscle. Methods: a reversed-phase isocratic high-performance liquid chromatographic method for linezolid analysis in piglet pulmonary tissue is described. Tissue samples and controls were prepared in 1 x TBE (1 M Tris, 0.9 M boric acid, 0.01 M EDTA). The mobile phase consisted of 20% ultrafiltered water and 80% of (A) 15 mM potassium monohydrogen phosphate buffer (pH = 5) with (B) acetonitrile (80%/20%; v/v). Samples were homogenized and precipitated with HClO(4) 3% (1/1, v/v). The injection volume was 100 microL. Ofloxacin was used as an internal standard. Results: the assay was linear over a linezolid concentration range: 1.6-100 microg/mL. The method provided good validation data (n = 15): inaccuracy (3.6%), intra and inter-day variability (4.2% and 5.2%, respectively), recovery (91.8%), limit of detection (0.8 microg/mL) and quantitation (1.6 microg/mL) and acceptable stability within 24 h in the auto-sampler. Conclusions: the method offers a fast and simple approach to determine linezolid in pulmonary tissue which could be of use in pharmacokinetic studies

Comparison of Nanopore and Synthesis-Based Next-Generation Sequencing Platforms for SARS-CoV-2 Variant Monitoring in Wastewater

Shortly after the beginning of the SARS-CoV-2 pandemic, many countries implemented sewage sentinel systems to monitor the circulation of the virus in the population. A fundamental part of these surveillance programs is the variant tracking through sequencing approaches to monitor and identify new variants or mutations that may be of importance. Two of the main sequencing platforms are Illumina and Oxford Nanopore Technologies. Here, we compare the performance of MiSeq (Illumina) and MinION (Oxford Nanopore Technologies), as well as two different data processing pipelines, to determine the effect they may have on the results. MiSeq showed higher sequencing coverage, lower error rate, and better capacity to detect and accurately estimate variant abundances than MinION R9.4.1 flow cell data. The use of different variant callers (LoFreq and iVar) and approaches to calculate the variant proportions had a remarkable impact on the results generated from wastewater samples. Freyja, coupled with iVar, may be more sensitive and accurate than LoFreq, especially with MinION data, but it comes at the cost of having a higher error rate. The analysis of MinION R10.4.1 flow cell data using Freyja combined with iVar narrows the gap with MiSeq performance in terms of read quality, accuracy, sensitivity, and number of detected mutations. Although MiSeq should still be considered as the standard method for SARS-CoV-2 variant tracking, MinION’s versatility and rapid turnaround time may represent a clear advantage during the ongoing pandemic

The Catalan Surveillance Network of SARS-CoV-2 in Sewage: design, implementation, and performance

Wastewater-based epidemiology has shown to be an efficient tool to track the circulation of SARS-CoV-2 in communities assisted by wastewater treatment plants (WWTPs). The challenge comes when this approach is employed to help Health authorities in their decision-making. Here, we describe the roadmap for the design and deployment of SARSAIGUA, the Catalan Surveillance Network of SARS-CoV-2 in Sewage. The network monitors, weekly or biweekly, 56 WWTPs evenly distributed across the territory and serving 6 M inhabitants (80% of the Catalan population). Each week, samples from 45 WWTPs are collected, analyzed, results reported to Health authorities, and finally published within less than 72 h in an online dashboard ( https://sarsaigua.icra.cat ). After 20 months of monitoring (July 20-March 22), the standardized viral load (gene copies/day) in all the WWTPs monitored fairly matched the cumulative number of COVID-19 cases along the successive pandemic waves, showing a good fit with the diagnosed cases in the served municipalities (Spearman Rho = 0.69). Here we describe the roadmap of the design and deployment of SARSAIGUA while providing several open-access tools for the management and visualization of the surveillance data.The authors wish to thank the staff from all the WWTPs monitored for their help and technical support during the sampling campaigns. The authors acknowledge the funding received from the ACA and the ASPCAT from the Catalan Government (Generalitat de Catalunya). ICRA authors acknowledge the funding provided by the Generalitat de Catalunya through the Consolidated Research Group grants ICRA-ENV 2017 SGR 1124 and ICRA-TiA 2017 SGR 1318. ICRA researchers also thank the funding from the CERCA program of the Catalan Government.Peer reviewe

Treatment with tocilizumab or corticosteroids for COVID-19 patients with hyperinflammatory state: a multicentre cohort study (SAM-COVID-19)

Objectives: The objective of this study was to estimate the association between tocilizumab or corticosteroids and the risk of intubation or death in patients with coronavirus disease 19 (COVID-19) with a hyperinflammatory state according to clinical and laboratory parameters. Methods: A cohort study was performed in 60 Spanish hospitals including 778 patients with COVID-19 and clinical and laboratory data indicative of a hyperinflammatory state. Treatment was mainly with tocilizumab, an intermediate-high dose of corticosteroids (IHDC), a pulse dose of corticosteroids (PDC), combination therapy, or no treatment. Primary outcome was intubation or death; follow-up was 21 days. Propensity score-adjusted estimations using Cox regression (logistic regression if needed) were calculated. Propensity scores were used as confounders, matching variables and for the inverse probability of treatment weights (IPTWs). Results: In all, 88, 117, 78 and 151 patients treated with tocilizumab, IHDC, PDC, and combination therapy, respectively, were compared with 344 untreated patients. The primary endpoint occurred in 10 (11.4%), 27 (23.1%), 12 (15.4%), 40 (25.6%) and 69 (21.1%), respectively. The IPTW-based hazard ratios (odds ratio for combination therapy) for the primary endpoint were 0.32 (95%CI 0.22-0.47; p < 0.001) for tocilizumab, 0.82 (0.71-1.30; p 0.82) for IHDC, 0.61 (0.43-0.86; p 0.006) for PDC, and 1.17 (0.86-1.58; p 0.30) for combination therapy. Other applications of the propensity score provided similar results, but were not significant for PDC. Tocilizumab was also associated with lower hazard of death alone in IPTW analysis (0.07; 0.02-0.17; p < 0.001). Conclusions: Tocilizumab might be useful in COVID-19 patients with a hyperinflammatory state and should be prioritized for randomized trials in this situatio

CIBERER : Spanish national network for research on rare diseases: A highly productive collaborative initiative

Altres ajuts: Instituto de Salud Carlos III (ISCIII); Ministerio de Ciencia e Innovación.CIBER (Center for Biomedical Network Research; Centro de Investigación Biomédica En Red) is a public national consortium created in 2006 under the umbrella of the Spanish National Institute of Health Carlos III (ISCIII). This innovative research structure comprises 11 different specific areas dedicated to the main public health priorities in the National Health System. CIBERER, the thematic area of CIBER focused on rare diseases (RDs) currently consists of 75 research groups belonging to universities, research centers, and hospitals of the entire country. CIBERER's mission is to be a center prioritizing and favoring collaboration and cooperation between biomedical and clinical research groups, with special emphasis on the aspects of genetic, molecular, biochemical, and cellular research of RDs. This research is the basis for providing new tools for the diagnosis and therapy of low-prevalence diseases, in line with the International Rare Diseases Research Consortium (IRDiRC) objectives, thus favoring translational research between the scientific environment of the laboratory and the clinical setting of health centers. In this article, we intend to review CIBERER's 15-year journey and summarize the main results obtained in terms of internationalization, scientific production, contributions toward the discovery of new therapies and novel genes associated to diseases, cooperation with patients' associations and many other topics related to RD research

Spatiotemporal Characteristics of the Largest HIV-1 CRF02_AG Outbreak in Spain: Evidence for Onward Transmissions

Background and Aim: The circulating recombinant form 02_AG (CRF02_AG) is the predominant clade among the human immunodeficiency virus type-1 (HIV-1) non-Bs with a prevalence of 5.97% (95% Confidence Interval-CI: 5.41–6.57%) across Spain. Our aim was to estimate the levels of regional clustering for CRF02_AG and the spatiotemporal characteristics of the largest CRF02_AG subepidemic in Spain.Methods: We studied 396 CRF02_AG sequences obtained from HIV-1 diagnosed patients during 2000–2014 from 10 autonomous communities of Spain. Phylogenetic analysis was performed on the 391 CRF02_AG sequences along with all globally sampled CRF02_AG sequences (N = 3,302) as references. Phylodynamic and phylogeographic analysis was performed to the largest CRF02_AG monophyletic cluster by a Bayesian method in BEAST v1.8.0 and by reconstructing ancestral states using the criterion of parsimony in Mesquite v3.4, respectively.Results: The HIV-1 CRF02_AG prevalence differed across Spanish autonomous communities we sampled from (p &lt; 0.001). Phylogenetic analysis revealed that 52.7% of the CRF02_AG sequences formed 56 monophyletic clusters, with a range of 2–79 sequences. The CRF02_AG regional dispersal differed across Spain (p = 0.003), as suggested by monophyletic clustering. For the largest monophyletic cluster (subepidemic) (N = 79), 49.4% of the clustered sequences originated from Madrid, while most sequences (51.9%) had been obtained from men having sex with men (MSM). Molecular clock analysis suggested that the origin (tMRCA) of the CRF02_AG subepidemic was in 2002 (median estimate; 95% Highest Posterior Density-HPD interval: 1999–2004). Additionally, we found significant clustering within the CRF02_AG subepidemic according to the ethnic origin.Conclusion: CRF02_AG has been introduced as a result of multiple introductions in Spain, following regional dispersal in several cases. We showed that CRF02_AG transmissions were mostly due to regional dispersal in Spain. The hot-spot for the largest CRF02_AG regional subepidemic in Spain was in Madrid associated with MSM transmission risk group. The existence of subepidemics suggest that several spillovers occurred from Madrid to other areas. CRF02_AG sequences from Hispanics were clustered in a separate subclade suggesting no linkage between the local and Hispanic subepidemics

Signaling pathways mTOR and AKT in epilepsy.

Introducción. La vía de señalización AKT / mTOR es un eje central en la regulación de procesos celulares, particularmente en enfermedades neurológicas. En el caso de la epilepsia, se ha observado alteración en el proceso fisiopatológico de la misma. Sin embargo, no han descrito todos los mecanismos de estas vías de señalización que podrían abrir la oportunidad a nuevas investigaciones y estrategias terapéuticas. Revisar las asociaciones existentes entre las vías de señalización intracelular AKT y mTOR en la fisiopatología de la epilepsia. Desarrollo. La epilepsia es una enfermedad con un alto impacto epidemiológico a nivel mundial, por lo que se investiga ampliamente con respecto a sus componentes fisiopatológicos. En esa búsqueda se han involucrado diferentes vías de señalización intracelular en las neuronas, como determinantes epileptógenos. Los avances en este campo incluso han permitido la implementación exitosa de nuevas estrategias terapéuticas y abrir el camino a nuevas investigaciones en el campo. Conclusiones. Mejorar el conocimiento sobre el papel fisiopatológico de la vía de señalización mTOR / AKT en la epilepsia puede generar nuevas investigaciones sobre alternativas terapéuticas. El uso de inhibidores de mTOR ha surgido en los últimos años como eficaz en el tratamiento de esta alternativa de entidad de enfermedad, sin embargo, es evidente la necesidad de continuar la investigación para nuevas terapias farmacológicas.Introduction. The signaling pathway AKT/mTOR is a central axis in regulating cellular processes, particularly in neurological diseases. In the case of epilepsy, it has been observed alteration in the pathophysiological process of the same. However, they have not described all the mechanisms of these signaling pathways that could open the opportunity to new research and therapeutic strategies.Aim. To review existing partnerships between intracellular signaling pathways AKT and mTOR in the pathophysiology of epilepsy.Development. Epilepsy is a disease with a high epidemiological impact globally, so it is widely investigated regarding the pathophysiological components thereof. In that search they have been involved different intracellular signaling pathways in neurons, as determinants epileptogenic. Advances in this field have even allowed the successful implementation of new therapeutic strategies and to open the way to new research in the field.Conclusions. Improving knowledge about the pathophysiological role of the signaling pathway mTOR/AKT in epilepsy can raise new investigations regarding therapeutic alternatives. The use of mTOR inhibitors, has emerged in recent years as effective in treating this disease entity alternative however is clear the necessity of continue the research for new drug therapies