Revealing Genomic Insights of the Unexplored Porcine Pathogen Actinobacillus pleuropneumoniae Using Whole Genome Sequencing

Actinobacillus pleuropneumoniae (APP) is the causative agent of pleuropneumonia in pigs, one of the most relevant bacterial respiratory diseases in the swine industry. To date, 19 serotypes have been described based on capsular polysaccharide typing with significant virulence dissimilarities. In this study, 16 APP isolates from Spanish origin were selected to perform antimicrobial susceptibility tests and comparative genomic analysis using whole genome sequencing (WGS). To obtain a more comprehensive worldwide molecular epidemiologic analyses, all APP whole genome assemblies available at the National Center for Biotechnology Information (NCBI) at the time of the study were also included. An in-house in silico PCR approach enabled the correct serotyping of unserotyped or incorrectly serotyped isolates and allowed for the discrimination between serotypes 9 and 11. A pangenome analysis identified the presence or absence of gene clusters to be serotype specific, as well as virulence profile analyses targeting the apx operons. Antimicrobial resistance genes were correlated to the presence of specific plasmids. Altogether, this study provides new insights into the genetic variability within APP serotypes, correlates phenotypic tests with bioinformatic analyses and manifests the benefits of populated databases for a better assessment of diversity and variability of relatively unknown pathogens. Overall, genomic comparative analysis enhances the understanding of transmission and epidemiological patterns of this species and suggests vertical transmission of the pathogen, including the resistance genes, within the Spanish integrated systems.info:eu-repo/semantics/publishedVersio

Client applications and server-side docker for management of RNASeq and/or VariantSeq workflows and pipelines of the GPRO suite

The GPRO suite is an in-progress bioinformatic project for -omics data analysis. As part of the continued growth of this project, we introduce a client- and server-side solution for comparative transcriptomics and analysis of variants. The client-side consists of two Java applications called “RNASeq” and “VariantSeq” to manage pipelines and workflows based on the most common command line interface tools for RNA-seq and Variant-seq analysis, respectively. As such, “RNASeq” and “VariantSeq” are coupled with a Linux server infrastructure (named GPRO Server-Side) that hosts all dependencies of each application (scripts, databases, and command line interface software). Implementation of the Server-Side requires a Linux operating system, PHP, SQL, Python, bash scripting, and third-party software. The GPRO Server-Side can be installed, via a Docker container, in the user’s PC under any operating system or on remote servers, as a cloud solution. “RNASeq” and “VariantSeq” are both available as desktop (RCP compilation) and web (RAP compilation) applications. Each application has two execution modes: a step-by-step mode enables each step of the workflow to be executed independently, and a pipeline mode allows all steps to be run sequentially. “RNASeq” and “VariantSeq” also feature an experimental, online support system called GENIE that consists of a virtual (chatbot) assistant and a pipeline jobs panel coupled with an expert system. The chatbot can troubleshoot issues with the usage of each tool, the pipeline jobs panel provides information about the status of each computational job executed in the GPRO Server-Side, while the expert system provides the user with a potential recommendation to identify or fix failed analyses. Our solution is a ready-to-use topic specific platform that combines the user-friendliness, robustness, and security of desktop software, with the efficiency of cloud/web applications to manage pipelines and workflows based on command line interface software.This work was supported by the Marie Sklodowska-Curie OPATHY project grant agreement 642095, the pre-doctoral research fellowship from MINECO Industrial Doctorates (Grant 659 DI-17-09134); Grant TSI-100903-2019-11 from the Secretary of State for Digital Advancement from Ministry of Economic Affairs and Digital Transformation, Spain; the Expedient IDI-2021-158274-a from the Ministry of Science and Innovation, Spain; and the ThinkInAzul program supported by MCIN with funding from European Union NextGenerationEU (PRTR-C17.I1) and Generalitat Valenciana (THINKINAZUL/2021/024).Peer Reviewed"Article signat per 18 autors/es: Ahmed Ibrahem Hafez, Beatriz Soriano, Aya Allah Elsayed,Ricardo Futami,Raquel Ceprian, Ricardo Ramos-Ruiz, Genis Martinez, Francisco Jose Roig, Miguel Angel Torres-Font, Fernando Naya-Catala, Josep Alvar Calduch-Giner, Lucia Trilla-Fuertes, Angelo Gamez Pozo, Vicente Arnau, Jose Maria Sempere-Luna, Jaume Perez-Sanchez, Toni Gabaldon and Carlos Llorens "Postprint (published version

Client Applications and Server-Side Docker for Management of RNASeq and/or VariantSeq Workflows and Pipelines of the GPRO Suite

The GPRO suite is an in-progress bioinformatic project for -omics data analysis. As part of the continued growth of this project, we introduce a client- and server-side solution for comparative transcriptomics and analysis of variants. The client-side consists of two Java applications called 'RNASeq' and 'VariantSeq' to manage pipelines and workflows based on the most common command line interface tools for RNA-seq and Variant-seq analysis, respectively. As such, 'RNASeq' and 'VariantSeq' are coupled with a Linux server infrastructure (named GPRO Server-Side) that hosts all dependencies of each application (scripts, databases, and command line interface software). Implementation of the Server-Side requires a Linux operating system, PHP, SQL, Python, bash scripting, and third-party software. The GPRO Server-Side can be installed, via a Docker container, in the user's PC under any operating system or on remote servers, as a cloud solution. 'RNASeq' and 'VariantSeq' are both available as desktop (RCP compilation) and web (RAP compilation) applications. Each application has two execution modes: a step-by-step mode enables each step of the workflow to be executed independently, and a pipeline mode allows all steps to be run sequentially. 'RNASeq' and 'VariantSeq' also feature an experimental, online support system called GENIE that consists of a virtual (chatbot) assistant and a pipeline jobs panel coupled with an expert system. The chatbot can troubleshoot issues with the usage of each tool, the pipeline jobs panel provides information about the status of each computational job executed in the GPRO Server-Side, while the expert system provides the user with a potential recommendation to identify or fix failed analyses. Our solution is a ready-to-use topic specific platform that combines the user-friendliness, robustness, and security of desktop software, with the efficiency of cloud/web applications to manage pipelines and workflows based on command line interface software

Актуальные вопросы создания и применения банков ДНК для целей криминалистики и смежных дисциплин

Review article presents essential information on DNA databases, forensic genomics for human identification and suspect characteristics. Author reports the essential information on the topic of forensic DNA databases and data processing. DNA databases are important tools for the improvement of performance of the security organizations and services with a final goal of national security enhancement.В статье-обзоре литературы приводятся основные сведения, касающиеся функционирования, разработки, развития и внедрения технических, лабораторных и кибернетических средств анализа и обработки геномных данных, предназначенных для улучшения результатов работы ряда криминалистических и судебно-медицинских служб, что имеет весомое значение для обеспечения безопасности граждан СНГ

Сhallenging Questions of Development and Application of DNA Banks for the Purposes of Criminology and Related Disciplines

В статье-обзоре литературы приводятся основные сведения, касающиеся функционирования, разработки, развития и внедрения технических, лабораторных и кибернетических средств анализа и обработки геномных данных, предназначенных для улучшения результатов работы ряда криминалистических и судебно-медицинских служб, что имеет весомое значение для обеспечения безопасности граждан СНГ

ПРОГРАММНО-ВЫЧИСЛИТЕЛЬНЫЙ КОМПЛЕКС «ОКУНЬ-2» ДЛЯ ОЦЕНКИ МУТАЦИОННОГО ПРОФИЛЯ ГЕНОВ РЕЗИСТЕНТНОСТИ И ВИРУЛЕНТНОСТИ СЕКВЕНИРОВАННЫХ ГЕНОМОВ МИКОБАКТЕРИИ ТУБЕРКУЛЕЗА

Authors describe a new software and computer complex designed and developed for the processing of the data of the whole genomes of mycobacterium tuberculosis with the purpose of obtaining information about the profile of tuberculosis resistance and virulence.Приводится описание нового программно-вычислительного комплекса, предназначенного для обработки данных полных геномов микобактерии туберкулеза человека с целью получения информации о профиле резистентности и вирулентности туберкулеза

Next generation sequencing study on RNA viruses of Vespa velutina and Apis mellifera sharing the same foraging area

The predator Asian hornet (Vespa velutina) represents one of the major threats to honeybee survival. Viral spillover from bee to wasp has been supposed in several studies, and this work aims to identify and study the virome of both insect species living simultaneously in the same foraging area. Transcriptomic analysis was performed on V. velutina and Apis mellifera samples, and replicative form of detected viruses was carried out by strand‐specific RT‐PCR. Overall, 6 and 9 different viral types were reported in V. velutina and A. mellifera, respectively, and five of these viruses were recorded in both hosts. Varroa destructor virus‐1 and Cripavirus NB‐1/2011/HUN (now classified as Triato‐like virus) were the most represented viruses detected in both hosts, also in replicative form. In this investigation, Triato‐like virus, as well as Aphis gossypii virus and Nora virus, was detected for the first time in honeybees. Concerning V. velutina, we report for the first time the recently detected honeybee La Jolla virus. A general high homology rate between genomes of shared viruses between V. velutina and A. mellifera suggests the efficient transmission of the virus from bee to wasp. In conclusion, our findings highlight the presence of several known and newly reported RNA viruses infecting A. mellifera and V. velutina. This confirms the environment role as an important source of infection and indicates the possibility of spillover from prey to predator

Using registries to integrate bioinformatics tools and services into workbench environments

The diversity and complexity of bioinformatics resources presents significant challenges to their localisation, deployment and use, creating a need for reliable systems that address these issues. Meanwhile, users demand increasingly usable and integrated ways to access and analyse data, especially within convenient, integrated “workbench” environments. Resource descriptions are the core element of registry and workbench systems, which are used to both help the user find and comprehend available software tools, data resources, and Web Services, and to localise, execute and combine them. The descriptions are, however, hard and expensive to create and maintain, because they are volatile and require an exhaustive knowledge of the described resource, its applicability to biological research, and the data model and syntax used to describe it. We present here the Workbench Integration Enabler, a software component that will ease the integration of bioinformatics resources in a workbench environment, using their description provided by the existing ELIXIR Tools and Data Services Registry

Prototyping a Tool for Processing Genetic Meta-Data in Microbiological Laboratories

Next generation sequencing (NGS) technologies allow improved understanding of pathogens. In the upstream processing of generating genomic data, there is still a lack of process-oriented tools for managing corresponding meta data. In this paper, we provide a description of how a process-oriented software prototype was developed that allowed the capture and collation of metadata involved when doing NGS. Our question was: How to develop an interactive web application that supports the process-oriented management of genetic data independent of any sequencing technique

Scandinavium goeteborgense gen. nov., sp. nov., a New Member of the Family Enterobacteriaceae Isolated From a Wound Infection, Carries a Novel Quinolone Resistance Gene Variant

The family Enterobacteriaceae is a taxonomically diverse and widely distributed family containing many human commensal and pathogenic species that are known to carry transferable antibiotic resistance determinants. Characterization of novel taxa within this family is of great importance in order to understand the associated health risk and provide better treatment options. The aim of the present study was to characterize a Gram-negative bacterial strain (CCUG 66741) belonging to the family Enterobacteriaceae, isolated from a wound infection of an adult patient, in Sweden. Initial phenotypic and genotypic analyses identified the strain as a member of the family Enterobacteriaceae but could not assign it to any previously described species. The complete 16S rRNA gene sequence showed highest similarity (98.8%) to four species. Whole genome sequencing followed by in silico DNA-DNA similarity analysis and average nucleotide identity (ANI) analysis confirmed that strain CCUG 66741 represents a novel taxon. Sequence comparisons of six house-keeping genes (16S rRNA, atpD, dnaJ, gyrB, infB, rpoB) with those of the type strains of the type species of related genera within the family Enterobacteriaceae indicated that the strain embodies a novel species within the family. Phylogenomic analyses (ANI-based and core genome-based phylogeny) showed that strain CCUG 66741 forms a distinct clade, representing a novel species of a distinct, new genus within the family Enterobacteriaceae, for which the name Scandinavium goeteborgense gen. nov., sp. nov. is proposed, with CCUG 66741T as the type strain (= CECT 9823T = NCTC 14286T). S. goeteborgense CCUG 66741T carries a novel variant of a chromosomally-encoded quinolone resistance gene (proposed qnrB96). When expressed in Escherichia coli, the qnrB96 gene conferred five-fold increase in minimum inhibitory concentration against ciprofloxacin. This study highlights the importance and the utility of whole genome sequencing for pathogen identification in clinical settings.publishedVersio