Estatuto de Redacción de la Agencia EFE, medio publico e internacional

Spain’s state-owned news agency, Agencia EFE, is the first of the major international wire services to establish an Editorial Council and a Charter to assure the independence of its journalists. Herein, the process of creating the Council and draughting (o drafting, en EEUU) the Charter, which the authors believe introduces important differences and innovations with respect to others.La Agencia EFE, de titularidad pública, es la primera de las internacionales que se dota de un Consejo y Estatuto de Redacción para garantizar la independencia de sus periodistas. Aquí se cuenta el proceso de creación de ese Consejo y de redacción del texto base, que los autores consideran con importantes diferencias e innovaciones respecto a otros Estatuto

CRISPR-Cas, a Revolution in the Treatment and Study of ESKAPE Infections: Pre-Clinical Studies

This article belongs to the Special Issue Non-antimicrobial Agents as Adjuvants against Bacterial Infections[Abstract] One of the biggest threats we face globally is the emergence of antimicrobial-resistant (AMR) bacteria, which runs in parallel with the lack in the development of new antimicrobials. Among these AMR bacteria pathogens belonging to the ESKAPE group can be highlighted (Enterococcus spp., Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp.) due to their profile of drug resistance and virulence. Therefore, innovative lines of treatment must be developed for these bacteria. In this review, we summarize the different strategies for the treatment and study of molecular mechanisms of AMR in the ESKAPE pathogens based on the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins’ technologies: loss of plasmid or cellular viability, random mutation or gene deletion as well directed mutations that lead to a gene’s loss of function.This study was funded by grants PI16/01163 and PI19/00878 awarded to M. Tomás within the State Plan for R+D+I 2013–2016 (National Plan for Scientific Research, Technological Development and Innovation 2008–2011) and cofinanced by the ISCIII-Deputy General Directorate for Evaluation and Promotion of Research-European Regional Development Fund “A way of Making Europe” and Instituto de Salud Carlos III FEDER, Spanish Network for the Research in Infectious Diseases (REIPI, RD16/0016/0006) and by the Study Group on Mechanisms of Action and Resistance to Antimicrobials, GEMARA (SEIMC, http://www.seimc.org/, Accessed on 21 June 2021). I. Bleriot was financially supported by pFIS program (ISCIII, FI20/00302). O. Pacios and M. López was financially supported by a grant IN606A-2020/035 and IN606B-2018/008, respectively, (GAIN, Xunta de Galicia), and M. Gonzalez-Bardanca was financially supported by the Rio Hortega program (ISCIII, CM20/00198)Xunta de Galicia; IN606A-2020/035Xunta de Galicia; IN606B-2018/00

Genomic Analysis of Molecular Bacterial Mechanisms of Resistance to Phage Infection

[Abstract] To optimize phage therapy, we need to understand how bacteria evolve against phage attacks. One of the main problems of phage therapy is the appearance of bacterial resistance variants. The use of genomics to track antimicrobial resistance is increasingly developed and used in clinical laboratories. For that reason, it is important to consider, in an emerging future with phage therapy, to detect and avoid phage-resistant strains that can be overcome by the analysis of metadata provided by whole-genome sequencing. Here, we identified genes associated with phage resistance in 18 Acinetobacter baumannii clinical strains belonging to the ST-2 clonal complex during a decade (Ab2000 vs. 2010): 9 from 2000 to 9 from 2010. The presence of genes putatively associated with phage resistance was detected. Genes detected were associated with an abortive infection system, restriction–modification system, genes predicted to be associated with defense systems but with unknown function, and CRISPR-Cas system. Between 118 and 171 genes were found in the 18 clinical strains. On average, 26% of these genes were detected inside genomic islands in the 2000 strains and 32% in the 2010 strains. Furthermore, 38 potential CRISPR arrays in 17 of 18 of the strains were found, as well as 705 proteins associated with CRISPR-Cas systems. A moderately higher presence of these genes in the strains of 2010 in comparison with those of 2000 was found, especially those related to the restriction–modification system and CRISPR-Cas system. The presence of these genes in genomic islands at a higher rate in the strains of 2010 compared with those of 2000 was also detected. Whole-genome sequencing and bioinformatics could be powerful tools to avoid drawbacks when a personalized therapy is applied. In this study, it allows us to take care of the phage resistance in A. baumannii clinical strains to prevent a failure in possible phage therapy.This study was funded by grants PI16/01163 and PI19/00878 awarded to MT within the State Plan for R + D + I 2013–2016 (National Plan for Scientific Research, Technological Development and Innovation 2008–2011) and co-financed by the ISCIII-Deputy General Directorate of evaluation and Promotion of Research-European Regional Development Fund “A way of Making Europe” and Instituto de Salud Carlos III FEDER. MT was financially supported by the Miguel Servet Research Programme (SERGAS and ISCIII

Latitudinal patterns and environmental drivers of taxonomic, functional, and phylogenetic diversity of woody plants in western Amazonian terra firme forests

Elucidating how environmental factors drive plant species distributions and how they affect latitudinal diversity gradients, remain essential questions in ecology and biogeography. In this study we aimed: 1) to investigate the relationships between all three diversity attributes, i.e., taxonomic diversity (TD), functional diversity (FD), and phylogenetic diversity (PD); 2) to quantify the latitudinal variation in these diversity attributes in western Amazonian terra firme forests; and 3) to understand how climatic and edaphic drivers contribute to explaining diversity patterns. We inventoried ca. 15,000 individuals from ca. 1,250 species, and obtained functional trait records for ca. 5,000 woody plant individuals in 50 plots of 0.1 ha located in five terra firme forest sites spread over a latitudinal gradient of 1200 km covering ca. 10°C in latitude in western Amazonia. We calculated all three diversity attributes using Hill numbers: q = 0 (richness), q = 1 (richness weighted by relative abundance), and q = 2 (richness weighted by dominance). Generalized linear mixed models were constructed for each diversity attribute to test the effects of different uncorrelated environmental predictors comprising the temperature seasonality, annual precipitation, soil pH and soil bulk density, as well as accounting for the effect of spatial autocorrelation, i.e., plots aggregated within sites. We confirmed that TD (q = 0, q = 1, and q = 2), FD (q = 0, q = 1, and q = 2), and PD (q = 0) increased monotonically towards the Equator following the latitudinal diversity gradient. The importance of rare species could explain the lack of a pattern for PD (q = 1 and q = 2). Temperature seasonality, which was highly correlated with latitude, and annual precipitation were the main environmental drivers of variations in TD, FD, and PD. All three diversity attributes increased with lower temperature seasonality, higher annual precipitation, and lower soil pH. We confirmed the existence of latitudinal diversity gradients for TD, FD, and PD in hyperdiverse Amazonian terra firme forests. Our results agree well with the predictions of the environmental filtering principle and the favourability hypothesis, even acting in a 10°C latitudinal range within tropical climate

Inter-rater reliability assessment for the new-born screening quality assurance

IntroductionTo ensure the quality of the new-born screening (NBS), our laboratory reviewed the analytical procedure to detect subjective steps that may represent a risk to the patient. Two subjective activities were identified in the extra-analytical phases: the classification of dried blood spots (DBS) according to their quality and the assignment of haemoglobin patterns. To keep these activities under control, inter-rater studies were implemented. This study aimed to evaluate the inter-rater reliability and the effectiveness of the measures taken to improve the agreement between observers, to assure NBS results’ quality. Materials and methodsDried blood spots specimens were used for the inter-rater studies. Ten studies were performed to assess DBS quality classification, and four to assess the assignment of haemoglobin patterns. Krippendorff’s alpha test was used to estimate inter-rater reliability. Causes were investigated when alpha values were below 0.80. ResultsFor both activities, the reliability obtained in the first studies was inadequate. After investigation, we detected that the criterion to classify a DBS as scant was not consolidated, and also a lack of consensus on whether or not to report Bart’s haemoglobin depending on its percentage. Alpha estimates became higher once the training was reinforced and a consensus about the appropriate criteria to be applied was reached. ConclusionInter-rater reliability assessment helped us to ensure the quality of subjective activities that could add variability to NBS results. Furthermore, the evolution of the alpha value over time allowed us to verify the effectiveness of the measures adopted

Newborn Screening for SCID: Experience in Spain (Catalonia)

Linfocitos T; Cribado de recién nacidos; Inmunodeficiencia combinada severaLimfòcits T; Cribratge de nounats; Immunodeficiència combinada severaT-lymphocytes; Newborn screening; Severe combined immunodeficiencyNewborn screening (NBS) for severe combined immunodeficiency (SCID) started in Catalonia in January-2017, being the first Spanish and European region to universally include this testing. In Spain, a pilot study with 5000 samples was carried out in Seville in 2014; also, a research project with about 35,000 newborns will be carried out in 2021–2022 in the NBS laboratory of Eastern Andalusia. At present, the inclusion of SCID is being evaluated in Spain. The results obtained in the first three and a half years of experience in Catalonia are presented here. All babies born between January-2017 and June-2020 were screened through TREC-quantification in DBS with the Enlite Neonatal TREC-kit from PerkinElmer. A total of 222,857 newborns were screened, of which 48 tested positive. During the study period, three patients were diagnosed with SCID: an incidence of 1 in 74,187 newborns; 17 patients had clinically significant T-cell lymphopenia (non-SCID) with an incidence of 1 in 13,109 newborns who also benefited from the NBS program. The results obtained provide further evidence of the benefits of early diagnosis and curative treatment to justify the inclusion of this disease in NBS programs. A national NBS program is needed, also to define the exact SCID incidence in Spain

Implementación del análisis del ADN libre circulante en plasma en el diagnóstico de pacientes con cáncer de pulmón de células no pequeñas

[spa] INTRODUCCIÓN: Las mutaciones en el gen EGFR son alteraciones comunes en pacientes con adenocarcinoma de pulmón. Los fármacos inhibidores de la tirosina quinasa son el tratamiento de elección en este grupo de pacientes, ya que han demostrado una mejora clara en la supervivencia frente a tratamientos convencionales. Las guías clínicas internacionales recomiendan el análisis de mutaciones en el gen EGFR en pacientes con un diagnóstico de adenocarcinoma avanzado. La biopsia de tejido continúa siendo el gold-standard para la caracterización molecular en pacientes con cáncer de pulmón de célula no pequeña. Sin embargo, en un alto porcentaje de pacientes no se dispone de muestra de tejido, o esta no presenta la calidad suficiente para realizar análisis moleculares. El ADN libre circulante (cfDNA) en plasma es una fuente alternativa para el análisis molecular indirecto del tumor, especialmente útil en aquellos pacientes de los que no se dispone de muestra de tejido. Junto con las características cualitativas del cfDNA, la información cuantitativa, como la concentración,y estructural, como el tamaño de sus fragmentos, está ganando interés en la práctica clínica. HIPÓTESIS: la caracterización molecular del gen EGFR en pacientes con cáncer de pulmón de células no pequeñas mediante el análisis de cfDNA en plasma representa una alternativa adecuada al análisis en biopsia de tejido. Además, parámetros derivados de este análisis como la concentración y tamaño de los fragmentos de cfDNA o el índice semicuantitativo (SQI) podrían proporcionar información complementaria en el diagnóstico y seguimiento de pacientes con cáncer de pulmón de células no pequeñas. OBJETIVOS: los objetivos de esta tesis son, en primer lugar, evaluar el impacto de la introducción en un entorno clínico real de un test tipo RT-PCR para el análisis de mutaciones en el gen EGFR en cfDNA en plasma. Además, determinar la utilidad clínica de la concentración del cfDNA y su fracción de fragmentos cortos como biomarcadores de estadificación de pacientes con cáncer de pulmón de células no pequeñas localmente avanzado o metastásico. Por otro lado, evaluar las características del índice semicuantitativo (SQI) obtenido en los pacientes con alteraciones en el gen EGFR y estudiar la asociación de la concentración del cfDNA y su patrón de fragmentos con parámetros derivados del FDG PET/TC. MÉTODOS: se ha realizado un análisis prospectivo en una cohorte clínica de pacientes diagnosticados con cáncer de pulmón de células no pequeñas localmente avanzado o metastásico. En todos los pacientes se realizó el estudio de alteraciones en el gen EGFR mediante el Cobas EGFR Mutation Test v2 en cfDNA en plasma y se determinó la concentración de cfDNA mediante fluorometría, y el patrón de fragmentos de cfDNA mediante electroforesis capilar. Se recogieron datos demográficos, clínicos, histopatológicos y el resultado molecular en tejido, siempre que estuviera disponible, de todos los pacientes. Se analizó la eficacia diagnóstica del estudio de mutaciones en plasma, el impacto de la introducción de esta metodología en la práctica clínica y la utilidad de la concentración de cfDNA y el tamaño de sus fragmentos como biomarcadores. En los pacientes en los que se disponía de análisis de imagen mediante FDG PET/TC y TC toracoabdominal se estudió su asociación con la concentración de cfDNA y el tamaño de sus fragmentos. En un subgrupo de pacientes con deleciones en el exón 19 del gen EGFR se realizó el análisis de mutaciones en el gen EGFR mediante una metodología alternativa (ddPCR) que proporcionó la fracción de alelo variante (VAF) para la mutación encontrada y se realizó un estudio de correlación de la misma con el SQI. PRINCIPALES RESULTADOS: el análisis de alteraciones en el gen EGFR en cfDNA en plasma mostró una alta eficacia diagnóstica comparado con el tejido. La concentración de cfDNA fue significativamente más alta en pacientes con estadios avanzados, y estos presentaron una fracción mayor de fragmentos cortos de cfDNA. Tanto la concentración de cfDNA como la fracción de fragmentos cortos presentaron una correlación positiva con los parámetros volumétricos y metabólicos derivados del FD PET/TC de la enfermedad metastásica. El SQI presentó una buena correlación con la VAF, tanto en pacientes al inicio del tratamiento, como durante el seguimiento longitudinal de los mismos. CONCLUSIONES: i) el análisis del cfDNA en plasma para la determinación de mutaciones en el gen EGFR es un método preciso y rápido para la caracterización molecular inicial de pacientes con cáncer de pulmón de célula no pequeña en la práctica clínica. ii) La introducción del Cobas EGFR mutation test v2 en la práctica clínica ha permitido el acceso a terapias dirigidas a los pacientes en los que no se dispone de muestra de tejido. iii) La concentración de cfDNA correlaciona con el estadio tumoral y con parámetros de imagen del tumor derivados de las lesiones metastásicas, por lo que tiene potencial como biomarcador en la estadificación de la neoplasia. iv) la fracción de fragmentos cortos de cfDNA correlaciona con parámetros volumétricos y metabólicos de las lesiones metastásicas obtenidos a partir del FDG PET/TC. v) El SQI es un parámetro cuantitativo robusto que refleja indirectamente la VAF y el número de copias mutadas/mL en pacientes con mutaciones en el exón 19 del gen EGFR

Technical Evaluation of the COBAS EGFR Semiquantitative Index (SQI) for Plasma cfDNA Testing in NSCLC Patients with EGFR Exon 19 Deletions

The cobas® EGFR Test provides a semiquantitative index (SQI) that reflects the proportion of mutated versus wild-type copies of the EGFR gene in plasma. The significance of SQI as an indirect measure of the variant allele frequency (VAF) or mutated copies/mL remains unclear. The aim of this study was to evaluate the correlation of SQI with the VAF and the number of mutated copies/mL obtained by a digital droplet PCR (ddPCR) test in NSCLC samples. The study included 118 plasma samples from a retrospective cohort of 25 stage IV adenocarcinoma patients with EGFR exon 19 deletions (Ex19Del), obtained before and during tyrosine kinase inhibitor (TKI) treatment. Both SQI and VAF and SQI and mutated copies/mL showed the same significant correlation (r2 = 0.79, p < 0.00001) across the whole study cohort. We found better correlation in samples collected at the baseline between SQI and VAF (r2 = 0.94, p < 0.00001) and SQI and mutated copies/mL (r2 = 0.97, p < 0.00001) compared to samples collected during TKI treatment: r2 = 0.76; p < 0.00001 for SQI and VAF and r2 = 0.75; p < 0.00001 for SQI and mutated copies/mL. The study indicates that SQI is a robust quantitative indirect measure of VAF and the number of mutated copies/mL in plasma from patients with an EGFR Ex19Del mutation. Further studies are desirable to assess the SQI cut-off values related to the clinical status of the patient

Brote de síndrome de shock tóxico estreptocócico en una guardería de Cantabría en 2006

Fundamento: Las infecciones por estreptococo beta-hemolítico grupo A (EGA) sólo excepcionalmente son agresivas y con letalidad alta. Más infrecuente aún es la ocurrencia de un brote. El objetivo de este estudio es la descripción de un brote epidémico por estreptococo beta-hemolítico grupo A en una guardería de Cantabria. Métodos: Estudio descriptivo de un brote de síndrome de shock tóxico estreptocócico (3 casos, uno letal) en una guardería, que motivó una intervención de salud pública con quimioprofilaxis, cierre de la guardería y estudio de los contactos. Se analizan los determinantes de la infección en los casos invasivos y no invasivos, y los resultados de los cultivos faríngeos de los contactos. Resultados: Se identificaron 3 casos invasivos y 14 no invasivos entre los 40 niños de la guardería (tasa de ataque 42,5%). Se estudiaron 19 posibles determinantes de la infección, asociándose sólo la edad mayor de 24 meses y la asistencia al aula de fichas (la de los niños más mayores). No se asoció a la varicela. Se investigaron microbiológicamente todos los niños de la guardería y su personal (4 cuidadoras) y 258 personas de contacto. En 12 de los niños se aisló el estreptococo emm 4, incluyendo 2 de los 3 casos con enfermedad invasiva. En 13 de los 258 contactos se aislaron otras cepas de estreptococo, pero en ninguno la causante del brote. Se hizo quimioprofilaxis con azitromicina a todos los niños y contactos, y a los positivos se les repitió el tratamiento hasta su negativización. Conclusiones: La cepa invasiva circuló sólo en la guardería. La quimioprofilaxis erradicó efectivamente la infección