Tools and methodology to in silico phage discovery in freshwater environments

Freshwater availability is essential, and its maintenance has become an enormous challenge. Due to population growth and climate changes, freshwater sources are becoming scarce, imposing the need for strategies for its reuse. Currently, the constant discharge of waste into water bodies from human activities leads to the dissemination of pathogenic bacteria, negatively impacting water quality from the source to the infrastructure required for treatment, such as the accumulation of biofilms. Current water treatment methods cannot keep pace with bacterial evolution, which increasingly exhibits a profile of multidrug resistance to antibiotics. Furthermore, using more powerful disinfectants may affect the balance of aquatic ecosystems. Therefore, there is a need to explore sustainable ways to control the spreading of pathogenic bacteria. Bacteriophages can infect bacteria and archaea, hijacking their host machinery to favor their replication. They are widely abundant globally and provide a biological alternative to bacterial treatment with antibiotics. In contrast to common disinfectants and antibiotics, bacteriophages are highly specific, minimizing adverse effects on aquatic microbial communities and offering a lower cost–benefit ratio in production compared to antibiotics. However, due to the difficulty involving cultivating and identifying environmental bacteriophages, alternative approaches using NGS metagenomics in combination with some bioinformatic tools can help identify new bacteriophages that can be useful as an alternative treatment against resistant bacteria. In this review, we discuss advances in exploring the virome of freshwater, as well as current applications of bacteriophages in freshwater treatment, along with current challenges and future perspectives

Boletim COVID-PA: relatos sobre projeções baseadas em inteligência artificial no enfrentamento da pandemia de COVID-19 no estado do Pará

Objective: Report the university research and extension product denominated ‘Boletim COVID-PA’ which presented projections about the pandemic in the State of Pará, Brazil, with practical, mathematically rigorous and computationally efficient approaches. Methods: The artificial intelligence technique known as Artificial Neural Networks was used to generate thirteen bulletins with short-term projections based on historical data from the State Department of Public Health system. Results: After eight months of projections, the technique generated reliable results with an average accuracy of 97% (147 days observed) for confirmed cases, 96% (161 observed days) for deaths and 86% (72 days observed) for occupancy of intensive care unit beds. Conclusion: These bulletins have become a useful tool for decision making by public managers, assisting in reallocating hospital resources and optimizing COVID-19 control strategies for the various regions of the State of Pará.Objetivo: Relatar o produto de pesquisa e extensão universitária denominado Boletim COVID-PA, que apresentou projeções sobre o comportamento da pandemia no estado do Pará, Brasil. Métodos: Utilizou-se da técnica de inteligência artificial conhecida como ‘redes neurais artificiais’, para gerar 13 boletins com projeções de curto prazo baseadas nos dados históricos do sistema da Secretaria de Estado de Saúde Pública. Resultados: Após oito meses de projeções, a técnica gerou resultados confiáveis, com precisão média de 97% (147 dias observados) para casos confirmados, 96% (161 dias observados) para óbitos e 86% (72 dias observados) para ocupação de leitos de unidade de terapia intensiva. Conclusão: Esses boletins tornaram-se um instrumento útil para a tomada de decisão de gestores públicos, auxiliando na realocação de recursos hospitalares e otimização das estratégias de controle da COVID-19 nas diversas regiões do estado do Pará

Genomic analysis of Klebsiella pneumoniae high-risk clone ST11 co-harbouring MCR-1.27 and KPC-2 recovered at a paediatric oncologic hospital in the Brazilian Amazon region

Evandro Chagas Institute (IEC), Secretariat for Science, Technology, Innovation and Strategic Health Inputs (SCTIE), Brazilian Ministry of Health (MS). Yan Corrêa Rodrigues’ scholarship is funded by PDPG - Pós-Doutorado Estratégico (PDPG-POSDOC), Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES/ Edital 16/2022).Ministério da Saúde. Secretaria de Vigilância em Saúde e Ambiente. Instituto Evandro Chagas. Laboratório de Biologia Molecular. Ananindeua, PA, Brasil.Universidade Federal do Pará. Laboratório de Engenharia Biológica. Belém, PA, Brazil.Universidade Federal do Pará. Laboratório de Engenharia Biológica. Belém, PA, Brazil.Ministério da Saúde. Secretaria de Vigilância em Saúde e Ambiente. Instituto Evandro Chagas. Laboratório de Biologia Molecular. Ananindeua, PA, Brasil / Ministério da Saúde. Secretaria de Vigilância em Saúde e Ambiente. Instituto Evandro Chagas. Programa de Pós-Graduação em Epidemiologia e Vigilância em Saúde. Ananindeua, PA, Brasil.Ministério da Saúde. Secretaria de Vigilância em Saúde e Ambiente. Instituto Evandro Chagas. Laboratório de Biologia Molecular. Ananindeua, PA, Brasil / Ministério da Saúde. Secretaria de Vigilância em Saúde e Ambiente. Instituto Evandro Chagas. Programa de Pós-Graduação em Epidemiologia e Vigilância em Saúde. Ananindeua, PA, Brasil.Objectives: The horizontal transfer of antibiotic resistance genes in Gram-negative bacteria, mainly through plasmids, is one of the greatest concerns for health systems worldwide and has been a growing threat in hospitals related to healthcare-associated infections by multidrug-resistant bacteria. Here we present phenotypic and genomic characterization of a KPC-2 and MCR-1.27-producing Klebsiella pneumoniae strain isolated from a paediatric patient at an oncologic hospital in Belém, Pará State, Brazilian Amazon region. Methods: Antibiotic susceptibility test, whole genome sequencing, and in silico analysis were used to characterize the bacterial isolate (IEC48020) received in the Evandro Chagas Institute. Results: The isolate was resistant to carbapenems, colistin, polymyxin B, and several other antimicrobials and was susceptible in vitro just to tigecycline, classified as an extensively drug-resistant phenotype. Genomic analysis revealed IEC48020 strain belonged to sequence type 11, clonal complex 258 high-risk clone and the presence of eight plasmids, two of them harbouring mcr-1.27 and blaKPC-2 genes, and the presence of virulence-related genes encoding yersiniabactin, phospholipase D, and traT genes. Conclusions: The presence and dissemination of high-risk clone bacteria with high disseminating plasmids containing antibiotic resistance genes for last resource antibiotics treatment options is a threat to the healthcare system and demands efforts in surveillance and epidemiological research for better knowledge of the actual situation of antibiotic resistance in the healthcare system, especially in the Amazon region, Brazil

Proksee sessions with GIPSy2 comparisons

<p><a href="https://proksee.ca">Proksee</a> sessions related to comparative analyses performed with GIPSy2.</p><p><i>Supporting material 1</i>. Comparative analyses carried out with the chromosome of <i>Acinetobacter baumannii</i> strain AYE against the chromosome of <i>A. baumannii</i> strain SDF.</p><p><i>Supporting material 2</i>. Comparative analysis carried out with the chromosome I of <i>Burkholderia pseudomallei</i> strain K96243 against the chromosome I of <i>B. pseudomallei</i> strain 668.</p><p><i>Supporting material 3</i>. Comparative analysis carried out with the chromosome II of <i>Burkholderia pseudomallei</i> strain K96243 against the chromosome chromosome II of <i>B. pseudomallei</i> strain 668.</p><p><i>Supporting material 4</i>. Comparative analyses carried out with the chromosome of <i>Escherichia coli</i> CFT073 against the chromosome of <i>E. coli</i> strain K-12 substrain MG1655.</p><p><i>Supporting material 5</i>. Comparative analyses carried out with the chromosome of <i>Mesorhizobium japonicum</i> MAFF 303099 against the chromosome of <i>Mesorhizobium sp</i>. strain BNC1.</p><p><i>Supporting material 6</i>. Comparative analyses carried out on the chromosome of <i>Mesorhizobium japonicum</i> MAFF 303099 against the chromosomes of <i>Mesorhizobium sp</i>. strain BNC1, <i>M. loti</i> strain TONO, <i>M. loti</i> strain R88b and <i>M. japonicum</i> strain R7Astar.</p><p> </p&gt

High efficiency application of a mate-paired library from next-generation sequencing to postlight sequencing: Corynebacterium pseudotuberculosis as a case study for microbial de novo genome assembly

Ramos RTJ, Carneiro AR, de Castro Soares S, et al. High efficiency application of a mate-paired library from next-generation sequencing to postlight sequencing: Corynebacterium pseudotuberculosis as a case study for microbial de novo genome assembly. Journal of microbiological methods. 2013;95(3):441-447.With the advent of high-throughput DNA sequencing platforms, there has been a reduction in the cost and time of sequencing. With these advantages, new challenges have emerged, such as the handling of large amounts of data, quality assessment, and the assembly of short reads. Currently, benchtop high-throughput sequencers enable the genomes of prokaryotic organisms to be sequenced within two hours with a reduction in coverage compared with the SOLiD, Illumina and 454 FLX Titanium platforms, making it necessary to evaluate the efficiency of less expensive benchtop instruments for prokaryotic genomics. In the present work, we evaluate and propose a methodology for the use of the Ion Torrent PGM platform for decoding the gram-positive bacterium Corynebacterium pseudotuberculosis, for which 15 complete genome sequences have already been deposited based on fragment and mate-paired libraries with a 3-kb insert size. Despite the low coverage, a single sequencing run using a mate-paired library generated 39 scaffolds after de novo assembly without data curation. This result is superior to that obtained by sequencing using libraries generated from fragments marketed by the equipment's manufacturer, as well as that observed for mate-pairs sequenced by SOLiD. The generated sequence added an extra 91kb to the genome available at NCBI

SATIN: a micro and mini satellite mining tool of total genome and coding regions with analysis of perfect repeats polymorphism in coding regions

Abstract Background Tandem repeats are specific sequences in genomic DNA repeated in tandem that are present in all organisms. Among the subcategories of TRs we have Satellite repeats, that is divided into macrosatellites, minisatellites, and microsatellites, being the last two of specific interest because they can identify polymorphisms between organisms due to their instability. Currently, most mining tools focus on Simple Sequence Repeats (SSR) mining, and only a few can identify SSRs in the coding regions. Results We developed a microsatellite mining software called SATIN (Micro and Mini SATellite IdentificatioN tool) based on a new sliding window algorithm written in C and Python. It represents a new approach to SSR mining by addressing the limitations of existing tools, particularly in coding region SSR mining. SATIN is available at https://github.com/labgm/SATIN.git . It was shown to be the second fastest for perfect and compound SSR mining. It can identify SSRs from coding regions plus SSRs with motif sizes bigger than 6. Besides the SSR mining, SATIN can also analyze SSRs polymorphism on coding-regions from pre-determined groups, and identify SSRs differentially abundant among them on a per-gene basis. To validate, we analyzed SSRs from two groups of Escherichia coli (K12 and O157) and compared the results with 5 known SSRs from coding regions. SATIN identified all 5 SSRs from 237 genes with at least one SSR on it. Conclusions The SATIN is a novel microsatellite search software that utilizes an innovative sliding window technique based on a numerical list for repeat region search to identify perfect, and composite SSRs while generating comprehensible and analyzable outputs. It is a tool capable of using files in fasta or GenBank format as input for microsatellite mining, also being able to identify SSRs present in coding regions for GenBank files. In conclusion, we expect SATIN to help identify potential SSRs to be used as genetic markers

Tips and tricks for the assembly of a Corynebacterium pseudotuberculosis genome using a semiconductor sequencer

New sequencing platforms have enabled rapid decoding of complete prokaryotic genomes at relatively low cost. The Ion Torrent platform is an example of these technologies, characterized by lower coverage, generating challenges for the genome assembly. One particular problem is the lack of genomes that enable reference-based assembly, such as the one used in the present study, Corynebacterium pseudotuberculosis biovar equi, which causes high economic losses in the US equine industry. The quality treatment strategy incorporated into the assembly pipeline enabled a 16-fold greater use of the sequencing data obtained compared with traditional quality filter approaches. Data preprocessing prior to the de novo assembly enabled the use of known methodologies in the next-generation sequencing data assembly. Moreover, manual curation was proved to be essential for ensuring a quality assembly, which was validated by comparative genomics with other species of the genus Corynebacterium. The present study presents a modus operandi that enables a greater and better use of data obtained from semiconductor sequencing for obtaining the complete genome from a prokaryotic microorganism, C. pseudotuberculosis, which is not a traditional biological model such as Escherichia coli

Influence of soil management for soybean production under microbial diversity in amazon soils

National Research Council (CNPq); Alliance Program for Education and Training—PAEC-OEA-GCUB 2017; Cooperation Agreement between the Organization of American States (OAS); Coimbra Group of Brazilian Universities (CGUB); L'Oréal Brasil-UNESCO-ABC “For Women in Science”; PROPESP/UFPA (Pró-Reitoria de Pesquisa e Pós-Graduação/Universidade Federal do Pará)Federal University of Pará. Institute of Biological Sciences. Center of Genomics and System Biology. Laboratory of Genomic and Bioinformatics. Belém, PA, Brazil.Federal University of Minas Gerais. Institute of Biological Sciences. Belo Horizonte, MG, Brazil.Federal Rural University of the Amazon. Paragominas, PA, Brazil.Ministério da Saúde. Secretaria de Ciência, Tecnologia, Inovação e Insumos Estratégicos. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Federal University of Pará. Institute of Biological Sciences. Center of Genomics and System Biology. Laboratory of Genomic and Bioinformatics. Belém, PA, Brazil.Ministério da Saúde. Secretaria de Ciência, Tecnologia, Inovação e Insumos Estratégicos. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Federal University of Pará. Institute of Biological Sciences. Center of Genomics and System Biology. Laboratory of Genomic and Bioinformatics. Belém, PA, Brazil / Federal University of Minas Gerais. Institute of Biological Sciences. Belo Horizonte, MG, Brazil.Federal University of Pará. Institute of Biological Sciences. Center of Genomics and System Biology. Laboratory of Genomic and Bioinformatics. Belém, PA, Brazil.The tropical Amazon has a unique biodiversity that has been affected by the development of pastures and economically important crops, such as soybeans. In the Amazon soil, the communities of microorganisms are diverse and act in different biogeochemical activities relevant to their adaptation to the environment. The assessment of changes in soil microorganism communities is essential to consider the impact of agribusiness action in one of the wealthiest regions in diversity in the world. Thus, the soil microbial diversity of the Amazon forest, the north region of Brazil, was evaluated regarding the influence of soybean farming with regions with periods of two and 14 years of exploitation, with regions of pasture and forest area, through the metagenomics approach with new generation sequencing technology, in addition, it was considered chemical characteristics such as pH value, organic matter content, macronutrients, micronutrients, and cations. High microbial diversity was identified at all collection sites and, despite this, bacterial, archaeal, and virus communities were very diverse between sites, with higher identification of Enterobacter cloacae and species of Pseudomonas, Pseudoplusia includens, Methanosarcina barkeri in the farmed and pasture, whose microbial diversity is influenced by the presence of cations and the interaction of organic matter with clay. It was evident that there is a change in the communities of native microorganisms for others adapted in the areas that had their vegetal cover eliminated

Genome sequence of a multidrug-resistant Corynebacterium striatum isolated from bloodstream infection from a nosocomial outbreak in Rio de Janeiro, Brazil

Multidrug-resistant (MDR) Corynebacterium striatum has been cited with increased frequency as pathogen of nosocomial infections. In this study, we report the draft genome of a C. striatum isolated from a patient with bloodstream infection in a hospital of Rio de Janeiro, Brazil. The isolate presented susceptibility only to tetracycline, vancomycin and linezolid. The detection of various antibiotic resistance genes is fully consistent with previously observed multidrug-resistant pattern in Corynebacterium spp. A large part of the pTP10 plasmid of MDR C. striatum M82B is present in the genome of our isolate. A SpaDEF cluster and seven arrays of CRISPR-Cas were found