A New Algorithm for Multivariate Genome Wide Association Studies Based on Differential Evolution and Extreme Learning Machines

Genome-wide association studies (GWAS) are observational studies of a large set of genetic variants, whose aim is to find those that are linked to a certain trait or illness. Due to the multivariate nature of these kinds of studies, machine learning methodologies have been already applied in them, showing good performance. This work presents a new methodology for GWAS that makes use of extreme learning machines and differential evolution. The proposed methodology was tested with the help of the genetic information (370,750 single-nucleotide polymorphisms) of 2049 individuals, 1076 of whom suffer from colorectal cancer. The possible relationship of 10 different pathways with this illness was tested. The results achieved showed that the proposed methodology is suitable for detecting relevant pathways for the trait under analysis with a lower computational cost than other machine learning methodologies previously proposed

Mobile genetic elements related to the diffusion of plasmid-mediated AmpC β-lactamases or carbapenemases from Enterobacteriaceae: findings from a multicenter study in Spain

We examined the genetic context of 74 acquired ampC genes and 17 carbapenemase genes from 85 out of 640 Enterobacteriaceae isolates collected in 2009. Using S1-PFGE and Southern hybridization, 37 out of 74 blaAmpC genes were located on large plasmids of different sizes belonging to six Inc groups. We used sequencing and PCR mapping to investigate the regions flanking the acquired ampC genes. The blaCMY-2like genes were associated with ISEcp1, the surrounding blaDHA genes were similar to Klebsiella pneumoniae plasmid pTN60013 associated with IS26 and the psp and sap operons, and blaACC-1 genes were associated with IS26 elements inserted into ISEcp1. All the carbapenemase genes (blaVIM-1, two blaIMP-22 and blaIMP-28) were located in class 1 integrons. Therefore, although plasmids are the main cause of the rapid dissemination of ampC genes among Enterobacteriaceae, we need to be aware that other mobile genetic elements, such as insertion sequences, transposons or integrons, can be involved in the mobilization of these genes of chromosomal origin. Additionally, three new integrons are described in this study (In846 to In848)

Recomendaciones del Comité Español del Antibiograma (COESANT) para la realización de los Informes de Sensibilidad Antibiótica Acumulada

[EN] The Spanish Antibiogram Committee (Comité Español del Antibiograma, COESANT) presents in this document a series of recommendations intending to unify how cumulative antibiogram reports must be made in Clinical Microbiology Spanish laboratories. This article is based on the information included in the Clinical Microbiology Procedure No. 51, «Preparation of cumulative reports on antimicrobial susceptibility» of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), published in 2014. The recommendations also include the modifications in the definition of clinical interpretive categories recently published by the European Committee on Antimicrobial Susceptibility Testing (EUCAST) in 2019. Its final objective is to establish a homogeneous way of preparing these summaries to compare results from different centers or aggregate the information from these in order to carry out an adequate local or even national surveillance regarding the evolution of antimicrobial susceptibility.[ES] El Comité Español del Antibiograma (COESANT) presenta en este documento una serie de recomendaciones cuya finalidad es unificar la forma en la que los Servicios y Unidades de Microbiología Clínica españoles realizan los informes de sensibilidad acumulada de las bacterias, aisladas en muestras clínicas, frente a los antimicrobianos. Las recomendaciones se fundamentan en las recogidas en el Procedimiento de Microbiología Clínica n° 51, «Preparación de informes acumulados de sensibilidad a los antimicrobianos» de la Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica (SEIMC), publicado en 2014, y recoge las modificaciones en las definiciones de las interpretaciones de las categorías clínicas publicadas en el año 2019 por el European Committee on Antimicrobial Susceptibility Testing (EUCAST). Su objetivo final es establecer una forma homogénea de elaborar estos resúmenes para poder comparar resultados de diferentes centros o sumar su información y así realizar una adecuada vigilancia local o incluso nacional de la evolución de la sensibilidad a los antimicrobianos.Peer reviewe

HIV in Spain 2017: policies for a new management of chronicity beyond virological control

The analysis of the available databases related to HIV/AIDS confirms a paradigm shift in the patient's life expectancy: now HIV has become a chronic disease, so patients are aging. However, this advance is accompanied by a negative counterpart: due to the increase in the number of years of life gained, there is a prevalence of comorbidities greater than the general population and at an earlier age. Reducing the risk associated with all the comorbidities that the ageing patient with HIV/AIDS may develop, must now be a health objective; it must be added to the traditional objectives that until now were part of the strategy to reduce the impact of the HIV infection. In the specific case of women, it is also necessary to train peri and postmenopausal women to increase their skills and motivation to care for their health; It is also very important to examine the role that hormone replacement therapy can play in reducing their symptoms.El análisis de las bases de datos disponibles relacionadas con VIH/SIDA confirma un cambio de paradigma en la esperanza de vida del pa-ciente: ahora el VIH se ha convertido en una enfermedad crónica, con la que los pacientes están envejeciendo. No obstante, este avance se acompaña de una contraparte negativa: debido al incremento en el número de años de vida ganados, se da una prevalencia de comorbilidades mayor a la de la población general y a una edad más temprana. Reducir el riesgo asociado a todas las comorbilidades que puede desarrollar el paciente con VIH/SIDA mientras envejece debe ser hoy en día un objetivo de salud, que se suma a los objetivos tradicionales que hasta ahora formaban parte de la estrategia para reducir el impacto de la infección por el VIH. En el caso específico de la mujer, además es necesario formar a las mujeres peri y postmenopáusi-cas para incrementar sus habilidades y su motivación para el cuidado de su salud; también es muy importante que se examine el rol que puede tener la terapia de reemplazo hormonal en la reducción de sus síntomas. Palabras clave: VIH, SIDA, Comorbilidad, Cronicidad, Envejeci-miento, Política sanitaria, Gestión clínicaEl presente trabajo ha sido editado por la Fundación Gaspar Casal, con ayuda del patrocinio de Gilead Sciences.S

Table_4_CARB-ES-19 Multicenter Study of Carbapenemase-Producing Klebsiella pneumoniae and Escherichia coli From All Spanish Provinces Reveals Interregional Spread of High-Risk Clones Such as ST307/OXA-48 and ST512/KPC-3.pdf

[Objectives] CARB-ES-19 is a comprehensive, multicenter, nationwide study integrating whole-genome sequencing (WGS) in the surveillance of carbapenemase-producing K. pneumoniae (CP-Kpn) and E. coli (CP-Eco) to determine their incidence, geographical distribution, phylogeny, and resistance mechanisms in Spain.[Methods] In total, 71 hospitals, representing all 50 Spanish provinces, collected the first 10 isolates per hospital (February to May 2019); CPE isolates were first identified according to EUCAST (meropenem MIC > 0.12 mg/L with immunochromatography, colorimetric tests, carbapenem inactivation, or carbapenem hydrolysis with MALDI-TOF). Prevalence and incidence were calculated according to population denominators. Antibiotic susceptibility testing was performed using the microdilution method (EUCAST). All 403 isolates collected were sequenced for high-resolution single-nucleotide polymorphism (SNP) typing, core genome multilocus sequence typing (cgMLST), and resistome analysis.[Results] In total, 377 (93.5%) CP-Kpn and 26 (6.5%) CP-Eco isolates were collected from 62 (87.3%) hospitals in 46 (92%) provinces. CP-Kpn was more prevalent in the blood (5.8%, 50/853) than in the urine (1.4%, 201/14,464). The cumulative incidence for both CP-Kpn and CP-Eco was 0.05 per 100 admitted patients. The main carbapenemase genes identified in CP-Kpn were blaOXA–48 (263/377), blaKPC–3 (62/377), blaVIM–1 (28/377), and blaNDM–1 (12/377). All isolates were susceptible to at least two antibiotics. Interregional dissemination of eight high-risk CP-Kpn clones was detected, mainly ST307/OXA-48 (16.4%), ST11/OXA-48 (16.4%), and ST512-ST258/KPC (13.8%). ST512/KPC and ST15/OXA-48 were the most frequent bacteremia-causative clones. The average number of acquired resistance genes was higher in CP-Kpn (7.9) than in CP-Eco (5.5).[Conclusion] This study serves as a first step toward WGS integration in the surveillance of carbapenemase-producing Enterobacterales in Spain. We detected important epidemiological changes, including increased CP-Kpn and CP-Eco prevalence and incidence compared to previous studies, wide interregional dissemination, and increased dissemination of high-risk clones, such as ST307/OXA-48 and ST512/KPC-3.Peer reviewe

All-cause mortality in the cohorts of the Spanish AIDS Research Network (RIS) compared with the general population: 1997Ł2010

Abstract Background: Combination antiretroviral therapy (cART) has produced significant changes in mortality of HIVinfected persons. Our objective was to estimate mortality rates, standardized mortality ratios and excess mortality rates of cohorts of the AIDS Research Network (RIS) (CoRIS-MD and CoRIS) compared to the general population. Methods: We analysed data of CoRIS-MD and CoRIS cohorts from 1997 to 2010. We calculated: (i) all-cause mortality rates, (ii) standardized mortality ratio (SMR) and (iii) excess mortality rates for both cohort for 100 personyears (py) of follow-up, comparing all-cause mortality with that of the general population of similar age and gender. Results: Between 1997 and 2010, 8,214 HIV positive subjects were included, 2,453 (29.9%) in CoRIS-MD and 5,761 (70.1%) in CoRIS and 294 deaths were registered. All-cause mortality rate was 1.02 (95% CI 0.91-1.15) per 100 py, SMR was 6.8 (95% CI 5.9-7.9) and excess mortality rate was 0.8 (95% CI 0.7-0.9) per 100 py. Mortality was higher in patients with AIDS, hepatitis C virus (HCV) co-infection, and those from CoRIS-MD cohort (1997. Conclusion: Mortality among HIV-positive persons remains higher than that of the general population of similar age and sex, with significant differences depending on the history of AIDS or HCV coinfection

Los estudios epidemiológicos sobre la poliomielitis en España antes de la vacunación

The eradication of polio in Spain is one of the most important health milestones of the twentieth century, not only for public health but also for the effect it had on scientific knowledge in our country, in the medical field. Knowledge of international literature by our epidemiologists and virologists, was important, as reflected in the studies of outbreaks, virological studies and clinical studies. For public health represented, throughout the twentieth century, an effort geared to make decisions based on scientific knowledge. For epidemiology represented the application of new ways of working and, therefore, its modernization.La erradicación de la poliomielitis en España es uno de los hitos sanitarios más importantes del siglo XX, no solo para la salud pública sino también por el efecto que su conocimiento científico tuvo en en el ámbito médico de nuestro país. El conocimiento de la literatura internacional por nuestros epidemiólogos y virólogos fue importante, como reflejan los estudios de los brotes epidémicos, los estudios virológicos y, lógicamente, los estudios clínicos. Para la salud pública representó, a lo largo de todo el siglo XX, un esfuerzo orientado a tomar decisiones basadas en el conocimiento científico. Para la epidemiología representó la aplicación de nuevas formas de trabajo y, por tanto, su modernización