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Genetic diversity of Mycobacterium tuberculosis affects immune responses and clinical outcomes of tuberculosis (TB). However, how bacterial diversity orchestrates immune responses to direct distinct TB severities is unknown. Here we study 681 patients with pulmonary TB and show that M. tuberculosis isolates from cases with mild disease consistently induce robust cytokine responses in macrophages across multiple donors. By contrast, bacteria from patients with severe TB do not do so. Secretion of IL-1 beta is a good surrogate of the differences observed, and thus to classify strains as probable drivers of different TB severities. Furthermore, we demonstrate that M. tuberculosis isolates that induce low levels of IL-1 beta production can evade macrophage cytosolic surveillance systems, including cGAS and the inflammasome. Isolates exhibiting this evasion strategy carry candidate mutations, generating sigA recognition boxes or affecting components of the ESX-1 secretion system. Therefore, we provide evidence that M. tuberculosis strains manipulate host-pathogen interactions to drive variable TB severities. Some strains of Mycobacterium tuberculosis seem to be able to avoid host defense systems. Here the authors stratify patients by severity of tuberculosis and find correlations with the level of IL-1 beta production by macrophages exposed to these isolates.

Glucocorticoid (GC) actions are mediated through two closely related ligand-dependent transcription factors, the GC receptor (GR) and the mineralocorticoid receptor (MR). Given the wide and effective use of GCs to combat skin inflammatory diseases, it is important to understand the relative contribution of these receptors to the transcriptional response to topical GCs. We evaluated the gene expression profiles in the skin of mice with epidermal-specific loss of GR-(GR(EKO)), MR-(MREKO), or both (double KO; DKO) in response to dexamethasone (Dex). The overall transcriptional response was abolished in GR(EKO) and DKO skin suggesting dependence of the underlying dermis on the presence of epidermal GR. Indeed, the observed dermal GC resistance correlated with a constitutive decrease in GR activity and up-regulation of p38 activity in this skin compartment. Upon Dex treatment, more than 90% of differentially expressed genes (DEGs) in CO overlapped with MREKO. However, the number of DEGs was fourfold increased and the magnitude of response was higher in MREKO vs CO, affecting both gene induction and repression. Taken together our data reveal that, in the cutaneous transcriptional response to GCs mediated through endogenous receptors, epidermal GR is mandatory while epidermal MR acts as a chief modulator of gene expression.

Motivation: Tuberculosis (TB) remains one of the main causes of death worldwide. The long and cumbersome process of culturing Mycobacterium tuberculosis complex (MTBC) bacteria has encouraged the development of specific molecular tools for detecting the pathogen. Most of these tools aim to become novel TB diagnostics, and big efforts and resources are invested in their development, looking for the endorsement of the main public health agencies. Surprisingly, no study has been conducted where the vast amount of genomic data available is used to identify the best MTBC diagnostic markers. Results: In this work, we used large-scale comparative genomics to identify 40 MTBC-specific loci. We assessed their genetic diversity and physiological features to select 30 that are good targets for diagnostic purposes. Some of these markers could be used to assess the physiological status of the bacilli. Remarkably, none of the most used MTBC markers is in our catalog. Illustrating the translational potential of our work, we develop a specific qPCR assay for quantification and identification of MTBC DNA. Our rational design of targeted molecular assays for TB could be used in many other fields of clinical and basic research.

Background Contaminant DNA is a well-known confounding factor in molecular biology and in genomic repositories. Strikingly, analysis workflows for whole-genome sequencing (WGS) data commonly do not account for errors potentially introduced by contamination, which could lead to the wrong assessment of allele frequency both in basic and clinical research. Results We used a taxonomic filter to remove contaminant reads from more than 4000 bacterial samples from 20 different studies and performed a comprehensive evaluation of the extent and impact of contaminant DNA in WGS. We found that contamination is pervasive and can introduce large biases in variant analysis. We showed that these biases can result in hundreds of false positive and negative SNPs, even for samples with slight contamination. Studies investigating complex biological traits from sequencing data can be completely biased if contamination is neglected during the bioinformatic analysis, and we demonstrate that removing contaminant reads with a taxonomic classifier permits more accurate variant calling. We used both real and simulated data to evaluate and implement reliable, contamination-aware analysis pipelines. Conclusion As sequencing technologies consolidate as precision tools that are increasingly adopted in the research and clinical context, our results urge for the implementation of contamination-aware analysis pipelines. Taxonomic classifiers are a powerful tool to implement such pipelines.

Mycobacterium tuberculosis (Mtb) infection results in a spectrum of clinical and histopathologic manifestations. It has been proposed that the environmental and immune pressures associated with different contexts of infection have different consequences for the associated bacterial populations, affecting drug susceptibility and the emergence of resistance. However, there is little concrete evidence for this model. We prospectively collected sputum samples from 18 newly diagnosed and treatment-naive patients with tuberculosis and sequenced 795 colony-derived Mtb isolates. Mutant accumulation rates varied considerably between different bacilli isolated from the same individual, and where high rates of mutation were observed, the mutational spectrum was consistent with reactive oxygen species-induced mutagenesis. Elevated bacterial mutation rates were identified in isolates from HIV-negative but not HIV-positive individuals, suggesting that they were immune-driven. These results support the model that mutagenesis of Mtb in vivo is modulated by the host environment, which could drive the emergence of variants associated with drug resistance in a host-dependent manner.

Tuberculosis (TB) surveillance is scarce in most African countries, even though it is the continent with the greatest disease incidence according to the World Health Organization. Liberia is within the 30 countries with the highest TB burden, probably as a consequence of the long civil war and the recent Ebola outbreak, both crippling the health system and depreciating the TB prevention and control programmes. Due to difficulties working in the country, there is a lack of resistance surveys and bacillus characterization. Here, we use genome sequencing of Mycobacterium tuberculosis clinical isolates to fill this gap. Our results highlight that the bacillus population structure is dominated by lineage 4 strains that harbour an outstanding genetic diversity, higher than in the rest of Africa as a whole. Coalescent analyses demonstrate that strains currently circulating in Liberia were introduced several times beginning in the early year 600 CE until very recently coinciding with migratory movements associated with the civil war and Ebola epidemics. A higher multidrug-resistant (MDR)-TB frequency (23.5 %) than current estimates was obtained together with non-catalogued drug-resistance mutations. Additionally, 39 % of strains were in genomic clusters revealing that ongoing transmission is a major contribution to the TB burden in the country. Our report emphasizes the importance of TB surveillance and control in African countries where bacillus diversity, MDR-TB prevalence and transmission are coalescing to jeopardize TB control programmes.

For the first time, next generation sequencing technologies provide access to genomic information at a price and scale that allow their implementation in routine clinical practice and epidemiology. While there are still many obstacles to their implementation, there are also multiple examples of their major advantages compared with previous methods. Their main advantage is that a single determination allows epidemiological information on the causative microorganism to be obtained simultaneously, as well as its resistance profile, although these advantages vary according to the pathogen under study. This review discusses several examples of the clinical and epidemiological use of next generation sequencing applied to complete genomes and microbiomes and reflects on its future in clinical practice. (C) 2020 Elsevier Espana, S.L.U. and Sociedad Espanola de Enfermedades Infecciosas y Microbiologia Clinica. All rights reserved.

Whole genome sequencing (WGS) has been proposed as a tool for the diagnosis of drug resistance in tuberculosis (TB); however, there have been few studies on its effectiveness in countries with significantly high drug resistance rates. This study therefore aimed to evaluate the effectiveness of WGS to identify mutations related to drug resistance in TB isolates from an endemic region of Mexico. The results showed that, of 35 multidrug-resistant isolates analyzed, the values of congruence found between the phenotypic drug susceptibility testing and polymorphisms were 94% for isoniazid, 97% for rifampicin, 90% for ethambutol, and 82% for pyrazinamide. It was also possible to identify eight isolates as potential pre-extensive drug resistant (XDR) and one as XDR. Twenty nine isolates were classified within L4 and two transmission clusters were identified. The results show the potential utility of WGS for predicting resistance against first- and second-line drugs, as well as providing a phylogenetic characterization of TB drug-resistant isolates circulating in Mexico.

Motivation Resistance co-occurrence within first-line anti-tuberculosis (TB) drugs is a common phenomenon. Existing methods based on genetic data analysis of Mycobacterium tuberculosis (MTB) have been able to predict resistance of MTB to individual drugs, but have not considered the resistance co-occurrence and cannot capture latent structure of genomic data that corresponds to lineages. Results We used a large cohort of TB patients from 16 countries across six continents where whole-genome sequences for each isolate and associated phenotype to anti-TB drugs were obtained using drug susceptibility testing recommended by the World Health Organization. We then proposed an end-to-end multi-task model with deep denoising auto-encoder (DeepAMR) for multiple drug classification and developed DeepAMR_cluster, a clustering variant based on DeepAMR, for learning clusters in latent space of the data. The results showed that DeepAMR outperformed baseline model and four machine learning models with mean AUROC from 94.4% to 98.7% for predicting resistance to four first-line drugs [i.e. isoniazid (INH), ethambutol (EMB), rifampicin (RIF), pyrazinamide (PZA)], multi-drug resistant TB (MDR-TB) and pan-susceptible TB (PANS-TB: MTB that is susceptible to all four first-line anti-TB drugs). In the case of INH, EMB, PZA and MDR-TB, DeepAMR achieved its best mean sensitivity of 94.3%, 91.5%, 87.3% and 96.3%, respectively. While in the case of RIF and PANS-TB, it generated 94.2% and 92.2% sensitivity, which were lower than baseline model by 0.7% and 1.9%, respectively. t-SNE visualization shows that DeepAMR_cluster captures lineage-related clusters in the latent space. Availability and implementation The details of source code are provided at http://www.robots.ox.ac.uk/∼davidc/code.php.

11 págs, 4 figuras y fórmulas matemáticas. Material suplementario en: http://dx.doi.org/10.1093/molbev/msaa069, The dN/dS ratio provides evidence of adaptation or functional constraint in protein-coding genes by quantifying the relative excess or deficit of amino acid-replacing versus silent nucleotide variation. Inexpensive sequencing promises a better understanding of parameters, such as dN/dS, but analyzing very large data sets poses a major statistical challenge. Here, I introduce genomegaMap for estimating within-species genome-wide variation in dN/dS, and I apply it to 3,979 genes across 10,209 tuberculosis genomes to characterize the selection pressures shaping this global pathogen. GenomegaMap is a phylogeny-free method that addresses two major problems with existing approaches: 1) It is fast no matter how large the sample size and 2) it is robust to recombination, which causes phylogenetic methods to report artefactual signals of adaptation. GenomegaMap uses population genetics theory to approximate the distribution of allele frequencies under general, parent-dependent mutation models. Coalescent simulations show that substitution parameters are well estimated even when genomegaMap's simplifying assumption of independence among sites is violated. I demonstrate the ability of genomegaMap to detect genuine signatures of selection at antimicrobial resistance-conferring substitutions in Mycobacterium tuberculosis and describe a novel signature of selection in the cold-shock DEAD-box protein A gene deaD/csdA. The genomegaMap approach helps accelerate the exploitation of big data for gaining new insights into evolution within species., D.J.W. is a Sir Henry Dale Fellow, jointly funded by the Wellcome Trust and the Royal Society (grant no. 101237/Z/13/B) and is a Big Data Institute Robertson Fellow. The CRyPTIC Consortium was supported by grants from the Bill and Melinda Gates Foundation (OPP1133541) and a Wellcome Trust/Newton Fund-MRC Collaborative Award (200205/Z/15/Z). F.A.D. was supported by the Imperial Biomedical Research Centre

Background: The analysis of transmission of tuberculosis (TB) is challenging in areas with a large migrant population. Standard genotyping may fail to differentiate transmission within the host country from new importations, which is key from an epidemiological perspective. Aim: To propose a new strategy to simplify and optimise cross-border surveillance of tuberculosis and to distinguish between recent transmission in the host country and new importations. Methods: We selected 10 clusters, defined by 24-locus mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR), from a population in Spain rich in migrants from eastern Europe, north Africa and west Africa and reanalysed 66 isolates by whole-genome sequencing (WGS). A multiplex-allele-specific PCR was designed to target strain-specific marker single nucleotide polymorphisms (SNPs), identified from WGS data, to optimise the surveillance of the most complex cluster. Results: In five of 10 clusters not all isolates showed the short genetic distances expected for recent transmission and revealed a higher number of SNPs, thus suggesting independent importations of prevalent strains in the country of origin. In the most complex cluster, rich in Moroccan cases, a multiplex allele-specific oligonucleotide-PCR (ASO-PCR) targeting the marker SNPs for the transmission subcluster enabled us to prospectively identify new secondary cases. The ASO-PCR-based strategy was transferred and applied in Morocco, demonstrating that the strain was prevalent in the country. Conclusion: We provide a new model for optimising the analysis of cross-border surveillance of TB transmission in the scenario of global migration.

The Mycobacterium tuberculosis complex (MTBC) members display different host-specificities and virulence phenotypes. Here, we have performed a comprehensive RNAseq and methylome analysis of the main clades of the MTBC and discovered unique transcriptional profiles. The majority of genes differentially expressed between the clades encode proteins involved in host interaction and metabolic functions. A significant fraction of changes in gene expression can be explained by positive selection on single mutations that either create or disrupt transcriptional start sites (TSS). Furthermore, we show that clinical strains have different methyltransferases inactivated and thus different methylation patterns. Under the tested conditions, differential methylation has a minor direct role on transcriptomic differences between strains. However, disruption of a methyltransferase in one clinical strain revealed important expression differences suggesting indirect mechanisms of expression regulation. Our study demonstrates that variation in transcriptional profiles are mainly due to TSS mutations and have likely evolved due to differences in host characteristics.

Background Whole genome sequencing (WGS) has been proposed as a tool for diagnosing drug resistance in tuberculosis. However, reports of its effectiveness in endemic countries with important numbers of drug resistance are scarce. The goal of this study was to evaluate the effectiveness of this procedure in isolates from a tuberculosis endemic region in Mexico. Methods WGS analysis was performed in 81 tuberculosis positive clinical isolates with a known phenotypic profile of resistance against first-line drugs (isoniazid, rifampin, ethambutol, pyrazinamide and streptomycin). Mutations related to drug resistance were identified for each isolate; drug resistant genotypes were predicted and compared with the phenotypic profile. Genotypes and transmission clusters based on genetic distances were also characterized. Findings Prediction by WGS analysis of resistance against isoniazid, rifampicin, ethambutol, pyrazinamide and streptomycin showed sensitivity values of 84%, 96%, 71%, 75% and 29%, while specificity values were 100%, 94%, 90%, 90% and 98%, respectively. Prediction of multidrug resistance showed a sensitivity of 89% and specificity of 97%. Moreover, WGS analysis revealed polymorphisms related to second-line drug resistance, enabling classification of eight and two clinical isolates as pre- and extreme drug-resistant cases, respectively. Lastly, four lineages were identified in the population (L1, L2, L3 and L4). The most frequent of these was L4, which included 90% (77) of the isolates. Six transmission clusters were identified; the most frequent was TC6, which included 13 isolates with a L4.1.1 and a predominantly multidrug-resistant condition. Conclusions The results illustrate the utility of WGS for establishing the potential for prediction of resistance against first and second line drugs in isolates of tuberculosis from the region. They also demonstrate the feasibility of this procedure for use as a tool to support the epidemiological surveillance of drug-and multidrug-resistant tuberculosis.

Al llarg de la seva vida, Pompeu Fabra va mantenir relacions amb diversos personatges de Mataró, com ara Jaume Baladia i Soler, Josep Puig i Cadafalch i Julià Gual i Masoller, o amb altres que tenien vincles maratonins, com Emili Guanyavents i Jané i Francesc Matheu i Fornells. En aquest article, Anna Comas i Valls ressegueix aquestes relacions i els vincles del Mestre amb la nostra ciutat, alhora que fa un recorregut per la seva bibliografia i per la dels personatges mataroninsamb qui es relacionà, tot contextualitzant-les en els diversos períodes històrics que travessen, des dels finals del segle XIX fins a mitjan segle XX.

Understanding why some multidrug-resistant tuberculosis cases are not detected by rapid phenotypic and genotypic routine clinical tests is essential to improve diagnostic assays and advance toward personalized tuberculosis treatment. Here, we combine whole-genome sequencing with single-colony phenotyping to identify a multidrug-resistant strain that had infected a patient for 9 years. Our investigation revealed the failure of rapid testing and genome-based prediction tools to identify the multidrug-resistant strain. The false-negative findings were caused by uncommon rifampicin and isoniazid resistance mutations. Although whole-genome sequencing data helped to personalize treatment, the patient developed extensively drug-resistant tuberculosis, highlighting the importance of coupling new diagnostic methods with appropriate treatment regimens.

13 páginas, 4 figuras. Contiene material suplementario., Whole genome sequencing (WGS) of Mycobacterium tuberculosis has rapidly progressed from a research tool to a clinical application for the diagnosis and management of tuberculosis and in public health surveillance. This development has been facilitated by drastic drops in cost, advances in technology and concerted efforts to translate sequencing data into actionable information. There is, however, a risk that, in the absence of a consensus and international standards, the widespread use of WGS technology may result in data and processes that lack harmonization, comparability and validation. In this Review, we outline the current landscape of WGS pipelines and applications, and set out best practices for M. tuberculosis WGS, including standards for bioinformatics pipelines, curated repositories of resistance-causing variants, phylogenetic analyses, quality control and standardized reporting., C.J.M., B.O.-A., L.R. and B.C.d.J. are supported by a European Research Council grant (INTERRUPTB; no. 311725). I.C. and G.A.G. are supported by a European Research Council grant (TB-ACCELERATE; no. 638553). T.C.R. receives salary support from the not-for-profit organization Foundation for Innovative New Diagnostics (the terms of this arrangement have been reviewed and approved by the University of California, San Diego). T.M.W. is an NIHR Academic Clinical Lecturer. J.L.G. and J.G. receive funding from the University of British Columbia, Vancouver, Canada. T.A.K., C.U., V.D. and S.N. receive funding from the German Center for Infection Research (DZIF) and are funded by the Deutsche Forschungsgemeinschaft (German Research Foundation) under Germany’s Excellence Strategy (EXC 22167–390884018). L.V., T.H.H. and A.V.R. are funded by FWO Odysseus G0F8316N. M.R.F. is supported by the US National Institutes of Health BD2K K01 (MRF ES026835). P.S. is supported by the Agence Nationale de la Recherche (ANR-16-CE35-0009).

L'agricultura periurbana o de proximitat proporciona nombrosos avantatges des del punt de vista social, econòmic i paisatgístic. Per exemple, la curta distància entre la zona productiva i el consumidor final proporciona productes molt frescos que ofereixen propietats organolèptiques i nutritives molt satisfactòries, alhora que redueix la petjada de carboni associada al transport. Un altre avantatge de les zones periurbanes és l'accés a les aigües regenerades de les plantes de depuració d'aigües residuals provinents de poblacions veïnes, cosa que n'assegura la disponibilitat durant el decurs de l'any. Nogensmenys, la presència d'infraestructures (aeroports, autopistes, ports) pot constituir una font de contaminació del medi atmosfèric per deposició humida i/o seca (partícules en suspensió: orgàniques i inorgàniques) i altres contaminants atmosfèrics en fase gas (O3, SOx, NOx) que poden generar un estrès abiòtic als cultius, i per tant afectar-ne el rendiment. D'altra banda, tot i que l'ús d'aigües regenerades i l'aplicació de biosòlids poden ser molt positius per als conreus pel seu elevat contingut en nutrients i matèria orgànica, la presència de contaminants químics (metalls i microcontaminants orgànics) i biològics (patògens) podria constituir un perill potencial per a la salut pública si s'incorporen als cultius. En aquest treball, es presenten els resultats d'un estudi desenvolupat al Parc Agrari del Baix Llobregat (PABL) (Barcelona, Catalunya), on l'aigua d'irrigació presenta diverses qualitats fisicoquímiques, així com concentracions variables de contaminants, els quals es poden transferir al sòl agrícola i alguns a certs cultius. No obstant això, a la zona d'estudi no s'han detectat efectes sobre la productivitat agrícola deguts a l'alteració de paràmetres fisiològics de la planta (contingut de lípids, sucres i clorofil·les)., Peri-urban or proximity agriculture provides numerous advantages for horticulture, mainly associated with the short distance between the crop production area and the final market, leading to products of improved organoleptic and nutritive properties. Likewise, peri-urban agriculture reduces the carbon footprint associated with the transportation of orchard products between the production and consumption zones. Furthermore, the peri-urban areas have access to reclaimed waters from wastewater treatment plants of neighbouring cities, ensuring their availability throughout the productive cycle. The surrounding infrastructures (namely airports, harbours and highways), however, can increase the air pollution associated with wet and/or dry deposition (organic or inorganic) and gas phase contaminants (O3, SOx, NOx) which can lead to abiotic stress for the crops, decreasing their yield. On the other hand, reclaimed wastewater and biosolids contain a high concentration of nutrients and organic matter that is clearly beneficial to crops, but they can also contain chemical pollutants (metals and organic micropollutants) and microbiological pathogens that can be a potential hazard if they are taken up by crops. In this paper, some of the findings of a study conducted at the Baix Llobregat Agricultural Park (PABL) (Barcelona, Catalonia), where the irrigation water has different physical-chemical properties and a variable concentration of pollutants, are presented. Concentrations of trace elements in soil such Mo, Ni, Pb and As exceeded the standards for agricultural soil but most crops grown in the area are compliant (except for Pb). With respect to emerging pollutants, an anticonvulsive drug (carbamazepine and its 9,10-epoxide) was detected in crops, which is consistent with the indirect water reuse. Fungicides used for crop production together with plasticizers released from irrigation tubing were detected in the drip-irrigated crops. Nevertheless, no effects on agricultural productivity or on physiological plant parameters (lipid, sugar and chlorophyll content) were observed., La agricultura periurbana o de proximidad proporciona numerosas ventajas desde el punto de vista social, económico y paisajístico. Por ejemplo, la corta distancia entre la zona productiva y el consumidor final ofrece productos muy frescos cuyas propiedades organolépticas y nutritivas son muy satisfactorias, además reduce la huella de carbono asociada a su transporte. Otra ventaja adicional de la agricultura periurbana es el acceso a aguas regeneradas de las plantas de depuración de aguas residuales provenientes de las poblaciones vecinas asegurando con ello su disponibilidad durante todo el ciclo productivo. Sin embargo, la presencia de infraestructuras (aeropuertos, autopistas, puertos) puede constituir una fuente de contaminación del medio atmosférico debido a la deposición húmeda y/o seca (partículas en suspensión: orgánicas e inorgánicas) y otros contaminantes atmosféricos en fase gas (O3, SOx, NOx) que pueden generar un estrés abiótico a los cultivos y por tanto afectar a su rendimiento. Por otra parte, aunque el uso de aguas regeneradas y la aplicación de biosólidos pueden ser muy positivos para los cultivos debido al elevado contenido en nutrientes y materia orgánica, la presencia de contaminantes químicos (metales y microcontaminantes orgánicos) y biológicos (patógenos) pueden constituir un peligro potencial para la salud pública si se incorporan a los cultivos. En este trabajo, se presentan los resultados de un estudio desarrollado en el Parque Agrario del Baix Llobregat (PABL) (Barcelona, Catalunya), donde el agua de irrigación presenta diversas calidades fisicoquímicas y concentraciones variables de contaminantes, los cuales se pueden transferir al suelo agrícola y algunos de ellos a ciertos cultivos. No obstante, en la zona de estudio no se han detectado efectos sobre la productividad agrícola debidos a la alteración de parámetros fisiológicos de la planta (contenido de lípidos, azúcares y clorofilas).

Background: Mycobacterium tuberculosis (MTB) has limited ability to acquire variability. Analysis of its microevolution might help us to evaluate the pathways followed to acquire greater infective success. Whole-genome sequencing (WGS) in the analysis of the transmission of MTB has elucidated the magnitude of variability in MTB. Analysis of transmission currently depends on the identification of clusters, according to the threshold of variability (

In this work, 12 spin-spin coupling constants (J) obtained experimentally for the Ala3 peptide are used to determine the secondary structure of its central amino acid. For this purpose, a procedure is used that does not assume any main conformation, but considers the entire Ramachandran diagram without limiting it to specific areas. In addition, the algorithm considers the possibility that the value of each observed J is the result of the contribution of different structures/conformations, with the corresponding weights. In order to apply this procedure, it is necessary to know the value of each J for any combination of the dihedral angles ɸ and Ψ of the central amino acid. This is achieved through the Density Functional Theory. Firstly, the 625 structures generated by fixing the dihedral angles ɸ and Ψ are optimized at intervals of 15o at the B3LYP/D95(d,p) level of theory. The values of the 12 J are calculated for each structure with different functionals and basis sets in order to determine their possible effects, and the results are represented as a function of ɸ and Ψ, thus obtaining two-dimensional plots for each J. With these grids it can be observed that one-dimensional Karplus equations are not applicable in general, since with the exception of the constants 3J(C6-H14), 3J(C6-C15) and 3J(C6-C16), the values of J show dependence with the two dihedral angles. The effect of the solvent in the J calculations is also introduced, although it is quickly discarded due to the large deviations obtained with respect to the experimental data. The combination of the functional MPW1WK and the basis set 6-31G-J gives the best results according to the mean deviation (RMSD) with respect to the experimental J values, but the structures that are obtained do not correspond to expected conformations. On the other hand, by calculating the J with the functional MPW1WK and the uncontracted basis set D95 (d,p), the error is slightly higher but the structures obtained fully correspond with alpha helix, beta sheet and polyproline II helix conformations. In this way the functional MPW1WK significantly improves the results obtained with respect to previous reference calculations, where the functional B3LYP with the base D95 (d, p) had been used

Background: The World Health Organization recommends drug-susceptibility testing of Mycobacterium tuberculosis complex for all patients with tuberculosis to guide treatment decisions and improve outcomes. Whether DNA sequencing can be used to accurately predict profiles of susceptibility to first-line antituberculosis drugs has not been clear.\ud \ud \ud \ud Methods: We obtained whole-genome sequences and associated phenotypes of resistance or susceptibility to the first-line antituberculosis drugs isoniazid, rifampin, ethambutol, and pyrazinamide for isolates from 16 countries across six continents. For each isolate, mutations associated with drug resistance and drug susceptibility were identified across nine genes, and individual phenotypes were predicted unless mutations of unknown association were also present. To identify how whole-genome sequencing might direct first-line drug therapy, complete susceptibility profiles were predicted. These profiles were predicted to be susceptible to all four drugs (i.e., pansusceptible) if they were predicted to be susceptible to isoniazid and to the other drugs or if they contained mutations of unknown association in genes that affect susceptibility to the other drugs. We simulated the way in which the negative predictive value changed with the prevalence of drug resistance.\ud \ud \ud \ud Results: A total of 10,209 isolates were analyzed. The largest proportion of phenotypes was predicted for rifampin (9660 [95.4%] of 10,130) and the smallest was predicted for ethambutol (8794 [89.8%] of 9794). Resistance to isoniazid, rifampin, ethambutol, and pyrazinamide was correctly predicted with 97.1%, 97.5%, 94.6%, and 91.3% sensitivity, respectively, and susceptibility to these drugs was correctly predicted with 99.0%, 98.8%, 93.6%, and 96.8% specificity. Of the 7516 isolates with complete phenotypic drug-susceptibility profiles, 5865 (78.0%) had complete genotypic predictions, among which 5250 profiles (89.5%) were correctly predicted. Among the 4037 phenotypic profiles that were predicted to be pansusceptible, 3952 (97.9%) were correctly predicted.\ud \ud \ud \ud Conclusions: Genotypic predictions of the susceptibility of M. tuberculosis to first-line drugs were found to be correlated with phenotypic susceptibility to these drugs. (Funded by the Bill and Melinda Gates Foundation and others.)

Every year, species of the Mycobacterium tuberculosis complex (MTBC) kill more people than any other infectious disease caused by a single agent. As a consequence of its global distribution and parallel evolution with the human host the bacteria is not genetically homogeneous. The observed genetic heterogeneity has relevance at different phenotypic levels, from gene expression to epidemiological dynamics. However, current systems biology datasets have focused on the laboratory reference strain H37Rv. By using large expression datasets testing the role of almost two hundred transcription factors, we have constructed computational models to grab the expression dynamics of Mycobacterium tuberculosis H37Rv genes. However, we have found that many of those transcription factors are deleted or likely dysfunctional across strains of the MTBC. As a result, we failed to predict expression changes in strains with a different genetic background when compared with experimental data. These results highlight the importance of designing systems biology approaches that take into account the genetic diversity of tubercle bacilli, or any other pathogen, if we want to identify universal targets for vaccines, diagnostics and treatments.

The role of clonal complexity has gradually been accepted in infection by Mycobacterium tuberculosis (MTB), although analyses of this issue are limited. We performed an in-depth study of a case of recurrent MTB infection by integrating genotyping, whole genome sequencing, analysis of gene expression and infectivity in in vitro and in vivo models. Four different clonal variants were identified from independent intrapatient evolutionary branches. One of the single-nucleotide polymorphisms in the variants mapped in mce3R, which encodes a repressor of an operon involved in virulence, and affected expression of the operon. Competitive in vivo and in vitro co-infection assays revealed higher infective efficiency for one of the clonal variants. A new clonal variant, which had not been observed in the clinical isolates, emerged in the infection assays and showed higher fitness than its parental strain. The analysis of other patients involved in the same transmission cluster revealed new clonal variants acquired through novel evolutionary routes, indicating a high tendency toward microevolution in some strains that is not host-dependent. Our study highlights the need for integration of various approaches to advance our knowledge of the role and significance of microevolution in tuberculosis.

L’epistolari de Víctor Balaguer és un enorme document a partir del qual s’accedeix a dades desconegudes del segle xix (polítiques i literàries) a causa de l’anonimat de molts dels seus corresponsals. L’ús adequat de la base de dades de les cartes esdevé una eina historiogràfica fonamental per detectar estats d’opinió o informacions rellevants que altrament quedarien amagades, The database of Victor Balaguer’s correspondence provides accessto nineteenth-century data (political and literary) that would otherwise be unknown because of the anonymity of many correspondents. The proper use of the letters database becomes a critical tool in detecting historiographical opinion states or relevant information that would otherwise remain hidden

Clonal variants of Mycobacterium tuberculosis (MTB) coexist in specific patients, although the dynamics of their emergence is unknown. We used MIRU-VNTR to detect microevolution leading to variants of MTB in 3 out of 19 patients (15%) soon after diagnosis (61-85 days). Most harbored SNPs and for some of them a potential functional role was suggested. Microevolution in tuberculosis seems to occur sooner and more often than expected and could affect tracking of transmission. (C) 2016 Elsevier GmbH. All rights reserved.

Resumen basado en el de la publicación Título, resumen y palabras clave en inglés y español Se trata una de las nuevas fuentes usadas para el estudio de la historia de la escuela: las memorias de prácticas de los estudiantes de Magisterio. Se utiliza como muestra una colección inédita de casi un centenar de memorias de prácticas de la Normal de Baleares, elaboradas entre 1939 y 1948. Permite evidenciar que, más allá de la visión estereotipada de la escuela, determinada por sus imposiciones ideológicas y sus normas legales, existen aspectos que sólo se pueden conocer estudiando la cotidianidad del aula. Se muestra que existieron determinadas continuidades que se resistieron a la voluntad política de imponer cambios, evidenciando la distancia que existente entre lo prescrito por la legislación y lo acontecido en la escuela. Se aconseja escapar de interpretaciones histórico-educativas basadas exclusivamente en fuentes administrativas, para añadir testimonios que acerquen a las realidades del aula. ESP

Tuberculosis (TB) has overtaken HIV (human immunodeficiency virus) and malaria as the leading cause of death by an infectious disease worldwide. The reduction in the TB incidence is a modest 2% of cases per year, thus we will need 200 years to eradicate the disease. Part of the problem is that TB control tools are decades old and cannot anymore contribute to accelerate eradication of TB. New diagnostics, treatments and vaccines are urgently needed. Next generation sequencing has the potential to become one of these new tools. Genomic characterization of TB isolates is already showing its potential for epidemiology and diagnostics, particularly to identify drug resistance mutations. However, the experimental and bioinformatics skills needed are still far from being standardized and are not easy to incorporate as a routine in clinical laboratories. In this review we will describe current next generation sequencing approaches applied to the Mycobacterium tuberculosis complex, their contribution to the diagnostics and epidemiology of the disease and the efforts that are being undertaken to make the technology accessible to public health and clinical microbiology laboratories.

Fruit de la investigació i el desenvolupament tecnològic, s’ha aconseguit tenir un control intel·ligent i autònom de les instal·lacions a temps real i de forma bidireccional que permet gestionar-les i analitzar-les remotament. El present projecte té com a objectiu monitoritzar una planta de gas natural liquat situada al municipi de Rialp, a la comarca del Pallars Sobirà, la qual és l’encarregada de subministrar el gas a tot el poble. Per a una òptima distribució i utilització, el gas s’ha de distribuir en unes condicions específiques de pressió i temperatura. Per assegurar-ho, es realitzarà el control mitjançant un datalogger. Aquest dispositiu disposarà d’una pantalla tàctil on s’hi mostraran els valors més importants i on també s’hi podran variar les consignes de funcionament de la maniobra. També hi haurà la possibilitat de controlar-ne i revisar-ne l’estat a temps real de forma remota mitjançant un ordinador amb connexió a Internet. A més a més, s’enviarà e-mails d’alarmes al personal específic per poder reaccionar ràpidament en cas d’alguna incidència. Per realitzar la monitorització es dissenyarà la instal·lació elèctrica de la planta. També s’escollirà i es programarà els components per realitzar la monitorització de la instal·lació, tant de forma local com de forma remota

A persistent 8-year infection by a Beijing Mycobacterium tuberculosis strain from a previous outbreak after importation from West Africa obliged us to investigate secondary cases. We developed a multiplex PCR method based on whole-genome sequencing to target strain-specific single nucleotide polymorphisms (SNPs). In 1 week, we analyzed 868 isolates stored over 6 years. Only 2 cases (immigrants from Guinea Conakry) harbored the strain, which ruled out transmission-despite opportunities- and challenged some of the advantages associated with Beijing strains.

Here, we report the draft genome sequence of Mycobacterium brumae type strain ATCC 51384. This is the first draft genome sequence of M. brumae, a nonpathogenic, rapidly growing, nonchromogenic mycobacterium, with immunotherapeutic capacities.

Current migratory movements require new strategies for rapidly tracking the transmission of high-risk imported Mycobacterium tuberculosis strains. Whole-genome sequencing (WGS) enables us to identify single-nucleotide polymorphisms (SNPs) and therefore design PCRs to track specific relevant strains. However, fast implementation of these strategies in the hospital setting is difficult because professionals working in diagnostics, molecular epidemiology, and genomics are generally at separate institutions. In this study, we describe the urgent implementation of a system that integrates genomics and molecular tools in a genuine high-risk epidemiological alert involving 2 independent importations of extensively drug resistant (XDR) and pre-XDR Beijing M. tuberculosis strains from Russia into Spain. Both cases involved commercial sex workers with long-standing tuberculosis (TB). The system was based on strain-specific PCRs tailored from WGS data that were transferred to the local node that was managing the epidemiological alert. The optimized tests were available for prospective implementation in the local node 33 working days after receiving the primary cultures of the XDR strains and were applied to all 42 new incident cases. An interpretable result was obtained in each case (directly from sputum for 27 stain-positive cases) and corresponded to the amplification profiles for strains other than the targeted pre-XDR and XDR strains, which made it possible to prospectively rule out transmission of these high-risk strains at diagnosis.

L’epistolari de Victor Balaguer es un enorme document a partir del qual s’accedeix a dades desconegudes del segle xix (politiques i literaries) a causa de l’anonimat de molts dels seus corresponsals. L’us adequat de la base de dades de les cartes esdeve una eina historiografica fonamental per detectar estats d’opinio o informacions rellevants que altrament quedarien amagades