Bridging the gap between molecular and genomic epidemiology in tuberculosis: inferring MIRU-VNTR patterns from genomic data.

The transition from MIRU-VNTR-based epidemiology studies in tuberculosis (TB) to genomic epidemiology has transformed how we track transmission. However, short-read sequencing is poor at analyzing repetitive regions such as the MIRU-VNTR loci. This causes a gap between the new genomic data and the large amount of information stored in historical databases. Long-read sequencing could bridge this knowledge gap by allowing analysis of repetitive regions. However, the feasibility of extracting MIRU-VNTRs from long reads and linking them to historical data has not been evaluated. In our study, an in silico arm, consisting of inference of MIRU patterns from long-read sequences (using MIRUReader program), was compared with an experimental arm, involving standard amplification and fragment sizing. We analyzed overall performance on 39 isolates from South Africa and confirmed reproducibility in a sample enriched with 62 clustered cases from Spain. Finally, we ran 25 consecutive incident cases, demonstrating the feasibility of correctly assigning new clustered/orphan cases by linking data inferred from genomic analysis to MIRU-VNTR databases. Of the 3,024 loci analyzed, only 11 discrepancies (0.36%) were found between the two arms: three attributed to experimental error and eight to misassigned alleles from long-read sequencing. A second round of analysis of these discrepancies resulted in agreement between the experimental and in silico arms in all but one locus. Adjusting the MIRUReader program code allowed us to flag potential in silico misassignments due to suboptimal coverage or unfixed double alleles. Our study indicates that long-read sequencing could help address potential chronological and geographical gaps arising from the transition from molecular to genomic epidemiology of tuberculosis. IMPORTANCE: The transition from molecular epidemiology in tuberculosis (TB), based on the analysis of repetitive regions (VNTR-based genotyping), to genomic epidemiology transforms in the precision with which we track transmission. However, short-read sequencing, the most common method for performing genomic analysis, is poor at analyzing repetitive regions. This means that we face a gap between the new genomic data and the large amount of information stored in historical databases, which is also an obstacle to cross-national surveillance involving settings where only molecular data are available. Long-read sequencing could help bridge this knowledge gap by allowing analysis of repetitive regions. Our study demonstrates that MIRU-VNTR patterns can be successfully inferred from long-read sequences, allowing the correct assignment of new cases as clustered/orphan by linking new data extracted from genomic analysis to historical MIRU-VNTR databases. Our data may provide a starting point for bridging the knowledge gap between the molecular and genomic eras in tuberculosis epidemiology.

A One Health approach revealed the long-term role of Mycobacterium caprae as the hidden cause of human tuberculosis in a region of Spain, 2003 to 2022.

IntroductionMycobacterium caprae is a member of the Mycobacterium tuberculosis complex (MTBC) not routinely identified to species level. It lacks specific clinical features of presentation and may therefore not be identified as the causative agent of tuberculosis. Use of whole genome sequencing (WGS) in the investigation of a family microepidemic of tuberculosis in Almería, Spain, unexpectedly identified the involvement of M. caprae.AimWe aimed to evaluate the presence of additional unidentified M. caprae cases and to determine the magnitude of this occurrence.MethodsFirst-line characterisation of the MTBC isolates was done by MIRU-VNTR, followed by WGS. Human and animal M. caprae isolates were integrated in the analysis.ResultsA comprehensive One Health strategy allowed us to (i) detect other 11 M. caprae infections in humans in a period of 18 years, (ii) systematically analyse M. caprae infections on an epidemiologically related goat farm and (iii) geographically expand the study by including 16 M. caprae isolates from other provinces. Integrative genomic analysis of 41 human and animal M. caprae isolates showed a high diversity of strains. The animal isolates' diversity was compatible with long-term infection, and close genomic relationships existed between isolates from goats on the farm and recent cases of M. caprae infection in humans.DiscussionZoonotic circulation of M. caprae strains had gone unnoticed for 18 years. Systematic characterisation of MTBC at species level and/or extended investigation of the possible sources of exposure in all tuberculosis cases would minimise the risk of overlooking similar zoonotic events.

Medium and long-term effects of low doses of Chlorpyrifos during the postnatal, preweaning developmental stage on sociability, dominance, gut microbiota and plasma metabolites.

Autism spectrum disorder (ASD) is a complex neurodevelopmental pathology characterized by altered verbalizations, reduced social interaction behavior, and stereotypies. Environmental factors have been associated with its development. Some researchers have focused on pesticide exposure. Chlorpyrifos (CPF) is the most used Organophosphate. Previous developmental studies with CPF showed decreased, enhanced or no effect on social outcomes eminently in mice. The study of CPF exposure during preweaning stages on social behavior is sparse in mice and non-existent in rats. d stressors could be at the basis of ASD development, and around postnatal day 10 in the rat is equivalent to the human birthday in neurodevelopmental terms. We explored the effects of exposure to low doses (1mg/kg/mL/day) of CPF during this stage regarding: sociability, dominance gut microbiome and plasma metabolomic profile, since alterations in these systems have also been linked to ASD. There was a modest influence of CPF on social behavior in adulthood, with null effects during adolescence. Dominance and hierarchical status were not affected by exposure. Dominance status explained the significant reduction in reaction to social novelty observed on the sociability test. CPF induced a significant gut microbiome dysbiosis and triggered a hyperlipidemic, hypoglycemic/hypogluconeogenesis and a general altered cell energy production in females. These behavioral results in rats extend and complement previous studies with mice and show novel influences on gut metagenomics and plasma lipid profile and metabolomics, but do not stablish a relation between the exposure to CPF and the ASD phenotype. The effects of dominance status on reaction to social novelty have an important methodological meaning for future research on sociability.

Plasmodium genomics: an approach for learning about and ending human malaria.

Malaria causes high levels of morbidity and mortality in human beings worldwide. According to the World Health Organization (WHO), about half a million people die of this disease each year. Malaria is caused by six species of parasites belonging to the Plasmodium genus: P. falciparum, P. knowlesi, P. vivax, P. malariae, P. ovale curtisi, and P. ovale wallikeri. Currently, malaria is being kept under control with varying levels of elimination success in different countries. The development of new molecular tools as well as the use of next-generation sequencing (NGS) technologies and novel bioinformatic approaches has improved our knowledge of malarial epidemiology, diagnosis, treatment, vaccine development, and surveillance strategies. In this work, the genetics and genomics of human malarias have been analyzed. Since the first P. falciparum genome was sequenced in 2002, various population-level genetic and genomic surveys, together with transcriptomic and proteomic studies, have shown the importance of molecular approaches in supporting malaria elimination.

The state of global research on social work and disability.

Two paradigms are used to define disability. On the one hand, the biological paradigm, which attends to a person's deficiencies and difficulties. And, on the other hand, the social, which does not treat disability as a pathology, but rather places the focus of interest on the deficient tools that society has to consider the capabilities of everyone. This article analyzes the scientific production on disability and social work, using bibliometric techniques and algorithms for the detection of communities, taking into account the current state of research worldwide. This analysis offers a holistic view of the characteristics of the work carried out in the world on this subject.

Trends in plant research using molecular markers.

MAIN CONCLUSION: A deep bibliometric analysis has been carried out, obtaining valuable parameters that facilitate the understanding around the research in plant using molecular markers. The evolution of the improvement in the field of agronomy is fundamental for its adaptation to the new exigencies that the current world context raises. In addition, within these improvements, this article focuses on those related to the biotechnology sector. More specifically, the use of DNA markers that allow the researcher to know the set of genes associated with a particular quantitative trait or QTL. The use of molecular markers is widely extended, including: restriction fragment length polymorphism, random-amplified polymorphic DNA, amplified fragment length polymorphism, microsatellites, and single-nucleotide polymorphisms. In addition to classical methodology, new approaches based on the next generation sequencing are proving to be fundamental. In this article, a historical review of the molecular markers traditionally used in plants, since its birth and how the new molecular tools facilitate the work of plant breeders is carried out. The evolution of the most studied cultures from the point of view of molecular markers is also reviewed and other parameters whose prior knowledge can facilitate the approach of researchers to this field of research are analyzed. The bibliometric analysis of molecular markers in plants shows that top five countries in this research are: US, China, India, France, and Germany, and from 2013, this research is led by China. On the other hand, the basic research using Arabidopsis is deeper in France and Germany, while other countries focused its efforts in their main crops as the US for wheat or maize, while China and India for wheat and rice.

Genetic approach towards a vaccine against malaria.

Malaria is a major concern for international health authorities. Millions of people contract it every year in the world due to a parasite of the Plasmodium genus. Due to the complexity of the parasite biology and genetics, there is currently no vaccine against the disease. However, due to the great resistance both to the medicines and to the insecticides used to combat the disease, it has become essential to obtain a vaccine as the necessary tool to prevent transmission and eliminate the disease. The bibliometric data indicate that interest in vaccines has been growing steadily since the 1980s. But nowadays, a powerful tool is used: the Plasmodium genome. This allows us to improve the fight against the disease. Knowing the sequences of the genes that favor the appearance of drug resistance, or those that encode for proteins with greater antigenic response, is a tool that can become fundamental. This article reviews the state of the art on vaccines and genetics, in the fight against malaria, and analyzes the fixed photo that the worldwide research on the disease poses.

Human parasitology worldwide research.

In this article, the trends in human parasitology have been studied through the analysis of the number of publications in this area. The parameters studied were: number of articles, language, countries and institutions with the highest number of publications, and keywords with greater presence in the articles of human parasitology. The results of the analysis confirm the growing interest in this area, observing an exponential growth in the number of publications in the last decades. We also verified that the main country in terms of scientific production is the USA, although among the most important institutions, we find non-US centres such as the Oswaldo Cruz Foundation and the London School of Hygiene and Tropical Medicine. For observing the relative importance of the journals that publish articles in this specific topic, an index has been created based on the h-index of the journal with publications related to human parasitology and divided by every 100 items. This rank is led fist by 'Journal of Medical Entomology' closely followed by 'Parasitology'. The analysis of the keywords allows to draw conclusions about the great importance of malaria in the current world research. A change in analytical methodology is also observed, and molecular techniques are now being imposed. These techniques, in the near future, have to influence in an improvement in the treatments and prevention of the diseases caused by parasites. Finally, it can be seen that diseases traditionally studied as helminthiasis and amebiasis are currently as well studied as others such as toxoplasmosis or leishmaniasis.

A new approach for detection and quantification of microalgae in industrial-scale microalgal cultures.

In industrial-scale microalgal cultures, non-target microalgae compete with the desired species for nutrients and CO2, thus reducing the growth rate of the target species and the quality of the produced biomass. Microalgae identification is generally considered a complicated issue; although, in the last few years, new molecular methods have helped to rectify this problem. Among the different techniques available, DNA barcoding has proven very useful in providing rapid, accurate, and automatable species identification; in this work, it is used to assess the genomic identity of the microalga species Scenedesmus sp. 'almeriensis', a common strain in industrial-scale cultures. Barcode markers rbcL and ITS1-5.8S-ITS2 were sequenced and the obtained genomic information was used to design a quantitative PCR assay to precisely quantify the S. almeriensis concentration in microalgal cultures of industrial interest. TaqMan chemistry was used to quantify down to 1 µg/L dry weight of S. almeriensis cells, including in the presence of concentrated mixed cultures of other microalgae. A simple direct qPCR approach was also investigated to avoid classic DNA extraction and to reduce total assay time to approximately 2 h. The objective was to design strain-specific tools able to confirm and quantify the presence of different strains in whatever microalgae culture so as to achieve maximal productivity and quality of the produced biomass.

The metagenomics worldwide research.

Metagenomics is the technique, or set of techniques, whose main objective is to determine the microbial population that can be found in a determined environment, studied in the context of its community. For this, it uses the techniques of massive sequencing, or next generation sequencing, due to the difficulties presented by traditional techniques when trying to transfer all the microorganisms present in a given environment to the laboratory. Metagenomics is a newly created technique, which was born at the beginning of the twenty-first century, and since then the interest of the world scientific community in fields as diverse as medicine, biotechnology, agriculture or genetics has not left to grow. In this article, the authors make a historical review of the metagenomics, analyze and evaluate the different massive sequencing platforms used for metagenomic assays, review the current literature on this subject and advance future problems with which researchers who decide to go deeper in this field could find. In this way, the prior knowledge of the researcher will facilitate the approach of his research.

Advanced microbial analysis for wastewater quality monitoring: metagenomics trend.

Urban Wastewater treatment plants (UWWTPs) have played an important and fundamental role in society for water purification of contaminated human wastewaters over the last decades. Microorganisms are very important in UWWTP as their metabolic activity significantly reduces the organic load of the UWW, although there is an uncertain gap in our knowledge regarding microbial consortium structure and their activity in UWWTP operation on a large scale. On the other hand, effluents of UWWTPs have come to be a new source of fresh water to ease water scarcity in many regions of the world, especially in intensive irrigation practices. Many concerns over health risks relating to the direct reuse of this water are very well known. However, if a proper disinfection treatment is applied, these are strongly reduced as conventional methodologies have demonstrated over the last decades. In line with this, the continuous development of new devices for analytical measurement that increase the sensitivities (limit of detection) are showing that other potential risks for both environmental and human health may be associated with UWW reuse. In this work, the most important aspects related to microorganisms in UWWTPs and UWW effluents are presented. Moreover, the new developments on genetic tools for detection of microorganisms are presented, with special emphasis on metagenomic methodology. A bibliometric analysis of what has been published so far is also carried out.

DNA Sequencing Sensors: An Overview.

The first sequencing of a complete genome was published forty years ago by the double Nobel Prize in Chemistry winner Frederick Sanger. That corresponded to the small sized genome of a bacteriophage, but since then there have been many complex organisms whose DNA have been sequenced. This was possible thanks to continuous advances in the fields of biochemistry and molecular genetics, but also in other areas such as nanotechnology and computing. Nowadays, sequencing sensors based on genetic material have little to do with those used by Sanger. The emergence of mass sequencing sensors, or new generation sequencing (NGS) meant a quantitative leap both in the volume of genetic material that was able to be sequenced in each trial, as well as in the time per run and its cost. One can envisage that incoming technologies, already known as fourth generation sequencing, will continue to cheapen the trials by increasing DNA reading lengths in each run. All of this would be impossible without sensors and detection systems becoming smaller and more precise. This article provides a comprehensive overview on sensors for DNA sequencing developed within the last 40 years.

Transfer of parasitology research to patents worldwide.

Mankind has known about different parasitic diseases since ancient times. There is no doubt that parasites are the infectious agents that have caused the most deaths throughout history. But even today, parasitic diseases affect more than one billion people worldwide. In this paper, the relationship between articles published in the area of parasitology and international patents in this field from 1996 to 2019 was analyzed. For this purpose, Scopus has been used. This is a database developed by Elsevier, which, in addition to having numerous indexed journals and books, has developed SciVal, an analysis tool with which the publications that have been cited in the patents of the 5 largest patent offices in the world have been analyzed. The analysis has allowed us to study 2814 publications, to know their time trend, their Authors, Affiliations, and Countries, as well as the journals in which they have been published. Also, the topics and topic clusters related to parasitology that appear in publications cited in international patents have been known. Thus, the existence of six Topic Clusters that group 94% of all publications has been discovered. Of all of them, the Topic Cluster referring to malaria stands out above all others, with 968 articles (34% of the total), probably due to the fact that malaria continues to be, to this day, one of the great challenges for both industry and basic research throughout the world.

Integrative transnational analysis to dissect tuberculosis transmission events along the migratory route from Africa to Europe.

BACKGROUND: Growing international migration has increased the complexity of tuberculosis transmission patterns. Italy's decision to close its borders in 2018 made of Spain the new European porte entrée for migration from the Horn of Africa (HA). In one of the first rescues of migrants from this region at the end of 2018, tuberculosis was diagnosed in eight subjects, mainly unaccompanied minors. METHODS: Mycobacterium tuberculosis isolates from these recently arrived migrants were analysed by Mycobacterial Interspersed Repetitive-Unit/Variable-Number of Tandem Repeat (MIRU-VNTR) and subsequent whole genome sequencing (WGS) analysis. Data were compared with those from collections from other European countries receiving migrants from the HA and a strain-specific PCR was applied for a fast searching of common strains. Infections in a cellular model were performed to assess strain virulence. RESULTS: MIRU-VNTR analysis allowed identifying an epidemiological cluster involving three of the eight cases from Somalia (0 single-nucleotide polymorphisms between isolates, HA cluster). Following detailed interviews revealed that two of these cases had shared the same migratory route in most of the trip and had spent a long time at a detention camp in Libya. To confirm potential en route transmission for the three cases, we searched the same strain in collections from other European countries receiving migrants from the HA. MIRU-VNTR, WGS and a strain-specific PCR for the HA strain were applied. The same strain was identified in 12 cases from Eritrea diagnosed soon after their arrival in 2018 to the Netherlands, Belgium and Italy. Intracellular replication rate of the strain did not reveal abnormal virulence. CONCLUSIONS: Our study suggests a potential en route transmission of a pan-susceptible strain, which caused at least 15 tuberculosis cases in Somalian and Eritrean migrants diagnosed in four different European countries.

Worldwide Research Trends on Medicinal Plants.

The use of medicinal plants has been done since ancient times and may even be considered the origin of modern medicine. Compounds of plant origin have been and still are an important source of compounds for drugs. In this study a bibliometric study of all the works indexed in the Scopus database until 2019 has been carried out, analyzing more than 100,000 publications. On the one hand, the main countries, institutions and authors researching this topic have been identified, as well as their evolution over time. On the other hand, the links between the authors, the countries and the topics under research have been analyzed through the detection of communities. The last two periods, from 2009 to 2014 and from 2015 to 2019, have been examined in terms of research topics. It has been observed that the areas of study or clusters have been reduced, those of the last period being those engaged in unclassified drug, traditional medicine, cancer, in vivo study-antidiabetic activity, and animals-anti-inflammatory activity. In summary, it has been observed that the trend in global research is focused more on the search for new medicines or active compounds rather than on the cultivation or domestication of plant species with this demonstrated potential.

The Contribution of Spanish Science to Patents: Medicine as Case of Study.

Investments in research and development (R&D) and innovation are expensive, and one wishes to be assured that there is positive feedback and to receive guidance on how to direct investments in the future. The social or economic benefits of investments in R&D are of particular interest to policymakers. In this regard, public expense in research, especially through universities, is sometimes being questioned. This paper establishes a measure of how research in Spain, and specifically in its universities, is involved. In this study, we have analyzed all the literature cited in the period 1998-2018 produced by Spanish institutions and which has been cited in at least one international patent, obtaining more than 40,000 publications from more than 160,000 different authors. The data have been surprisingly positive, showing that practically all public universities contribute to this subject and that there is a great deal of international collaboration, both in terms of the number of countries with which they collaborate and the prestige of the institutions involved. Regarding the specific scientific fields in which this collaboration is most relevant, biochemistry, genetics and molecular biology, and medicine together account for almost 40% of the total works. The topics most used by these publications were those of diseases or medical problems such as: Neoplams, Carcinoma, Alzheimer Disease, or human immunodeficiency virus (HIV-1). Oncology was according to the All Science Journal Classification (ASJC) the leading and central issue. Therefore, although the result of basic research is difficult to quantify, when it is observed that there is a return in fields such as medicine or global health, it can be said that it is well employed. In terms of journals from a purely bibliometric point of view, it has been observed that some journals do not have a great impact or relative position within their categories, but they do have a great relevance in this area of patent support. Therefore, it would be worthwhile to set up a rank for scientific journals based on the citations of patents, so the percentage of articles cited in patents with Field-Weighted Citation Impact (FWCI) >1, and as an indicator of scientific transfer from universities or research centres, the transference index in patents (TIP) is also proposed.

Long-term effects of low doses of Chlorpyrifos exposure at the preweaning developmental stage: A locomotor, pharmacological, brain gene expression and gut microbiome analysis.

Development is especially sensitive to Chlorpyrifos (CPF) toxicity, associated with several neurodegenerative and neurodevelopmental disorders where motor function dysfunction is a core symptom. Amongst the alternative molecular targets to cholinesterases inhibition, developmental CPF alters different components in the most important neurotransmitter systems, although this depends on the exposure period. Exposure during the late postnatal preweaning stage is the least studied by far. This period includes essential neurodevelopmental processes and has an important translational meaning. The present study analyzed the influence of low doses of CPF on this developmental window on locomotor activity and the state of the different neurotransmitter systems by pharmacological challenges. Brain gene expression and microbiome modulation following CPF were also analyzed. CPF exposure long-term increased spontaneous vertical activity, female's activity following acute stress, hyposensitized the cholinergic system and hypersensitized the GABAergic system, up-regulated both muscarinic 2 receptor and GABA-A-α2 receptor subunit in the dorsal striatum and the frontal cortex, respectively and induced gut microbiota dysbiosis at both genus and species levels. The present study supports alternative molecular targets than the ChEs following late postnatal, preweaning exposure to low doses of CPF, focusing on both cholinergic and GABAergic systems and the gut microbiome as an important factor.

Plasmodium vivax Cysteine-Rich Protective Antigen Polymorphism at Exon-1 Shows Recombination and Signatures of Balancing Selection.

Plasmodium vivax Cysteine-Rich Protective Antigen (CyRPA) is a merozoite protein participating in the parasite invasion of human reticulocytes. During natural P. vivax infection, antibody responses against PvCyRPA have been detected. In children, low anti-CyRPA antibody titers correlated with clinical protection, which suggests this protein as a potential vaccine candidate. This work analyzed the genetic and amino acid diversity of pvcyrpa in Mexican and global parasites. Consensus coding sequences of pvcyrpa were obtained from seven isolates. Other sequences were extracted from a repository. Maximum likelihood phylogenetic trees, genetic diversity parameters, linkage disequilibrium (LD), and neutrality tests were analyzed, and the potential amino acid polymorphism participation in B-cell epitopes was investigated. In 22 sequences from Southern Mexico, two synonymous and 21 nonsynonymous mutations defined nine private haplotypes. These parasites had the highest LD-R2 index and the lowest nucleotide diversity compared to isolates from South America or Asia. The nucleotide diversity and Tajima's D values varied across the coding gene. The exon-1 sequence had greater diversity and Rm values than those of exon-2. Exon-1 had significant positive values for Tajima's D, ß-α values, and for the Z (HA: dN > dS) and MK tests. These patterns were similar for parasites of different origin. The polymorphic amino acid residues at PvCyRPA resembled the conformational B-cell peptides reported in PfCyRPA. Diversity at pvcyrpa exon-1 is caused by mutation and recombination. This seems to be maintained by balancing selection, likely due to selective immune pressure, all of which merit further study.

Wastewater Treatment by Advanced Oxidation Process and Their Worldwide Research Trends.

Background: Water is a scarce resource and is considered a fundamental pillar of sustainable development. The modern development of society requires more and more drinking water. For this cleaner wastewater, treatments are key factors. Among those that exist, advanced oxidation processes are being researched as one of the sustainable solutions. The main objective of this manuscript is to show the scientific advances in this field. Methods: In this paper, a systematic analysis of all the existing scientific works was carried out to verify the evolution of this line of research. Results: It was observed that the three main countries researching this field are China, Spain, and the USA. Regarding the scientific collaboration between countries, three clusters were detected-one of Spain, one of China and the USA, and one of Italy and France. The publications are grouped around three types of water: industrial, urban, and drinking. Regarding the research, 15 clusters identified from the keywords analyzed the advanced oxidation process (alone or combined with biological oxidation) with the type of wastewater and the target pollutant, removal of which is intended. Finally, the most important scientific communities or clusters detected in terms of the number of published articles were those related to the elimination of pollutants of biological origin, such as bacteria, and of industrial nature, such as pesticides or pharmaceutical products.

Analysis of Global Research on Malaria and Plasmodium vivax.

Background: Malaria is one of the infectious diseases of greatest interest to the scientific community and of greatest concern to international health authorities. Traditionally, the focus has been on Plasmodium falciparum, the parasite that causes the most severe form of the disease in Africa. However, in the last twenty years, the Plasmodium vivax parasite, responsible for a large number of cases in Latin America, the Middle East, South and Southeast Asia, the Horn of Africa, and Oceania, has also generated enormous interest due, among other things, to the published evidence that it can cause severe malaria. Methods: In this paper, the international scientific publication on malaria and P. vivax has been analyzed using the Scopus database to try to define global trends in this field of study. Results: It has been shown that events such as the emergence of resistance to certain drugs can break a trend. The important role of non-malaria-endemic countries such as the USA or Switzerland in malaria research is also evident. Conclusions: International cooperation will be essential for the eradication of the disease. Moreover, in this sense, the general vision given by the bibliometric analysis of malaria caused by P. vivax is fundamental to paint the picture regarding the current situation and encourage international cooperation and control efforts.