Corrigendum: In-depth analysis of IS genomic variability in the complex.

[This corrects the article DOI: 10.3389/fmicb.2022.

Corrigendum: In-depth analysis of IS genomic variability in the complex.

[This corrects the article DOI: 10.3389/fmicb.2022.

Diversity and botanical composition of native species in the Pampa biome in vineyards cultivated on soils with high levels of copper, zinc and manganese and phytoremediation potential.

Viticulture allows the preservation of native species inside vineyards in the Pampa biome. However, phytosanitary treatments in these areas can increase the levels of Cu, Zn and Mn. The study aimed to (i) verify the influence of Cu, Zn and Mn contents in Pampa biome soils; (ii) identify variables related to Cu, Zn and Mn that most contribute to the variation in richness, diversity, and dry matter production of native vegetation, (iii) investigate the phytoremediation potential of species present in vineyards.

Qualitative soil quality assessment is efficient in a grazing system with or without trees.

Background: Soil quality (SQ) assessment is affected by methods that convert data sets into indices, and such analyses are expensive and time-consuming. Qualitative SQ assessments are faster and cheaper than quantitative methods and they can be repeated to monitor SQ in crop and pasture systems. We evaluated SQ using qualitative and quantitative SQ indicators of two grazing systems under Voisin rational grazing (VRG) with trees (WT) or without trees (NT).

Transcriptomic profile of the most successful strain in Aragon, the MtZ strain, during exponential and stationary growth phases.

Aragon Community suffered, during the first years of the beginning of this century, a large outbreak caused by the MtZ strain, producing more than 240 cases to date. MtZ strain and the outbreak have been previously studied from an epidemiological and molecular point of view. In this work, we analyzed the transcriptomic profile of the strain for better understanding of its success among our population.

Phytoremediation of Cu-contaminated vineyard soils in Brazil: A compendium of Brazilian pot studies.

Vineyard soils can be contaminated by copper (Cu) due to successive applications of fungicides and organic fertilizers. Soil remediation can be addressed by altering soil properties or selecting efficient Cu-extracting cover crops tolerant to Cu toxicity. Our objectives were to synthesize the Cu-extracting efficiency by plant species tested in Brazil, classify them according to Cu resistance to toxicity, and assess the effect of soil properties on attenuating Cu toxicity.

Rapid Identification of Lineage and Drug Resistance in Clinical Samples of .

Background: is a slow-growing bacterium, which could delay its diagnosis and, therefore, promote the spread of the disease. Whole-genome sequencing allows us to obtain the complete drug-resistance profile of the strain; however, bacterial cultivation of clinical samples, along with complex processing, is required.

Methods: In this work, we explore AmpliSeq, an amplicon-based enrichment method for preparing libraries for targeted next-generation sequencing, to identify lineage and drug resistance directly from clinical samples.

Deciphering the Tangible Spatio-Temporal Spread of a 25-Year Tuberculosis Outbreak Boosted by Social Determinants.

Outbreak strains of Mycobacterium tuberculosis are promising candidates as targets in the search for intrinsic determinants of transmissibility, as they are responsible for many cases with sustained transmission; however, the use of low-resolution typing methods and restricted geographical investigations represent flaws in assessing the success of long-lived outbreak strains. We can now address the nature of outbreak strains by combining large genomic data sets and phylodynamic approaches. We retrospectively sequenced the whole genome of representative samples assigned to an outbreak circulating in the Canary Islands (the GC strain) since 1993, which accounts for ~20% of local tuberculosis cases.

Analysis of the twenty-six largest outbreaks of tuberculosis in Aragon using whole-genome sequencing for surveillance purposes.

The incidence of tuberculosis in Aragon, Spain, is around ten cases per 100,000 inhabitants. Since 2004, a molecular surveillance protocol has been carried out; therefore, all M. tuberculosis strains are genotyped.

Estimation of the mutation rate of Mycobacterium tuberculosis in cases with recurrent tuberculosis using whole genome sequencing.

The study of tuberculosis latency is problematic due to the difficulty of isolating the bacteria in the dormancy state. Despite this, several in vivo approaches have been taken to mimic the latency process. Our group has studied the evolution of the bacteria in 18 cases of recurrent tuberculosis.

Proposition of critical thresholds for copper and zinc transfer to solution in soils.

Several studies have reported increased copper (Cu) and zinc (Zn) levels in agricultural soils worldwide, mainly due to organic waste and successive leaf fungicide applications in crops. However, the critical transfer thresholds in soils, which can indicate the real risk of environmental contamination and toxicity to plants, remain poorly understood. This study aimed to define the maximum Cu and Zn adsorption capacity (MAC) and threshold (T-Cu and T-Zn) in different soils in Southern Brazil, which present different clay and organic matter (OM) levels.

The MtZ Strain: Molecular Characteristics and Outbreak Investigation of the Most Successful Strain in Aragon Using Whole-Genome Sequencing.

Since 2004, a tuberculosis surveillance protocol has been carried out in Aragon, thereby managing to detect all tuberculosis outbreaks that take place in the community. The largest outbreak was caused by a strain named (MtZ), causing 242 cases as of 2020. The main objective of this work was to analyze this outbreak and the molecular characteristics of this successful strain that could be related to its greater transmission.

In-depth Analysis of IS Genomic Variability in the Complex.

The insertion sequence (IS) is a repetitive mobile element specific for the complex (MTBC) used for years to diagnose and genotype this pathogen. It contains the overlapping reading frames and that encode a transposase. Its genetic variability is difficult to study because multiple copies are present in the genome.

Identification and phytoremediation potential of spontaneous species in vineyard soils contaminated with copper.

Copper (Cu) contents in vineyard soils due to the application of cupric fungicides cause changes in the native covering flora. Under these conditions, the surviving individuals accumulate the metal in and decrease its availability in the soil, reducing the potential toxicity to grapevine. We have identified spontaneous plant species and their phytoremediation potential from vineyards of Isabella () on two distinct soil types (Inceptisol and Entisol) contaminated with Cu.

Natural abundance analysis of the role played by N as indicator for the certification of organic-system deriving food.

Background: The natural abundance of stable isotope N (δ N) in production systems has emerged as an alternative to distinguish organic products from conventional ones. This study evaluated the use of δ N values recorded for nitrogen fertilizers, soil and plant tissue in order to set the differences between organic and conventional agricultural production systems applied to rice, potatoes, apple and banana crops.

Results: Values of δ N recorded for N sources ranged from +5.

Consensus on improving the comprehensive care of patients with acute heart failure.

The latest acute heart failure (AHF) consensus document from the Spanish Society of Cardiology (SEC, for its initials in Spanish), Spanish Society of Internal Medicine (SEMI), and Spanish Society of Emergency Medicine (SEMES) was published in 2015, which made an update covering the main novelties regarding AHF from the last few years necessary. These include publication of updated European guidelines on HF in 2016, new studies on the pharmacological treatment of patients during hospitalization, and other recent developments regarding AHF such as early treatment, intermittent treatment, advanced HF, and refractory congestion. This consensus document was drafted with the aim of updating all aspects related to AHF and to create a document that comprehensively describes the diagnosis, treatment, and management of this disease.

Analysis of Mycobacterium africanum in the last 17 years in Aragon identifies a specific location of IS6110 in Lineage 6.

The purpose of this study was to increase our knowledge about Mycobacterium africanum and report the incidence and characteristics of tuberculosis (TB) due to their lineages in Aragon, Spain, over the period 2003-2019. The study includes all the cases in our region, where all the M. tuberculosis complex isolates are systematically characterised.

Discrimination of soils managed with different sources of fertilization and plant species in organic and conventional farming through near-infrared spectroscopy and chemometrics.

Background: The combination of near-infrared (NIR) spectroscopy and chemometrics can be used to group or discriminate soils based on spectral response. In this study, we conducted discrimination and classification analyses on soils managed with different sources of fertilization and plant species grown in organic and conventional farming systems.

Results: Principal component analysis explained 96% (PC1) and 3% (PC2) of the data variability and separated the soil samples of organic and conventional management systems.

Consensus on improving the comprehensive care of patients with acute heart failure.

The latest acute heart failure consensus document from the Spanish Society of Cardiology, Spanish Society of Internal Medicine, and Spanish Society of Emergency Medicine was published in 2015, which made an update covering the main novelties regarding acute heart failure from the last few years necessary. These include publication of updated European guidelines on heart failure in 2016, new studies on the pharmacological treatment of patients during hospitalization, and other recent developments regarding acute heart failure such as early treatment, intermittent treatment, advanced heart failure, and refractory congestion. This consensus document was drafted with the aim of updating all aspects related to acute heart failure and to create a document that comprehensively describes the diagnosis, treatment, and management of this disease.

A whole-genome sequencing study of an X-family tuberculosis outbreak focus on transmission chain along 25 years.

Lineage 4/X-family of Mycobacterium tuberculosis is not very notorious, except for the CDC1551 strain. One strain of this family, named Ara50, caused one of the largest tuberculosis outbreaks of the Aragon region, Spain, during the 1990s and remained until 2018. These X-strains are characterised by high transmissibility and by carrying a low copy number of IS6110 in their genomes.

The value of the continuous genotyping of multi-drug resistant tuberculosis over 20 years in Spain.

Molecular epidemiology of circulating clinical isolates is crucial to improve prevention strategies. The Spanish Working Group on multidrug resistant tuberculosis (MDR-TB) is a network that monitors the MDR-TB isolates in Spain since 1998. The aim of this study was to present the study of the MDR-TB and extensively drug-resistant tuberculosis (XDR-TB) patterns in Spain using the different recommended genotyping methods over time by a national coordinated system.

Bioinformatic analysis of RHO family of GTPases identifies RAC1 pharmacological inhibition as a new therapeutic strategy for hepatocellular carcinoma.

Objective: The RHO family of GTPases, particularly RAC1, has been linked with hepatocarcinogenesis, suggesting that their inhibition might be a rational therapeutic approach. We aimed to identify and target deregulated RHO family members in human hepatocellular carcinoma (HCC).

Design: We studied expression deregulation, clinical prognosis and transcription programmes relevant to HCC using public datasets.